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Portal Experiment Replicate @@ -541,7 +544,7 @@ pattern: - homepage: http://www.sparontologies.net/ontologies/bido name: Bibliometric Data Ontology prefix: bido -- homepage: null +- homepage: http://4dx.embl.de/4DXpress name: Bilateria anatomy prefix: bila - homepage: https://bioregistry.io @@ -1466,7 +1469,7 @@ wikidata: - homepage: http://bigg.ucsd.edu/universal/reactions name: BiGG Reaction prefix: bigg.reaction -- homepage: null +- homepage: http://4dx.embl.de/4DXpress name: Bilateria anatomy prefix: bila - homepage: https://www.bindingdb.org diff --git a/docs/img/bioregistry_coverage.svg b/docs/img/bioregistry_coverage.svg index fc1205bf4..7a7123e72 100644 --- a/docs/img/bioregistry_coverage.svg +++ b/docs/img/bioregistry_coverage.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:57:10.837605 + 2022-07-30T11:27:54.351642 image/svg+xml @@ -63,7 +63,7 @@ C 117.995311 124.398596 124.546335 123.597445 130.776805 121.603415 C 137.007274 119.609385 142.806124 116.458021 147.868677 112.314899 C 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opacity: 0.4"/> +" clip-path="url(#p171bd32590)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p171bd32590)" style="fill: #cab2d6; opacity: 0.4"/> +" clip-path="url(#p171bd32590)" style="fill: #ffffff; opacity: 0.4"/> @@ -1907,7 +1907,7 @@ C 109.468294 552.111194 115.704996 551.898449 121.756796 550.593235 C 127.808596 549.28802 133.578572 546.911239 138.793866 543.575287 C 144.00916 540.239335 148.586248 535.99764 152.308681 531.050786 C 156.031115 526.103933 158.839278 520.531148 160.600376 514.595965 -" clip-path="url(#pbb5f53c623)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p189d848559)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p189d848559)" style="fill: #6a3d9a; opacity: 0.4"/> +" clip-path="url(#p189d848559)" style="fill: #d1b1f2; opacity: 0.4"/> @@ -2012,7 +2012,7 @@ C 340.097693 552.042823 346.300624 551.876089 352.328983 550.626489 C 358.357342 549.376889 364.115457 547.064255 369.333454 543.796975 C 374.551452 540.529696 379.146521 536.359624 382.9033 531.482204 C 386.660078 526.604783 389.518944 521.09742 391.345908 515.218235 -" clip-path="url(#p24aac03269)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p3a48a5a306)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p3a48a5a306)" style="fill: #ffff99; opacity: 0.4"/> +" clip-path="url(#p3a48a5a306)" style="fill: #fffff2; opacity: 0.4"/> @@ -2110,7 +2110,7 @@ C 569.434415 551.863089 575.502934 551.893317 581.440005 550.880298 C 587.377075 549.86728 593.092219 547.826453 598.328065 544.849723 C 603.563912 541.872993 608.24067 538.005723 612.147731 533.422068 C 616.054792 528.838414 619.132613 523.608227 621.242593 517.967039 -" clip-path="url(#p670a8d9369)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p0d2291ec23)" style="fill: #c0c0c0; opacity: 0.4"/> +" clip-path="url(#p0d2291ec23)" style="fill: #b15928; opacity: 0.4"/> +" clip-path="url(#p0d2291ec23)" style="fill: #ffc5a2; opacity: 0.4"/> @@ -2234,7 +2234,7 @@ C 110.719659 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739.84904 1382.738055 748.69911 1387.01435 758.164404 1387.740345 - + @@ -4115,81 +4115,81 @@ C 739.84904 1382.738055 748.69911 1387.01435 758.164404 1387.740345 - + - + - + - - + + - + - + - + - + @@ -4197,7 +4197,7 @@ C 135.211019 1532.034733 135.783229 1533.965406 136.857974 1535.61927 - + @@ -4210,83 +4210,83 @@ C 135.211019 1532.034733 135.783229 1533.965406 136.857974 1535.61927 - + - + - + - - + + - + - - + + - + - - + + - + - + @@ -4294,7 +4294,7 @@ C 291.485696 1538.020159 293.913809 1545.791672 298.444209 1552.334026 - + @@ -4311,78 +4311,78 @@ C 291.485696 1538.020159 293.913809 1545.791672 298.444209 1552.334026 - + - + - + - - + + - + - + - + - + @@ -4390,7 +4390,7 @@ C 542.853193 1547.907851 546.780079 1551.045415 551.353655 1552.846957 - + @@ -4406,81 +4406,81 @@ C 542.853193 1547.907851 546.780079 1551.045415 551.353655 1552.846957 - + - + - + - - + + - - + + - + - + - + @@ -4488,7 +4488,7 @@ C 777.437322 1532.62583 778.329657 1535.111072 779.960298 1537.089077 - + @@ -4503,84 +4503,84 @@ C 777.437322 1532.62583 778.329657 1535.111072 779.960298 1537.089077 - + - + - + - - + + - + - - + + - + - - + + - + - + @@ -4588,7 +4588,7 @@ C 71.966629 1715.786406 73.195073 1721.547815 75.571608 1726.867433 - + @@ -4601,95 +4601,95 @@ C 71.966629 1715.786406 73.195073 1721.547815 75.571608 1726.867433 - + - + - + - - + + - - + + - + - + - + @@ -4697,7 +4697,7 @@ C 364.400225 1721.19328 365.528936 1720.020481 366.452772 1718.69271 - + @@ -4710,68 +4710,68 @@ C 364.400225 1721.19328 365.528936 1720.020481 366.452772 1718.69271 - + - + - + - - + + - + - + @@ -4779,13 +4779,13 @@ C 536.303008 1713.125996 536.913138 1716.262463 538.099949 1719.197527 - + - + @@ -4793,7 +4793,7 @@ C 536.303008 1713.125996 536.913138 1716.262463 538.099949 1719.197527 - + @@ -10392,7 +10392,7 @@ C 532.001265 4447.789108 536.714686 4447.595533 541.281494 4446.573638 C 545.848303 4445.551742 550.194719 4443.718036 554.113436 4441.159978 C 558.032154 4438.60192 561.459865 4435.360838 564.233081 4431.591318 C 567.006296 4427.821798 569.080215 4423.584738 570.355918 4419.082229 -" clip-path="url(#p4e0e72ead5)" style="fill: #e31a1c; opacity: 0.4"/> +" clip-path="url(#p7ad7d95923)" style="fill: #e31a1c; opacity: 0.4"/> +" clip-path="url(#p7ad7d95923)" style="fill: #b2df8a; opacity: 0.4"/> +" clip-path="url(#p7ad7d95923)" style="fill: #ffae74; opacity: 0.4"/> @@ -15278,7 +15278,7 @@ C 97.852361 6781.061926 101.993565 6780.757447 105.977186 6779.714422 C 109.960807 6778.671397 113.719858 6776.907365 117.067847 6774.509844 C 120.415835 6772.112322 123.296463 6769.121626 125.566816 6765.68613 C 127.837169 6762.250634 129.45907 6758.428107 130.352054 6754.408192 -" clip-path="url(#pfefbf00ba9)" style="fill: #6a3d9a; opacity: 0.4"/> +" clip-path="url(#pbf7a67cef3)" style="fill: #6a3d9a; opacity: 0.4"/> +" clip-path="url(#pbf7a67cef3)" style="fill: #b2df8a; opacity: 0.4"/> +" clip-path="url(#pbf7a67cef3)" style="fill: #c7c7cc; opacity: 0.4"/> @@ -17858,7 +17858,7 @@ C 73.651883 8019.405249 74.969655 8019.707751 76.310275 8019.810085 C 77.650895 8019.912419 78.999313 8019.813435 80.31062 8019.516431 C 81.621926 8019.219427 82.881398 8018.727737 84.047089 8018.057737 C 85.212779 8017.387737 86.271601 8016.546949 87.18829 8015.563375 -" clip-path="url(#pc3a3668fd5)" style="fill: #a6cee3; opacity: 0.4"/> +" clip-path="url(#p8845690d81)" style="fill: #a6cee3; opacity: 0.4"/> +" clip-path="url(#p8845690d81)" style="fill: #33a02c; opacity: 0.4"/> +" clip-path="url(#p8845690d81)" style="fill: #98ffbe; opacity: 0.4"/> @@ -18811,7 +18811,7 @@ C 500.136326 8352.253257 497.944601 8354.54296 496.424746 8357.266323 C 494.904891 8359.989686 494.106867 8363.057187 494.106867 8366.175947 C 494.106867 8369.294707 494.904891 8372.362207 496.424746 8375.08557 C 497.944601 8377.808933 500.136326 8380.098637 502.790661 8381.736065 -" clip-path="url(#ped227892ef)" style="fill: #1f78b4; opacity: 0.4"/> +" clip-path="url(#p8133323bad)" style="fill: #1f78b4; opacity: 0.4"/> +" clip-path="url(#p8133323bad)" style="fill: #fdbf6f; opacity: 0.4"/> +" clip-path="url(#p8133323bad)" style="fill: #c7dacc; opacity: 0.4"/> @@ -19330,7 +19330,7 @@ C 68.64193 8730.98943 69.179478 8731.066071 69.718972 8731.056804 C 70.258466 8731.047536 70.793065 8730.952478 71.302685 8730.7752 C 71.812304 8730.597921 72.290483 8730.340671 72.719255 8730.013114 C 73.148027 8729.685556 73.521957 8729.291844 73.826996 8728.84677 -" clip-path="url(#p306408a1c2)" style="fill: #b2df8a; opacity: 0.4"/> +" clip-path="url(#pe110f0a1ed)" style="fill: #b2df8a; opacity: 0.4"/> +" clip-path="url(#pe110f0a1ed)" style="fill: #fdbf6f; opacity: 0.4"/> +" clip-path="url(#pe110f0a1ed)" style="fill: #ffffae; opacity: 0.4"/> @@ -19999,7 +19999,7 @@ C 736.615374 8936.177352 740.223692 8936.065818 743.727441 8935.323171 C 747.23119 8934.580524 750.57448 8933.21861 753.599834 8931.301578 C 756.625189 8929.384545 759.284349 8926.942975 761.452062 8924.09187 C 763.619775 8921.240764 765.261463 8918.025603 766.299798 8914.597828 -" clip-path="url(#p1d8ad6764a)" style="fill: #33a02c; opacity: 0.4"/> +" clip-path="url(#pdd5206cf49)" style="fill: #33a02c; opacity: 0.4"/> +" clip-path="url(#pdd5206cf49)" style="fill: #cab2d6; opacity: 0.4"/> +" clip-path="url(#pdd5206cf49)" style="fill: #b1edb5; opacity: 0.4"/> @@ -20496,7 +20496,7 @@ C 64.587634 9266.697751 64.8746 9267.710899 65.416408 9268.590607 C 65.958217 9269.470315 66.733865 9270.182485 67.656526 9270.647394 C 68.579186 9271.112303 69.613095 9271.31193 70.642511 9271.223929 C 71.671928 9271.135927 72.656951 9270.763708 73.487313 9270.148939 -" clip-path="url(#pe496f75b04)" style="fill: #e31a1c; opacity: 0.4"/> +" clip-path="url(#p1e04a6efc1)" style="fill: #e31a1c; opacity: 0.4"/> +" clip-path="url(#p1e04a6efc1)" style="fill: #fdbf6f; opacity: 0.4"/> +" clip-path="url(#p1e04a6efc1)" style="fill: #ff9861; opacity: 0.4"/> @@ -20949,7 +20949,7 @@ z - + - - + + - - + + @@ -21151,62 +21151,62 @@ z - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + @@ -21385,7 +21385,7 @@ z - + @@ -21535,7 +21535,7 @@ z - + @@ -21619,7 +21619,7 @@ z - + @@ -21649,7 +21649,7 @@ z - + @@ -21667,7 +21667,7 @@ z - + @@ -21688,7 +21688,7 @@ z - + @@ -21703,7 +21703,7 @@ z - + diff --git a/docs/img/has_attribute.svg b/docs/img/has_attribute.svg index 5e6b8c35d..92f1a3716 100644 --- a/docs/img/has_attribute.svg +++ b/docs/img/has_attribute.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:57:09.722806 + 2022-07-30T11:27:53.760770 image/svg+xml @@ -1828,40 +1828,40 @@ z - - - + @@ -1869,7 +1869,7 @@ z - + @@ -1877,14 +1877,14 @@ z - + - + @@ -2455,7 +2455,7 @@ z - + - - + + diff --git a/docs/img/licenses.svg b/docs/img/licenses.svg index baffbb470..1e08af6ca 100644 --- a/docs/img/licenses.svg +++ b/docs/img/licenses.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:56:48.139752 + 2022-07-30T11:27:37.979752 image/svg+xml @@ -696,7 +696,7 @@ L 565.2 10.8 - + - - - + + diff --git a/docs/img/providers.svg b/docs/img/providers.svg index 586233a70..7b3f7f4a7 100644 --- a/docs/img/providers.svg +++ b/docs/img/providers.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:59:55.331375 + 2022-07-30T11:29:58.607741 image/svg+xml @@ -577,7 +577,7 @@ z - + @@ -587,7 +587,7 @@ z - + @@ -690,66 +690,66 @@ z - - - - - - - - @@ -775,7 +775,7 @@ L 565.2 10.8 - + - - - + + diff --git a/docs/img/regex_report.svg b/docs/img/regex_report.svg index af21d8c35..553ce78c9 100644 --- a/docs/img/regex_report.svg +++ b/docs/img/regex_report.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:59:56.281108 + 2022-07-30T11:29:59.255008 image/svg+xml diff --git a/docs/img/xrefs.svg b/docs/img/xrefs.svg index 86f4b44dd..f58a9cba9 100644 --- a/docs/img/xrefs.svg +++ b/docs/img/xrefs.svg @@ -6,7 +6,7 @@ - 2022-07-29T13:59:51.376816 + 2022-07-30T11:29:57.312871 image/svg+xml @@ -1107,7 +1107,7 @@ z - + @@ -1117,7 +1117,7 @@ z - + @@ -1181,189 +1181,189 @@ z - - - - - - - - - - - - - - - - - - - - - - - @@ -1379,13 +1379,13 @@ L 565.2 210.04 - + - + @@ -1395,7 +1395,7 @@ L 565.2 210.04 - + @@ -1403,38 +1403,38 @@ L 565.2 210.04 - + - + - + - + - - + + - + - + @@ -1442,7 +1442,7 @@ L 565.2 210.04 - + @@ -1450,47 +1450,47 @@ L 565.2 210.04 - + - + - + - + - + - + - + @@ -1502,13 +1502,13 @@ L 565.2 210.04 - + - + @@ -1538,7 +1538,7 @@ L 565.2 210.04 - + - + @@ -1611,7 +1611,7 @@ z - + - - + + diff --git a/exports/contexts/bioregistry.context.jsonld b/exports/contexts/bioregistry.context.jsonld index 6c5a32495..e8dab0144 100644 --- a/exports/contexts/bioregistry.context.jsonld +++ b/exports/contexts/bioregistry.context.jsonld @@ -245,7 +245,6 @@ "cosmic.cell": "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=", "covid19": "https://covid19.sfb.uit.no/api/records/", "cpc": "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=", - "cpga": "http://purl.obolibrary.org/obo/GRO_", "cpt": "https://www.aapc.com/codes/cpt-codes/", "crisprdb": "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=", "cro": "http://purl.obolibrary.org/obo/CRO_", @@ -1210,7 +1209,6 @@ "yetfasco": "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=", "yid": "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=", "ymdb": "http://www.ymdb.ca/compounds/", - "ypo": "http://purl.obolibrary.org/obo/YPO_", "yrcpdr": "http://yeastrc.org/pdr/viewProtein.do?id=", "zea": "http://purl.obolibrary.org/obo/ZEA_", "zeco": "http://purl.obolibrary.org/obo/ZECO_", diff --git a/exports/contexts/bioregistry.context.ttl b/exports/contexts/bioregistry.context.ttl index 5d0735934..65e539522 100644 --- a/exports/contexts/bioregistry.context.ttl +++ b/exports/contexts/bioregistry.context.ttl @@ -247,7 +247,6 @@ [ sh:prefix "cosmic.cell" ; sh:namespace "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=" ; sh:pattern "^\d+$" ], [ sh:prefix "covid19" ; sh:namespace "https://covid19.sfb.uit.no/api/records/" ; sh:pattern "^\w+_COVID19_[-\w]+$" ], [ sh:prefix "cpc" ; sh:namespace "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=" ; sh:pattern "^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$" ], - [ sh:prefix "cpga" ; sh:namespace "http://purl.obolibrary.org/obo/GRO_" ], [ sh:prefix "cpt" ; sh:namespace "https://www.aapc.com/codes/cpt-codes/" ; sh:pattern "^\d+$" ], [ sh:prefix "crisprdb" ; sh:namespace "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=" ; sh:pattern "^[0-9]+$" ], [ sh:prefix "cro" ; sh:namespace "http://purl.obolibrary.org/obo/CRO_" ; sh:pattern "^\d{7}$" ], @@ -1212,7 +1211,6 @@ [ sh:prefix "yetfasco" ; sh:namespace "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=" ; sh:pattern "^\w+\_\d+(\.\d+)?$" ], [ sh:prefix "yid" ; sh:namespace "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=" ; sh:pattern "^[A-Z0-9]+$" ], [ sh:prefix "ymdb" ; sh:namespace "http://www.ymdb.ca/compounds/" ; sh:pattern "^YMDB\d+$" ], - [ sh:prefix "ypo" ; sh:namespace "http://purl.obolibrary.org/obo/YPO_" ], [ sh:prefix "yrcpdr" ; sh:namespace "http://yeastrc.org/pdr/viewProtein.do?id=" ; sh:pattern "^\d+$" ], [ sh:prefix "zea" ; sh:namespace "http://purl.obolibrary.org/obo/ZEA_" ], [ sh:prefix "zeco" ; sh:namespace "http://purl.obolibrary.org/obo/ZECO_" ; sh:pattern "^\d{7}$" ], diff --git a/exports/contexts/obo.context.jsonld b/exports/contexts/obo.context.jsonld index 1ba7581f8..a440c56ef 100644 --- a/exports/contexts/obo.context.jsonld +++ b/exports/contexts/obo.context.jsonld @@ -5,7 +5,7 @@ "4dn.replicate": "https://data.4dnucleome.org/experiment-set-replicates/", "AAO": "http://purl.obolibrary.org/obo/AAO_", "ADO": "http://purl.obolibrary.org/obo/ADO_", - "ADW": "http://purl.obolibrary.org/obo/ADW_", + "ADW": "https://animaldiversity.org/accounts/", "AEO": "http://purl.obolibrary.org/obo/AEO_", "AERO": "http://purl.obolibrary.org/obo/AERO_", "AGRO": "http://purl.obolibrary.org/obo/AGRO_", @@ -75,7 +75,7 @@ "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", "ENSEMBL": "https://www.ensembl.org/id/", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EO": "http://purl.obolibrary.org/obo/EO_", + "EO": "http://archive.gramene.org/db/ontology/search?query=EO:", "EPIO": "http://purl.obolibrary.org/obo/EPIO_", "EPO": "http://purl.obolibrary.org/obo/EPO_", "ERO": "http://purl.obolibrary.org/obo/ERO_", @@ -107,7 +107,6 @@ "GEOGEO": "http://purl.obolibrary.org/obo/GEO_", "GNO": "http://purl.obolibrary.org/obo/GNO_", "GO": "http://purl.obolibrary.org/obo/GO_", - "GRO": "http://purl.obolibrary.org/obo/GRO_", "GSSO": "http://purl.obolibrary.org/obo/GSSO_", "HABRONATTUS": "http://purl.obolibrary.org/obo/HABRONATTUS_", "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", @@ -125,7 +124,6 @@ "IEV": "http://purl.obolibrary.org/obo/IEV_", "IMR": "http://purl.obolibrary.org/obo/IMR_", "INO": "http://purl.obolibrary.org/obo/INO_", - "IPR": "http://purl.obolibrary.org/obo/IPR_", "KISAO": "http://purl.obolibrary.org/obo/KISAO_", "LABO": "http://purl.obolibrary.org/obo/LABO_", "LEPAO": "http://purl.obolibrary.org/obo/LEPAO_", @@ -168,7 +166,7 @@ "NIF_CELL": "http://purl.obolibrary.org/obo/NIF_CELL_", "NIF_DYSFUNCTION": "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_", "NIF_GROSSANATOMY": "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_", - "NMR": "http://purl.obolibrary.org/obo/NMR_", + "NMR": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:", "NOMEN": "http://purl.obolibrary.org/obo/NOMEN_", "OAE": "http://purl.obolibrary.org/obo/OAE_", "OARCS": "http://purl.obolibrary.org/obo/OARCS_", @@ -223,13 +221,13 @@ "PdumDv": "http://purl.obolibrary.org/obo/PdumDv_", "PuRO": "http://purl.org/spar/pro/", "RBO": "http://purl.obolibrary.org/obo/RBO_", - "RESID": "http://purl.obolibrary.org/obo/RESID_", + "RESID": "https://proteininformationresource.org/cgi-bin/resid?id=", "REX": "http://purl.obolibrary.org/obo/REX_", "RNAO": "http://purl.obolibrary.org/obo/RNAO_", "RO": "http://purl.obolibrary.org/obo/RO_", "RS": "http://purl.obolibrary.org/obo/RS_", "RXNO": "http://purl.obolibrary.org/obo/RXNO_", - "SAO": "http://purl.obolibrary.org/obo/SAO_", + "SAO": "http://uri.neuinfo.org/nif/nifstd/sao", "SBO": "http://purl.obolibrary.org/obo/SBO_", "SCDO": "http://purl.obolibrary.org/obo/SCDO_", "SCTID": "http://www.snomedbrowser.com/Codes/Details/", @@ -256,7 +254,7 @@ "UBERON": "http://purl.obolibrary.org/obo/UBERON_", "UMLS": "http://linkedlifedata.com/resource/umls/id/", "UO": "http://purl.obolibrary.org/obo/UO_", - "UPA": "http://purl.obolibrary.org/obo/UPA_", + "UPA": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", "VHOG": "http://purl.obolibrary.org/obo/VHOG_", "VO": "http://purl.obolibrary.org/obo/VO_", @@ -272,7 +270,6 @@ "XCO": "http://purl.obolibrary.org/obo/XCO_", "XLMOD": "http://purl.obolibrary.org/obo/XLMOD_", "XPO": "http://purl.obolibrary.org/obo/XPO_", - "YPO": "http://purl.obolibrary.org/obo/YPO_", "ZEA": "http://purl.obolibrary.org/obo/ZEA_", "ZECO": "http://purl.obolibrary.org/obo/ZECO_", "ZFA": "http://purl.obolibrary.org/obo/ZFA_", @@ -736,6 +733,7 @@ "intact": "https://www.ebi.ac.uk/intact/interaction/", "intact.molecule": "https://www.ebi.ac.uk/intact/molecule/", "interlex": "https://scicrunch.org/scicrunch/interlex/view/ilx_", + "interpro": "https://www.ebi.ac.uk/interpro/entry/", "ird.segment": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=", "irefweb": "http://wodaklab.org/iRefWeb/interaction/show/", "iro": "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:", diff --git a/exports/contexts/obo.context.ttl b/exports/contexts/obo.context.ttl index ebf6a37dd..a4a2dfe47 100644 --- a/exports/contexts/obo.context.ttl +++ b/exports/contexts/obo.context.ttl @@ -7,7 +7,7 @@ [ sh:prefix "4dn.replicate" ; sh:namespace "https://data.4dnucleome.org/experiment-set-replicates/" ], [ sh:prefix "AAO" ; sh:namespace "http://purl.obolibrary.org/obo/AAO_" ], [ sh:prefix "ADO" ; sh:namespace "http://purl.obolibrary.org/obo/ADO_" ], - [ sh:prefix "ADW" ; sh:namespace "http://purl.obolibrary.org/obo/ADW_" ; sh:pattern "^[A-Z_a-z]+$" ], + [ sh:prefix "ADW" ; sh:namespace "https://animaldiversity.org/accounts/" ; sh:pattern "^[A-Z_a-z]+$" ], [ sh:prefix "AEO" ; sh:namespace "http://purl.obolibrary.org/obo/AEO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "AERO" ; sh:namespace "http://purl.obolibrary.org/obo/AERO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "AGRO" ; sh:namespace "http://purl.obolibrary.org/obo/AGRO_" ; sh:pattern "^\d{8}$" ], @@ -77,7 +77,7 @@ [ sh:prefix "EMAPA" ; sh:namespace "http://purl.obolibrary.org/obo/EMAPA_" ; sh:pattern "^\d+$" ], [ sh:prefix "ENSEMBL" ; sh:namespace "https://www.ensembl.org/id/" ; sh:pattern "^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" ], [ sh:prefix "ENVO" ; sh:namespace "http://purl.obolibrary.org/obo/ENVO_" ; sh:pattern "^\d{7,8}$" ], - [ sh:prefix "EO" ; sh:namespace "http://purl.obolibrary.org/obo/EO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "EO" ; sh:namespace "http://archive.gramene.org/db/ontology/search?query=EO:" ; sh:pattern "^\d{7}$" ], [ sh:prefix "EPIO" ; sh:namespace "http://purl.obolibrary.org/obo/EPIO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "EPO" ; sh:namespace "http://purl.obolibrary.org/obo/EPO_" ], [ sh:prefix "ERO" ; sh:namespace "http://purl.obolibrary.org/obo/ERO_" ; sh:pattern "^\d{7}$" ], @@ -109,7 +109,6 @@ [ sh:prefix "GEOGEO" ; sh:namespace "http://purl.obolibrary.org/obo/GEO_" ; sh:pattern "^\d{9}$" ], [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^\d{8}$" ], [ sh:prefix "GO" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "GRO" ; sh:namespace "http://purl.obolibrary.org/obo/GRO_" ], [ sh:prefix "GSSO" ; sh:namespace "http://purl.obolibrary.org/obo/GSSO_" ; sh:pattern "^\d{6}$" ], [ sh:prefix "HABRONATTUS" ; sh:namespace "http://purl.obolibrary.org/obo/HABRONATTUS_" ], [ sh:prefix "HANCESTRO" ; sh:namespace "http://purl.obolibrary.org/obo/HANCESTRO_" ; sh:pattern "^\d{4}$" ], @@ -127,7 +126,6 @@ [ sh:prefix "IEV" ; sh:namespace "http://purl.obolibrary.org/obo/IEV_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "IMR" ; sh:namespace "http://purl.obolibrary.org/obo/IMR_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "INO" ; sh:namespace "http://purl.obolibrary.org/obo/INO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "IPR" ; sh:namespace "http://purl.obolibrary.org/obo/IPR_" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "KISAO" ; sh:namespace "http://purl.obolibrary.org/obo/KISAO_" ; sh:pattern "^\d+$" ], [ sh:prefix "LABO" ; sh:namespace "http://purl.obolibrary.org/obo/LABO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "LEPAO" ; sh:namespace "http://purl.obolibrary.org/obo/LEPAO_" ; sh:pattern "^\d{7}$" ], @@ -170,7 +168,7 @@ [ sh:prefix "NIF_CELL" ; sh:namespace "http://purl.obolibrary.org/obo/NIF_CELL_" ], [ sh:prefix "NIF_DYSFUNCTION" ; sh:namespace "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_" ], [ sh:prefix "NIF_GROSSANATOMY" ; sh:namespace "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_" ], - [ sh:prefix "NMR" ; sh:namespace "http://purl.obolibrary.org/obo/NMR_" ; sh:pattern "^\d+$" ], + [ sh:prefix "NMR" ; sh:namespace "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:" ; sh:pattern "^\d+$" ], [ sh:prefix "NOMEN" ; sh:namespace "http://purl.obolibrary.org/obo/NOMEN_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "OAE" ; sh:namespace "http://purl.obolibrary.org/obo/OAE_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "OARCS" ; sh:namespace "http://purl.obolibrary.org/obo/OARCS_" ; sh:pattern "^\d{7}$" ], @@ -225,13 +223,13 @@ [ sh:prefix "PdumDv" ; sh:namespace "http://purl.obolibrary.org/obo/PdumDv_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "PuRO" ; sh:namespace "http://purl.org/spar/pro/" ], [ sh:prefix "RBO" ; sh:namespace "http://purl.obolibrary.org/obo/RBO_" ; sh:pattern "^\d{8}$" ], - [ sh:prefix "RESID" ; sh:namespace "http://purl.obolibrary.org/obo/RESID_" ; sh:pattern "^AA\d{4}$" ], + [ sh:prefix "RESID" ; sh:namespace "https://proteininformationresource.org/cgi-bin/resid?id=" ; sh:pattern "^AA\d{4}$" ], [ sh:prefix "REX" ; sh:namespace "http://purl.obolibrary.org/obo/REX_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "RNAO" ; sh:namespace "http://purl.obolibrary.org/obo/RNAO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "RO" ; sh:namespace "http://purl.obolibrary.org/obo/RO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "RS" ; sh:namespace "http://purl.obolibrary.org/obo/RS_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "RXNO" ; sh:namespace "http://purl.obolibrary.org/obo/RXNO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "SAO" ; sh:namespace "http://purl.obolibrary.org/obo/SAO_" ; sh:pattern "^\d+$" ], + [ sh:prefix "SAO" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/sao" ; sh:pattern "^\d+$" ], [ sh:prefix "SBO" ; sh:namespace "http://purl.obolibrary.org/obo/SBO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "SCDO" ; sh:namespace "http://purl.obolibrary.org/obo/SCDO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "SCTID" ; sh:namespace "http://www.snomedbrowser.com/Codes/Details/" ; sh:pattern "^(\w+)?\d+$" ], @@ -258,7 +256,7 @@ [ sh:prefix "UBERON" ; sh:namespace "http://purl.obolibrary.org/obo/UBERON_" ; sh:pattern "^\d+$" ], [ sh:prefix "UMLS" ; sh:namespace "http://linkedlifedata.com/resource/umls/id/" ; sh:pattern "^C\d+$" ], [ sh:prefix "UO" ; sh:namespace "http://purl.obolibrary.org/obo/UO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "UPA" ; sh:namespace "http://purl.obolibrary.org/obo/UPA_" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], + [ sh:prefix "UPA" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], [ sh:prefix "UPHENO" ; sh:namespace "http://purl.obolibrary.org/obo/UPHENO_" ], [ sh:prefix "VHOG" ; sh:namespace "http://purl.obolibrary.org/obo/VHOG_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "VO" ; sh:namespace "http://purl.obolibrary.org/obo/VO_" ; sh:pattern "^\d{7}$" ], @@ -274,7 +272,6 @@ [ sh:prefix "XCO" ; sh:namespace "http://purl.obolibrary.org/obo/XCO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "XLMOD" ; sh:namespace "http://purl.obolibrary.org/obo/XLMOD_" ; sh:pattern "^\d{5}$" ], [ sh:prefix "XPO" ; sh:namespace "http://purl.obolibrary.org/obo/XPO_" ; sh:pattern "^\d+$" ], - [ sh:prefix "YPO" ; sh:namespace "http://purl.obolibrary.org/obo/YPO_" ], [ sh:prefix "ZEA" ; sh:namespace "http://purl.obolibrary.org/obo/ZEA_" ], [ sh:prefix "ZECO" ; sh:namespace "http://purl.obolibrary.org/obo/ZECO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "ZFA" ; sh:namespace "http://purl.obolibrary.org/obo/ZFA_" ; sh:pattern "^\d{7}$" ], @@ -738,6 +735,7 @@ [ sh:prefix "intact" ; sh:namespace "https://www.ebi.ac.uk/intact/interaction/" ; sh:pattern "^EBI\-[0-9]+$" ], [ sh:prefix "intact.molecule" ; sh:namespace "https://www.ebi.ac.uk/intact/molecule/" ; sh:pattern "^EBI\-[0-9]+$" ], [ sh:prefix "interlex" ; sh:namespace "https://scicrunch.org/scicrunch/interlex/view/ilx_" ; sh:pattern "^[0-9]+$" ], + [ sh:prefix "interpro" ; sh:namespace "https://www.ebi.ac.uk/interpro/entry/" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "ird.segment" ; sh:namespace "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=" ; sh:pattern "^\w+(\_)?\d+(\.\d+)?$" ], [ sh:prefix "irefweb" ; sh:namespace "http://wodaklab.org/iRefWeb/interaction/show/" ; sh:pattern "^\d+$" ], [ sh:prefix "iro" ; sh:namespace "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:" ; sh:pattern "^\d{7}$" ], diff --git a/exports/contexts/obo_synonyms.context.jsonld b/exports/contexts/obo_synonyms.context.jsonld index 2dcdce7e6..3db929dae 100644 --- a/exports/contexts/obo_synonyms.context.jsonld +++ b/exports/contexts/obo_synonyms.context.jsonld @@ -6,7 +6,7 @@ "4dn.replicate": "https://data.4dnucleome.org/experiment-set-replicates/", "AAO": "http://purl.obolibrary.org/obo/AAO_", "ADO": "http://purl.obolibrary.org/obo/ADO_", - "ADW": "http://purl.obolibrary.org/obo/ADW_", + "ADW": "https://animaldiversity.org/accounts/", "AEO": "http://purl.obolibrary.org/obo/AEO_", "AEO_RETIRED": "http://purl.obolibrary.org/obo/AEO_", "AERO": "http://purl.obolibrary.org/obo/AERO_", @@ -121,7 +121,7 @@ "EMAPA_RETIRED": "http://purl.obolibrary.org/obo/EMAPA_", "ENSEMBL": "https://www.ensembl.org/id/", "ENVO": "http://purl.obolibrary.org/obo/ENVO_", - "EO": "http://purl.obolibrary.org/obo/EO_", + "EO": "http://archive.gramene.org/db/ontology/search?query=EO:", "EPIO": "http://purl.obolibrary.org/obo/EPIO_", "EPO": "http://purl.obolibrary.org/obo/EPO_", "ERO": "http://purl.obolibrary.org/obo/ERO_", @@ -162,7 +162,6 @@ "GFAM": "https://www.genenames.org/cgi-bin/genefamilies/set/", "GNO": "http://purl.obolibrary.org/obo/GNO_", "GO": "http://purl.obolibrary.org/obo/GO_", - "GRO": "http://purl.obolibrary.org/obo/GRO_", "GR_GENE": "http://www.gramene.org/db/genes/search_gene?acc=", "GR_PROTEIN": "http://www.gramene.org/db/protein/protein_search?protein_id=", "GR_QTL": "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=", @@ -205,9 +204,9 @@ "IMR": "http://purl.obolibrary.org/obo/IMR_", "INN_ID": "https://mednet-communities.net/inn/db/ViewINN.aspx?i=", "INO": "http://purl.obolibrary.org/obo/INO_", - "IP": "http://purl.obolibrary.org/obo/IPR_", + "IP": "https://www.ebi.ac.uk/interpro/entry/", "IPD-IMGT/HLA": "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?", - "IPR": "http://purl.obolibrary.org/obo/IPR_", + "IPR": "https://www.ebi.ac.uk/interpro/entry/", "ISBN-10": "http://isbndb.com/search-all.html?kw=", "ISBN-13": "http://isbndb.com/search-all.html?kw=", "IUPHAR_GPCR": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=", @@ -215,7 +214,7 @@ "IUPHAR_LIGAND_ID": "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=", "IUPHARfam": "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=", "IUPHARobj": "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=", - "InterPro": "http://purl.obolibrary.org/obo/IPR_", + "InterPro": "https://www.ebi.ac.uk/interpro/entry/", "JGI Phytozome": "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:", "KEGG": "http://www.kegg.jp/entry/", "KEGG COMPOUND": "https://www.kegg.jp/entry/", @@ -318,7 +317,7 @@ "NLXQUAL": "http://uri.neuinfo.org/nif/nifstd/nlx_qual_", "NLXRES": "http://uri.neuinfo.org/nif/nifstd/nlx_res_", "NLXSUB": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_", - "NMR": "http://purl.obolibrary.org/obo/NMR_", + "NMR": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:", "NOMEN": "http://purl.obolibrary.org/obo/NOMEN_", "NXP": "https://www.nextprot.org/db/entry/", "NXPFA": "https://www.nextprot.org/term/FA-", @@ -400,7 +399,7 @@ "RE": "https://reactome.org/content/detail/", "REACT": "https://reactome.org/content/detail/", "REFSEQ_PROT": "https://www.ncbi.nlm.nih.gov/protein/", - "RESID": "http://purl.obolibrary.org/obo/RESID_", + "RESID": "https://proteininformationresource.org/cgi-bin/resid?id=", "RETIRED_EHDAA2": "http://purl.obolibrary.org/obo/EHDAA2_", "REX": "http://purl.obolibrary.org/obo/REX_", "RGD": "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=", @@ -412,7 +411,7 @@ "RXCUI": "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=", "RXNO": "http://purl.obolibrary.org/obo/RXNO_", "SABIO-RK": "http://sabiork.h-its.org/reacdetails.jsp?reactid=", - "SAO": "http://purl.obolibrary.org/obo/SAO_", + "SAO": "http://uri.neuinfo.org/nif/nifstd/sao", "SBO": "http://purl.obolibrary.org/obo/SBO_", "SCDO": "http://purl.obolibrary.org/obo/SCDO_", "SCTID": "http://www.snomedbrowser.com/Codes/Details/", @@ -487,12 +486,12 @@ "UMLS_CUI": "http://linkedlifedata.com/resource/umls/id/", "UO": "http://purl.obolibrary.org/obo/UO_", "UP": "http://purl.uniprot.org/uniprot/", - "UPA": "http://purl.obolibrary.org/obo/UPA_", + "UPA": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", "UPHENO": "http://purl.obolibrary.org/obo/UPHENO_", "UPISO": "http://www.uniprot.org/uniprot/", "UPLOC": "https://www.uniprot.org/locations/", "UPPRO": "http://purl.uniprot.org/annotation/", - "UPa": "http://purl.obolibrary.org/obo/UPA_", + "UPa": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", "Uber-anatomy ontology": "http://purl.obolibrary.org/obo/UBERON_", "Uberon": "http://purl.obolibrary.org/obo/UBERON_", "UniProt": "http://purl.uniprot.org/uniprot/", @@ -520,7 +519,6 @@ "XLMOD": "http://purl.obolibrary.org/obo/XLMOD_", "XPO": "http://purl.obolibrary.org/obo/XPO_", "Xenbase": "https://www.xenbase.org/entry/", - "YPO": "http://purl.obolibrary.org/obo/YPO_", "ZEA": "http://purl.obolibrary.org/obo/ZEA_", "ZECO": "http://purl.obolibrary.org/obo/ZECO_", "ZFA": "http://purl.obolibrary.org/obo/ZFA_", @@ -1014,6 +1012,7 @@ "intact.molecule": "https://www.ebi.ac.uk/intact/molecule/", "intenz": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=", "interlex": "https://scicrunch.org/scicrunch/interlex/view/ilx_", + "interpro": "https://www.ebi.ac.uk/interpro/entry/", "inxight": "https://drugs.ncats.io/drug/", "inxight-drugs": "https://drugs.ncats.io/drug/", "ird.segment": "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=", @@ -1201,7 +1200,7 @@ "nlx.res": "http://uri.neuinfo.org/nif/nifstd/nlx_res_", "nlx.sub": "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_", "nmdc": "https://drs.microbiomedata.org/objects/", - "nmrcv": "http://purl.obolibrary.org/obo/NMR_", + "nmrcv": "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:", "nmrshiftdb2": "https://nmrshiftdb.nmr.uni-koeln.de/molecule/", "noaa": "https://www.fisheries.noaa.gov/species/", "noncodev3": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=", @@ -1473,9 +1472,9 @@ "unii": "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=", "unimod": "http://www.unimod.org/modifications_view.php?editid1=", "uniparc": "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=", - "unipathway": "http://purl.obolibrary.org/obo/UPA_", + "unipathway": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", "unipathway.compound": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=", - "unipathway.pathway": "http://purl.obolibrary.org/obo/UPA_", + "unipathway.pathway": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", "unipathway.reaction": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=", "uniprot": "http://purl.uniprot.org/uniprot/", "uniprot.chain": "http://purl.uniprot.org/annotation/", diff --git a/exports/contexts/obo_synonyms.context.ttl b/exports/contexts/obo_synonyms.context.ttl index 4e92648b3..017f118a9 100644 --- a/exports/contexts/obo_synonyms.context.ttl +++ b/exports/contexts/obo_synonyms.context.ttl @@ -8,7 +8,7 @@ [ sh:prefix "4dn.replicate" ; sh:namespace "https://data.4dnucleome.org/experiment-set-replicates/" ], [ sh:prefix "AAO" ; sh:namespace "http://purl.obolibrary.org/obo/AAO_" ], [ sh:prefix "ADO" ; sh:namespace "http://purl.obolibrary.org/obo/ADO_" ], - [ sh:prefix "ADW" ; sh:namespace "http://purl.obolibrary.org/obo/ADW_" ; sh:pattern "^[A-Z_a-z]+$" ], + [ sh:prefix "ADW" ; sh:namespace "https://animaldiversity.org/accounts/" ; sh:pattern "^[A-Z_a-z]+$" ], [ sh:prefix "AEO" ; sh:namespace "http://purl.obolibrary.org/obo/AEO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "AEO_RETIRED" ; sh:namespace "http://purl.obolibrary.org/obo/AEO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "AERO" ; sh:namespace "http://purl.obolibrary.org/obo/AERO_" ; sh:pattern "^\d{7}$" ], @@ -123,7 +123,7 @@ [ sh:prefix "EMAPA_RETIRED" ; sh:namespace "http://purl.obolibrary.org/obo/EMAPA_" ; sh:pattern "^\d+$" ], [ sh:prefix "ENSEMBL" ; sh:namespace "https://www.ensembl.org/id/" ; sh:pattern "^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$" ], [ sh:prefix "ENVO" ; sh:namespace "http://purl.obolibrary.org/obo/ENVO_" ; sh:pattern "^\d{7,8}$" ], - [ sh:prefix "EO" ; sh:namespace "http://purl.obolibrary.org/obo/EO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "EO" ; sh:namespace "http://archive.gramene.org/db/ontology/search?query=EO:" ; sh:pattern "^\d{7}$" ], [ sh:prefix "EPIO" ; sh:namespace "http://purl.obolibrary.org/obo/EPIO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "EPO" ; sh:namespace "http://purl.obolibrary.org/obo/EPO_" ], [ sh:prefix "ERO" ; sh:namespace "http://purl.obolibrary.org/obo/ERO_" ; sh:pattern "^\d{7}$" ], @@ -164,7 +164,6 @@ [ sh:prefix "GFAM" ; sh:namespace "https://www.genenames.org/cgi-bin/genefamilies/set/" ; sh:pattern "^\d+$" ], [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^\d{8}$" ], [ sh:prefix "GO" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "GRO" ; sh:namespace "http://purl.obolibrary.org/obo/GRO_" ], [ sh:prefix "GR_GENE" ; sh:namespace "http://www.gramene.org/db/genes/search_gene?acc=" ; sh:pattern "^GR\:\d+$" ], [ sh:prefix "GR_PROTEIN" ; sh:namespace "http://www.gramene.org/db/protein/protein_search?protein_id=" ; sh:pattern "^\d+$" ], [ sh:prefix "GR_QTL" ; sh:namespace "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=" ; sh:pattern "^\w+$" ], @@ -207,9 +206,9 @@ [ sh:prefix "IMR" ; sh:namespace "http://purl.obolibrary.org/obo/IMR_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "INN_ID" ; sh:namespace "https://mednet-communities.net/inn/db/ViewINN.aspx?i=" ], [ sh:prefix "INO" ; sh:namespace "http://purl.obolibrary.org/obo/INO_" ; sh:pattern "^\d{7}$" ], - [ sh:prefix "IP" ; sh:namespace "http://purl.obolibrary.org/obo/IPR_" ; sh:pattern "^IPR\d{6}$" ], + [ sh:prefix "IP" ; sh:namespace "https://www.ebi.ac.uk/interpro/entry/" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "IPD-IMGT/HLA" ; sh:namespace "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?" ; sh:pattern "^[A-Z0-9*:]+$" ], - [ sh:prefix "IPR" ; sh:namespace "http://purl.obolibrary.org/obo/IPR_" ; sh:pattern "^IPR\d{6}$" ], + [ sh:prefix "IPR" ; sh:namespace "https://www.ebi.ac.uk/interpro/entry/" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "ISBN-10" ; sh:namespace "http://isbndb.com/search-all.html?kw=" ; sh:pattern "^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$" ], [ sh:prefix "ISBN-13" ; sh:namespace "http://isbndb.com/search-all.html?kw=" ; sh:pattern "^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$" ], [ sh:prefix "IUPHAR_GPCR" ; sh:namespace "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=" ; sh:pattern "^\d+$" ], @@ -217,7 +216,7 @@ [ sh:prefix "IUPHAR_LIGAND_ID" ; sh:namespace "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=" ; sh:pattern "^\d+$" ], [ sh:prefix "IUPHARfam" ; sh:namespace "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=" ; sh:pattern "^\d+$" ], [ sh:prefix "IUPHARobj" ; sh:namespace "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=" ; sh:pattern "^\d+$" ], - [ sh:prefix "InterPro" ; sh:namespace "http://purl.obolibrary.org/obo/IPR_" ; sh:pattern "^IPR\d{6}$" ], + [ sh:prefix "InterPro" ; sh:namespace "https://www.ebi.ac.uk/interpro/entry/" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "JGI Phytozome" ; sh:namespace "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:" ; sh:pattern "^[A-Za-z0-9]+$" ], [ sh:prefix "KEGG" ; sh:namespace "http://www.kegg.jp/entry/" ; sh:pattern "^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$" ], [ sh:prefix "KEGG COMPOUND" ; sh:namespace "https://www.kegg.jp/entry/" ; sh:pattern "^C\d+$" ], @@ -320,7 +319,7 @@ [ sh:prefix "NLXQUAL" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/nlx_qual_" ; sh:pattern "^\d+$" ], [ sh:prefix "NLXRES" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/nlx_res_" ; sh:pattern "^\d+$" ], [ sh:prefix "NLXSUB" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_" ; sh:pattern "^\d+$" ], - [ sh:prefix "NMR" ; sh:namespace "http://purl.obolibrary.org/obo/NMR_" ; sh:pattern "^\d+$" ], + [ sh:prefix "NMR" ; sh:namespace "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:" ; sh:pattern "^\d+$" ], [ sh:prefix "NOMEN" ; sh:namespace "http://purl.obolibrary.org/obo/NOMEN_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "NXP" ; sh:namespace "https://www.nextprot.org/db/entry/" ; sh:pattern "^NX_\w+$" ], [ sh:prefix "NXPFA" ; sh:namespace "https://www.nextprot.org/term/FA-" ; sh:pattern "^\d+$" ], @@ -402,7 +401,7 @@ [ sh:prefix "RE" ; sh:namespace "https://reactome.org/content/detail/" ; sh:pattern "^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$" ], [ sh:prefix "REACT" ; sh:namespace "https://reactome.org/content/detail/" ; sh:pattern "^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$" ], [ sh:prefix "REFSEQ_PROT" ; sh:namespace "https://www.ncbi.nlm.nih.gov/protein/" ; sh:pattern "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$" ], - [ sh:prefix "RESID" ; sh:namespace "http://purl.obolibrary.org/obo/RESID_" ; sh:pattern "^AA\d{4}$" ], + [ sh:prefix "RESID" ; sh:namespace "https://proteininformationresource.org/cgi-bin/resid?id=" ; sh:pattern "^AA\d{4}$" ], [ sh:prefix "RETIRED_EHDAA2" ; sh:namespace "http://purl.obolibrary.org/obo/EHDAA2_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "REX" ; sh:namespace "http://purl.obolibrary.org/obo/REX_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "RGD" ; sh:namespace "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=" ; sh:pattern "^\d{4,}$" ], @@ -414,7 +413,7 @@ [ sh:prefix "RXCUI" ; sh:namespace "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=" ; sh:pattern "^[0-9]{1,7}$" ], [ sh:prefix "RXNO" ; sh:namespace "http://purl.obolibrary.org/obo/RXNO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "SABIO-RK" ; sh:namespace "http://sabiork.h-its.org/reacdetails.jsp?reactid=" ; sh:pattern "^\d+$" ], - [ sh:prefix "SAO" ; sh:namespace "http://purl.obolibrary.org/obo/SAO_" ; sh:pattern "^\d+$" ], + [ sh:prefix "SAO" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/sao" ; sh:pattern "^\d+$" ], [ sh:prefix "SBO" ; sh:namespace "http://purl.obolibrary.org/obo/SBO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "SCDO" ; sh:namespace "http://purl.obolibrary.org/obo/SCDO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "SCTID" ; sh:namespace "http://www.snomedbrowser.com/Codes/Details/" ; sh:pattern "^(\w+)?\d+$" ], @@ -489,12 +488,12 @@ [ sh:prefix "UMLS_CUI" ; sh:namespace "http://linkedlifedata.com/resource/umls/id/" ; sh:pattern "^C\d+$" ], [ sh:prefix "UO" ; sh:namespace "http://purl.obolibrary.org/obo/UO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "UP" ; sh:namespace "http://purl.uniprot.org/uniprot/" ; sh:pattern "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$" ], - [ sh:prefix "UPA" ; sh:namespace "http://purl.obolibrary.org/obo/UPA_" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], + [ sh:prefix "UPA" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], [ sh:prefix "UPHENO" ; sh:namespace "http://purl.obolibrary.org/obo/UPHENO_" ], [ sh:prefix "UPISO" ; sh:namespace "http://www.uniprot.org/uniprot/" ; sh:pattern "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\-\d+)$" ], [ sh:prefix "UPLOC" ; sh:namespace "https://www.uniprot.org/locations/" ; sh:pattern "^SL-\d+$" ], [ sh:prefix "UPPRO" ; sh:namespace "http://purl.uniprot.org/annotation/" ; sh:pattern "^PRO_[0-9]{10}$" ], - [ sh:prefix "UPa" ; sh:namespace "http://purl.obolibrary.org/obo/UPA_" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], + [ sh:prefix "UPa" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], [ sh:prefix "Uber-anatomy ontology" ; sh:namespace "http://purl.obolibrary.org/obo/UBERON_" ; sh:pattern "^\d+$" ], [ sh:prefix "Uberon" ; sh:namespace "http://purl.obolibrary.org/obo/UBERON_" ; sh:pattern "^\d+$" ], [ sh:prefix "UniProt" ; sh:namespace "http://purl.uniprot.org/uniprot/" ; sh:pattern "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$" ], @@ -522,7 +521,6 @@ [ sh:prefix "XLMOD" ; sh:namespace "http://purl.obolibrary.org/obo/XLMOD_" ; sh:pattern "^\d{5}$" ], [ sh:prefix "XPO" ; sh:namespace "http://purl.obolibrary.org/obo/XPO_" ; sh:pattern "^\d+$" ], [ sh:prefix "Xenbase" ; sh:namespace "https://www.xenbase.org/entry/" ; sh:pattern "^XB\-\w+\-\d+$" ], - [ sh:prefix "YPO" ; sh:namespace "http://purl.obolibrary.org/obo/YPO_" ], [ sh:prefix "ZEA" ; sh:namespace "http://purl.obolibrary.org/obo/ZEA_" ], [ sh:prefix "ZECO" ; sh:namespace "http://purl.obolibrary.org/obo/ZECO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "ZFA" ; sh:namespace "http://purl.obolibrary.org/obo/ZFA_" ; sh:pattern "^\d{7}$" ], @@ -1016,6 +1014,7 @@ [ sh:prefix "intact.molecule" ; sh:namespace "https://www.ebi.ac.uk/intact/molecule/" ; sh:pattern "^EBI\-[0-9]+$" ], [ sh:prefix "intenz" ; sh:namespace "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=" ; sh:pattern "^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$" ], [ sh:prefix "interlex" ; sh:namespace "https://scicrunch.org/scicrunch/interlex/view/ilx_" ; sh:pattern "^[0-9]+$" ], + [ sh:prefix "interpro" ; sh:namespace "https://www.ebi.ac.uk/interpro/entry/" ; sh:pattern "^IPR\d{6}$" ], [ sh:prefix "inxight" ; sh:namespace "https://drugs.ncats.io/drug/" ], [ sh:prefix "inxight-drugs" ; sh:namespace "https://drugs.ncats.io/drug/" ], [ sh:prefix "ird.segment" ; sh:namespace "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=" ; sh:pattern "^\w+(\_)?\d+(\.\d+)?$" ], @@ -1203,7 +1202,7 @@ [ sh:prefix "nlx.res" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/nlx_res_" ; sh:pattern "^\d+$" ], [ sh:prefix "nlx.sub" ; sh:namespace "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_" ; sh:pattern "^\d+$" ], [ sh:prefix "nmdc" ; sh:namespace "https://drs.microbiomedata.org/objects/" ; sh:pattern "^[\w\-.]{3,}$" ], - [ sh:prefix "nmrcv" ; sh:namespace "http://purl.obolibrary.org/obo/NMR_" ; sh:pattern "^\d+$" ], + [ sh:prefix "nmrcv" ; sh:namespace "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:" ; sh:pattern "^\d+$" ], [ sh:prefix "nmrshiftdb2" ; sh:namespace "https://nmrshiftdb.nmr.uni-koeln.de/molecule/" ; sh:pattern "^[0-9]+$" ], [ sh:prefix "noaa" ; sh:namespace "https://www.fisheries.noaa.gov/species/" ; sh:pattern "^[a-z]+(\-[a-z]+)*$" ], [ sh:prefix "noncodev3" ; sh:namespace "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=" ; sh:pattern "^\d+$" ], @@ -1475,9 +1474,9 @@ [ sh:prefix "unii" ; sh:namespace "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=" ; sh:pattern "^[A-Z0-9]+$" ], [ sh:prefix "unimod" ; sh:namespace "http://www.unimod.org/modifications_view.php?editid1=" ; sh:pattern "^\d+$" ], [ sh:prefix "uniparc" ; sh:namespace "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=" ; sh:pattern "^UPI[A-F0-9]{10}$" ], - [ sh:prefix "unipathway" ; sh:namespace "http://purl.obolibrary.org/obo/UPA_" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], + [ sh:prefix "unipathway" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], [ sh:prefix "unipathway.compound" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=" ; sh:pattern "^UPC\d{5}$" ], - [ sh:prefix "unipathway.pathway" ; sh:namespace "http://purl.obolibrary.org/obo/UPA_" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], + [ sh:prefix "unipathway.pathway" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=" ; sh:pattern "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$" ], [ sh:prefix "unipathway.reaction" ; sh:namespace "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=" ; sh:pattern "^UCR\d{5}$" ], [ sh:prefix "uniprot" ; sh:namespace "http://purl.uniprot.org/uniprot/" ; sh:pattern "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$" ], [ sh:prefix "uniprot.chain" ; sh:namespace "http://purl.uniprot.org/annotation/" ; sh:pattern "^PRO_[0-9]{10}$" ], diff --git a/exports/rdf/bioregistry.jsonld b/exports/rdf/bioregistry.jsonld index 2e9fe1730..3b91cf122 100644 --- a/exports/rdf/bioregistry.jsonld +++ b/exports/rdf/bioregistry.jsonld @@ -15,7 +15,6 @@ "cheminf": "https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_", "cropoct": "https://www.cropontology.org/ontology/", "dc": "http://purl.org/dc/elements/1.1/", - "dcterms": "http://purl.org/dc/terms/", "ecoportal": "http://ecoportal.lifewatch.eu/ontologies/", "edam.data": "http://edamontology.org/data_", "fairsharing": "https://fairsharing.org/", @@ -24,7 +23,8 @@ "miriam": "https://registry.identifiers.org/registry/", "n2t": "https://bioregistry.io/metaregistry/n2t/", "ncbi.resource": "https://bioregistry.io/metaregistry/ncbi/", - "ns1": "http://www.w3.org/2004/02/skos/core#", + "ns1": "http://purl.org/dc/terms/", + "ns2": "http://www.w3.org/2004/02/skos/core#", "obofoundry": "http://www.obofoundry.org/ontology/", "ols": "https://www.ebi.ac.uk/ols/ontologies/", "ontobee": "http://www.ontobee.org/ontology/", @@ -41,1756 +41,1291 @@ }, "@graph": [ { - "@id": "https://fairsharing.org/FAIRsharing.78d3ad", + "@id": "https://bioregistry.io/metaregistry/cellosaurus/NHCDR", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/cellosaurus" } }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/CIO", + "@id": "https://registry.identifiers.org/registry/pride.project", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/metaregistry/n2t/panther.family", + "@id": "https://bioregistry.io/metaregistry/biocontext/GMD.REF", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" + "@id": "https://bioregistry.io/metaregistry/biocontext" } }, { - "@id": "https://orcid.org/0000-0001-5809-9523", - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Darren Natale" + "@id": "http://www.obofoundry.org/ontology/sbo", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/obofoundry" } }, { - "@id": "https://bioregistry.io/metaregistry/n2t/tigrfam", + "@id": "https://www.ebi.ac.uk/ols/ontologies/mamo", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" + "@id": "https://bioregistry.io/metaregistry/ols" } }, { - "@id": "https://fairsharing.org/FAIRsharing.5701h1", + "@id": "https://registry.identifiers.org/registry/dbgap", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/registry/fbbt", + "@id": "https://bioregistry.io/registry/biotools", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "An ontology of Drosophila 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"https://bioregistry.io/schema/#0000018": [ - { - "@id": "https://bioregistry.io/registry/pcl" - }, - { - "@id": "https://bioregistry.io/registry/scdo" - }, - { - "@id": "https://bioregistry.io/registry/ecto" - } - ], - "https://bioregistry.io/schema/#0000019": { - "@id": "https://orcid.org/0000-0002-2061-091X" + "http://xmlns.com/foaf/0.1/homepage": "https://ega-archive.org/", + "https://bioregistry.io/schema/#0000005": "EGAD00000000001", + "https://bioregistry.io/schema/#0000006": "https://www.ebi.ac.uk/ega/datasets/$1", + "https://bioregistry.io/schema/#0000008": "^EGAD\\d{11}$", + "https://bioregistry.io/schema/#0000012": false + }, + { + "@id": "https://registry.identifiers.org/registry/dragondb.dna", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/registry/merops", - "http://purl.org/dc/terms/hasPart": [ - { - "@id": "https://bioregistry.io/registry/merops.family" - }, - { - "@id": "https://bioregistry.io/registry/merops.clan" - } - ] + "@id": "https://fairsharing.org/FAIRsharing.c86b48", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/fairsharing" + } }, { - "@id": "http://www.ontobee.org/ontology/OPL", + "@id": "https://fairsharing.org/FAIRsharing.rvz0m9", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/fairsharing" + } + }, + { + "@id": "http://www.ontobee.org/ontology/FIX", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/ontobee" } }, { - "@id": "https://registry.identifiers.org/registry/rfam", + "@id": "https://registry.identifiers.org/registry/mesh.2013", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://www.uniprot.org/database/DB-Rouge", + "@id": "https://bioregistry.io/registry/geonames", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge.", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/uniprot" - } + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "GeoNames" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": { + "@id": "https://fairsharing.org/FAIRsharing.56a0Uj" + }, + "http://xmlns.com/foaf/0.1/homepage": "https://www.geonames.org", + "https://bioregistry.io/schema/#0000005": "3532759", + "https://bioregistry.io/schema/#0000006": "https://www.geonames.org/$1", + "https://bioregistry.io/schema/#0000008": "^\\d+$", + "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://prefixcommons.org/?q=smpdb", + "@id": "https://registry.identifiers.org/registry/hcvdb", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://fairsharing.org/FAIRsharing.6bc7h9", + "@id": "https://registry.identifiers.org/registry/wikigenes", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://prefixcommons.org/?q=wikipedia", + "@id": "https://bioregistry.io/metaregistry/ncbi/PomBase", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" + "@id": "https://bioregistry.io/metaregistry/ncbi" } }, { - "@id": "https://bioregistry.io/registry/psdo", + "@id": "https://bioregistry.io/registry/ardb", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed.", + "http://purl.org/dc/elements/1.1/description": "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Performance Summary Display Ontology" + "@value": "Antibiotic Resistance Genes Database" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "http://aber-owl.net/ontology/PSDO" - }, - { - "@id": "http://www.ontobee.org/ontology/PSDO" - }, - { - "@id": "https://www.ebi.ac.uk/ols/ontologies/psdo" - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/PSDO" - }, - { - "@id": "http://www.obofoundry.org/ontology/PSDO" - } - ], - "http://xmlns.com/foaf/0.1/homepage": "https://github.com/Display-Lab/psdo", - "https://bioregistry.io/schema/#0000005": "0000055", - "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/PSDO_$1", - "https://bioregistry.io/schema/#0000008": "^\\d{7}$", - "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000017": [ - { - "@id": "https://bioregistry.io/registry/stato" - }, - { - "@id": "https://bioregistry.io/registry/ro" + "@id": "https://bioregistry.io/metaregistry/n2t/ardb" }, { - "@id": "https://bioregistry.io/registry/bfo" + "@id": "https://registry.identifiers.org/registry/ardb" }, { - "@id": "https://bioregistry.io/registry/iao" + "@id": "https://bioregistry.io/metaregistry/biocontext/ARDB" } ], - "https://bioregistry.io/schema/#0000019": { - "@id": "https://orcid.org/0000-0002-9117-9338" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/n2t/cas", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" - } + "http://xmlns.com/foaf/0.1/homepage": "http://ardb.cbcb.umd.edu/", + "https://bioregistry.io/schema/#0000005": "CAE46076", + "https://bioregistry.io/schema/#0000006": "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1", + "https://bioregistry.io/schema/#0000008": "^[A-Z_]{3}[0-9]{4,}$", + "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://fairsharing.org/FAIRsharing.y2qkst", + "@id": "https://registry.identifiers.org/registry/arrayexpress", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/registry/eupath", + "@id": "https://bioregistry.io/registry/vto", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available.", + "http://purl.org/dc/elements/1.1/description": "Comprehensive hierarchy of extinct and extant vertebrate taxa.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "VEuPathDB ontology" + "@value": "Vertebrate Taxonomy Ontology" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://bioportal.bioontology.org/ontologies/EUPATH" + "@id": "https://www.ebi.ac.uk/ols/ontologies/vto" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/EUPATH" + "@id": "http://aber-owl.net/ontology/VTO" }, { - "@id": "http://aber-owl.net/ontology/EUPATH" + "@id": "http://www.ontobee.org/ontology/VTO" }, { - "@id": "https://fairsharing.org/FAIRsharing.9rhr9j" + "@id": "https://bioportal.bioontology.org/ontologies/VTO" }, { - "@id": "http://www.ontobee.org/ontology/EUPATH" + "@id": "http://www.obofoundry.org/ontology/vto" }, { - "@id": "https://www.ebi.ac.uk/ols/ontologies/eupath" + "@id": "https://fairsharing.org/FAIRsharing.akmeb9" }, { - "@id": "http://www.obofoundry.org/ontology/EUPATH" + "@id": "https://bioregistry.io/metaregistry/biocontext/VTO" } ], - "http://xmlns.com/foaf/0.1/homepage": "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology", - "https://bioregistry.io/schema/#0000005": "0010316", - "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/EUPATH_$1", + "http://xmlns.com/foaf/0.1/homepage": "https://github.com/phenoscape/vertebrate-taxonomy-ontology", + "https://bioregistry.io/schema/#0000005": "9008500", + "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/VTO_$1", "https://bioregistry.io/schema/#0000008": "^\\d{7}$", "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000018": { - "@id": "https://bioregistry.io/registry/scdo" - }, "https://bioregistry.io/schema/#0000019": { - "@id": "https://orcid.org/0000-0002-2999-0103" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/biocontext/IRD.SEGMENT", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" + "@id": "https://orcid.org/0000-0002-8688-6599" } }, { - "@id": "https://bioregistry.io/registry/span", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality.", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Span" - }, - "http://xmlns.com/foaf/0.1/homepage": "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf", - "https://bioregistry.io/schema/#0000012": false - }, - { - "@id": "https://bioregistry.io/registry/gold.meta", + "@id": "https://bioregistry.io/registry/treefam", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples.", + "http://purl.org/dc/elements/1.1/description": "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "GOLD metadata" + "@value": "TreeFam" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://bioregistry.io/metaregistry/biocontext/GOLD.META" + "@id": "https://prefixcommons.org/?q=treefam" }, { - "@id": "https://bioregistry.io/metaregistry/n2t/gold.meta" + "@id": "https://registry.identifiers.org/registry/treefam" }, { - "@id": "https://registry.identifiers.org/registry/gold.meta" + "@id": "https://bioregistry.io/metaregistry/biocontext/TREEFAM" + }, + { + "@id": "https://www.uniprot.org/database/DB-TreeFam" + }, + { + "@id": "https://bioregistry.io/metaregistry/n2t/treefam" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi", - "https://bioregistry.io/schema/#0000005": "Gm00047", - "https://bioregistry.io/schema/#0000006": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1", - "https://bioregistry.io/schema/#0000008": "^Gm\\d+$", + "http://xmlns.com/foaf/0.1/homepage": "http://www.treefam.org/", + "https://bioregistry.io/schema/#0000005": "TF101014", + "https://bioregistry.io/schema/#0000006": "http://www.treefam.org/family/$1", + "https://bioregistry.io/schema/#0000008": "^\\w{1,2}\\d+$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioregistry.io/registry/ark", + "@id": "https://bioregistry.io/registry/fideo", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type.", + "http://purl.org/dc/elements/1.1/description": "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Archival Resource Key" + "@value": "Food Interactions with Drugs Evidence Ontology" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://bioregistry.io/metaregistry/n2t/ark" + "@id": "https://www.ebi.ac.uk/ols/ontologies/fideo" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/ARK" + "@id": "http://www.ontobee.org/ontology/FIDEO" }, { - "@id": "https://registry.identifiers.org/registry/ark" + "@id": "http://aber-owl.net/ontology/FIDEO" + }, + { + "@id": "https://bioportal.bioontology.org/ontologies/FIDEO" + }, + { + "@id": "http://www.obofoundry.org/ontology/fideo" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://n2t.net/", - "https://bioregistry.io/schema/#0000005": "/12345/fk1234", - 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"@id": "https://www.ebi.ac.uk/ols/ontologies/co_338", + "@id": "https://bioregistry.io/metaregistry/n2t/psipar", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/ols" + "@id": "https://bioregistry.io/metaregistry/n2t" } }, { - "@id": "https://www.ebi.ac.uk/ols/ontologies/po", + "@id": "https://www.ebi.ac.uk/ols/ontologies/dpo", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/ols" } }, { - "@id": "https://bioportal.bioontology.org/ontologies/EPIO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/biocontext/OAE", + "@id": "http://aber-owl.net/ontology/ECO", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" + "@id": "https://bioregistry.io/metaregistry/aberowl" } }, { - "@id": "https://bioregistry.io/registry/schema", + "@id": "https://bioregistry.io/registry/labo", "@type": "https://bioregistry.io/schema/#0000001", - 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It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. 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The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "C. elegans Gross Anatomy Ontology" + "@value": "Minimum Anformation About a Phylogenetic Analysis Ontology" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://fairsharing.org/FAIRsharing.phk7dd" - }, - { - "@id": "http://www.ontobee.org/ontology/WBbt" - }, - { - "@id": "https://bioregistry.io/metaregistry/biolink/WBbt" - }, - { - "@id": "https://prefixcommons.org/?q=wbbt" + "@id": "https://bioportal.bioontology.org/ontologies/MIAPA" }, { - "@id": "https://bioportal.bioontology.org/ontologies/WB-BT" + "@id": "https://www.ebi.ac.uk/ols/ontologies/miapa" }, { - "@id": "http://www.obofoundry.org/ontology/WBbt" + "@id": "http://www.obofoundry.org/ontology/miapa" }, { - "@id": "https://bioregistry.io/metaregistry/go/WBbt" + "@id": "https://bioregistry.io/metaregistry/biocontext/MIAPA" }, { - "@id": "http://aber-owl.net/ontology/WBBT" + "@id": "http://aber-owl.net/ontology/MIAPA" }, { - "@id": "https://www.ebi.ac.uk/ols/ontologies/wbbt" + "@id": "https://fairsharing.org/FAIRsharing.ca48xs" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/WBbt" + "@id": "http://www.ontobee.org/ontology/MIAPA" } ], - "http://xmlns.com/foaf/0.1/homepage": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology", - "https://bioregistry.io/schema/#0000005": "0001290", - "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/WBbt_$1", + "http://xmlns.com/foaf/0.1/homepage": "http://www.evoio.org/wiki/MIAPA", + "https://bioregistry.io/schema/#0000005": "0000010", + "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/MIAPA_$1", "https://bioregistry.io/schema/#0000008": "^\\d{7}$", "https://bioregistry.io/schema/#0000012": false, "https://bioregistry.io/schema/#0000019": { - "@id": "https://orcid.org/0000-0002-8151-7479" - } - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/PO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" + "@id": "https://orcid.org/0000-0001-9107-0714" } }, { - "@id": "http://www.ontobee.org/ontology/CDAO", + "@id": "https://registry.identifiers.org/registry/ecoliwiki", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/ontobee" + "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/metaregistry/biolink/foodb.food", + "@id": "https://bioregistry.io/registry/aphidbase.transcript", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information.", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biolink" - } - }, - { - "@id": "https://orcid.org/0000-0002-1509-4981", + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Matúš Kalaš" - } + "@value": "AphidBase Transcript" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "https://bioregistry.io/metaregistry/n2t/aphidbase.transcript" + }, + { + "@id": "https://registry.identifiers.org/registry/aphidbase.transcript" + }, + { + "@id": "https://bioregistry.io/metaregistry/biocontext/APHIDBASE.TRANSCRIPT" + } + ], + "http://xmlns.com/foaf/0.1/homepage": "http://www.aphidbase.com/aphidbase", + "https://bioregistry.io/schema/#0000005": "ACYPI000159", + "https://bioregistry.io/schema/#0000006": "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1", + "https://bioregistry.io/schema/#0000008": "^ACYPI\\d{6}(-RA)?$", + "https://bioregistry.io/schema/#0000012": false } ] } \ No newline at end of file diff --git a/exports/rdf/bioregistry.nt b/exports/rdf/bioregistry.nt index e0933beee..cc631075c 100644 --- a/exports/rdf/bioregistry.nt +++ b/exports/rdf/bioregistry.nt @@ -1,31857 +1,31859 @@ - "false"^^ . - "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . - . - . - . - . - . - . - . -_:Ne896ab818ea343789462ac9fa7e3e18f "Jonathan Bard" . - . - . - "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . - . - "^FB\\w{2}\\d{7}$"^^ . - "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . - "http://geneontology.org/docs/guide-go-evidence-codes/"^^ . - "^[0-9]+$"^^ . - . - . - . - "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . - . - . - "http://www.cropontology.org/ontology/CO_327/Pearl%20millet"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TTO_$1"^^ . - . - . - "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - "https://signor.uniroma2.it/"^^ . - "The Food Ontology" . - . - . - . - . - "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . - . - . - . - . - "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . - . - "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . - . - "^[A-Z-a-z0-9]+$"^^ . - "https://archive.softwareheritage.org"^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_325:$1"^^ . - "false"^^ . - "https://pharmacodb.ca/datasets/$1"^^ . - . - "http://www.geneontology.org/gocam"^^ . - "https://github.com/monarch-initiative/SEPIO-ontology"^^ . - . - "Observational Medical Outcomes Partnership" . - . - . - "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . - . - . - . - . - . - . - . - . - "Rice Genome Annotation Project" . - . - "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . - . - . - "^IM-\\d+(-?)(\\d+?)$"^^ . - . - "FlyBase Qualifiers" . - . - . - . - . - . - "false"^^ . - . - "Brassica ontology" . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "Common Bean ontology" . - . - . - . - "^\\d{7}$"^^ . - . - "Mutant Mouse Resource and Research Centers" . - . - . - . - . - . - . - . - "TreeFam" . - . - "AKR-270"^^ . - . - . - . - . - "false"^^ . - . - "Circular double stranded DNA sequences composed" . - "Suggested Ontology for Pharmacogenomics" . - . - "^UPC\\d{5}$"^^ . - . - "Glyma0021s00410"^^ . - . - . - . - "Environmental conditions, treatments and exposures ontology" . - . - . - . - . - "TIGR protein families" . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . - . - "0000001"^^ . - "Telethon Network of Genetic Biobanks" . - . - . - . - "false"^^ . - . - "ChEMBL target" . - "^[0-9]+$"^^ . - . - . - "Google Patents" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . - . - "InterPro" . - . - . - . - . - . - . - "SSF57615"^^ . - . - "https://horizondiscovery.com/en/search?searchterm=$1"^^ . - . - . - . - . - . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - "http://www.gramene.org/db/ontology/search?id=$1"^^ . - . - "http://www.w3.org/2002/07/owl#$1"^^ . - "true"^^ . - . - . - . - "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . - . - . - . - . - "190000021540"^^ . - . - "A database for Triticeae and Avena gene symbols."^^ . -_:N8ebd69fb45dc4921afb4d7643fbcd91c "GenBank Support" . - . - "https://w3id.org"^^ . - "^\\d{7}$"^^ . - . - "Tom Gillespie" . - . - . - . - . - . - "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . - . - . - . - "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . - . - . - "^[1-9]\\d{0,5}$"^^ . - "Gene Regulation Ontology" . - . - . - . - "http://www.gramene.org/"^^ . - "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html"^^ . - "http://purl.obolibrary.org/obo/FBSP_$1"^^ . -_:N159387d952584bb48466cc3880fbdbeb "Jonathan Bard" . - "Kerafast cell lines" . - "4007166"^^ . - . - "Molecule role (INOH Protein name/family name ontology)" . - . - . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - . - . - . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv"^^ . - . - . - . - . - . - . - . - "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . - . - . - "MCDS_C_0000000001"^^ . - "http://www.alanwood.net/pesticides"^^ . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - "^\\d+$"^^ . - . - . - . - _:Nce7fed9968da4026a9656318875caf42 . - . - "RF00230"^^ . - "G-Rich Sequences Database" . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . - . - . - . - . - "https://thebiogrid.org/"^^ . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1"^^ . - . - . - . - . - "P29894"^^ . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . - . - . - . - . - . - "true"^^ . - . - . - "The Drug-Drug Interactions Ontology" . - . - . - . - . - "false"^^ . - . - "P00747__P07355"^^ . - "http://neuinfo.org/"^^ . - . - . - "http://www.jcvi.org/mpidb/about.php"^^ . - . - "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . - . - . - . - . - . - . - . - "^PAR:\\d+$"^^ . - . - . - "^HGVST\\d+$"^^ . - . - . - "false"^^ . - . - . - . - "Cell line collections"^^ . - . - "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://www.nescent.org/phenoscape/Main_Page"^^ . - . - . - "http://euhcvdb.ibcp.fr"^^ . - . - . - "45539"^^ . - . - "miRNEST" . - . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . - . - . - "http://purl.obolibrary.org/obo/BSPO_$1"^^ . - "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . - . - . - . - "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . - . - "https://github.com/DiseaseOntology/PathogenTransmissionOntology"^^ . - . - . - . - . - . - . - . - . - "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . - . - "https://www.ebi.ac.uk/metagenomics"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - "http://www.nlm.nih.gov/mesh/"^^ . - "http://www.unimod.org/"^^ . - "false"^^ . - . - "miRTarBase" . - "LK99"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "https://cryptodb.org/cryptodb/"^^ . - "Homology Ontology" . - "Computer Retrieval of Information on Science Projects Thesaurus" . - "3966782"^^ . - . - "http://bugs.sgul.ac.uk/E-BUGS"^^ . - . - . - . - . - . - . - . - "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . - . - . - . - . - . - . - "3hB06"^^ . - . - . - . - . - . - "http://amoebadb.org/amoeba/"^^ . - . - . - . - . - . - . - . - "Fababean ontology" . - . - "1017"^^ . - . - . - "false"^^ . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . - . - . - "National Library of Medicine Catalog" . - . - . - . - "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . - . - . - . - . - "^(cl|tum)\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . - . - . - "false"^^ . - . - "Brian Aevermann" . - "https://github.com/PlantPhenoOntology/PPO"^^ . - "false"^^ . - . - . -_:Nb989cb7dedee4004a9c97f1355271a9f "Pantelis Topalis" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "4145692"^^ . - . - . - . - "Span" . - "Signaling Pathways Project" . - . - . - . - "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . - "Gerhard Mayer" . - . - . - . - "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^ . - . - . - . - . - . - . - . - . - . - . - . - "60316"^^ . - . - "https://proconsortium.org/app/entry/PR:$1"^^ . - . - "false"^^ . - . - . - . - . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . - "Gramene Gene" . - . - . - "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . - "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . - "false"^^ . - . - . - "Regulation of Transcription Ontology" . - "OpenAlex" . - "DP00003"^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - "PB000166"^^ . - . - . - . - . - . - "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Tom Gillespie" . - "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . - "false"^^ . - . - "http://viralzone.expasy.org/all_by_protein/$1.html"^^ . - . - . - . - . - "^\\d{7}$"^^ . - "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . - . - . - . - . - . - . - . - . - . - . - . - "Protein Data Bank Ligand" . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "^\\d+$"^^ . - "feature"^^ . - . - "Mental Functioning Ontology" . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - "Biological Collections Ontology" . - "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . - . - "Gene Ontology Causal Assembly Model" . - . - . - . - . - . - . - . - . - . - "UniProt Keywords" . - . - . - . - . - . - . - "http://www.cathdb.info/cathnode/$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - "NIF Standard Ontology: OEN Terms in Neurolex" . - . - . - . - "false"^^ . - "https://github.com/geneontology/go-ontology"^^ . -_:N5a204fe83f08423aa66671d566c22e9c "Jonathan Bard" . - . - . - . - . - . - . - . - "https://tree.opentreeoflife.org"^^ . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - . - . - . - . - "^\\d{6}$"^^ . - . - . - . - "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "ABC"^^ . - . - . - . - "https://cordis.europa.eu/project/id/$1"^^ . - . - . - "false"^^ . - . - "Wheat ontology" . - . - . - . - . - . - . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . - "https://www.ebi.ac.uk/metabolights/"^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - . - . - . - . - "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . - "WikiPathways" . - . - "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1"^^ . - . - "veNOG12876"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "90901"^^ . - . - "COG Categories" . - "Name-to-Thing" . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "http://www.jcvi.org/charprotdb"^^ . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - "https://bioportal.bioontology.org/" . - . - "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . - . - . - . - . - . - . - . - . - . - "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . - . - "http://bioinformatics.ramapo.edu/GRSDB2/"^^ . - . - "ASPL0000349247"^^ . - . - . - . - . - . - "Database portal containing replicate experiments of different assays and samples"^^ . - . - . - . - . - . - . - . - . - . - "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . - . - "Genatlas" . - "GWAS Central Marker" . - "Maize ontology" . - . - "http://planttfdb.cbi.pku.edu.cn"^^ . - "http://purl.obolibrary.org/obo/PSDO_$1"^^ . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/EMAP_$1"^^ . - . - . - "InChI" . - "http://edamontology.org/format_$1"^^ . - . - . - . - . - . - . - "https://github.com/monarch-initiative/MAxO"^^ . - "638309541"^^ . - . - "Identifier for an entity in open tree of life"^^ . - "^\\d{7}$"^^ . - . - "Gene Ontology Annotation Database" . - . - . - "CharProt" . - "NeuroVault Collection" . - . - "2023"^^ . - . - . - "https://vocab.lternet.edu/vocab/vocab/index.php"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . - "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . - . - "4447"^^ . - . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . - . - . - "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . - . - "PMC3084216"^^ . - "false"^^ . - . - "BitterDB Compound" . - . - "false"^^ . - . - . - "false"^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "^\\d{8}$"^^ . - . - . - . - . - . - "NIF Cell" . - . - "WormBase RNAi" . - . - "Fyler" . - . - . - "Core Ontology for Biology and Biomedicine" . - . - "https://idr.openmicroscopy.org"^^ . - . - . - . - . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - . - "Wikidata" . - "^[A-Za-z0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "Dataset"^^ . - "https://www.kegg.jp/entry/$1"^^ . - . - "https://biopragmatics.github.io/providers/sfam/$1"^^ . - . - "http://bioassayontology.org"^^ . - . - . - . - . - "false"^^ . - "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . - "https://bioregistry.io/$1:$2" . - . - . - . - "002678"^^ . - . - "false"^^ . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - "TTHERM_00648910"^^ . - . - "Transcription Factor Database" . - . - . - . - . - . - . - . - "37232"^^ . - "false"^^ . - "https://www.ebi.ac.uk/pride/archive/assays/$1"^^ . - . - . - . - . - "Ensembl Gene" . - . - . - "0000001"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "0002005"^^ . - . - . - "https://flowrepository.org/id/$1"^^ . - . - "KEGG Metagenome" . - . - . - "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - "https://cropontology.org/ontology/CO_358/Cotton"^^ . - . - . - "Eukaryotic Promoter Database" . - . - . - "0001157"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Phenoscape Publication" . - . - . - "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . - . - . - . - "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . - . - . - . - . - . - "0000288"^^ . - "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . - "1868"^^ . - . - . - . - . - . - . - . - . - "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . - . - "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^ . - . - "false"^^ . - . - . - . - "https://www.cameo3d.org/sp/targets/target/$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology"^^ . - "false"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MOP_$1"^^ . - "https://www.insdc.org/"^^ . - . - . - "false"^^ . - "5688061"^^ . - . - "http://www.mirbase.org/"^^ . - . - "http://europepmc.org/articles/$1"^^ . - "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . - "false"^^ . - "Studies in dbVar."^^ . - . - . - . - . - . - . - "0000295"^^ . - . - . - . - "BRAF"^^ . - "http://browser.planteome.org/amigo"^^ . - . - . - . - . - . - "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^ . - . - . - . - "0000001"^^ . - . - . - . - . - . - . - "https://github.com/HajoRijgersberg/OM"^^ . - . - . - . - . - "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MO_$1"^^ . - "http://edamontology.org/operation_$1"^^ . - "1351341"^^ . - "NX_O00165"^^ . - . - . - . - . - . - . - . - "ADM1"^^ . - . - "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . - . - "false"^^ . - "^\\w+$"^^ . - . - "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . - . - . - . - . - "http://xmlns.com/foaf/0.1/$1"^^ . - . - "http://sideeffects.embl.de/"^^ . - . - . - . - . - . - . - . - . - . - "3"^^ . - "https://github.com/obcs/obcs"^^ . - . - . - "https://www.ebi.ac.uk/ols" . - . - "SwissRegulon" . - . - . - "NIF Dysfunction" . - . - "false"^^ . - "false"^^ . - "Fossilworks Taxon" . - . - . - "^\\d+$"^^ . - . - . - . - . - "JCGG-STR008690"^^ . - . - . - . - . - . - "http://aps.unmc.edu/AP/"^^ . - . - . - "http://purl.obolibrary.org/obo/fbcv"^^ . - . - . - "false"^^ . - . - . - . - . - . - "^[A-Za-z0-9-]+$"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - "ICEberg family" . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "^MGYA\\d+$"^^ . - . - "false"^^ . - "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "RSC3"^^ . - . - . - . - . - . - . - "https://bioinformatics.cineca.it/PMDB/"^^ . - . - "https://www.psidev.info/peff"^^ . - "http://www.drugbank.ca"^^ . - "Ontology for genetic interval" . - . - . - . - . - "ArrayMap" . - . - . - "^PS\\d{5}$"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OMO_$1"^^ . - "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . - "PA447218"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "0058"^^ . - . - "^TIGR\\d+$"^^ . - . - . - . - . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/"^^ . - . - . - . - "http://unite.ut.ee/"^^ . - . - . - "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . - . - . - . - . - . - . - . - . - . - "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/medgen/"^^ . - "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . - . - . - "EasyChair Topic" . - . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - . - . - "SysBioCancer2022"^^ . - . - . - . - "^\\d+$"^^ . - "Identifiers.org Terms" . - . - . - . - . - "BitterDB Receptor" . - "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . - "https://github.com/obophenotype/ncbitaxon"^^ . - "http://4dx.embl.de/platy"^^ . - . - . - . - . - "false"^^ . - . - . - "0000590"^^ . - . - . - . - . - "http://www.obofoundry.org/" . - . - . - "false"^^ . - . - "https://www.w3.org/TR/owl-features/"^^ . - . - . - . - . - . - . - . - "https://web.www.healthdatagateway.org/dataset/$1"^^ . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - "^\\d+$"^^ . - . - "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^ . - . - "Sebastian Koehler" . - . - . - . - "https://github.com/qfo/OrthologyOntology"^^ . - . - "sbgn.er.level-1.version-1.2"^^ . - . - . - "0000773"^^ . - "^\\d+$"^^ . - "HIP000030660"^^ . - "false"^^ . - "^M\\d{4}$"^^ . - . - "^\\d{7}$"^^ . - . - "http://vocab.deri.ie/void"^^ . - . - . - . - "000912"^^ . - "^SMP\\d+$"^^ . - . - . - . - . - . - . - . - "https://github.com/arpcard/aro"^^ . - "0440"^^ . - . - . - . - "AOPWiki" . - "https://fcs-free.org"^^ . - "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . - . - . - . - . - . - . - . - . - . - . - "https://github.com/$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . - "https://www.nlm.nih.gov/research/umls/rxnorm/"^^ . - . - "E-MEXP-1712"^^ . - "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . - "false"^^ . - . - . - "https://scicrunch.org/resolver"^^ . - . - . - . - . - "Sequence Read Archive" . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "^ACH-\\d+$"^^ . - . - "COG Pathways" . - "Molecular Interactions Controlled Vocabulary" . - "false"^^ . - . - . - . - . - . - . - . - "T06648"^^ . - . - . - . - . - "https://www.hivreagentprogram.org/Home.aspx"^^ . - "Bambara groundnut ontology" . - . - . - . - . - . - . - "FlyBase Controlled Vocabulary" . - . - . - . - . - . - "^DB-\\d{4}$"^^ . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "https://smpdb.ca/view/$1"^^ . - . - . - . - "false"^^ . - . - . - "Chemical Information Ontology" . - . - . - . - "http://www.informatics.jax.org/expression.shtml"^^ . - "false"^^ . - . - "^\\d{6}$"^^ . - "Laurel Cooper" . - "0000001"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^ . - "^GLDS-\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^ . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . - . - "http://www.amphibanat.org"^^ . - . - . - . - . - . - "^\\d{6,7}$"^^ . - "https://fair-research.org"^^ . - . - . - . - . - . - . - . - . - "DDB0191090"^^ . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . - "https://kidsfirstdrc.org"^^ . - "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . - . - . - . - . - . - "101"^^ . - . - . - "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . - . - . - "biopragmatics/bioregistry"^^ . - . - . - . - . - "9861/3"^^ . - . - "http://www.obofoundry.org/ontology/$1" . - "Microbial Conditions Ontology" . - . - . - . - . - . - . - . - . - . - "^[0-9]*$"^^ . - . - "false"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . - . - "splash10-0zq2000000-77302b0326a418630a84"^^ . - . - . - . - . - . - . - . - "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology"^^ . - "false"^^ . - . - . - . - "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . - . - "false"^^ . - "FunderRegistry" . - . - . - . - "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . - . - . - . - . - "https://cropontology.org/ontology/CO_346/Mungbean"^^ . - . - . - . - "false"^^ . - . - "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . - . - . - . - "Subcellular Anatomy Ontology" . - . - "false"^^ . - . - . - . - . - . - "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . - "false"^^ . - . - . - "XB-GENE-922462"^^ . - "false"^^ . - . - . - . - . - . - "0001655"^^ . - "PubChem Element" . - "http://www.accessdata.fda.gov/scripts/cder/ndc/"^^ . - . - . - . - "FuncBase Yeast" . - . - . - . - . - . - "^XB\\-\\w+\\-\\d+$"^^ . - . - "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . - . - "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . - . - "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^ . - . - . - . - . - . - . - "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . - . - "Alzheimer's Disease Ontology" . - . - . - . - . - . - . - . - "DP00086r013"^^ . - . - "PASS01237"^^ . - "false"^^ . - . - . - "http://pax-db.org/"^^ . - "false"^^ . - "https://pictar.mdc-berlin.de/"^^ . - . - "Clinical Trials Ontology" . - . - . - . - "https://github.com/semanticchemistry/semanticchemistry" . - . - "false"^^ . - . - . - . - "ECU03_0820i"^^ . - "^\\d+$"^^ . - . - . - . - . - "JWS Online" . - . - . - "title"^^ . - . - "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . - "NONHSAG00001"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"^^ . - "https://www.ebi.ac.uk/intact/interaction/$1"^^ . - . - . - . - . - . - . - . - "2170610"^^ . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . - . - "^\\d+$"^^ . - "785"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PECO_$1"^^ . - . - "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . - . - . - "https://doulix.com/constructs/$1"^^ . - "0001114"^^ . - "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . - "DiscoverX cell line products" . - . - . - . - . - . - . - "false"^^ . - . - "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . - . - . - . - "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . - . - . - . - "Social Behavior in insects"^^ . - . - "00005254"^^ . - . - . - "TIGR00010"^^ . - . - . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . - . - . - . - . - "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - "http://www.cellsignal.com/products/$1.html"^^ . - "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GAZ_$1"^^ . - . - . - . - . - . - . - . - "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . - . - . - . - . - . - . - . - "CAA71118.1"^^ . - . - . - "http://www.ontobee.org/ontology/$1" . - . - . - . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . - "false"^^ . - . - "1-FEH+w3"^^ . - . - . - . - "MU9_3181"^^ . - . - "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . - . - . - . - . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . - . - "Catalogue of Life in Taiwan" . - "https://health.uconn.edu/"^^ . - "false"^^ . - . - "Plant Environment Ontology" . - "false"^^ . - . - . - _:N2b596d6f851d445d873ed6f8a3aeda5a . - . - "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . - . - "Chris Grove" . - . - . - . - . - . - "^[A-Z0-9*:]+$"^^ . - "MicroScope" . - "https://reporter.nih.gov/project-details/$1"^^ . - . - "ViralZone" . - . - . - "Intelligence Task Ontology" . - . - "Charles Ettensohn" . - . - . - "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . - . - "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . - "MarDB" . - . - "http://zinc15.docking.org/substances/$1"^^ . - "GrassBase" . - . - . - "^[A-Z_]{3}[0-9]{4,}$"^^ . - "false"^^ . - "http://mged.sourceforge.net/ontologies/MGEDontology.php"^^ . - "European Genome-phenome Archive Study" . - "false"^^ . - . - . - . - "http://www.sparontologies.net/ontologies/pro"^^ . - . - . - "http://proconsortium.org"^^ . - . - . - . - . - "46"^^ . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . - . - . - "4201PAT-CCTCC00348"^^ . - . - . - "Sequencing Initiative Suomi" . - . - . - . - . - . - "true"^^ . - "false"^^ . - . - . - . - . - "http://www-bionet.sscc.ru/sitex/"^^ . - . - . - . - "http://ncim.nci.nih.gov/"^^ . - . - "^\\d{7}$"^^ . - "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . - . - "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . - . - . - . - . - "http://www.sparontologies.net/ontologies/biro"^^ . - "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . - . - . - "http://purl.uniprot.org/uniprot/$1"^^ . - . - . - . - . - "Cell Line Database" . - . - . - "Uberon Property" . - . - "https://www.novusbio.com"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - "http://www.swisslipids.org/#/"^^ . - "https://cropontology.org/ontology/CO_326/Coconut"^^ . - . - . - "http://purl.obolibrary.org/obo/AAO_$1"^^ . - . - . - . - "http://www.3dmet.dna.affrc.go.jp/"^^ . - . - "https://www.ebi.ac.uk/arrayexpress/"^^ . - . - . - "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . - "http://purl.obolibrary.org/obo/OHMI_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.imanislife.com/collections/cell-lines/"^^ . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . - . - "Cell line collections"^^ . - "EDAM Ontology" . - . - . - "Edison Ong" . - . - . - . - "http://www.mycobank.org/"^^ . - "https://web.expasy.org/cellosaurus/"^^ . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "16S rRNA gene database" . - . - . - . - . - "false"^^ . - "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . - . - . - . - "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . - . - . - "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"^^ . - . - . - "0000093"^^ . - "false"^^ . - . - . - "NIST Chemistry WebBook" . - . - . - . - . - "http://greengenes.lbl.gov/"^^ . - . - . - . - . - "https://bioregistry.io/resolve/github/pull/$1"^^ . - . - . - "SEED Compound" . - . - . - "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^ . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - "MycoBrowser smegmatis" . - . - . - "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed."^^ . - "^\\d+$"^^ . - . - . - . - "0000639"^^ . - . - "https://glycopost.glycosmos.org"^^ . - . - "TGME49_053730"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "^[A-Za-z]+$"^^ . - . - . - "Conferences in EasyChair"^^ . - . - . - "http://umbbd.ethz.ch/"^^ . - "63250"^^ . - . - . - . - "CATH domain" . - . - . - . - . - "Sorghum TDv5 - Oct 2019"^^ . - . - . - . - . - . - "false"^^ . - . - "https://www.gbif.org/species"^^ . - . - "^\\d{7}$"^^ . - . - . - "https://www.ebi.ac.uk/gxa/genes/$1"^^ . - . - . - "http://sabiork.h-its.org/"^^ . - . - . - "Habronattus courtship" . - "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . - . - . - . - . - "Dictybase Gene" . - . - . - "WBGene00000001"^^ . - "http://purl.obolibrary.org/obo/OBA_$1"^^ . - . - . - . - . - . - . - "Catalog of purchasable reagents and building blocks"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Terminologia Embryologica" . - "https://omim.org/phenotypicSeries/$1"^^ . - . - "1829126"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://depmap.org/portal/cell_line/$1"^^ . - . - . - "https://flowrepository.org/"^^ . - . - . - "0000001"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - . - "Ontology of Precision Medicine and Investigation" . - "10343835"^^ . - . - "false"^^ . - . - . - . - "^\\w+$"^^ . - . - . - "false"^^ . - . - . - "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . - "false"^^ . - . - . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . - . - "0000001"^^ . - . - "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . - . - "false"^^ . - "https://www.w3.org/2004/02/skos/"^^ . - "^\\d+$"^^ . - . - . - "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . - . - "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . - . - "Eukaryotic Linear Motif Resource" . - . - . - . - . - "false"^^ . - . - "Mouse adult gross anatomy" . - "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . - . - "https://www.worldwildlife.org/ecoregions/$1"^^ . - "laml_tcga_pub"^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - . - . - "https://www.kyinno.com/"^^ . - "^\\d+$"^^ . - . - "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^ . - "GitLab" . - . - "^\\d{7}$"^^ . - . - . - . - "Funding, Research Administration and Projects Ontology" . - . - . - "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - "false"^^ . - "https://github.com/BiodiversityOntologies/bco"^^ . - "BioData Catalyst" . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^ . - "Plant Stress Ontology" . - . - . - . - "false"^^ . - . - . - "https://www.wikidata.org/wiki/Property:$1"^^ . - . - . - . - . - . - . - . - "COSMIC Cell Lines" . - . - . - . - "PharmacoDB Tissues" . - "Petra Fey" . - . - "https://knowledge.lonza.com"^^ . - "Human developmental anatomy, abstract version" . - . - . - "KNApSAcK" . - "NIF Standard Ontology: External" . - . - "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . - "^\\d+$"^^ . - "http://www.ymdb.ca"^^ . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/TADS_$1"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/gwas/studies/$1"^^ . - . - . - . - . - "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "https://w3id.org/biolink/vocab/$1"^^ . - "Human Induced Pluripotent Stem Cells Initiative" . - . - . - . - . - . - . - . - . - . - "An ontology built for representating the organizational components of trauma centers and trauma systems."^^ . - "European Searchable Tumour Line Database" . - "EMLSAT00000003403"^^ . - . - . - . - . - "cpd15380"^^ . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt"^^ . - "^\\w+$"^^ . - . - . - . - . - . - "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d{3}$"^^ . - . - "NLXCELL conatins cell types with a focus on neuron types."^^ . - . - . - . - "false"^^ . - _:N5a204fe83f08423aa66671d566c22e9c . - . - "^\\d+$"^^ . - . - "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . - . - . - . - "Cell line databases/resources"^^ . - . - . - "^Y[A-Z]{2}\\d+[CW]$"^^ . - . - "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . - "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . - . - . - "https://www.icd10data.com/ICD10CM"^^ . - . - "174"^^ . - . - . - "Prefix Commons" . - "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . - "Medaka fish anatomy and development" . - . - . - "false"^^ . - . - "false"^^ . - . - "https://bams1.org"^^ . - . - "00050"^^ . - "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . - "OMIM Phenotypic Series" . - . - "http://vocab.getty.edu/page/tgn/$1"^^ . - . - . - . - . - . - . - . - . - "https://www.aepc.org/european-paediatric-cardiac-coding"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . - "PubChem Classification" . - . - "false"^^ . - . - . - . - . - . - "https://bykdb.ibcp.fr/BYKdb/"^^ . - . - . - . - "has pattern" . - "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"^^ . - . - "BloodPAC" . - . - "0009089"^^ . - . - "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . - "http://www.sparontologies.net/ontologies/fr"^^ . - . - . - "false"^^ . - "http://ccr.coriell.org/"^^ . - . - . - . - . - . - . - . - "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^ . - "false"^^ . - "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "2029"^^ . - . - . - . - . - . - . - . - "0000030"^^ . - . - . - . - . - "Human Ancestry Ontology" . - "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . - . - . - "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . - . - . - . - "http://github.com/ga4gh/data-object-service-schemas"^^ . - "false"^^ . - "false"^^ . - "BIOMD0000000048"^^ . - "090201"^^ . - "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . - . - . - . - "false"^^ . - . - "Selventa legacy disease namespace used with the Biological Expression Language"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://www.who.int/teams/health-product-and-policy-standards/inn"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . - . - . - . - "^\\d+$"^^ . - "has canonical" . - "http://gmd.mpimp-golm.mpg.de/"^^ . - "Medical Data Models" . - . - . - . - . - . - . - . - . - "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . - "https://cells.ebisc.org/$1"^^ . - . - "false"^^ . - "FishBase" . - . - . - . - . - "https://github.com/sparontologies/fabio"^^ . - . - "Genetic Code" . - "false"^^ . - "identifierPattern"^^ . - . - . - . - "Kyoto Encyclopedia of Genes and Genomes" . - "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters"^^ . - . - . - . - . - . - . - . - "AT1402"^^ . - . - . - . - "00000098"^^ . - . - "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . - . - . - . - . - "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . - . - . - . - . - . - . - . - . - "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . - "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x"^^ . - . - . - . - . - "^RF\\d{5}$"^^ . - . - . - "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - "^\\w+$"^^ . - . - "^\\d{7}$"^^ . - "https://www.biozol.de/en"^^ . - "https://www.nextprot.org/"^^ . - . - "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . - . - . - "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . - . - . - "http://www.pocketome.org/sfSearch.cgi?act=browseall"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "2555646"^^ . - . - "false"^^ . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^ . - "Nico Matentzoglu" . - . - . - "^[A-Za-z_0-9]+$"^^ . - . - "Coconut ontology" . - . - . - . - . - "RxNorm" . - . - . - . - . - "https://repeatsdb.org/protein/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "DB14938"^^ . - . - "Radiomics Ontology" . - . - . - "false"^^ . - "AOPWiki (Key Event Relationship)" . - . - . - . - "false"^^ . - . - . - "N0000001662"^^ . - . - "OriDB Schizosaccharomyces" . - . - . - . - . - . - "Developmental stages of the Zebrafish"^^ . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . - "10087"^^ . - . - . - . - "74"^^ . - "Cell Signaling Technology Antibody" . - . - . - . - "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . - . - . - "false"^^ . - . - "true"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/gene"^^ . - . - "false"^^ . - "Integrated Canine Data Commons" . - "^\\d+$"^^ . - "BioProject" . - . - . - "CASRAI Contributor Roles Taxonomy" . - . - . - "MCDS_L_0000000001"^^ . - . - . - . - . - . - . - . - . - . - "BioAssay Ontology" . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - "Document Components Ontology" . - . - . - . - . - . - "true"^^ . - . - "https://www.python.org/psf/"^^ . - "false"^^ . - . - "PS214100"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "Intrinsically Disordered Proteins Ontology" . - . - "^PWY\\w{2}\\-\\d{3}$"^^ . - . - "Cereal Plant Gross Anatomy" . - . - "false"^^ . - . - "1.1.1.1"^^ . - . - "http://www.pharmgkb.org/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "ConoServer" . - . - . - "https://bioportal.bioontology.org/ontologies/SWEET"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . - . - "http://pax-db.org/#!species/$1"^^ . - . - "^\\d{8}$"^^ . - . - . - . - "false"^^ . - . - . - . - "http://masspec.scripps.edu/"^^ . - . - . - . - . - "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . - . - "the FAIR Cookbook" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "NeuronDB" . -_:Nf71ae981eae34cd8a4f065e8adea91b3 "WikiData Support" . - . - "http://ligand-depot.rutgers.edu/index.html"^^ . - . - . - "Bio-Pesticides DataBase" . - . - . - . - "SIDER Drug" . - . - . - . - . - . - . - . - "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . - . - "https://www.ebi.ac.uk/miriam/"^^ . - . - . - . -_:N30ac1120786448ac972d9fafdef5ad63 "Fahim Imam" . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - "^SM\\d{5}$"^^ . - "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . - . - "^[A-Z][a-z][0-9]+$"^^ . - . - . - . - . - "^D\\d{4}$"^^ . - . - . - . - . - . - . - . - "104674"^^ . - . - "true"^^ . - . - . - . - . - . - . - . - "GLDS-141"^^ . - . - "false"^^ . - . - . - . - "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . - . - "https://w3id.org/reproduceme/research"^^ . - "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . - . - "false"^^ . - . - "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . - . - . - . - . - "^\\w+$"^^ . - . - . - "https://protists.ensembl.org"^^ . - . - . - . - . - "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . - . - . - "Social Insect Behavior Ontology" . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - "3075966"^^ . - . - . - . - . - . - . - . - "Enzyme Commission Code" . - "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . - . - "http://purl.obolibrary.org/obo/OVAE_$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "https://n2t.net/$1:"^^ . - . - . - . - . - "http://dictybase.org/gene/$1"^^ . - . - . - . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . - . - . - "http://www.ebi.ac.uk/chebi"^^ . - . - "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . - "CNBG_0001"^^ . - "PROSITE" . - . - . - . - . - . - . - . - . - . - . - . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . - . - . - . - . - "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . - "false"^^ . - . - . - "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906"^^ . - . - . - . - . - . - . - "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . - "^\\d+$"^^ . - "https://dgrc.bio.indiana.edu/cells/Catalog"^^ . - "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . - "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . - "^PA\\d+$"^^ . - . - "false"^^ . - . - . - . - "http://www.conoserver.org/"^^ . - . - . - . - "9001411"^^ . - . - . - . - . - . - . - . - . - . - . - "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . - . - "WGS-95-1333"^^ . - . - . - "http://cell-lines.toku-e.com"^^ . - "^\\d{7}$"^^ . - . - . - . - "Discourse Elements Ontology" . - . - . - "A modeling paradigm-specific registry of prefixes and their URL expansions" . - . - . - . - . - "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . - . - . - "An ontology of core ecological entities" . - . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . - . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - . - . - "https://www.disprot.org/idpo/IDPO:$1"^^ . - . - . - . - . - . - . - . - . - . - "http://www.ebi.ac.uk/efo/EFO_$1"^^ . - "PTPN1"^^ . - . - . - . - "PhosphoSite Residue" . - "false"^^ . - . - . - . - "http://www-is.biotoul.fr/i"^^ . - . - . - . - "CellBank Australia" . - . - . - . - . - . - . - . - . - . - . - "General Multilingual Environmental Thesaurus" . - . - "Proteomic Data Commons" . - . - . - . - . - "SitEx" . - . - . - . - . - . - . - "GE86325"^^ . - . - "https://www.kegg.jp/entry/$1"^^ . - "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . - . - "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . - . - . - . - . - "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . - "https://github.com/cido-ontology/cido"^^ . - . - . - "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . - "^\\d{7}$"^^ . - . - . - . - . - "0.7-123"^^ . - "false"^^ . - . - . - "false"^^ . - . - "http://www.hipsci.org/lines/#/lines/$1"^^ . - "^\\d+$"^^ . - . - . - . - "http://genatlas.medecine.univ-paris5.fr/"^^ . - . - . - . - "http://data.europa.eu/89h/$1"^^ . - . - . - . - "http://n2t.net/"^^ . - . - "https://cropontology.org/ontology/CO_350/Oat"^^ . - . - "false"^^ . - . - "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . - "Decentralized Biomedical Ontology" . - . - "false"^^ . - . - . - . - . - . - "https://github.com/PRIDE-Utilities/pride-ontology"^^ . - . - "AB0"^^ . - . - "true"^^ . - . - . - . - . - . - . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . - . - . - . - . - . - "Bioregistry" . - . - "^\\d+$"^^ . - "https://www.kew.org/data/grasses-syn/index.htm"^^ . - . - "https://www.ncbi.nlm.nih.gov/research/cog/pathways"^^ . - . - . - . - . - "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . - "https://github.com/VEuPathDB-ontology/MIRO"^^ . - . - . - . - "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . - . - . - "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . - . - "http://purl.obolibrary.org/obo/COLAO_$1"^^ . - . - "LiceBase" . - "^\\d+$"^^ . - . - "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . - . - . - . - . - . - . - "UniProt Diseases" . - . - . - . - . - . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "^[A-Z0-9]+$"^^ . - . - . - "Vertebrate skeletal anatomy ontology."^^ . - "Health Surveillance Ontology" . - . - . - . - "http://purl.obolibrary.org/obo/ICO_$1"^^ . - . - "miRBase Families" . - . - "MM00040"^^ . - "http://multicellds.org/MultiCellDB/$1"^^ . - "http://purl.obolibrary.org/obo/OLATDV_$1"^^ . - "http://www.gramene.org/plant_ontology/"^^ . - . - "http://www.peptideatlas.org/"^^ . - . - "false"^^ . - "3304"^^ . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - "http://www.allergome.org/"^^ . - "^\\d{7}$"^^ . - . - "0000125"^^ . - . - . - . - . - . - . - "http://www.humanproteomemap.org/index.php"^^ . - "false"^^ . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . - . - . - . - "^MMP\\d+.\\d+$"^^ . - . - . - "0000010"^^ . - . - . - . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"^^ . - . - . - . - "http://jaxmice.jax.org/"^^ . - "MetaCyc Reaction" . - . - . - . - "6472"^^ . - . - . - . - . - "https://glygen.org/glycan/"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/TAO_$1"^^ . - . - . - "PSI Extended File Format" . - . - . - . - . - "000000021"^^ . - . - . - . - "http://www.protonet.cs.huji.ac.il/"^^ . - "http://aims.fao.org/aos/agrovoc/c_$1"^^ . - . - . - . - . - "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^C\\d+$"^^ . - "https://www.alzforum.org/mutations"^^ . - . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . - "Allergome" . - . - . - "A vendor of antibodies and other biologics"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . - "^D\\d+$"^^ . - . - . - . - . - "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . - "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . - . - "https://monarch-initiative.github.io/mondo"^^ . - . - "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . - "0000021"^^ . - . - . - . - "The set of prefixes used in the Cellosaurus resource"^^ . - . - "false"^^ . - . - . - "false"^^ . - . - "https://www.ebi.ac.uk/gxa/"^^ . - "Ontology of Medically Related Social Entities" . - . - . - . - . - . - "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . - . - . - . - "SMP0000219"^^ . - "Cell line databases/resources"^^ . - "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . - . - "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . - . - . - . - "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . - "Paul Schofield" . - "false"^^ . - . - . - . - . - . - . - . - . - . - "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . - . - . - "OBO Metadata Ontology" . - "Costal and Marine Ecological Classification Standard" . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "1"^^ . - "^[A-Za-z0-9+_.%-:]+$"^^ . - "09200010"^^ . - . - . - . - . - "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "true"^^ . - "Plant Phenology Ontology" . - . - . - . - "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . - . - "http://bioportal.bioontology.org/ontologies/MEDDRA"^^ . - . - . - "Daniel C. Berrios" . - "ExAC Transcript" . - . - . - . - . - . - . - . - "https://www.ndexbio.org/viewer/networks/$1"^^ . - . - "false"^^ . - . - . - . - . - "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . - "434"^^ . - . - "^\\d+$"^^ . - "12dgr161"^^ . - "Comprehensive Resource of Mammalian protein complexes" . - "RL3R1_HUMAN"^^ . - "RCV000033555.3"^^ . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - "^\\d+$"^^ . - "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . - . - . - . - . - . - "GR_tax:013681"^^ . - "Dictyostelium discoideum phenotype ontology" . - . - "http://purl.obolibrary.org/obo/ATO_$1"^^ . - . - . - . - "BugBase Expt" . - . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . - . - "http://www.indexfungorum.org"^^ . - . - . - . - . - "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . - . - . - "^\\d+$"^^ . - . - "0376"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "Genome assembly database" . - "false"^^ . - . - "7123"^^ . - . - . - . - "ab-1-ha"^^ . - . - . - . - . - . - . - . - "^MNEST\\d+$"^^ . - . - . - "https://github.com/IHCC-cohorts/GECKO"^^ . - "^MMP\\d+.\\d+$"^^ . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . - . - . - . - . - . - "^\\d+$"^^ . - "^\\d{7}$"^^ . - . - . - . - "https://pir.georgetown.edu/"^^ . - "http://www.sparontologies.net/ontologies/deo"^^ . - . - . - "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . - . - "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . - . - . - . - . - _:N78c2686ae6ab4cdf82c7b9bca90a884a . - "^\\d+$"^^ . - "http://www.pseudomonas.com/"^^ . - . - . - . - "GeoNames Feature Code" . - . - . - . - . - "Nathan Edwards" . - "https://glycopost.glycosmos.org/entry/$1"^^ . - . - . - . - . - "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CVDO_$1"^^ . - . - . - "National Academic Research and Collaborations Information System" . - . - . - . - . - . - . - . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - . - . - . - . - "http://eggnog.embl.de/version_3.0/"^^ . - "KEGG Glycan" . - "https://flybase.org"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/SYMP_$1"^^ . - "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . - . - . - . - . - . - . - . - "nstd102"^^ . - . - "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . - . - "E5.11.2.0.0.0.4"^^ . - . - . - . - "false"^^ . - "Wasila Dahdul" . - "false"^^ . - "false"^^ . - . - . - "http://lisanwanglab.org/DASHR/"^^ . - . - . - "^LTS\\d{7}$"^^ . - "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . - "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/fbdv"^^ . - . - . - . - "false"^^ . - . - . - . - "9002859"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . - . - "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . - "http://geneontology.org/" . - "Michael Y Galperin" . - . - . - "false"^^ . - . - . - . - . - . - "Universal Spectrum Identifier" . - . - "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . - . - "^TTDS\\d+$"^^ . - "https://lncipedia.org"^^ . - . - "https://fair-research.org"^^ . - . - "VFDB Gene" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . - "false"^^ . - . - . - "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . - "false"^^ . - . - . - "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MFO_$1"^^ . - "TS-0285"^^ . - . - "https://herv.img.cas.cz/"^^ . - . - . - "true"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . - . - "https://cellmodelpassports.sanger.ac.uk/"^^ . - "589462"^^ . - "is deprecated" . - "https://www.worldwildlife.org/biomes"^^ . - . - . - . - . - . - . - "NONCODE v4 Gene" . - . - . - . - "BCRTi001-A"^^ . - . - . - . - . - . - "CHEMBL465070"^^ . - . - "Q9UKQ2"^^ . - . - . - "https://www.novusbio.com/products/$1"^^ . - . - . - . - "Cancer Staging Terms" . - "Biolink Model Registry" . - . - . - . - . - "CHEBI" . - . - . - . - . - . - . - "98034"^^ . - . - "https://horizondiscovery.com/"^^ . - . - . - "false"^^ . - . - . - . - "http://cicblade.dep.usal.es:8080/APID/"^^ . - "LINCS Cell" . - . - . - . - . - "Tick Cell Biobank" . - . - "false"^^ . - . - "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . - . - "http://www.york.ac.uk/"^^ . - . - "http://environmentontology.github.io/gaz/"^^ . - . - . - . - . - . - "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^ . - . - . - "http://www.uniprot.org/"^^ . - "https://www.w3.org/ns/dcat"^^ . - "^\\d{7}$"^^ . - . - . - . - "Anatomical Therapeutic Chemical Vetinary" . - . - . - _:N97cbfa9779f94043ab3e07f690355ec4 . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"^^ . - . - . - . - "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . - . - . - "0000009"^^ . - "https://bioregistry.io/metaregistry/$1"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/RBO_$1"^^ . - "Cell line collections"^^ . - "https://www.cropontology.org/rdf/CO_350:$1"^^ . - . - . - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - . - "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . - "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . - . - . - . - "has responsible" . - "false"^^ . - "false"^^ . - . - . - . - "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . - . - "false"^^ . - "8000221"^^ . - . - . - "IntellectualContribution"^^ . - . - . - "false"^^ . - "Blue Brain Project Knowledge Graph" . - . - . - . - . - . - "^\\d+$"^^ . - "Gene Ontology Registry" . - . - "0000062"^^ . - . - "false"^^ . - "http://sideeffects.embl.de/se/$1"^^ . - . - . - . - . - . - . - . - . - . - "UniRef" . - . - _:N0b78bd2c53ed4e6baaea94e059f19c70 . - . - . - . - . - . - . - "1755"^^ . - "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . - "false"^^ . - . - "https://vectorbase.org/vectorbase/app/record/gene/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - "GenProp0699"^^ . - . - "https://datalab.rwth-aachen.de/MINDER"^^ . - . - . - "false"^^ . - . - "Natural Product Activity and Species Source Database" . - . - . - . - "0000069"^^ . - "http://purl.obolibrary.org/obo/CLO_$1"^^ . - . - "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . - . - . - "false"^^ . - . - . - . - "http://research.nhgri.nih.gov/apps/homeodomain/web/"^^ . - . - . - . - . - "true"^^ . - "false"^^ . - . - "^MMP\\d+.\\d+$"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . - . - . - "^\\w+(\\.)?(\\d+)?$"^^ . - "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . - . - "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . - "BioNumbers" . - "https://lhncbc.nlm.nih.gov/semanticnetwork/"^^ . - . - . - . - . - "rsk00410"^^ . - "cho"^^ . - . - "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . - . - . - . - . - "https://data.4dnucleome.org/biosources"^^ . - "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . - . - "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . - . - "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . - . - . - . - . - . - . - . - . - "https://code.google.com/p/epidemiology-ontology/"^^ . - "0003463"^^ . - "false"^^ . - . - . - . - "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . - . - . - "UCR00226"^^ . - . - . - "http://ecmdb.ca/compounds/$1"^^ . - "0000001"^^ . - . - . - "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "http://www.chemspider.com/$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . - . - "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . - . - "http://dictybase.org/"^^ . - "^\\d{7}$"^^ . - . - "Software Heritage is the universal archive of software source code."^^ . - . - . - . - . - . - "true"^^ . - "0001807"^^ . - "https://www.biocatalogue.org/services/$1"^^ . - . - . - "false"^^ . - . - . - . - "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . - "Benchmark Energy & Geometry Database" . - . - . - "^C\\d{8}$"^^ . - "NIF Standard Ontology" . - . - . - . - "0002999"^^ . - . - . - . - . - . - . - "false"^^ . - "http://braininfo.rprc.washington.edu/"^^ . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/TGMA_$1"^^ . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - . - "http://purl.org/spar/scoro/$1"^^ . - . - . - "http://stormo.wustl.edu/ScerTF/"^^ . - . - . - . - " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - . - . - "http://browser.planteome.org/amigo"^^ . - . - . - . - . - "^MI\\d{7}$"^^ . - . - . - "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . - . - . - . - . - "https://github.com/Planteome/plant-stress-ontology"^^ . - . - _:Nac2201223a8747d1a31b9c6dcc856983 . - . - . - . - "https://foodon.org/"^^ . - . - . - "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - "ProtoNet ProteinCard" . - "http://www.snomedbrowser.com/Codes/Details/$1"^^ . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "EY223054.1"^^ . - . - . - . - . - "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . - . - "HOMD Sequence Metainformation" . - "Vaccine Ontology" . - . - . - . - . - . - "0000008"^^ . - . - "https://www.cropontology.org/rdf/CO_321:$1"^^ . - . - . - . - "http://www.cathdb.info/"^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . - . - . - . - "^\\d{4}$"^^ . - "^\\w+$"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d{4,}((_[asx])?_at)$"^^ . - . - . - . - . - . - . - "has example" . - . - . - "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . - . - . - . - "Diseases Database" . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . - "https://data.4dnucleome.org/biosources/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Michelle Giglio" . - . - . - . - "Collection"^^ . - "Online Mendelian Inheritance in Animals" . - . - "Q-2958"^^ . - "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license."^^ . - "Online Mendelian Inheritance in Man" . - . - "false"^^ . - "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . - "0000690"^^ . - "false"^^ . - "Kidney and Urinary Pathway Ontology" . -_:N570bb9b9d35a491eb45adc922195e29b "Fahim Imam" . - . - . - . - "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "Human Dermatological Disease Ontology" . - . - . - . - . - . - . - . - . - "https://www.ada.org/publications/CDT"^^ . - "RAP-DB Transcript" . - . - "^[\\d.]+$"^^ . - . - . - . - . - . - . - . - . - "https://www.uniprot.org/database/DB-$1" . - "Richard Cyganiak" . - . - . - . - . - . - "^[CN]*\\d{4,7}$"^^ . - . - "https://www.ncbi.nlm.nih.gov/books/$1"^^ . - . - . - . - . - . - . - . - . - . - "Amazon Standard Identification Number" . - . - "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . - . - . - . - . - . - . - . - . - . - "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . - "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . - . - "EMD-1001"^^ . - . - "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . - . - . - . - . - "http://www.guidetopharmacology.org/"^^ . - "0000003"^^ . - . - . - . - "Mental Disease Ontology" . - "Ensembl Protists" . - . - "4.2.78"^^ . - "Identifiers.org Registry" . - . - . - . - . - "^\\d+$"^^ . - . - "hasOpenAccessRating"^^ . - . - "https://github.com/infectious-disease-ontology-extensions/ido-virus"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . - "false"^^ . - . - . - . - . - "BioCatalogue Service" . - . - . - . - . - "false"^^ . - . - . - . - "https://www.addexbio.com/productdetail?pid=$1"^^ . - "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . - . - "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . - "http://www.wikipathways.org/"^^ . - . - . - . - "^[A-Z0-9]+$"^^ . - . - . - "http://www.disease-ontology.org"^^ . - . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . - "false"^^ . - . - . - . - . - "https://w3id.org/hso"^^ . - . - "SNHG3"^^ . - . - . - "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . - "International Medical Device Regulators Forum" . - . - . - "Sustainable Development Goals Interface Ontology" . - "http://www.cazy.org/$1.html"^^ . - . - . - . - "MSMEG_3769"^^ . - "Plant Experimental Conditions Ontology" . - "false"^^ . - . - . - . - . - . - . - . - "4390079"^^ . - "Manually curated collections of resources stored in the bioregistry"^^ . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . - "https://www.uniprot.org/tissues/$1"^^ . - . - "Lucas Leclere" . - . - "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . - . - "false"^^ . - "http://en.wikipedia.org/wiki/Gene_Wiki"^^ . - . - "CategorialBibliometricData"^^ . - "Affymetrix Probeset" . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "FAIRsharing" . - . - "neXtProt family" . - . - . - "false"^^ . - . - "Human Gene Mutation Database" . - . - "^\\d{7}$"^^ . - "ABE-0009634"^^ . - . - "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . - . - . - "false"^^ . - "health_care_quality_assessment"^^ . - . - . - "10595"^^ . - . - . - . - . - . - "imp10873"^^ . - . - . - . - . - . - . - "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . - "^\\d{7}$"^^ . - . - . - "0004"^^ . - . - . - . - . - . - . - . - . - "Yeast Deletion and the Mitochondrial Proteomics Project" . - "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . - "0000029"^^ . - . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . - . - . - . - . - . - "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/ZFA_$1"^^ . - . - . - . - . - "https://www.wikidata.org/"^^ . - . - . - . - "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . - . - . - . - . - "^[A-Z\\-]+$"^^ . - . - . - . - . - "http://rgd.mcw.edu/rgdweb/search/strains.html"^^ . - . - . - "https://pav-ontology.github.io/pav/"^^ . - . - "http://emouseatlas.org"^^ . - . - . - . - "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . - "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . - . - . - . - . - . - "Exposure ontology" . - . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . - . - . - . - . - . - "Antimicrobial Peptide Database" . - . - . - . - . - "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . - . - . - "https://www.nlm.nih.gov/research/umls"^^ . - . - "ARP-1513"^^ . - . - . - . - . - "^\\d+$"^^ . - "Lipid Ontology" . - . - . - . - . - . - . - "false"^^ . - . - "0174" . - . - . - . - "http://www.sbgnbricks.org/"^^ . - "false"^^ . - . - . - . - "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . - "^\\d+$"^^ . - . - . - "051"^^ . - . - . - . - "Sol Genomics Network" . - . - "https://www.uniprot.org/journals/$1"^^ . - . - "ClinGen Allele Registry" . - "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . - . - "https://www-snorna.biotoul.fr/"^^ . - . - "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . - "AddexBio cell line products" . - "https://www.ncbi.nlm.nih.gov/dbvar"^^ . - "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . - . - . - . - . - . - . - . - "^EMD-\\d{4}$"^^ . - . - . - . - . - . - . - . - . - . - . - "0000512"^^ . - . - . - . - . - "https://doulix.com"^^ . - . - . - . - . - . - . - "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . - . - . - . - . - . - . - . - "https://www.reaxys.com"^^ . - "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . - . - . - "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . - "http://www.sparontologies.net/ontologies/scoro"^^ . - "https://www.phosphosite.org"^^ . - "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "false"^^ . - . - . - . - "HsapDO:0000004"^^ . - "false"^^ . - . - . - . - "Continuous Automated Model Evaluation" . - . - . - . - . - "^[0-9A-Za-z\\-.]+$"^^ . - "Open Data Commons for Spinal Cord Injury" . - . - . - "CGH Data Base" . - "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . - . - . - . - "https://www.thermofisher.com/antibody/product/$1"^^ . - . - "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . - "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . - . - . - . - "Oryzabase Stage" . - "http://bigg.ucsd.edu/models/$1"^^ . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . - "NeuroVault Image" . - . - . - . - . - . - . - "false"^^ . - "true"^^ . - . - . - . - . - . - . - "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"^^ . - "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . - "HUGO Gene Nomenclature Committee" . - . - . - . - . - . - "MagnitudeValueType"^^ . - . - . - . - . - . - "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . - "false"^^ . - . - "^\\d{7}$"^^ . - "377550"^^ . - "https://www.ebi.ac.uk/ega/studies/$1"^^ . - "Toxin and Toxin Target Database" . - "false"^^ . - "^\\d{9}$"^^ . - . - . - . - . - . - "http://www.gramene.org/"^^ . - . - . - "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . - . - . - . - "hsa-let-7a-2-3p"^^ . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "000410"^^ . - . - "false"^^ . - . - . - . - "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^ . - . - "https://www.biocarta.com/"^^ . - "Ontology for MicroRNA Target" . - . - "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . - . - . - . - . - . - "https://www.xenbase.org/entry/$1"^^ . - "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . - . - "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . - "false"^^ . - "http://www.sparontologies.net/ontologies/datacite"^^ . - "false"^^ . - . - . - . - . - . - . - "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . - . - . - . - . - "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . - . - . - "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . - . - "48439"^^ . - . - . - "Gmelins Handbuch der anorganischen Chemie" . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - . - . - . - . - . - . - . - . - "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . - . - . - . - "http://modelseed.org/"^^ . - "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . - "Spectra Hash Code" . - "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . - . - . - "false"^^ . - . - "AntiBodies Chemically Defined database" . - . - "Terms from the source appear in the target resource" . - . - . - "Sweet Potato ontology" . - . - "http://www.pombase.org/spombe/result/$1"^^ . - . - . - "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . - . - . - . - . - . - "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . - "https://glytoucan.org"^^ . - . - . - "http://purl.org/spar/datacite/$1"^^ . - . - "SCC111"^^ . - . - "^PR\\d{5}$"^^ . - . - . - "GR:0080039"^^ . - . - "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"^^ . - . - . - . - . - . - . - "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . - . - "Topology Data Bank of Transmembrane Proteins" . - "Ion Channel Electrophysiology Ontology" . - . - "ACC-1"^^ . - . - . - . - . - . - . - "http://antibodyregistry.org/AB_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . - . - . - "https://icahn.mssm.edu/"^^ . - . - "^\\d{5}$"^^ . - "https://w3id.org/oc/corpus"^^ . - . - . - "https://www.bio.di.uminho.pt/"^^ . - . - . - . - "http://www.phosphosite.org/siteAction.do?id=$1"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - "Protein covalent bond" . - . - . - . - . - . - "https://www.flymine.org/come/entry?gn=$1"^^ . - . - . - . - . - . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/VHOG_$1"^^ . - . - . - . - "Maize gross anatomy" . - . - . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - "REBASE restriction enzyme database" . - "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . - . - "ClassyFire" . - "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . - "false"^^ . - . - . - . - . - . - "IMGT/HLA human major histocompatibility complex sequence database" . - "https://aopwiki.org/"^^ . - "false"^^ . - . - . - . - . - . - "http://www.pantherdb.org/"^^ . - "SM_UB-81"^^ . - "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . - . - . - "0000003"^^ . - . - . - "false"^^ . - "false"^^ . - "^[A-Z]+[A-Z-0-9]{2,}$"^^ . - . - . - . - "Cell Lines Service" . - "uc001rvw.5"^^ . - . - . - . - . - . - . - . - . - . - "Oryzabase Reference" . - . - . - "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . - . - . - . - "90806"^^ . - . - "Mosquito insecticide resistance" . - . - . - . - "CORDIS Project" . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - "false"^^ . - "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . - . - . - . - . - . - "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . - . - . - . - . - . - . - . - "http://umbbd.ethz.ch/"^^ . - "https://web.expasy.org/variant_pages"^^ . - "https://www.abmgood.com/Cell-Biology.html"^^ . - . - "^\\w+$"^^ . - . - . - "https://hpo.jax.org/app/browse/term/HP:$1"^^ . - . - . - . - . - "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . - "^\\d+$"^^ . - "Cube db" . - "1050"^^ . - . - . - . - "https://cropontology.org/ontology/CO_320/Rice"^^ . - . - . - . - "Tom Gillespie" . - "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . - . - "Eschmeyer's Catalog of Fishes" . - . - "http://biobanknetwork.telethon.it/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://drugcentral.org"^^ . - . - . - "OMA Group" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/SPD_$1"^^ . - "DDB0016567"^^ . - . - . - "true"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . - "^(\\w){3}$"^^ . - . - . - "http://neuinfo.org/"^^ . - "ENSG00000026508"^^ . - . - . - . - . - . - . - . - . - "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . - "Bioregistry Collections" . - "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . - "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "1398574"^^ . - . - . - "https://omabrowser.org"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . - . - . - "^Gm\\d+$"^^ . - "https://github.com/OOSTT/OOSTT"^^ . - . - . - . - . - "false"^^ . - "http://www.aspgd.org/"^^ . - "0000411"^^ . - "http://www.semantic-systems-biology.org/apo"^^ . - . - . - . - "https://open.med.harvard.edu/wiki/display/eaglei/Ontology"^^ . - "Hazardous Substances Data Bank" . - . - . - "PharmGKB Disease" . - . - . - "^\\d{7}$"^^ . - "Human Developmental Stages" . - "Immune Epitope Database" . - . - . - . - "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . - "http://sabiork.h-its.org/"^^ . - . - . - "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . - . - . - "Unimod protein modification database for mass spectrometry" . - "false"^^ . - . - . - . - "false"^^ . - . - . - "https://giardiadb.org/giardiadb/"^^ . - "false"^^ . - "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . - . - . - "http://www.semantic-systems-biology.org/apo"^^ . - . - "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . - . - "Proteoform Atlas" . - . - . - . - "https://easychair.org/cfp/"^^ . - "http://epd.vital-it.ch/"^^ . - . - "An ontology covering the taxonomy of teleosts (bony fish)"^^ . - . - "Cross-linker reagents ontology" . - . - . - . - . - "http://purl.org/spar/bido/$1"^^ . - . - "Browser for the periodic table of the elements"^^ . - "http://www.phytozome.net/"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "http://www.pharmgkb.org/gene/$1"^^ . - "PED00037"^^ . - . - "eVOC mouse development stage" . - . - . - "false"^^ . - . - "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . - . - "0000712_1"^^ . - . - . - "811"^^ . - "Vitis ontology" . - "0010039"^^ . - . - . - . - . - "https://publons.com/researcher/$1"^^ . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://purl.org/spar/pwo/$1"^^ . - . - "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . - . - "None"^^ . - . - . - "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^ . - "53504"^^ . - "Ontology from the APA"^^ . - "P4355"^^ . - "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . - . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . - . - "Chemical Methods Ontology" . - "false"^^ . - . - . - "5"^^ . - . - . - . - . - . - "https://flybase.org/reports/FBtc$1"^^ . - . - "^EB\\d+$"^^ . - . - . - "https://progenetix.org/"^^ . - "http://www.informatics.jax.org/"^^ . - "http://korkinlab.org/dommino"^^ . - . - . - . - . - . - . - . - "https://hamap.expasy.org/unirule/$1"^^ . - . - . - . - . - . - "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . - . - . - "https://github.com/monarch-initiative/GENO-ontology/"^^ . - "https://bioregistry.io/metaregistry/scholia/$1"^^ . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . - . - . - "false"^^ . - . - "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . - "https://medlineplus.gov/genetics/condition"^^ . - "Human Metabolome Database" . - . - . - . - "http://www.pharmgkb.org/disease/$1"^^ . - . - "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . - "Mike Tyers" . - "https://cropontology.org/ontology/CO_345/Brachiaria"^^ . - . - . - . - "AutDB" . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - "true"^^ . - . - "http://purl.obolibrary.org/obo/MPATH_$1"^^ . - . - . - . - "https://github.com/futres/fovt"^^ . - . - . - . - "DrugBank" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . - . - . - "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^ . - . - "Ontology of Biological Attributes" . - . - . - . - . - . - "http://www.kegg.jp/kegg/module.html"^^ . - "https://www.cropontology.org/rdf/CO_331:$1"^^ . - . - "Anatomical Therapeutic Chemical Classification System" . - "BacMap Biography" . - . - "^\\w+(\\.\\d+)$"^^ . - "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . - . - . - . - . - . - . - "https://bitbucket.org/hegroup/ogg"^^ . - "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . - . - . - . - . - . - . - . - "https://www.google.com/patents/"^^ . - "A formal ontology of phenotypes observed in fission yeast."^^ . - . - . - . - . - "^[A-Z0-9]+$"^^ . - . - . - . - . - . - "https://www.swisslipids.org/#/entity/SLM:$1"^^ . - . - "Golm Metabolome Database GC-MS spectra" . - . - . - . - . - . - . - . - . - "CoVoc Coronavirus Vocabulary" . - "TAIR Protein" . - . - . - . - . - . - "^\\d+$"^^ . - . - "145"^^ . - . - . - "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . - . - . - . - . - . - . - "http://www.bioinfo.org/NONCODEv4/"^^ . - . - . - . - . - . - . - . - "^PAp[0-9]{8}$"^^ . - . - "46977"^^ . - . - "https://icd.codes/icd10cm/$1"^^ . - . - . - . - . - . - . - "http://purl.bioontology.org/ontology/MEDDRA/$1"^^ . - . - . - . - "0000198"^^ . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . - . - "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . - . - "http://autism.mindspec.org/autdb/"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^ . - . - "http://sideeffects.embl.de/drugs/$1"^^ . - . - . - . - . - . - . - . - "https://europepmc.org/article/CTX/$1"^^ . - "CorrDB" . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - "^[0-9]+$"^^ . - . - . - . - "0000047"^^ . - . - "BindingDB" . - "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . - "172"^^ . - . - . - "true"^^ . - . - . - "A representation of the variety of methods used to make clinical and phenotype measurements. "^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . - "^\\w\\d+$"^^ . - . - "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . - "https://plants.ensembl.org/"^^ . - "2404"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - "Gramene Reference" . - . - "true"^^ . - . - . - "false"^^ . - . - "DICOM Controlled Terminology" . - . - . - . - "Cell line databases/resources"^^ . - . - . - . - "^[A-Z0-9]+$"^^ . - "false"^^ . - . - . - "01001"^^ . - . - . - "https://aopwiki.org/"^^ . - . - . - . - "349124"^^ . - . - "false"^^ . - "Cell Ontology" . - "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . - . - . - . - . - "http://swift.cmbi.kun.nl/swift/hssp/"^^ . - . - . - . - . - "false"^^ . - . - . - . - "Biomedical Informatics Research Network Lexicon" . - "MMP3312982.2"^^ . - . - . - . - . - . - "An ontology of Drosophila melanogaster developmental stages."^^ . - "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . - . - . - "http://trichdb.org/trichdb/"^^ . - . - "http://aclame.ulb.ac.be/"^^ . - . - "http://img.jgi.doe.gov/"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GRO_$1"^^ . - . - "false"^^ . - "Contributor Role Ontology" . - . - "^Q[A-Z0-9]+$"^^ . - . - . - . - "http://edamontology.org"^^ . - . - . - . - "^\\d{7}$"^^ . - "prefLabel"^^ . - . - . - "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . - . - . - . - . - "https://bacteria.ensembl.org/id/$1"^^ . - . - "https://www.phenxtoolkit.org/"^^ . - "false"^^ . - . - . - "http://www.t3db.org/"^^ . - . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^ . - . - . - "https://sed-ml.org/urns.html#format:$1"^^ . - . - . - . - . - . - . - . - . - "https://bdsc.indiana.edu/about/mission.html"^^ . - "https://bioregistry.io"^^ . - . - . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home"^^ . - . - . - . - . - . - "^PTN\\d{9}$"^^ . - "false"^^ . - "https://www.wormbase.org/"^^ . - . - . - . - . - "Metabolomics Standards Initiative Ontology" . - . - . - . - "false"^^ . - . - "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm"^^ . - "0000111"^^ . - "https://www.merckmillipore.com/catalogue/item/$1"^^ . - . - . - . - "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . - . - . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - "https://github.com/flora-phenotype-ontology/flopoontology"^^ . - . - "https://uniresolver.io/#did:$1"^^ . - . - . - "https://www.mlcommons.org/mlc-id/$1"^^ . - "false"^^ . - . - . - . - "Publons Researcher" . - "1"^^ . - "Cancer cell LInes GEne fusions portAl" . - . - "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . - "https://www.ebi.ac.uk"^^ . - "Physico-chemical methods and properties" . - . - . - . - "https://swissmodel.expasy.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . - . - . - . - "87"^^ . - "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . - . - . - . - "John Kunze" . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - . - . - . - "aaeA"^^ . - "http://mona.fiehnlab.ucdavis.edu/"^^ . - . - . - "DrugBank Drug Category" . - . - . - . - . - "Arabidopsis Small RNA Project" . - . - . - "false"^^ . - . - "false"^^ . - . - "Human Protein Reference Database" . - "https://www.deciphergenomics.org/syndrome/$1"^^ . - . - "http://neurovault.org"^^ . - . - "false"^^ . - "false"^^ . - . - "4DNESWX1J3QU"^^ . - . - . - "^\\d+$"^^ . - . - "19-T4"^^ . - . - "MEROPS Clan" . - "false"^^ . - . - . - . - "Barcode of Life database" . - . - . - . - "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . - "The allele registry provides and maintains identifiers for genetic variants"^^ . - . - . - . - . - . - "http://ecolexicon.ugr.es/en/index.htm"^^ . - . - . - "1433C_TOBAC_1_252"^^ . - . - . - "Identifiers.org namespace" . - . - . - . - . - . - . -_:N0dd9101a4c25485d820090171fbe6905 "Julie Thompson" . - . - . - . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/VSAO_$1"^^ . - . - . - . - . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - "European Nucleotide Archive" . - "0000485"^^ . - . - . - . - . - "^[0-9]+$"^^ . - . - "0011124"^^ . - . - "http://www.mgc.ac.cn/VFs/"^^ . - "IRD Segment Sequence" . - . - "https://doi.org/$1"^^ . - "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . - . - "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . - . - "^\\d+$"^^ . - "0000187"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Q0VCA6"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "4238"^^ . - . - . - . - "false"^^ . - . - "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . - . - "MF_01400"^^ . - "false"^^ . - . - . - . - "nasa/kepler-exoplanet-search-results"^^ . - . - . - "OBO in OWL" . - "Carissa Park" . - "https://arxiv.org/abs/$1"^^ . - . - . - . - "true"^^ . - "http://jjj.biochem.sun.ac.za/models/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.jax.org/strain"^^ . - . - . - "^\\d+$"^^ . - . - . - "0000252"^^ . - . - "1000560"^^ . - . - . - "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "TubercuList knowledge base" . - . - . - "3905431"^^ . - . - . - . - . - "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . - . - "Rice ontology" . - . - . - . - . - . - . - "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . - . - "0000041"^^ . - . - . - . - . - . - "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . - . - . - "https://glygen.org/glycan/$1"^^ . - . - . - . - . - . - . - . - . - "EDAM Operation" . - "false"^^ . - . - . - . - "https://metacyc.org"^^ . - "true"^^ . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - "1"^^ . - "^\\d{4,}$"^^ . - . - . - "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . - . - . - . - . - "Cluster of orthologous genes" . - . - . - "false"^^ . - "https://github.com/obophenotype/provisional_cell_ontology"^^ . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "biopragmatics/bioregistry/416"^^ . - . - "https://www.wicell.org"^^ . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - . - . - . - "Castor bean ontology" . - . - "^GPST[0-9]{6}$"^^ . - "A01M1/026"^^ . - "128011350"^^ . - "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . - "false"^^ . - . - . - . - "PRIDE Project" . - "^(G|P|U|C|S)\\d{5}$"^^ . - . - "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . - "https://github.com/pato-ontology/pato/"^^ . - . - . - . - . - . - . - "https://www.cancerrxgene.org/translation/Drug/$1"^^ . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . - . - . - . - "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . - "http://www.mgc.ac.cn/VFs/"^^ . - . - . - "0000630"^^ . - . - . - . - . - . - . - . - . - . - . - "LOTUS Initiative for Open Natural Products Research" . - "21393"^^ . - "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure"^^ . - "https://github.com/OMIABIS/omiabis-dev"^^ . - . - . - "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . - . - . - . - "CORDIS Article" . - . - . - "https://orcid.org/$1"^^ . - "Open Data for Access and Mining" . - . - "ViralZone" . - . - "https://www.animalgenome.org/QTLdb"^^ . - "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . - "https://www.vmh.life/#reaction/$1"^^ . - . - . - "Locus Reference Genomic" . - . - "false"^^ . - . - . - . - . - "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . - . - "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . - "Universal Natural Products Database" . - . - . - . - . - "Asiyah Yu Lin" . - . - . - . - . - . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - "KIAA0001"^^ . - . - . - . - . - . - . - . - . -_:Nb2d09a7498bc40199aa734cfcb455768 "Plant Ontology Administrators" . - . - . - . - . - . - . - . - . - . - . - "005012"^^ . - . - . - . - . - . - . - "https://w3c-ccg.github.io/did-spec/"^^ . - "https://link.springer.com/bookseries/562"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Pfam" . - . - . - "false"^^ . - . - . - . - . - . - "oct 2016"^^ . - . - . - . - "Ontology of Genetic Susceptibility Factor" . - . - "^C\\d+$"^^ . - . - "http://beetlebase.org/"^^ . - . - "NIF Standard Ontology: Subcellular Entities" . - . - . - . - . - . - . - . - "Protein Affinity Reagents" . - "familyName"^^ . - "https://bioportal.bioontology.org/ontologies/IDODEN"^^ . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - "http://purl.obolibrary.org/obo/fbbt"^^ . - . - "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . - . - . - . - . - . - . - . - . - . - "Ceri Van Slyke" . - . - . - "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . - "chebi"^^ . - . - . - "GLIDA Ligand" . - . - . - . - "cd00400"^^ . - "https://www.ncbi.nlm.nih.gov/assembly/$1"^^ . - . - . - "^\\w+$"^^ . - . - "http://phenol-explorer.eu/foods/$1"^^ . - "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . - . - "true"^^ . - "https://github.com/EBISPOT/clyh_ontology"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "BiGG Reaction" . - . - . - "KC-0979"^^ . - . - . - . - "003070"^^ . - "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "PD10000"^^ . - . - . - "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^ . - . - . - . - . - "^GPM\\d+$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . - "http://microsporidiadb.org/micro/"^^ . - . - "Mass spectrometry ontology" . - . - . - . - . - . - . - "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . - . - . - "^\\d+$"^^ . - "false"^^ . - . - "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . - . - . - . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - . - . - . - . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . - . - . - "A-GEOD-50"^^ . - . - . - "false"^^ . - . - "Experimental condition ontology" . - . - . - "^\\d{7}$"^^ . - . - . - . - "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . - . - . - . - . - . - "false"^^ . - "http://microbialphenotypes.org"^^ . - . - "GeneFarm" . - . - . - . - . - "false"^^ . - "false"^^ . - . - "^[A-Z]+[0-9]+$"^^ . - "false"^^ . - "https://www.oclc.org/en/about.html"^^ . - "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . - "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/BCGO_$1"^^ . - "https://www.ncbi.nlm.nih.gov/sra"^^ . - "https://data.apps.fao.org/catalog/organization/agrovoc"^^ . - "NCBI Probe database Public registry of nucleic acid reagents" . - . - "false"^^ . - . - . - "ENVO" . - . - "Multum MediSource Lexicon" . - "3305"^^ . - . - . - . - . - . - . - . - . - . - . - "Cambridge Structural Database" . - . - . - . - "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . - . - . - . - "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . - . - . - . - . - . - "CTD Gene" . -_:N2fde3ed72d8f4e8ba8c8aa6ce10c384e "Pantelis Topalis" . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "ITO_01625"^^ . - . - . - . - . - "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^ . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - "false"^^ . - "^[A-Za-z-0-9_]+$"^^ . - . - "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . - . - . - . - "http://compbio.cs.queensu.ca/F-SNP/"^^ . - . - . - "C. elegans Small Molecule Identifier Database" . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "0221"^^ . - . - . - "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . - "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "0002-1975-61"^^ . - "http://www.gabipd.org/"^^ . - . - "^P\\w+$"^^ . - . - "Relation Ontology" . - "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . - . - . - . - . - . - "https://metacyc.org/compound?orgid=META&id=$1"^^ . - . - . - . - . - "^((VGNC|vgnc):)?\\d{1,9}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/genome"^^ . - . - . - . - "https://comptox.epa.gov/dashboard"^^ . - . - "Food-Biomarker Ontology" . - . - . - . - "Database of Arabidopsis Transcription Factors" . - . - "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . - . - . - . - . - "Tribolium Genome Database -- Insertion" . - "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "LINCS Data" . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - . - . - . - "http://www.pharmgkb.org/"^^ . - . - . - . - . - . - "BioCyc collection of metabolic pathway databases" . - . - . - . - "https://bioregistry.io/collection/$1"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . - . - . - "http://aber-owl.net" . - "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^ . - . - "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies."^^ . - . - . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . - "Luis A. Gonzalez-Montana" . - "https://bioregistry.io/registry/$1" . - . - . - . - . - . - "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . - . - . - . - . - . - . - "false"^^ . - . - "http://www.russelllab.org/miRNAs/"^^ . - . - . - . - . - . - "^M\\d+$"^^ . - "EAWAG Biocatalysis/Biodegradation Database" . - "74"^^ . - . - "Drosophila Genomics Resource Center" . - . - . - "http://string.embl.de/"^^ . - . - . - "LL379-9"^^ . - . - "false"^^ . - "P3DB Protein" . - . - . - . - . - . - . - . - "c"^^ . - . - "GXA Gene" . - . - . - . - . - . - . - . - . - . - "Egon Willighagen" . - "h_aktPathway"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "Protein modification" . - . - . - . - . - "https://www.cropontology.org/rdf/CO_366:$1"^^ . - "https://www.vmh.life/"^^ . - "false"^^ . - . - . - . - . - . - . - "A type for entries in the Bioregistry's collections" . - "NINDS Human Cell and Data Repository" . - "http://www.imdrf.org/"^^ . - "SNR17A"^^ . - . - . - . - . - "Biolink Model" . - . - . - "false"^^ . - . - "false"^^ . - . - . - "http://www.cellsignal.com/pathways/index.html"^^ . - "SubstrateDB" . - . - . - . - . - . - "https://www.proteomicsdb.org/#peptideSearch"^^ . - . - . - "^\\d{7}$"^^ . - "APID Interactomes" . - . - . - . - . - "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . - "^\\d{7}$"^^ . - . - "Software Heritage" . - "Jennifer C. Girón" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . - "E. coli Metabolite Database" . - "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . - . - . - "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . - . - "http://search.sisuproject.fi/#/variant/$1"^^ . - "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . - . - . - . - . - . - "false"^^ . - "https://topfind.clip.msl.ubc.ca"^^ . - . - . - . - "false"^^ . - "^M\\d+$"^^ . - . - . - "0000184"^^ . - "NCBI Bookshelf" . - . - . - . - "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . - . - "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^ . - . - "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . - . - "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^ . - "https://lincs.hms.harvard.edu/db/sm/"^^ . - . - . - . - . - . - . - . - "http://www.w3.org/ns/prov#$1"^^ . - . - . - . - . - . - . - . - "688"^^ . - "PR00001"^^ . - "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . - . - . - "81944ba1-81d0-436e-8552-33d77a27834b"^^ . - . - . - . - . - "A001094"^^ . - . - . - . - . - "0001"^^ . - "true"^^ . - . - . - . - "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . - . - . - . - . - "Yuki Yamagata" . - "^\\d{7}$"^^ . - "^[A-Za-z0-9_-]+$"^^ . - . - . - "http://napp.u-psud.fr/"^^ . - . - . - . - . - . - "http://www.animaldiversity.org"^^ . - . - . - . - . - . - "NIH HIV Reagent Program" . - . - . - "https://coconut.naturalproducts.net"^^ . - "false"^^ . - . - . - . - . - . - "0001011"^^ . - . - . - . - "http://www.sequenceontology.org/miso/current_release/term/SO:$1"^^ . - "http://purl.obolibrary.org/obo/MAXO_$1"^^ . - . - . - . - . - . - . - . - . - . - . - "DIP-743N"^^ . - . - . - . - . - . - . - "http://sabiork.h-its.org/"^^ . - . - "http://purl.obolibrary.org/obo/TAHE_$1"^^ . - . - . - . - "false"^^ . - "Identifiers.org Ontology" . - . - . - . - "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . - "2.1.1"^^ . - . - . - "3000887619"^^ . - . - "https://spdx.org/licenses"^^ . - . - . - "ECMDB00005"^^ . - "http://www.obofoundry.org/"^^ . - . - . - . - "https://sed-ml.org/urns.html#language:$1"^^ . - . - . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . - . - "https://web.expasy.org/variant_pages/VAR_$1.html"^^ . - "https://biopragmatics.github.io/debio/$1"^^ . - . - . - . - . - . - "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . - . - "false"^^ . - . - . - . - "KEGG Pathways Database" . - "PIR Superfamily Classification System" . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - "NIF Standard Ontology: Digital Resources" . - "^A\\d{4}$"^^ . - "https://medical-data-models.org/forms/$1"^^ . - . - . - . - . - . - . - "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . - . - "George Gkoutos" . - . - . - "^\\d{7}$"^^ . - "https://cropontology.org/ontology/CO_330/Potato"^^ . - "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - . - "DUO is an ontology which represent data use conditions."^^ . - . - "https://www.wikidata.org"^^ . - "^MSMEG\\w+$"^^ . - . - . - "F0001"^^ . - . - "ENST00000407236"^^ . - "James C. Hu" . - "^\\d{5}$"^^ . - . - . - . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . - . - "false"^^ . - "depends on" . - . - . - . - . - . - . - . - . - . - . - . - "latitude"^^ . - "447860"^^ . - . - . - "false"^^ . - "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . - . - . - "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . - "http://www.sanger.ac.uk/Users/mb4/PLO/"^^ . - . - "false"^^ . - . - "http://virtualflybrain.org/reports/$1"^^ . - . - "https://fungidb.org/fungidb"^^ . - . - . - . - _:Ne0ea286e6e0c4fe3a14b5392c427c8ab . - . - "https://www.ebi.ac.uk/uniparc/"^^ . - . - . - . - "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . - . - "false"^^ . - "https://pdc.cancer.gov/pdc"^^ . - "P12345"^^ . - . - . - . - "Minimal Viable Identifier" . - . - "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . - "A controlled vocabulary to support the study of transcription in the human brain"^^ . - . - . - "EcoPortal" . - . - . - . - . - "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "^[0-9]{1,7}$"^^ . - "Minimum PDDI Information Ontology" . - . - "^\\d+$"^^ . - . - "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . - "PR000001"^^ . - "false"^^ . - . - . - "h2o"^^ . - "https://www.nextprot.org/"^^ . - . - . - "http://www.w3.org/2000/01/rdf-schema#$1"^^ . - "^\\d{7}$"^^ . - "false"^^ . - "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . - . - "https://www.w3.org/TR/xml/"^^ . - . - . - "Drug Central" . - "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . - . - . - . - . - . - "0000001"^^ . - . - . - . - . - . - "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . - "false"^^ . - . - . - "false"^^ . - . - "LMPR0102010012"^^ . - . - . - "^\\d{7}$"^^ . - "PKDB00198"^^ . - . - . - . - . - . - . - . - "false"^^ . - "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . - . - . - . - . - . - . - . - "http://www.begdb.com"^^ . - . - . - . - "Drosophila development" . - . - . - . - "^[0-9]+$"^^ . - . - . - "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . - "https://fungi.ensembl.org/"^^ . - . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . - . - . - "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . - . - "http://www.geneontology.org/formats/oboInOwl#$1"^^ . - . - . - "https://www.metanetx.org/"^^ . - . - "false"^^ . - . - . - "ValidatorDB" . - . - . - . - . - . - . - . - "https://biological-expression-language.github.io/"^^ . - . - . - . - . - . - . - "EcoliWiki from EcoliHub" . - . - . - . - . - . - . - . - "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . - "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . - . - . - . - . - . - "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . - . - "^\\d+$"^^ . - "^LSM-\\d+$"^^ . - . - . - . - "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - . - "http://rgd.mcw.edu/"^^ . - "^\\w{1,3}$"^^ . - . - "https://europepmc.org/article/ppr/$1"^^ . - . - . - "http://www.coloncanceratlas.org"^^ . - . - "I31.952"^^ . - . - "3G6A5W338E"^^ . - . - . - "Name Reaction Ontology" . - . - . - . - . - . - . - "https://stemcells.nindsgenetics.org?line=$1"^^ . - "https://www.ebi.ac.uk/ega/datasets/$1"^^ . - . - "false"^^ . - . - . - "Antibiotic Resistance Ontology" . - "0000519"^^ . - "PharmGKB Drug" . - . - . - . - . - . - "^DTXSID\\d+$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/nucest"^^ . - . - . - "00000000"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "^\\d+$"^^ . - . - . - "https://github.com/PHI-base/phipo"^^ . - . - "002368"^^ . - "SABIO-RK Reaction" . - . - "false"^^ . - . - "false"^^ . - . - . - "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - "1"^^ . - "nextProt" . - "false"^^ . - . - . - "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . - . - "http://exac.broadinstitute.org/"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm"^^ . - . - "http://geneontology.org/"^^ . - . - "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "https://www.crossref.org/"^^ . - . - "https://aopwiki.org/aops/$1"^^ . - . - "http://plasmodb.org/plasmo/"^^ . - . - "https://ifaa.unifr.ch/"^^ . - . - . - . - "http://fossilworks.org"^^ . - "European Paediatric Cardiac Codes" . - . - . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/"^^ . - . - "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . - . - . - . - "http://mint.bio.uniroma2.it/mint/"^^ . - "CL070"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GNO_$1"^^ . - . - . - . - "Rahuman Sheriff" . - "0000111"^^ . - "10.1621/vwN2g2HaX3"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "https://github.com/OBOFoundry/COB"^^ . - . - . - . - "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . - . - . - . - "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . - . - . - . - "^\\d+$"^^ . - . - "^\\d{7}$"^^ . - "0000001"^^ . - . - . - . - . - "International Molecular Exchange" . - "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . - . - . - . - . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - "http://www.wikidata.org/entity/$1"^^ . - . - "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . - . - "3618"^^ . - . - "ppr103739"^^ . - . - "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . - . - . - "International Classifications of Diseases" . - "https://www.cdc.gov/nchs/icd/icd9.htm"^^ . - . - "NOR00681"^^ . - "MeSH 2012" . - "http://purl.obolibrary.org/obo/CIO_$1"^^ . - "http://bis.zju.edu.cn/ricenetdb"^^ . - "154022"^^ . - . - . - . - . - . - . - . - . - "Phy000CLXM_RAT"^^ . - . - "http://purl.obolibrary.org/obo/LABO_$1"^^ . - . - . - . - "Human developmental anatomy, timed version" . - . - "https://gen3.theanvil.io"^^ . - . - . - "Cardiovascular Disease Ontology" . - "^[a-z0-9]{32,32}$"^^ . - "false"^^ . - . - "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^ . - . - "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . - "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . - . - . - "G77500AY"^^ . - . - . - "^\\d+$"^^ . - "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^ . - "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . - . - . - "http://n2t.net/ark:$1"^^ . - . - . - . - "http://dictybase.org/gene/$1"^^ . - . - "^\\d+$"^^ . - "false"^^ . - "https://e-cyanobacterium.org/models/model/$1"^^ . - . - . - . - "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . - . - "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . - . - . - "https://doulix.com/biomodules/$1"^^ . - . - . - . - "http://www.loria.fr/~coulet/sopharm2.0_description.php"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OGMS_$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "Ascomycete phenotype ontology" . - "http://research.amnh.org/atol/files/"^^ . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - "false"^^ . - "Cell line collections"^^ . - "90000018"^^ . - "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . - "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . - . - "false"^^ . - . - "https://web.expasy.org/abcd/ABCD_$1"^^ . - "0000008"^^ . - . - "http://agroportal.lirmm.fr" . - . - . - "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . - . - "Alzforum Mutations" . - "COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1"^^ . - . - . - . - "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . - "5.A.1.1.1"^^ . - . - . - "http://purl.obolibrary.org/obo/RXNO_$1"^^ . - "Unified Medical Language System Concept Unique Identifier" . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . - "37"^^ . - "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . - . - "0000006"^^ . - . - . - . - . - . - "Cancer Data Standards Registry and Repository" . - . - . - . - . - "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . - . - "https://www.biozol.de/en/product/$1"^^ . - . - . - . - "Friend of a Friend" . - "0000128"^^ . - . - "Scholia Registry" . - . - . - . - "http://www.semantic-systems-biology.org/apo"^^ . - . - "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . - . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000"^^ . - "https://lotus.naturalproducts.net"^^ . - . - . - "100000"^^ . - "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . - . - "false"^^ . - "http://www.massbank.jp"^^ . - . - . - "BioModels Database" . - . - . - . - . - "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait"^^ . - . - "https://www.merckmillipore.com/"^^ . - "https://www.ebi.ac.uk/ega/studies"^^ . - . - . - . - . - . - . - "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . - . - "https://www.flymine.org/come"^^ . - . - . - . - "http://purl.obolibrary.org/obo/AEO_$1"^^ . - . - . - . - . - . - . - . - "HMDB00001"^^ . - "Grant"^^ . - . - . - . - "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . - . - . - "ICARDA - TDv5 - Sept 2018"^^ . - . - . - . - . - "0000000"^^ . - . - . - _:N732b3ccdbc224eba875ae6978752abdd . - "^\\d{7}$"^^ . - . - . - . - . - "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . - "Sierra Moxon" . - . - . - . - "Pathogen Transmission Ontology" . - . - . - . - . - . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt"^^ . - . - . - "ML0224"^^ . - "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "https://github.com/obo-behavior/behavior-ontology/"^^ . - "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^ . - . - "false"^^ . - "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . - "^\\d{6}$"^^ . - . - "https://www.cropontology.org/rdf/CO_346:$1"^^ . - "https://n2t.net" . - "false"^^ . - "0000078"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://addgene.org/$1"^^ . - . - . - . - . - "DRSC05221"^^ . - "false"^^ . - . - . - . - . - . - "true"^^ . - . - "https://www.animalgenome.org"^^ . - . - . - "^P\\d+$"^^ . - . - "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . - . - . - . - . - . - . - . - "HOSAPI0399"^^ . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PDUMDV_$1"^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1"^^ . - . - . - . - . - . - "https://github.com/evoinfo/cdao"^^ . - . - "1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Luis González-Montaña" . - . - . - . - "^R\\d+$"^^ . - "false"^^ . - "Orthology Ontology" . - . - . - . - "40565"^^ . - "https://civicdb.org/links/assertions/$1"^^ . - . - . - . - . - "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . - "false"^^ . - . - "Microbial Conditions Ontology is an ontology..."^^ . - . - . - "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . - . - . - . - "false"^^ . - "^\\w+:[\\w\\d\\.-]*$"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "00020007"^^ . - . - . - _:Ne896ab818ea343789462ac9fa7e3e18f . - . - . - . - . - . - . - . - . - . - . - . - "https://doulix.com"^^ . - . - . - . - "Hepatitis C Virus Database" . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . - . - "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . - . - "false"^^ . - "0045310"^^ . - . - . - "https://mips.helmholtz-muenchen.de/genre/proj/corum/"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . - . - "https://github.com/ufbmi/dron"^^ . - "https://github.com/obophenotype/planarian-phenotype-ontology"^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . - . - . - "https://cordis.europa.eu/"^^ . - . - "Identifiers.org" . - . - "false"^^ . - "Network Data Exchange" . - . - . - "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . - "false"^^ . - . - . - . - . - "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . - "FAIR* Reviews Ontology" . - "https://cropontology.org/ontology/CO_336/Soybean"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . - "http://stato-ontology.org/"^^ . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - "https://mmp.sfb.uit.no/databases/marref/"^^ . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - "achcar11"^^ . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . - . - . - . - "false"^^ . - "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . - . - . - "An ontology of minimum information regarding potential drug-drug interaction information."^^ . - . - "Symptom Ontology" . - . - . - "International repository of Adverse Outcome Pathways."^^ . - . - . - . - "http://purl.obolibrary.org/obo/PLO_$1"^^ . - . - "https://www.grid.ac/institutes/$1"^^ . - "Fernanda Farinelli" . - . - . - . - "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . - . - "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . - "br/1"^^ . - "^[A-Z0-9]+$"^^ . - "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . - "EAWAG Biocatalysis/Biodegradation Database" . - "Variation Ontology" . - . - "CUT"^^ . - "https://www.genome.jp/kegg/glycan/"^^ . - . - . - "A formal represention for drug-drug interactions knowledge."^^ . - . - . - . - . - . - . - . - . - "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . - "false"^^ . - . - "Coronavirus Infectious Disease Ontology" . - . - . - . - . - . - "0002927"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://senselab.med.yale.edu/OrDB/"^^ . - . - . - . - "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . - . - . - . - . - "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . - "10004892"^^ . - . - . - "false"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . - "true"^^ . - . - . - . - . - . - . - "false"^^ . - "http://ecocyc.org/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/MAT_$1"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "HGVST1828"^^ . - . - . - "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . - . - . - "https://cmecscatalog.org/cmecs"^^ . - . - "false"^^ . - . - . - "https://www.fdilab.org"^^ . - . - "http://www.cathdb.info/"^^ . - "Drosophila Phenotype Ontology" . - . - . - "614"^^ . - . - . - "false"^^ . - . - . - "Software ontology" . - . - . - . - . - "Online Computer Library Center WorldCat" . - . - . - . - . - . - . - . - . - . - "Oryza Tag Line" . - "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . - . - . - . - . - "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes."^^ . - "https://biosimulators.org/simulators/$1"^^ . - . - "https://data.4dnucleome.org/experiment-set-replicates/"^^ . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . - . - "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://pk-db.com/data/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/EBISPOT/amphx_ontology"^^ . - . - . - "BAMSC981"^^ . - "ENSGT00550000074763"^^ . - . - "Protein Model Portal" . - "false"^^ . - . - "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . - . - . - . - . - . - . - "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . - . - "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto"^^ . - "false"^^ . - "false"^^ . - . - "Yeast phenotypes" . - . - "http://code.google.com/p/mirna-ontology/"^^ . - . - "false"^^ . - . - . - "Ontology about the development and life stages of the C. elegans"^^ . - . - . - "false"^^ . - "^HGVPM\\d+$"^^ . - . - . - "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . - . - "^C\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . - . - . - . - . - . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - . - . - . - . - . - "0001350"^^ . - . - . - . - "Veterans Health Administration (VHA) unique identifier" . - "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^ . - . - "PhosphoSite Protein" . - . - . - . - . - . - "^[A-Za-z-0-9]+$"^^ . - . - "http://opm.phar.umich.edu/"^^ . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv"^^ . - . - . - . - . - . - "MI0026471"^^ . - "http://wheat.pw.usda.gov"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.genenames.org"^^ . - . - "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . - . - "https://datanator.info/"^^ . - . - . - . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . - . - . - "0000057"^^ . - . - . - . - . - . - . - . - . - "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . - "https://www.uniprot.org/docs/tisslist.txt"^^ . - "Jade Hotchkiss" . - . - . - . - . - . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . - . - . - . - . - "^rs\\d+$"^^ . - . - "^\\d{7}$"^^ . - "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . - . - "http://www.gpcrdb.org/"^^ . - . - "^([hm]\\_)?\\w+Pathway$"^^ . - "false"^^ . - . - . - . - . - "^S\\w+(\\.)?\\w+(\\.)?$"^^ . - . - . - . - . - "false"^^ . - "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . - . - . - . - . - "false"^^ . - . - "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . - . - "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . - . - . - "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$"^^ . - "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . - . - . - . - . - . - . - "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . - . - "An application ontology built for beta cell genomics studies."^^ . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . - . - "Michel Dumontier" . - . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1"^^ . - . - . - "42840"^^ . - . - "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "SPIKE Map" . - . - . - . - "http://dictybase.org/"^^ . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - "https://www.ncbi.nlm.nih.gov/Genbank/"^^ . - . - . - . - "HGNC Symbol" . - . - . - . - . - . - . - . - . - . - "eggNOG" . - . - "00103"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . - _:N41d82a5714aa4f9bbd5fea9efb312782 . - "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . - . - . - . - . - . - . - . - "AgentIdentifierScheme"^^ . - . - . - "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . - "false"^^ . - "http://ardb.cbcb.umd.edu/"^^ . - . - . - . - . - . - . - . - "false"^^ . - "00000099"^^ . - . - . - "false"^^ . - "N1899"^^ . - "1001"^^ . - . - "1h68"^^ . - . - . - . - "Resources mentioned in \"Sharing biological data: why, when, and how\"" . - . - . - "https://omabrowser.org/oma/hog/HOG:$1"^^ . - . - "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FBbi_$1"^^ . - . - . - . - . - "AICARTRANSIMPCYCLO-CPLX"^^ . - . - . - . - . - . - "^F\\d{4}$"^^ . - . - . - "icdom:8500_3"^^ . - . - "Barry Smith" . - . - "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . - . - . - . - "CA981206459"^^ . - "http://ecoportal.lifewatch.eu/ontologies/$1" . - . - "https://odc-tbi.org/data/$1"^^ . - . - . - . - . - . - . - . - . - "Fetal Calf Serum-Free Database" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.cropontology.org/rdf/CO_365:$1"^^ . - . - . - "^DI-\\d{5}$"^^ . - "false"^^ . - "https://neurovault.org/collections/$1"^^ . - . - . - . - "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . - . - . - "GiardiaDB" . - . - "false"^^ . - . - . - "false"^^ . - . - "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . - . - . - . - "http://ascl.net/"^^ . - "false"^^ . - . - "https://www.genome.jp/kegg/reaction/"^^ . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . - "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . - . - . - . - . - . - . - "http://www.tcdb.org/search/result.php?tc=$1"^^ . - . - . - . - "Gemina Symptom Ontology" . - . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - _:N3991e431e80949699eef7263bacf932b . - "http://vegbank.org/cite/$1"^^ . - "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^ . - . - "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . - . - . - . - . - . - . - "Alexander Diehl" . - "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . - . - "PANTHER Node" . - "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . - "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . - . - . - . - "http://purl.obolibrary.org/obo/XAO_$1"^^ . - . - . - . - "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^ . - . - . - . - . - . - . - . - . - "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . - . - . - "Web Ontology Language" . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CDNO_$1"^^ . - "https://www.wormbase.org/"^^ . - "https://www.ebi.ac.uk"^^ . - . - . - . - . - "Ruili Huang" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "http://omia.angis.org.au/$1/"^^ . - . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp"^^ . - . - . - . - . - . - . - . - . - . - . - "https://icahn.mssm.edu/"^^ . - "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . - . - . - . - "http://www.pathwaycommons.org/pc/"^^ . - "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . - . - . - "false"^^ . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - "^GCST\\d{6}\\d*$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - "https://proteininformationresource.org/resid/"^^ . - . - "Golm Metabolome Database Reference Substance" . - "true"^^ . - "KEGG Genome" . - . - . - . - . - . - . - "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules"^^ . - . - . - "Add"^^ . - "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . - "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . - . - "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . - . - . - . - "https://www.ebi.ac.uk/chembldb/"^^ . - "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/PORO_$1"^^ . - "http://www.sparontologies.net/ontologies/cito"^^ . - . - "false"^^ . - . - . - "http://img.jgi.doe.gov/"^^ . - . - "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . - "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . - . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^ . - . - "EG10173"^^ . - "false"^^ . - . - . - "^ML\\w+$"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "^[A-Za-z0-9]+$"^^ . - _:N159387d952584bb48466cc3880fbdbeb . - . - . - . - "UniProt Subcellular Locations" . - . - . - . - "^UCR\\d{5}$"^^ . - . - . - . - "^PGS[0-9]{6}$"^^ . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/UBERON_$1"^^ . - . - . - . - . - . - . - . - . - . - "^[A-Za-z0-9-]+$"^^ . - . - "^[0-9]*$"^^ . - . - "https://www.rhea-db.org/rhea/$1"^^ . - "http://www.antweb.org/specimen.do?name=$1"^^ . - "^\\d{7}$"^^ . - "0002350"^^ . - "SUPERFAMILY" . - . - "WGS84 Geo Positioning" . - . - . - . - . - . - . - . - . - . - . - . - "http://www.cellsignal.com/catalog/index.html"^^ . - . - . - . -_:Nefa30c915878425fa1cb9bca02259543 "Pierre Sprumont" . - . - . - . - . - "Current Dental Terminology" . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . - . - . - . - "false"^^ . - "https://www.uniprot.org/journals"^^ . - . - "http://planteome.org/"^^ . - . - . - "data_1664"^^ . - "true"^^ . - . - . - . - . - . - . - . - . - "221058"^^ . - "http://ctdbase.org/"^^ . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . - "0000947"^^ . - . - . - . - . - "https://rarediseases.info.nih.gov/diseases"^^ . - . - . - . - . - . - "https://hpscreg.eu/cell-line/$1"^^ . - . - . - . - . - "false"^^ . - . - "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . -_:N732b3ccdbc224eba875ae6978752abdd "SEP developers via the PSI and MSI mailing lists" . - "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . - . - . - "PAR:0116"^^ . - . - . - . - . - . - "re3data" . - "Yeast Metabolome Database" . - . - . - "Molecular Process Ontology" . - . - . - . - . - . - . - . - "http://www.oid-info.com/introduction.htm"^^ . - . - . - "HOMD Taxonomy" . - "false"^^ . - "https://gold.jgi.doe.gov/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Comparative Data Analysis Ontology" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . - "http://dictybase.org"^^ . - . - "https://portal.issn.org"^^ . - "Consensus CDS" . - . - "^CONSO\\d{5}$"^^ . - "^\\d{6}$"^^ . - . - "https://comptox.epa.gov/dashboard/$1"^^ . - . - . - . - "false"^^ . - "https://prosite.expasy.org/$1"^^ . - . - . - . - "0000054"^^ . - . - "^[a-zA-Z]+.+$"^^ . - . - "https://pharmacodb.ca/datasets"^^ . - . - . - . - . - . - . - . - "^[A-Za-z0-9\\-\\_]+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "PharmacoDB Datasets" . - "http://sabiork.h-its.org/"^^ . - . - . - . - . - "http://www.cropontology.org/ontology/CO_335/Common%20Bean"^^ . - "131"^^ . - . - . - "https://skip.stemcellinformatics.org/en/"^^ . - "SNOMED CT (International Edition)" . - . - . - . - . - . - . - . - . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - "http://pbil.univ-lyon1.fr/databases/hogenom/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . - "Natural Product-Drug Interaction Research Data Repository" . - "Quantities, Units, Dimensions, and Types Ontology" . - . - . - . - "Vertebrate trait ontology" . - . - "70"^^ . - . - . - "false"^^ . - . - . - . - "https://github.com/echinoderm-ontology/ecao_ontology"^^ . - . - . - "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . - . - . - "https://nanocommons.github.io/identifiers/registry#$1"^^ . - . - . - . - . - . - . - . - . - "https://www.uniprot.org/database/$1"^^ . - . - "true"^^ . - . - . - . - . - . - "1981638"^^ . - "https://eol.org/pages/$1"^^ . - . - . - "false"^^ . - "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^ . - . - . - . - "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"^^ . - "Life cycle stages for Platynereis dumerilii"^^ . - "Bioregistry" . - . - . - "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . - "RC00001"^^ . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/OHD_$1"^^ . - . - "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . - "KEGG Genes" . - . - "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - "Physico-chemical process" . - "false"^^ . - . - . - . - . - . - . - "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . - . - "Sanger Cell Model Passports" . - . - . - "TB2:S1000"^^ . - "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . - . - . - . - "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . - . - . - . - . - . - "GDS1234"^^ . - . - . - "https://gitlab.com/fortunalab/ontoavida"^^ . - "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^ . - . - "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . - . - "false"^^ . - . - . - "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies"^^ . - . - . - . - . - "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^ . - . - . - . - . - . - "http://www.imgt.org/ligmdb/view?id=$1"^^ . - . - . - . - "^GN_[A-Za-z0-9_:]+$"^^ . - "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . - . - " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . - . - "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . - . - . - "https://www.aapc.com"^^ . - "WormBase database of nematode biology" . - "false"^^ . - "068078"^^ . - . - . - . - . - . - . - "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . - "false"^^ . - "Minimal Anatomical Terminology" . - . - . - "1a05"^^ . - "^\\d{8}$"^^ . - . - . - "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html"^^ . - . - "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . - "false"^^ . - "https://cropontology.org/ontology/CO_323/Barley"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . -_:Ne436db2047a8466592218d4a04b072df "Pierre Sprumont" . - . - . - . - "An ontology of traits covering vertebrates"^^ . - . - "http://senselab.med.yale.edu/OdorDB"^^ . - . - . - "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . - "0000001"^^ . - . - "Meghan Balk" . - . - . - . - . - "https://panoramaweb.org/$1.url"^^ . - . - "31"^^ . - "Event (INOH pathway ontology)" . - "arXiv" . - . - . - "false"^^ . - . - "VEuPathDB ontology" . - . - . - . - . - "International Classification of Diseases, 10th Revision, Procedure Coding System" . - . - . - . - . - "false"^^ . - . - . - "https://www.uniprot.org/database/"^^ . - . - . - . - . - . - . - . - . - "http://e-cyanobacterium.org/models/"^^ . - . - . - . - "C34"^^ . - . - . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "01406"^^ . - . - . - . - . - "http://flybase.org/"^^ . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . - . - . - . - . - . - "http://edamontology.org/data_$1" . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - "http://multicellds.org/MultiCellDB.php"^^ . - "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes."^^ . - . - . - "82"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "100"^^ . - . - . - . - . - "https://www.vectorbase.org/ontology-browser"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "https://biopragmatics.github.io/providers/scomp/$1"^^ . - . - . - . - . - . - "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . - . - _:N5b5cb92149e84d5181fc7daa005ced76 . - . - "BioGRID" . - . - . - "^[A-Za-z_0-9]+$"^^ . - . - . - . - . - "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/INO_$1"^^ . - . - "Simple Knowledge Organization System" . - . - . - . - . - "10153"^^ . - . - . - "1466"^^ . - _:Nfac200ed2c064af48ed9910ac7785fc4 . - "National Center for Advancing Translation Sciences BioPlanet" . - "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - "0001290"^^ . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - "^PS\\d+$"^^ . - . - "Database of Escherichia coli Sequence and Function" . - "AURKA"^^ . - . - . - . - . - . - . - . - "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . - . - . - . - . - "Semantic Web for Earth and Environment Technology Ontology" . - "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . - "false"^^ . - . - "http://www.xenbase.org/anatomy/xao.do?method=display"^^ . - . - . - "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . - "TA_H3"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . - . - "101"^^ . - . - . - "false"^^ . - "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^ . - . - . - . - "Vocabulary used in the RDF representation of SBML models."^^ . - "false"^^ . - "http://purl.org/spar/deo/$1"^^ . - . - . - "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "^[\\w\\d\\.-]*$"^^ . - . - . - . - . - "5.1"^^ . - "AntWeb ID" . - . - . - . - . - "https://www.worldcat.org/oclc/$1"^^ . - . - "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . - "DAPK1"^^ . - . - "false"^^ . - . - "false"^^ . - . - "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . - "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . - "ATL98012"^^ . - . - "Digital archive of scholarly articles" . - . - "true"^^ . - . - . - . - "http://pax-db.org/#!protein/$1"^^ . - "http://purl.obolibrary.org/obo/HSO_$1"^^ . - . - . - . - "Decentralized Identifier" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "true"^^ . - . - "https://www.w3.org/2003/01/geo/wgs84_pos"^^ . - . - . - . - . - . - . - "Network of Different Plant Genomic Research Projects" . - . - "https://pathbank.org/view/$1"^^ . - "http://www.sparontologies.net/ontologies/doco"^^ . - "http://uberon.org"^^ . - . - . - "http://paleodb.org/"^^ . - . - "false"^^ . - "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . - . - . - "http://biomodels.net/rdf/vocabulary.rdf"^^ . - . - . - . - . - . - . - "Bilateria anatomy" . - . - . - . - . - . - "https://www.ebi.ac.uk/biomodels/"^^ . - "Human Medical Genetics" . - . - . - . - "https://www.ebi.ac.uk/arrayexpress/"^^ . - . - "Database of human Major Histocompatibility Complex" . - . - . - . - . - . - . - . - . - . - . - "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . - "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . - "^PA\\w+$"^^ . - . - . - "0187632"^^ . - . - "http://purl.obolibrary.org/obo/DINTO_$1"^^ . - "AU124"^^ . - . - "https://bioregistry.io/metaregistry/biocontext/$1" . - . - "^MF_\\d+$"^^ . - . - "false"^^ . - . - "^K\\d+$"^^ . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - "International Classification of Diseases, 10th Revision, Clinical Modification" . - "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . - . - . - . - . - "http://www.narcis.nl"^^ . - . - "^(doi\\:)?\\d{2}\\.\\d{4}.*$"^^ . - . - . - "false"^^ . - . - . - "Cowpea ontology" . - . - . - "http://exac.broadinstitute.org/variant/$1"^^ . - . - . - . - . - . - "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^ . - . - . - "ToxoDB" . - . - "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . - . - . - . - . - "^\\d+$"^^ . - . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^ . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "OrthoDB" . - . - "Soybean ontology" . - . - "AT1G73965"^^ . - . - . - "Datanator Gene" . - . - . - . - . - . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . - . - . - "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^ . - . - . - . - . - . - . - "Multiple alignment" . - "^\\d+$"^^ . - "^(imp|gen)\\d{5}$"^^ . - . - "Tom Gillespie" . - . - . - "1731"^^ . - "Animal TFDB Family" . - "false"^^ . - . - . - . - "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . - . - . - . - . - "https://github.com/enpadasi/Ontology-for-Nutritional-Studies"^^ . - "^\\d+$"^^ . - "false"^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . - . - . - "11"^^ . - . - "long-finned-pilot-whale"^^ . - . - "Ontology of Host-Microbiome Interactions" . - . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . - "http://purl.obolibrary.org/obo/MMUSDV_$1"^^ . - "http://www.ncbi.nlm.nih.gov/unigene"^^ . - . - . - "Veterans Administration National Drug File" . - . - . - "Schema.org" . - . - . - . - "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1"^^ . - "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . - . - . - . - . - . - "http://purl.org/dc/terms/$1"^^ . - . - . - . - "https://www.araport.org/"^^ . - . - "https://pubchem.ncbi.nlm.nih.gov/classification/"^^ . - . - . - . - "https://github.com/EcologicalSemantics/ecocore"^^ . - . - . - . - . - . - . - "false"^^ . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - "BIOZIL" . - "false"^^ . - "http://purl.org/spar/biro/$1"^^ . - "UniProt Resource" . - . - . - . - "true"^^ . - "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"^^ . - . - . - "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . - "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . - . - "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . - . - "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . - . - . - . - . - . - . - "https://www.cropontology.org/rdf/CO_357:$1"^^ . - . - _:N670300cc4f4e45b8a8b3cfa32ce48e3e . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - "https://github.com/rsc-ontologies/rxno"^^ . - "https://www.brainspan.org/"^^ . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . - "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . - . - . - . - . - . - . - . - "https://www.expasy.org/prosite/"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - . - "false"^^ . - . - . - "true"^^ . - . - "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . - "https://www.cropontology.org" . - . - . - "ECOCYC" . - . - . - "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "dictyBase" . - . - . - . - . - . - "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . - . - . - . - "false"^^ . - . - . - . - "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . - . - . - . - "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries."^^ . - "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . - . - . - . - "http://purl.obolibrary.org/obo/FOBI_$1"^^ . - . - "^EDI_\\d+$"^^ . - "53504"^^ . - . - . - . - "false"^^ . - "Pazar Transcription Factor" . - "http://zinc15.docking.org/"^^ . - . - . - . - . - . - . - . - . - . - . - "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . - . - . - . - "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . - "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . - "1199"^^ . - "03307879"^^ . - "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . - "http://umbbd.ethz.ch/"^^ . - "1000003"^^ . - . - . - "Citlalli Mejía-Almonte" . - . - "^\\d{7}$"^^ . - . - "https://aopwiki.org/"^^ . - "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . - . - "Linear double stranded DNA sequences" . - "chromium"^^ . - . - "Registry" . - . - . - "http://purl.obolibrary.org/obo/CDAO_$1"^^ . - . - . - "Scopus Researcher" . - "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . - "GenPept" . - . - . - . - . - . - . - . - "Carrine Blank" . - . - "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "Resource" . - . - . - "false"^^ . - . - . - . - . - "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^ . - . - . - . - "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . - "http://purl.obolibrary.org/obo/LPT_$1"^^ . - "The pattern for identifiers in the given resource" . - . - "^\\d{7}$"^^ . - . - . - "Teleost taxonomy ontology" . - . - . - . - . - . - "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . - "DailyMed" . - . - . - "^\\d+$"^^ . - "false"^^ . - . - "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "http://modelseed.org/biochem/reactions/"^^ . - . - . - . - . - . - . - . - . - . - . - "SABIO-RK Compound" . - . - "sourceDateStart"^^ . - "false"^^ . - "eagle-i" . - "https://ssbd.riken.jp/database/project/$1"^^ . - . - . - . - "Legacy disease classes that later became MONDO"^^ . - . - "https://github.com/phenoscape/taxrank"^^ . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - "false"^^ . - . - "0002058"^^ . - . - . - "Bibliographic Reference Ontology" . - . - "^ILMN_\\d+$"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "Cell line collections"^^ . - . - . - "false"^^ . - "Identifier for a species on the noaa fisheries website"^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . - . - "Phenol-Explorer" . - "VFDB Genus" . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . - . - . - . - . - . - . - . - "^AT\\d+$"^^ . - "^\\d{7}$"^^ . - "^.+$"^^ . - "AADB12"^^ . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . - . - "http://www.w3.org/2004/02/skos/core#$1"^^ . - "^PRO_[0-9]{10}$"^^ . - "https://github.com/SDG-InterfaceOntology/sdgio"^^ . - . - "https://datanator.info/reaction/$1"^^ . - "ScerTF" . - . - . - "Animal natural history and life history" . - "false"^^ . - . - . - . - . - "AHR"^^ . - . - . - . - . - . - . - . - . - . - "Porifera Ontology" . - "The Statistical Methods Ontology" . - . - "^\\d+$"^^ . - . - . - . - . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - . - . - "false"^^ . - . - . - . - . - "0001885"^^ . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - "ALA"^^ . - . - . - . - . - "CHEMBL3307800"^^ . - . - . - "^\\d+$"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/$1"^^ . - . - . - . - "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . - . - . - . - . - "Encyclopedia of DNA Elements" . - . - . - . - . - . - "http://crdd.osdd.net/servers/virsirnadb"^^ . - . - . - . - "^\\d{7}$"^^ . - "000000341"^^ . - . - . - . - . - . - "false"^^ . - . - . -_:N0b6dc46b862b41399ea93d23b5a47653 "David Blackburn" . - . - . - . - . - "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . - . - "https://glytoucan.org/"^^ . - . - . - "0000011"^^ . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/RS_$1"^^ . - . - . - "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . - "https://github.com/linikujp/OGSF"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://amigo.geneontology.org/amigo/term/GO:$1"^^ . - . - . - . - "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^ . - . - "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . - . - . - . - . - . - "ChemSpider" . - . - . - "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . - . - . - . - . - "BiGG Model" . - "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^EBI\\-[0-9]+$"^^ . - . - "https://github.com/obophenotype/porifera-ontology"^^ . - "https://www.uniprot.org/diseases/"^^ . - . - . - "https://github.com/github/linguist"^^ . - . - "Snapshot" . - "An ontology designed to support the semantic annotation of epidemiology resources"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . - "^Os\\S+t\\d{7}-\\d{2}$"^^ . - . - . - . - "https://dailymed.nlm.nih.gov/dailymed/"^^ . - . - . - "^\\d+$"^^ . - "ENCSR163RYW"^^ . - . - "https://rfam.xfam.org/family/$1"^^ . - "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^ . - . - . - . - . - . - . - "T039"^^ . - . - . - "36"^^ . - "PhylomeDB" . - "^\\d{8}$"^^ . - . - . - . - . - . - . - . - "https://www.metanetx.org/equa_info/$1"^^ . - . - . - . - . - . - . - "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . - "A controlled vocabulary to describe phenotypic traits in plants."^^ . - . - . - . - . - "VFG2154"^^ . - . - "NA06985"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - "ERP004492"^^ . - . - . - "2008-005144-16"^^ . - . - . - . - . - "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . - . - "http://www.yeastgenome.org/"^^ . - . - "http://purl.obolibrary.org/obo/CHMO_$1"^^ . - . - . - "false"^^ . - . - . - "https://bio.tools/"^^ . - . - "LIPID MAPS" . - "^(Gi|Gc)\\d+$"^^ . - . - "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . - . - . - . - . - . - . - . - . - "5277619"^^ . - . - . - . - "0000066"^^ . - "^\\d{7}$"^^ . - . - "LRG_1"^^ . - . - "Redistributor of bilogics and biomedical supplies"^^ . - . - "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . - "https://flybase.org/reports/$1"^^ . - "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . - . - . - "Gm00047"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - . - . - . - . - . - . - "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . - . - "https://www.cropontology.org/rdf/CO_359:$1"^^ . - "Oat ontology" . - . - "false"^^ . - . - . - . - . - . - _:Nb2d09a7498bc40199aa734cfcb455768 . - "fluticasone"^^ . - "https://www.ideal-db.org"^^ . - "https://foodb.ca/foods/$1"^^ . - . - . - . - . - . - "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^ . - . - "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . - . - . - . - . - . - . - "false"^^ . - "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^ . - . - . - . - . - . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . - "002804"^^ . - . - . - . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . - . - . - . - "https://www.genedb.org/gene/$1"^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - "https://www.ebi.ac.uk/pdbe/emdb/"^^ . - . - . - . - "false"^^ . - "false"^^ . - "http://func.mshri.on.ca/mouse/"^^ . - "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . - "Ontology of Biological and Clinical Statistics" . - . - . - . - . - . - . - . - . - "^r\\d+$"^^ . - "ISCW007415"^^ . - "The International Standard Book Number (ISBN) is for identifying printed books."^^ . - . - . - . - . - . - "http://psb.kobic.re.kr/STAP/refinement/"^^ . - . - "Loggerhead nesting" . - . - . - . - . - . - . - . - . - "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . - . - . - . - . - . - . - "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . - . - "John Graybeal" . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . - . - . - "MobiDB is a database of protein disorder and mobility annotations."^^ . - . - . - . - . - . - "SBGN Bricks data and ontology" . - . - "false"^^ . - . - . - . - . - "John Beverly" . - . - . - "https://medical-data-models.org/"^^ . - . - . - "http://edamontology.org"^^ . - . - . - . - "false"^^ . - "http://rebase.neb.com/rebase/enz/$1.html"^^ . - . - . - . - . - . - . - "^C\\d+$"^^ . - . - "false"^^ . - "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . - . - . - . - "http://130.88.97.239/dbbrowser/sprint/"^^ . - . - "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . - . - "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "Health Data Research Innovation Gateway" . - . - "http://topdb.enzim.hu/?m=show&id=$1"^^ . - . - . - . - . - . - . - "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . - "https://www.brenda-enzymes.org/"^^ . - . - . - . - "PjrpzUIAAAAJ"^^ . - "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . - "http://bioinfo.iitk.ac.in/MIPModDB"^^ . - . - "SNR17A"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "Mathematical modeling ontology" . - . - "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^ . - . - "https://www.geonames.org/$1"^^ . - "E-cyanobacterium Experimental Data" . - . - . - "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "http://jcggdb.jp/index_en.html"^^ . - "Provenance, Authoring, and Versioning Vocabulary" . - . - . - "^[1-9][0-9]*$"^^ . - "false"^^ . - . - . - . - "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . - . - . - . - . - . - "P00266"^^ . - . - "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . - . - . - "http://purl.obolibrary.org/obo/EPIO_$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/CARO_$1"^^ . - "NMR-instrument specific component of metabolomics investigations" . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/ONS_$1"^^ . - . - . - . - . - . - "https://www.phenxtoolkit.org/protocols/view/$1"^^ . - . - "2005080"^^ . - "false"^^ . - . - "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^ . - . - "PANTHER Pathway" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^rs[0-9]+$"^^ . - "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . - . - "false"^^ . - . - . - "78"^^ . - . - "NanoParticle Ontology" . - . - "https://www.kegg.jp/entry/$1"^^ . - . - . - "Rat Genome Database qTL" . - "DICOM Controlled Terminology"^^ . - "false"^^ . - . - . - . - "http://www.atol-ontology.com"^^ . - . - "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . - . - . - . - . - . - "http://www.ubio.org"^^ . - . - "https://www.glycoepitope.jp/epitopes/$1"^^ . - . - "http://pombe.oridb.org/details.php?id=$1"^^ . - . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits."^^ . - . - . - . - . - . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . - . - . - "Unified Medical Language System Atomic Unique Identifier" . - . - "false"^^ . - . - "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . - . - "^(R)?PXD\\d{6}$"^^ . - . - . - . - "Insect Resistance Ontology" . - . - . - . - . - "ChEMBL" . - "^\\d+$"^^ . - . - . - . - . - . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Molecular database for the identification of fungi" . - "http://purl.obolibrary.org/obo/PLANA_$1"^^ . - . - . - . - . - . - "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . - . - . - . - "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . - . - "false"^^ . - . - . - . - . - "European Registry of Materials" . - . - . - . - . - "^\\d{7}$"^^ . - "Chinese Biological Abstracts" . - . - . - . - "BibliographicRecord"^^ . - . - . - . - . - . - . - . - "false"^^ . - "Zebrafish Information Network Gene" . - "^[1-9][0-9]{3,6}$"^^ . - . - . - . - . - . - "2022.07.08.499378"^^ . - "Draft version"^^ . - . - . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . - . - "Information for ligands in the BRENDA database."^^ . - "0000022"^^ . - . - . - . - "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/VO_$1"^^ . - . - . - . - . - . - . - . - . - . - "Drosophila gross anatomy" . - . - "Lutz Fischer" . - . - . - . - . - . - . - . - . - . - . - "https://www.va.gov/health"^^ . - "2.16.840"^^ . - . - "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . - . - . - . - . - . - "JCRB1355"^^ . - . - "PRJDB3"^^ . - . - "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . - "GPST000024"^^ . - . - . - "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . - . - . - . - . - . - . - "^[\\w\\-:,]{3,64}$"^^ . - . - "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . - "false"^^ . - . - . - . - "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . - . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - . - . - . - . - . - . - . - . - . - . - "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . - "34"^^ . - . - "Catalytic Site Atlas" . - . - . - . - . - . - . - . - "Mouse Genome Informatics" . - . - "http://purl.org/dc/dcmitype/$1"^^ . - . - "THE1B"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ZECO_$1"^^ . - "DragonDB DNA" . - . - . - . - . - . - . - "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records."^^ . - "AC119"^^ . - "AAA35559"^^ . - "chebi" . - . - "https://www.cropontology.org/rdf/CO_358:$1"^^ . - . - . - "^\\d{7}$"^^ . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . - "^\\d{8}$"^^ . - . - . - . - . - . - . - "http://intron.ucsc.edu/yeast4.3/"^^ . - "28"^^ . - "false"^^ . - "WBRNAi00086878"^^ . - "Cellular Phenotypes" . - . - . - "MassIVE" . - . - . - "https://pubchem.ncbi.nlm.nih.gov/"^^ . - . - . - . - . - . - "InTextReferencePointer"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page"^^ . - . - . - "false"^^ . - "Cell line collections"^^ . - . - . - "E-cyanobacterium entity" . - . - . - . - . - . - . - "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . - . - "false"^^ . - "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . - . - . - "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . - "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "PaxDb Organism" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://www.genome.jp/kegg/drug/"^^ . - . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "An ontology to describe entities related to cardiovascular diseases"^^ . - "0000066"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.blueprintnhpatlas.org/"^^ . - . - "NIF Standard Ontology: Qualities" . - . - "0000139"^^ . - . - . - "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - "true"^^ . - . - . - "GPM32310002988"^^ . - . - "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . - . - . - . - . - "https://envipath.org/package/$1"^^ . - . -_:Ne83bc53683cc401c8d9aa32085d472b2 "Nathan Baker" . - . - . - . - . - "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . - . - "0000728"^^ . - "Odor Molecules DataBase" . - . - . - . - "https://flybrain-ndb.virtualflybrain.org"^^ . - "^[0-9]{8}$"^^ . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^ . - . - . - . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . - . - "http://www.imgt.org/"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . - "NIA Mouse cDNA Project" . - . - "http://www.fungalbarcoding.org/"^^ . - "https://microbiomedata.org/"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CTO_$1"^^ . - . - . - "102l"^^ . - . - . - . - . - "COG0001"^^ . - "Biological Imaging Methods Ontology" . - . - "http://bgee.unil.ch/bgee/bgee"^^ . - . - . - . - . - . - . - "Clair Kronk" . - "http://www.genome.jp/kegg/genes.html"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://hawaii.eagle-i.net"^^ . - "Bactibase" . - "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . - . - . - "^YMDB\\d+$"^^ . - . - . - . - . - "false"^^ . - "https://www.lgresearch.ai"^^ . - "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "^[1-9]\\d{0,5}$"^^ . - "CryptoDB" . - "Contains information about cells and data sheets related to transfection."^^ . - . - . - . - "Plant Trait Ontology" . - . - . - "GlycomeDB" . - . - . - . - . - "false"^^ . - "^[1-9][0-9]*$"^^ . - . - . - . - "http://www.geosamples.org/"^^ . - . - . - "http://topdb.enzim.hu/"^^ . - . - . - . - . - . - _:Nad7b44867b004956a38c44d46d8c39ba . - . - . - . - "https://gpcrdb.org/protein/$1"^^ . - "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . - . - _:N81701af170f54963a1109ab1bda92df0 . - . - . - "An ontology of human and animal behaviours and behavioural phenotypes"^^ . - . - . - . - . - . - . - "https://asrp.danforthcenter.org/"^^ . - . - . - . - . - . - "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . - . - . - "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . - . - . - . - . - . - . - "Jennifer Smith" . - . - . - "^\\d+$"^^ . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . - . - "^(\\w+)?\\d+$"^^ . - . - . - . - . - . - . - . - "NONCODE v3" . - . - "SwissLipid" . - . - . - . - "PRO_0000016681"^^ . - . - . - "https://www.cropontology.org/rdf/CO_343:$1"^^ . - . - "Polygenic Score Catalog" . - . - . - . - . - . - . - . - "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . - . - . - . - "http://www.yeastgenome.org/"^^ . - . - "false"^^ . - . - "false"^^ . - "false"^^ . - "Ontology about C. elegans and other nematode phenotypes"^^ . - "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^ . - "Histopathology Ontology" . - "rs17852708"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "A0014"^^ . - . - "Cryo Electron Microscopy ontology" . - "0000460"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/"^^ . - . - . - . - . - . - "http://substrate.burnham.org/protein/annotation/$1/html"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "https://www.bindingdb.org"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://www.receptors.org/nucleardb/proteins/$1"^^ . - "TRQ"^^ . - . - "true"^^ . - "^\\d{7}$"^^ . - . - . - . - "Call for paper topics in EasyChair"^^ . - . - "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . - . - . - . - "T3D0001"^^ . - . - . - . - "0000598"^^ . - "Zebrafish anatomy and development ontology" . - "GWAS Central Phenotype" . - "http://scipion.i2pc.es/ontology/cryoem"^^ . - . - "false"^^ . - . - . - "https://www.kaggle.com/$1"^^ . - . - "RNA Modification Database" . - . - . - . - . - . - . - "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . - "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . - . - "https://pharmacodb.ca/tissues/$1"^^ . - . - . - . - "https://dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - . - . - "^\\d{7}$"^^ . - "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . - . - . - . - . - "false"^^ . - "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . - . - "false"^^ . - . - . - "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - "http://thebiogrid.org/$1"^^ . - . - "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . - . - "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . - "1200"^^ . - "^RCB\\d+$"^^ . - "Ontology Lookup Service" . - "false"^^ . - "Daniel Himmelstein" . - . - . - "C12345"^^ . - . - . - . - . - . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . - "EGAS00000000001"^^ . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Val Wood" . - . - . - . - . - . - "http://compluyeast2dpage.dacya.ucm.es/"^^ . - . - . - "https://mmp.sfb.uit.no/databases/marcat/"^^ . - "M58335"^^ . - "https://github.com/micheldumontier/semanticscience"^^ . - . - "ChemDB" . - . - . - "false"^^ . - . - . - . - . - "https://github.com/calipho-sib/controlled-vocabulary"^^ . - "prgr_human"^^ . - . - _:N2fde3ed72d8f4e8ba8c8aa6ce10c384e . - . - . - "0001410"^^ . - . - . - . - . - . - "ForwardStrandPosition"^^ . - . - "http://www.proteinatlas.org/"^^ . - "Metabolomics Workbench Project" . - . - . - . - . - . - "3SBPLMKKVEVR"^^ . - . - "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^ . - "Gene Ontology Database references" . - . - . - . - "https://caninecommons.cancer.gov/#/"^^ . - "^M[0-9]{4,}$"^^ . - . - "http://scicrunch.org/resolver/SCR_$1"^^ . - . - . - "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . - "Digital Object Identifier" . - . - . - . - . - . - "NIF Standard Ontology: Neurolex" . - "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . - . - . - . - . - "1000000"^^ . - "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . - "Integrated Genomic Resources of human Cell Lines for Identification" . - . - . -_:N0b78bd2c53ed4e6baaea94e059f19c70 "David Blackburn" . - . - . - . - . - . - "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . - . - "false"^^ . - . - . - "Pesticide Properties DataBase" . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - . - . - . - . - . - . - . - . - . - "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . - "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . - . - "ALIENSPECIES" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://www.imanislife.com/?s=$1"^^ . - . - . - . - . - . - . - . - . - . - "LinJ.20.0070"^^ . - "false"^^ . - "http://smart.embl-heidelberg.de/"^^ . - . - . - . - . - . - . - . - . - "307"^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . - . - . - . - . - . - . - "MCDS_S_0000000001"^^ . - . - "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . - "^\\S+$"^^ . - "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . - "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . - "https://github.com/OPMI/opmi"^^ . - "^MMP\\d+.\\d+$"^^ . - . - "Gene Wiki" . - "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . - . - "^[A-Z]C\\d{1,3}$"^^ . - . - . - . - "RiceNetDB Gene" . - . - "http://pid.nci.nih.gov/"^^ . - . - . - . - . - . - . - . - "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . - . - . - . - . - "http://www.pathbase.net"^^ . - "The Drug Ontology" . - . - . - "false"^^ . - "4019477"^^ . - . - . - . - . - . - . - "https://www.kew.org/data/grasses-db/www/$1"^^ . - . - "https://pfam.xfam.org/"^^ . - . - "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . - . - . - "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . - . - "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . - . - "false"^^ . - . - . - . - . - . - . - "https://www.nextprot.org/db/entry/$1"^^ . - "https://biopragmatics.github.io/debio"^^ . - . - "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . - . - "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . - . - "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . - . - . - . - . - . - "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "CIAT Common bean trait dictionary - version August 2014"^^ . - . - "Microbial Protein Interaction Database" . - . - "false"^^ . - . - . - "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . - "CHEMBL3467"^^ . - "https://www.internationalgenome.org/"^^ . - . - "false"^^ . - . - . - . - . - . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . - . - . - . - . - . - "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . - . - . - "BRIP1"^^ . - . - . - "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . - . - . - . - . - . - "Applied Biological Materials cell line products" . - "^\\d+$"^^ . - "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . - . - "^A\\d{6}$"^^ . - . - "Cell line collections"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - "Signaling Gateway" . - . - . - . - "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . - . - . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - "false"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - "00000001"^^ . - "https://www.gwascentral.org/study/$1"^^ . - . - . - "http://www.pantherdb.org/"^^ . - . - "880798137"^^ . - . - . - . - . - . - "b97957"^^ . -_:N97cbfa9779f94043ab3e07f690355ec4 "Animal Diversity Web technical staff" . - . - "http://www.enanomapper.net/"^^ . - . - "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . - . - "https://www.gwascentral.org/markers"^^ . - . - "false"^^ . - . - . - . - . - . - "Mouse Developmental Stages" . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - "false"^^ . - "PharmacoDB Cells" . - . - "https://www.ebi.ac.uk/chembl"^^ . - . - . - . - . - . - . - "ClinVar Record" . - . - "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . - . - "https://github.com/obophenotype/planaria-ontology"^^ . - . - . - . - "http://patft.uspto.gov/netahtml/PTO/index.html"^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^ . - . - . - . - . - . - . - "http://www.drugbank.ca/biodb/bio_entities/$1"^^ . - . - "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . - . - "http://www.hipsci.org"^^ . - "^\\d{7}$"^^ . - . - . - "http://purl.obolibrary.org/obo/ICEO_$1"^^ . - . - "ACH-000001"^^ . - . - . - "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . - . - . - "^COG\\d+$"^^ . - . - . - . - "G00054MO"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "LINCS Protein" . - . - "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . - "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . - "^\\d+$"^^ . - . - . - "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . - . - . - "TR0000001"^^ . - . - . - . - . - . - "true"^^ . - "http://wheat.pw.usda.gov"^^ . - . - "NONCODE v4 Transcript" . - . - . - . - . - "https://www.pgscatalog.org/pgs/$1"^^ . - "https://www.humancellatlas.org"^^ . - . - . - . - "true"^^ . - . - . - . - . - . - "1915"^^ . - "Schema for the export of the Bioregistry as RDF"^^ . - . - . - . - . - "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . - . - . - . - . - "26"^^ . - . - . - "Trish Whetzel" . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "Global Biodiversity Information Facility" . - . - "https://www.ebi.ac.uk/chembldb/"^^ . - . - . - . - . - "P3DB Site" . - "true"^^ . - . - "https://hamap.expasy.org/"^^ . - . - "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"^^ . - . - . - . - . - . - . - . - . - . - "CO_010" . - . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all"^^ . - "http://genex.hgu.mrc.ac.uk/"^^ . - "XML Schema Definition" . - . - "^ENSG\\d{11}$"^^ . - "false"^^ . - "Probability Distribution Ontology" . - . - "false"^^ . - "https://github.com/bgsu-rna/rnao"^^ . - "Amanda Hicks" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Reaxys eMolecules" . - "false"^^ . - . - "^EG\\d+$"^^ . - . - "http://www.violinet.org/ovae/"^^ . - . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . - "http://purl.obolibrary.org/obo/VARIO_$1"^^ . - . - . - "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . - . - "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . - . - . - . - "https://www.noguchi.or.jp/"^^ . - "false"^^ . - "true"^^ . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . - . - . - "Database of small human noncoding RNAs" . - . - . - "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . - "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . - . - "BindingDB is the first public database of protein-small molecule affinity data."^^ . - . - . - . - . - . - "^e\\d+$"^^ . - . - . - "14"^^ . - . - "2842"^^ . - . - "00573"^^ . - . - . - . - . - . - . - "Tom Gillespie" . - . - "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . - . - . - "http://www.antweb.org/"^^ . - "http://www.sparontologies.net/ontologies/frbr"^^ . - . - . - "false"^^ . - . - "false"^^ . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - "rs11603840"^^ . - . - . - . - "https://www.cropontology.org/rdf/CO_333:$1"^^ . - . - . - . - "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . - . - . - "http://caps.ncbs.res.in/pass2"^^ . - "Person" . - . - . - "^\\d+$"^^ . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . - . - "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . - "true"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"^^ . - . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . - . - . - . - . - "false"^^ . - . - . - "^SCV\\d+(\\.\\d+)?$"^^ . - "false"^^ . - . - . - . - . - . - "Getty Thesaurus of Geographic Names" . - . - . - . - "https://w3id.org/oc/oci/$1"^^ . - . - . - . - . - "http://www.proteinatlas.org/$1"^^ . - . - "^[AEP]-\\w{4}-\\d+$"^^ . - . - . - . - "false"^^ . - . - . - . - "^(ZINC)?\\d+$"^^ . - . - . - "https://www.ebi.ac.uk/metagenomics"^^ . - . - . - . - . - . - . - . - . - . - . - "NLXFUNC covers terms for cognitive function."^^ . - . - . - "Close to 5K Categorizations for drugs, similar to ATCC."^^ . - . - . - "Jim Balhoff" . - "OID Repository" . - . - "false"^^ . - . - . - "http://www.metabolomicsworkbench.org/"^^ . - "0000095"^^ . - . - . - . - "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . - . - "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . - . - . - "true"^^ . - . - . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - . - "http://www.w3.org/1999/02/22-rdf-syntax-ns"^^ . - . - "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . - . - . - "Candida Genome Database" . - "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1"^^ . - . - "^\\d+$"^^ . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . - "SED-ML model format" . - "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . - . - . - . - "^[A-Za-z0-9]+$"^^ . - "false"^^ . - . - . - "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . - . - . - . - . - . - "CranioMaxilloFacial ontology" . - . - . - "NPC139585"^^ . - . - "false"^^ . - "false"^^ . - "0002533"^^ . - . - . - . - "Coli Genetic Stock Center" . - . - "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF"^^ . - . - . - . - . - . - . - "http://modelseed.org/biochem/compounds/$1"^^ . - . - "https://www.vmh.life/"^^ . - . - . - "^[0-9]*$"^^ . - "false"^^ . - . - . - . - "15000"^^ . - . - . - . - _:Nb10cfdfe8ec745368a2e70a3b46283ad . - . - . - "090803"^^ . - "nb100-56351"^^ . - "http://www.ebi.ac.uk/cmpo"^^ . - . - . - "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . - . - . - . - . - . - "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . - . - "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/obophenotype/sibo"^^ . - "https://www.ebi.ac.uk/biomodels/$1"^^ . - "false"^^ . - . - . - "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - "chebi" . - . - . - . - . - . - . - "0807.4956v1"^^ . - . - . - "1354581"^^ . - . - "GenBank" . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/gtr/"^^ . - . - . - . - "Electron Microscopy Data Bank" . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . - . - . - "OntoBee" . - . - . - . - . - . - . - "http://kinase.bioinformatics.tw/"^^ . - "false"^^ . - . - . - . - . - . - "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . - . - "0290"^^ . - . - . - . - "^\\d{7}$"^^ . - "Glycine max Genome Database" . - . - . - . - . - . - "Units of measurement ontology" . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - "051"^^ . - "European Bank for induced pluripotent Stem Cells" . - . - "Name-to-Thing" . - . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . - . - . - . - . - . - "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . - "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . - . - . - . - . - . - "AKR"^^ . - . - . - . - . - . - . - . - . - "5359"^^ . - . - . - . - . - . - "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . - "^\\d+$"^^ . - "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . - "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . - . - . - "false"^^ . - "Molecular Interaction Database" . - . - . - "false"^^ . - . - . - . - "International Standard Serial Number" . - "http://www.bindingdb.org/compact/$1"^^ . - . - . - . - . - . - . - . - . - "https://mobidb.org/$1"^^ . - "false"^^ . - "CAL0003079"^^ . - . - . - . - "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . - . - . - "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . - . - . - . - . - "^IS\\w+(\\-\\d)?$"^^ . - "MNXC15"^^ . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . - "Ontology about the gross anatomy of the C. elegans"^^ . - . - . - . - . - "0471491039"^^ . - . - "false"^^ . - . - "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^ . - . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . - . - . - . - "Zebrafish Experimental Conditions Ontology" . - . - . - . - . - . - . - "false"^^ . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . - . - . - . - "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^ . - . - . - . - . - . - "http://www.antirrhinum.net/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "0000062"^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - . - "miRNA Target Prediction at EMBL" . - . - . - "http://oncotree.mskcc.org"^^ . - . - . - . - . - "http://cutdb.burnham.org/relation/show/$1"^^ . - . - . - . - "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . - "^\\d+$"^^ . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - . - . - . - . - . - . - . - "^PR\\d{5}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Chickpea ontology" . - . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . - . - . - . - "https://www.ebi.ac.uk/pride/"^^ . - "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . - . - "None"^^ . - . - "12345"^^ . - . - . - . - . - . - . - . - . - . - . - "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . - . - "false"^^ . - "https://www.dataone.org"^^ . - . - "Antibiotic Resistance Genes Database" . - "493771"^^ . - "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . - "A gazetteer constructed on ontological principles"^^ . - "http://func.mshri.on.ca/yeast"^^ . - "2701"^^ . - . - . - . - . - . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . - "GOLD metadata" . - . - "^[a-z0-9-]+$"^^ . - "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . - . - "false"^^ . - . - . - . - "Saccharomyces genome database pathways" . - . - . - . - "MetaNetX compartment" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://webapps2.ucalgary.ca/~groupii/"^^ . - "https://spdx.org/licenses/$1"^^ . - "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - . - . - "CHEBI"^^ . - "true"^^ . - "http://neuromorpho.org/index.jsp"^^ . - . - . - . - . - . - . - . - . - . - "https://www.metanetx.org/chem_info/$1"^^ . - . - "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^ . - "0745-4570"^^ . - "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . - . - "false"^^ . - "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . - . - . - "An ontology of physico-chemical methods and properties."^^ . - . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - . - . - "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . - . - "https://www.cellbankaustralia.com/$1.html"^^ . - "https://github.com/ufbmi/geographical-entity-ontology/wiki"^^ . - . - . - . - . - . - . - . - . - . - "046"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "0000205"^^ . - "http://purl.obolibrary.org/obo/SWO_$1"^^ . - "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . - "false"^^ . - . - "http://www.bmrb.wisc.edu/"^^ . - . - . - "false"^^ . - "^BAMSC\\d+$"^^ . - . - . - . - "http://www.transcriptionfactor.org/"^^ . - . - . - . - "An ontology of phenotypes covering microbes"^^ . - . - . - . - . - . - "http://nbn-resolving.org/resolve_urn.htm"^^ . - "NeuroLex Anatomy" . - . - "288"^^ . - . - "true"^^ . - . - . - "AphidBase Transcript" . - "https://www.opengalen.org"^^ . - . - . - . - . - . - "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . - . - . - "^\\w+\\d+$"^^ . - . - . - "contributor"^^ . - . - . - "https://civicdb.org/"^^ . - "http://www.drugbank.ca/targets"^^ . - . - . - . - "http://www.genome.jp/dbget-bin/www_bfind?enzyme"^^ . - "Pol Castellano Escuder" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Database of the dielectric properties of biological tissues."^^ . - . - . - "KEGG Drug" . - . - . - . - . - . - "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . - "19803"^^ . - "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . - . - . - . - . - "Damion Dooley" . - . - . - . - . - . - . - . - . - . - "2000191"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . - . - . - "Flora Phenotype Ontology" . - "https://pharmacodb.ca/tissues"^^ . - . - "Chris Mungall" . - "https://www.ebi.ac.uk/ena/data/view/$1"^^ . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . - "http://doqcs.ncbs.res.in/"^^ . - . - . - . - . - "https://aopwiki.org/stressors/$1"^^ . - "http://www.genome.jp/kegg/reaction/"^^ . - . - . - "^\\d{7}$"^^ . - "SNP to Transcription Factor Binding Sites" . - . - . - "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - . - "http://purl.obolibrary.org/obo/MMO_$1"^^ . - . - "http://treebase.org/"^^ . - . - . - . - . - "SciCrunch Registry" . - . - . - . - . - . - . - "http://www.genome.jp/kegg/ko.html"^^ . - "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . - "false"^^ . - "^\\d+$"^^ . - "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . - . - . - . - . - . - "true"^^ . - "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . - . - "false"^^ . - "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^ . - . - . - "^\\d+$"^^ . - "https://web.expasy.org/cellosaurus/" . - . - . - . - . - . - "LNCipedia" . - "^CH_\\d+$"^^ . - . - "^[A-Za-z0-9]+$"^^ . - . - . - . - . - . - "https://www.doi.org/"^^ . - "Cell line collections"^^ . - . - . - . - . - . - . - . - . - "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html"^^ . - . - "IUPHAR family" . - . - . - . - . - . - . - . - . - . - . - "ProteomicsDB Protein" . - . - . - . - . - "false"^^ . - "http://ascl.net/$1"^^ . - . - . - "International repository of Adverse Outcome Pathways."^^ . - . - . - "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^ . - "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . - . - . - "Alliance of Genome Resources Knowledge Base" . - . - . - . - . - . - . - . - . - "false"^^ . - "https://cropontology.org/ontology/CO_340/Cowpea"^^ . - . - . - . - . - . - . - . - . - . - "1000160"^^ . - . - "Pablo Porras Millán" . - "false"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/geo/"^^ . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . - . - "SKIP001214"^^ . - . - . - . - . - . - . - "http://isbndb.com/"^^ . - . - . - . - "https://jcoin.datacommons.io"^^ . - . - . - . - "http://www.diseasesdatabase.com/"^^ . - "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - "Disease Drivers Ontology" . - . - . - "Quality"^^ . - . - "^HGVM\\d+$"^^ . - . - . - . - "^WBRNAi\\d{8}$"^^ . - . - "101"^^ . - . - . - "http://www.atol-ontology.com"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PROCO_$1"^^ . - . - . - . - . - . - . - "Antibiotic resistance genes and mutations"^^ . - . -_:Nad7b44867b004956a38c44d46d8c39ba "Burke Squires" . - . - . - . - . - . - "NIF Standard Ontology: Organisms" . - "https://download.nextprot.org/pub/current_release/controlled_vocabularies/"^^ . - . - . - . - . - . - . - "Yongqun Oliver He" . - "Chlamydia"^^ . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . - . - . - "4776"^^ . - . - . - "^IID\\d+$"^^ . - . - . - . - . - "https://schema.org"^^ . - . - . - . - "5282"^^ . - . - "http://www.genome.jp/kegg/drug/environ.html"^^ . - . - "http://edamontology.org/data_$1"^^ . - "Gender, Sex, and Sexual Orientation Ontology" . - . - . - . - . - "^\\d+$"^^ . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "ProtClustDB" . - . - . - "9-1-1 Complex"^^ . - "https://amzn.com/$1"^^ . - . - "EDAM Format" . - "http://pgscatalog.org"^^ . - . - "false"^^ . - . - . - "Tom Gillespie" . - "http://bcrj.org.br/celula/$1"^^ . - . - . - "^\\d+$"^^ . - "PyPI" . - "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . - . - "Heather Piwowar" . - "627"^^ . - . - "Ontology for Biobanking" . - . - "^\\d+$"^^ . - . - . - . - . - "^.*?--%3E.*?$"^^ . - . - . - "MTBLS1"^^ . - "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . - . - . - . - "^\\d{7}$"^^ . - . - "485991"^^ . - "false"^^ . - . - . - "https://www.biomodels.net/kisao/KISAO#KISAO_$1"^^ . - . - . - "Molecular Modeling Database" . - . - . - "false"^^ . - "Nucleotide" . - "Arabidopsis Information Portal" . - . - . - . - . - "false"^^ . - . - . - . - . - . - "https://reporter.nih.gov/"^^ . - "NITE Biological Resource Center" . - . - "https://cropontology.org/ontology/CO_348/Brassica"^^ . - . - . - . - "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . - . - "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . - . - . - . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index"^^ . - . - . - . - "July 2018"^^ . - . - . - . - . - . - "DEF"^^ . - . - "false"^^ . - . - "Entrez Gene" . - . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . - . - . - . - . - . - . - "https://www.re3data.org/repository/$1"^^ . - . - "Signaling Network Open Resource" . - _:N0dd9101a4c25485d820090171fbe6905 . - "An ontology of prokaryotic phenotypic and metabolic characters"^^ . - . - "AGRO" . - . - "http://purl.obolibrary.org/obo/CLYH_$1"^^ . - "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . - . - . - . - "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . - . - . - . - . - . - "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - . - "NBK331"^^ . - . - . - . - . - "EasyChair Call for Paper" . - "Stemcell Knowledge and Information Portal" . - . - "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . - . - . - . - . - . - . - "false"^^ . - . - "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . - . - . - "http://tolweb.org/tree/"^^ . - . - . - . - "https://github.com/ClinicalTrialOntology/CTO/"^^ . - "FxnI151FMs"^^ . - "https://scdontology.h3abionet.org/"^^ . - . - . - . - . - "CTD Chemical" . - . - . - "FlyBase Reference Report" . - "false"^^ . - . - . - . - "http://pax-db.org/"^^ . - . - "false"^^ . - . - . - . - "http://mirtarbase.mbc.nctu.edu.tw/"^^ . - . - . - . - "4DN" . - "http://www.jstor.org/"^^ . - "false"^^ . - "false"^^ . - "^UPI[A-F0-9]{10}$"^^ . - "001"^^ . - . - . - . - "false"^^ . - . - . - "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . - "http://igsn.org/$1"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.picb.ac.cn/limore/home"^^ . - "Animal Genome QTL" . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - "NIH RePORTER" . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . - "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . - . - . - "^\\w+$"^^ . - . - "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . - . - . - "http://purl.obolibrary.org/obo/OBIB_$1"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . - . - . - . - "http://func.mshri.on.ca/fly"^^ . - "CCDS13573.1"^^ . - . - . - . - . - . - "false"^^ . - . - "^PA\\d+$"^^ . - . - . - . - . - . - . - . - . - "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^ . - . - . - . - "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . - . - . - "https://ega-archive.org/"^^ . - . - "false"^^ . - "System Science of Biological Dynamics dataset" . - . - . - . - "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . - . - . - "http://www.w3.org/2001/XMLSchema"^^ . - . - "https://github.com/pcastellanoescuder/FoodBiomarkerOntology"^^ . - . - . - . - "HUMAN16963"^^ . - "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . - . - . - . - . - "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . - "http://www.gudmap.org/"^^ . - "TTDS00056"^^ . - "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . - . - "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . - "false"^^ . - . - . - . - . - "false"^^ . - . - "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . - . - "false"^^ . - . - . - "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut"^^ . - . - . - "https://cameo3d.org"^^ . - . - "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . - . - "https://pharmacodb.ca/cell_lines"^^ . - . - . - "true"^^ . - "^\\d{7}$"^^ . - . - "https://pharmacome.github.io/conso/"^^ . - . - "https://github.com/obophenotype/fungal-anatomy-ontology/"^^ . - "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . - "http://omia.angis.org.au/"^^ . - . - "Tree of Life Web Project ID" . - . - . - "Golm Metabolome Database" . - . - . - "BiGG Metabolite" . - . - . - . - . - "http://www.pantherdb.org/"^^ . - . - "https://www.who.int/classifications/icd/adaptations/oncology/en/"^^ . - . - . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt"^^ . - . - "0000449"^^ . - . - . - . - . - "http://cbg.garvan.unsw.edu.au/pina/"^^ . - . - . - . - "false"^^ . - "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . - . - "http://www.ebi.ac.uk/interpro/index.html"^^ . - . - "PhenX Toolkit" . - . - . - . - . - "1242"^^ . - . - . - . - . - "Enzo Life Sciences is an antibody vendor."^^ . - . - . - . - . - "false"^^ . - . - "NCBI Protein" . - . - . - . - . - "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^ . - . - . - "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . - "https://www.wormbase.org/db/seq/protein?name=$1"^^ . - . - "https://www.salk.edu/"^^ . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . - . - . - "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . - "Contains entries for various database identifiers" . - . - "NIF Standard Ontology: Brain Regions" . - "Pathogen Host Interaction Phenotype Ontology" . - "false"^^ . - . - "DAP000773"^^ . - . - . - "http://cellimagelibrary.org/"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "http://www.geneontology.org/cgi-bin/references.cgi"^^ . - . - "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . - . - "PF11_0344"^^ . - . - . - "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . - . - . - . - "0000052"^^ . - . - . - . - "^[A-Za-z0-9\\/]+$"^^ . - "2gc4E"^^ . - . - . - . - "https://www.ebi.ac.uk/sbo/main/SBO:$1"^^ . - "http://purl.obolibrary.org/obo/EHDA_$1"^^ . - . - . - "^\\d+$"^^ . - "Hymenoptera Anatomy Ontology" . - . - "^P\\d{5}$"^^ . - . - . - . - . - . - . - . - . - . - "https://publons.com/researcher"^^ . - "https://www.ncbi.nlm.nih.gov/homologene/"^^ . - "http://rna.rega.kuleuven.be/rnamods/"^^ . - . - . - "https://vcell.org/biomodel-$1"^^ . - . - . - . - "^((HGNC|hgnc):)?\\d{1,5}$"^^ . - . - . - "^[A-Z0-9]{4}$"^^ . - . - . - "Cell Line Ontology [derivative]" . - . -_:Nc09f0b1a44ab40779fcac26a35eea2ef "Thorsten Henrich" . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "dsmz_mutz-id:ACC 291"^^ . - . - . - "0000101"^^ . - "https://www.cropontology.org/ontology/$1" . - . - . - "^LGCEDe-S-\\d{9}$"^^ . - . - . - . - "http://www.cellresource.cn"^^ . - . - . - "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . - "4214"^^ . - . - "DepMap Cell Lines" . - "Protein Ensemble Database ensemble" . - . - "9"^^ . - . - . - . - "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . - . - . - . - . - "https://nmrshiftdb.nmr.uni-koeln.de"^^ . - . - "false"^^ . - . - "https://bioregistry.io/resolve/github/issue/$1"^^ . - . - . - "appears in" . - "^TA\\d+$"^^ . - . - . - . - . - . - . - . - "117"^^ . - . - "miRBase pre-miRNA" . - . - . - . - "FAIRsharing Subject Ontology" . - . - . - . - "https://github.com/pombase/fypo"^^ . - "RIKEN Bioresource Center Cell Bank" . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - _:N570bb9b9d35a491eb45adc922195e29b . - . - . - "http://lgsun.grc.nia.nih.gov/cDNA/"^^ . - . - "2019-08-03_00000089_1"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PAO_$1"^^ . - . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^ . - . - . - "https://openalex.org/"^^ . - "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . - . - "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - . - "http://biohackathon.org/resource/faldo"^^ . - . - "false"^^ . - . - . - "https://www.vectorbase.org/ontology-browser"^^ . - "Saccharomyces Genome Database" . - "https://www.ncbi.nlm.nih.gov/dbEST/index.html"^^ . - "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://biocyc.org/getid?id=$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . - . - . - "false"^^ . - . - "0000012b-5661-2f63-2f73-b43980000000"^^ . - . - . - . - . - . - . - . - "Search Tool for Retrieval of Interacting Genes/Proteins" . - . - "iRefWeb" . - "https://omim.org/"^^ . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "KEGG Drug Group" . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - "https://arxiv.org/"^^ . - . - "Archival Resource Key" . - . - . - "^\\d{7}$"^^ . - . - "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^ . - "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . - . - . - . - . - . - . - "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines)."^^ . - . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "Groundnut ontology" . - . - "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . - . - "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . - . - "2gc4"^^ . - . - "false"^^ . - . - "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . - . - . - . - . - . - "Chris Stoeckert" . - . - . - . - . - . - . - "^\\d{4}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "None"^^ . - "RXN-14904"^^ . - . - . - "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . - "^\\d{7}$"^^ . - . - . - "http://ecoportal.lifewatch.eu" . - . - . - . - "KEGG Reaction" . - "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . - "false"^^ . - "CADAFLAT00006211"^^ . - "0007133"^^ . - . - . - . - . - . - . - "Xenopus Anatomy Ontology" . - "http://www.hmdb.ca/"^^ . - . - . - . - "Polymorphism and mutation databases"^^ . - . - . - . -_:N78c2686ae6ab4cdf82c7b9bca90a884a "Onard Mejino" . - . - . - . - . - . - . - "http://hpc-bioinformatics.cineca.it/fusion/main"^^ . - "https://github.com/OPL-ontology/OPL"^^ . - . - . - . - . - "GlycoPOST" . - . - . - . - . - . - . - . - . - . - . - "ISA1083-2"^^ . - . - . - . - . - "http://www.chemspider.com/inchikey=$1"^^ . - "^[\\w\\-.]{3,}$"^^ . - . - "^HIX\\d{7}(\\.\\d+)?$"^^ . - . - "KG09531"^^ . - . - "http://soybase.org/"^^ . - . - . - . - . - "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . - . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - "true"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "https://ccg.epfl.ch/snp2tfbs/"^^ . - . - "^\\w+$"^^ . - . - "^T3\\d+$"^^ . - . - . - . - . - "https://toxpilot.nibiohn.go.jp/"^^ . - . - . - . - . - . - "C. elegans phenotype" . - . - . - "false"^^ . - "PaxDb Protein" . - . - . - . - "http://compbio.soe.ucsc.edu/yeast_introns.html"^^ . - . - . - . - . - . - . - . - "false"^^ . - "The reviewer of a prefix" . - . - . - "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . - "http://www.iclc.it"^^ . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . - . - "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . - "CL0192"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.aapc.com/codes/cpt-codes/$1"^^ . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . - . - . - . - . - . - "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . - "SCV000151292"^^ . - . - . - "Citation Typing Ontology" . - . - "false"^^ . - . - . - . - . - . - . - . - "SWISS-MODEL Repository" . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "CompTox Chemistry Dashboard" . - . - "2639"^^ . - "false"^^ . - "http://agroportal.lirmm.fr/ontologies/$1" . - . - "Colin Batchelor" . - . - . - . - . - "https://github.com/aellenhicks/htn_owl"^^ . - . - . - . - . - . - "https://www.yeastgenome.org/"^^ . - "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . - . - "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . - . - . - . - . - . - . - . - . - . - . - . - "Lepidoptera Anatomy Ontology" . - . - . - "RA01.0"^^ . - "Description of Plant Viruses" . - . - . - "^(STUDY|FILE|DATASET)\\d+$"^^ . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - . - "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . - . - . - . - . - "2679240"^^ . - . - "https://www.ebi.ac.uk/ipd/estdab/"^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "http://purl.obolibrary.org/obo/VTO_$1"^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - . - "false"^^ . - "false"^^ . - . - . - "^[A-Z-_0-9]+$"^^ . - . - . - . - . - "https://ecmdb.ca"^^ . - "http://degradome.uniovi.es/"^^ . - . - . - "false"^^ . - . - "Orientations of Proteins in Membranes Database" . - . - "http://prism.case.edu/prism/index.php/EpilepsyOntology"^^ . - . - . - . - "YOR172W_571.0"^^ . - . - . - . - . - . - . - "bsg-000052"^^ . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - "http://www.wormbase.org/get?name=$1"^^ . - "273"^^ . - . - . - . - . - "^rxn\\d+$"^^ . - "http://linkedlifedata.com/resource/umls/id/$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . - . - . - . - . - . - . - . - "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . - . - . - . - . - . - . - . - . - . - . - "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . - "r0001"^^ . - . - . - "Genetic and Rare Diseases Information Center" . - . - . - . - "http://en.wikipedia.org/wiki/$1"^^ . - "http://elm.eu.org/elms/elmPages/$1.html"^^ . - . - . - "https://sitem.herts.ac.uk/aeru/bpdb/index.htm"^^ . - . - . - . - . - . - "NCBI Genome" . - . - . - "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . - . - . - . - . - . - "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . - . - "GO Chemicals" . - . - "false"^^ . - "56586"^^ . - . - . - . - . - "1a24"^^ . - . - "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . - . - . - . - "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo"^^ . - . - . - "false"^^ . - "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . - . - . - . - . - . - . - "http://cgsc.biology.yale.edu/index.php"^^ . - . - . - . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . - . - . - "Psychology Ontology" . - "https://www.genenames.org/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "cgd7_230"^^ . - . - . - . - "false"^^ . - "^RC\\d+$"^^ . - . - . - "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."^^ . - . - . - . - . - . - . - "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - "Homeodomain Research" . - . - "^[A-Za-z]+\\/[0-9]+$"^^ . - _:Nf71ae981eae34cd8a4f065e8adea91b3 . - . - . - "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^ . - . - . - . - . - . - . - "Degradome Database" . - . - . - . - . - "BioLegend is a life sciences supply vendor."^^ . - . -_:Ndcdd7944f57c41f490bd5019a483aef6 "Jonathan Bard" . - . - . - . - . - . - . - . - . - . - . - . - "https://disprot.org/$1"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "Feature Type Thesaurus" . - . - "https://scicrunch.org/resolver/RRID:$1"^^ . - . - . - . - . - . - "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . - . - "http://sideeffects.embl.de/"^^ . - "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . - . - . - . - "Sickle Cell Disease Ontology" . - "1"^^ . - . - "http://www.uniprot.org/keywords/"^^ . - . - . - . - . - . - . - . - "https://www.goreni.org/gr3_nomenclature.php"^^ . - "false"^^ . - "https://genome.ucsc.edu/"^^ . - "false"^^ . - . - "Sample processing and separation techniques" . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . - . - "Addgene Plasmid Repository" . - . - "^[A-Z0-9]+$"^^ . - "Biosapiens Protein Feature Ontology" . - . - . - . - "version 2019 - pvs"^^ . - . - "http://www.jstor.org/stable/$1"^^ . - . - . - . - . - . - . - "https://www.ensembl.org/"^^ . - "https://github.com/ICO-ontology/ICO"^^ . - . - "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb"^^ . - . - . - . - "https://gold.jgi.doe.gov/resolver?id=$1"^^ . - . - . - "false"^^ . - "^[a-z][a-zA-Z]+$"^^ . - . - "http://www.w3.org/ns/dcat#$1"^^ . - . - "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . - "rs121909098"^^ . - . - . - . - . - . - . - . - "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . - . - "https://mmp.sfb.uit.no/databases/marfun"^^ . - . - . - . - "http://www.semantic-systems-biology.org/apo"^^ . - . - . - "^B\\d{5}$"^^ . - . - "C0017565"^^ . - "SPAR Ontologies" . - . - "^LRG_\\d+$"^^ . - "http://tuberculist.epfl.ch/"^^ . - . - . - . - . - . - . - . - "http://exac.broadinstitute.org/gene/$1"^^ . - . - "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . - . - . - . - . - "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . - . - "00000001"^^ . - . - "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology"^^ . - . - . - . - . - . - . - . - "Semanticscience Integrated Ontology" . - . - . - "https://aopwiki.org/"^^ . - "MultiCellDS Digital Cell Line" . - . - . - "https://www.gsea-msigdb.org"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - " http://edamontology.org" . - "^P(X|R)D\\d{6}$"^^ . - . - . - . - . - . - . - "Guide to Pharmacology Target" . - "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . - . - "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . - . - . - "false"^^ . - . - . - . - "Fungal Nomenclature and Species Bank" . - "https://www.allotrope.org/"^^ . - . - . - "http://thebiogrid.org/"^^ . - . - . - . - "http://www.w3.org/ns/activitystreams"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "Mammalian Phenotype Ontology" . - "https://bioregistry.io/registry/$1"^^ . - "false"^^ . - . - . - . - "25512"^^ . - . - . - . - . - . - . - . - "chebi" . - . - . - . - . - . - . - . - "AY109603"^^ . - "http://data.jrc.ec.europa.eu/"^^ . - . - . - . - . - . - . - . - . - . - "LigandBox" . - . - "https://bioregistry.io/metaregistry/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://www.encodeproject.org"^^ . - . - . - _:N10bcddcc6f3e4cb885115dbe30c41186 . - . - . - . - . - "^\\d{7}$"^^ . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - "5046"^^ . - "hasDbXref"^^ . - . - . - "https://bioportal.bioontology.org/ontologies/BIRNLEX"^^ . - . - . - . - . - . - . - . - . - "MHC Restriction Ontology" . - . - . - . - . - . - "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . - . - "An ontology to capture confidence information about annotations."^^ . - . - . - . - . - "Human Phenotype Ontology" . - "International Genome Sample Resource" . - "^\\d+$"^^ . - "https://registry.identifiers.org/registry?query=\"MIR:$1\""^^ . - . - . - . - . - "^\\d{8}$"^^ . - "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . - . - . - . - "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . - . - . - . - . - . - . - . - "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . - . - "83088"^^ . - . - . - . - . - "760050"^^ . - . - . - "^[8-9]\\d{3}(/[0-3])?$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "PROB_c0000005"^^ . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - "true"^^ . - "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"^^ . - . - . - "Adriano Rutz" . - "Pocketome" . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - . - . - "DragonDB Protein" . - "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FOVT_$1"^^ . - . - . - "10001-101"^^ . - . - . - . - . - . - "Environment Ontology for Livestock" . - . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - "Developing Mouse Brain Atlas" . - . - "58788"^^ . - . - . - . - . - . - . - "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . - "^\\d{7}$"^^ . - . - . - . - "0000109"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . - "y3ax-8bq3-60"^^ . - "^\\w+$"^^ . - . - "https://mouse.brain-map.org"^^ . - . - . - . - "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . - . - . - "75121530"^^ . - . - "The main contact person for a registry" . - . - . - "3403"^^ . - . - . - "^(Q|P)\\d+$"^^ . - . - "^\\d{5}$"^^ . - . - "http://teddyontology.sourceforge.net/"^^ . - "false"^^ . - "false"^^ . - "https://zenodo.org"^^ . - "http://purl.obolibrary.org/obo/WBbt_$1"^^ . - "^\\d{7}$"^^ . - "LipidBank" . - . - . - "false"^^ . - . - . - . - "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . - . - "ST000900"^^ . - "40000617"^^ . - "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . - "0000024"^^ . - "http://purl.obolibrary.org/obo/OMP_$1"^^ . - . - . - . - "^\\w+$"^^ . - . - . - . - . - "true"^^ . - "false"^^ . - "false"^^ . - . - . - "https://repo.napdi.org/study/$1"^^ . - "PerkinElmer cell line collection" . - . - . - . - "4685"^^ . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - "https://www.genome.jp/kegg/ligand.html"^^ . - "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology"^^ . - . - . - "false"^^ . - . - . - . - "ChEBI"^^ . - "https://www.storedb.org/"^^ . - . - . - "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml"^^ . - "https://www.gtexportal.org/home/gene/$1"^^ . - . - "morpheus.lab/morpheus"^^ . - . - . - . - . - . - "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "^NCT\\d{8}$"^^ . - . - "https://github.com/SCAI-BIO/EpilepsyOntology"^^ . - "Rosa2"^^ . - "FCB005"^^ . - "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"^^ . - . - "Ligand Expo" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "GL50803_102438"^^ . - . - . - . - . - . - . - . - "GM17027"^^ . - . - . - . - "^[0-9]+$"^^ . - . - . - . - . - . - "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . - "false"^^ . - "false"^^ . - "https://icahn.mssm.edu/"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . - . - . - . - . - "https://signor.uniroma2.it"^^ . - . - . - . - "^[0-9]+$"^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . - . - . - "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . - "BioSample" . - . - . - . - "https://www.wwpdb.org/pdb?id=$1"^^ . - "European Food Information Resource Network" . - "http://sourceforge.net/p/mamo-ontology/wiki/Home/"^^ . - . - "http://mycobrowser.epfl.ch/leprosy.html"^^ . - . - . - . - "DBG2 Introns" . - . - "http://fishbase.org"^^ . - . - . - . - . - "MobiDB" . - . - . - "true"^^ . - . - . - . - "^\\d{7}$"^^ . - "MetaboLights Compound" . - "3532759"^^ . - "The set of prefixes used in the Cellosaurus resource" . - . - "false"^^ . - "Cephalopod Ontology" . - . - . - . - . - . - "false"^^ . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . - "http://phylomedb.org/"^^ . - . - "false"^^ . - . - "Nucleotide Sequence Database" . - . - . - . - "0001998"^^ . - . - "false"^^ . - . - . - . - "HWUPKR0MPOU8FGXBT394"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Japan Collection of Microorganisms" . - "0000032"^^ . - . - "Cell Cycle Ontology" . - . - . - . - "d4e2515"^^ . - . - . - . - . - . - . - . - . - . - "0000080"^^ . - "https://www.wormbase.org/get?name=$1"^^ . - . - . - "false"^^ . - . - . - "MolMeDB" . - "0000319"^^ . - . - . - . - . - . - "Rat Genome Database strain" . - . - . - "http://purl.obolibrary.org/obo/NBO_$1"^^ . - . - "0000001"^^ . - . - . - "false"^^ . - . - . - . - "Ontology of rat strains"^^ . - "0000435"^^ . - . - "Protein Ontology" . - "https://www.enzolifesciences.com/$1"^^ . - "false"^^ . - . - "^[A-Z]{6}(\\d{2})?$"^^ . - "^\\d{6}$"^^ . - "037727"^^ . - . - . - . - "http://purl.obolibrary.org/obo/DUO_$1"^^ . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - . - . - "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . - "Donny Winston" . - . - . - . - "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/CEPH_$1"^^ . - . - . - "EP0311"^^ . - . - . - "false"^^ . - . - . - . - "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . - _:N02c0d5f52cd9416fb3689c022283dd41 . - . - . - "00000268"^^ . - . - . - . - . - . - "TreeBASE" . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . - "https://github.com/DIDEO/DIDEO"^^ . - . - . - . - . - . - . - "CHEMBL4303805"^^ . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "UniPathway Compound" . - "3"^^ . - . - . - "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . - . - "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . - . - . - "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . - . - . - . - "^BG\\d+$"^^ . - . - . - "Mammalian Feeding Muscle Ontology" . - "^\\d{7}$"^^ . - "hsa00190"^^ . - "https://n2t.net/$1:$2" . - . - "false"^^ . - . - . - . - "^OSC\\d{4}$"^^ . - . - . - "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . - . - . - . - . - "4544"^^ . - . - . - "^IPR\\d{6}$"^^ . - . - . - "^TTHERM\\_\\d+$"^^ . - . - "Crop Ontology Curation Tool" . - "https://fungi.ensembl.org/id/$1"^^ . - . - . - "sbml.level-3.version-2"^^ . - "false"^^ . - . - . - . - "ND50028"^^ . - "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . - . - "true"^^ . - "http://genome.crg.es/datasets/abs2005/"^^ . - . - . - _:N6286b2e88eb043c48cb2a7df2ec973b8 . - "0010316"^^ . - "false"^^ . - "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . - "https://fairsharing.org/" . - . - "http://neuinfo.org/"^^ . - . - "https://cropontology.org/ontology/CO_324/Sorghum"^^ . - . - "Ontology for the Anatomy of the Insect SkeletoMuscular system" . - "https://cellrepo.ico2s.org/"^^ . - "RiceNetDB Compound" . - . - "0000389"^^ . - . - . - "Integrative and Conjugative Element Ontology" . - . - . - . - . - . - . - "Activity"^^ . - "0000041"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/TAHH_$1"^^ . - . - . - . - . - . - . - "https://ligandbook.org/"^^ . - . - . - . - "PXD000500"^^ . - . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . - . - . - . - . - "BioContext contains modular JSON-LD contexts for bioinformatics data." . - . - . - . - . - . - _:Nceb4566787ea45869d0bbc6c2b7d5379 . - "http://polbase.neb.com/"^^ . - "Rat Genome Database" . - . - "^\\d+$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PCL_$1"^^ . - "false"^^ . - "0000194"^^ . - . - . - . - "FAIRsharing.62qk8w" . - . - "https://www.uniprot.org/uniref/$1"^^ . - . - "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . - . - "DragonDB Locus" . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . - "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . - . - . - "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . - . - . - . - . - . - "https://www.arraymap.org/pgx:$1"^^ . - . - . - "FooDB Food" . - . - . - . - "false"^^ . - . - . - . - "Kids First" . - . - . - . - . - "https://www.cropontology.org/rdf/CO_330:$1"^^ . - . - . - . - . - . - . - "https://www.cellbiolabs.com/search?keywords=$1"^^ . - . - . - "MIRIAM Registry resource" . - . - . - . - . - . - . - "20090303"^^ . - . - "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . - "Electron Microscopy Public Image Archive" . - . - . - . - . - . - . - "GlycoEpitope" . - . - "Genomics of Drug Sensitivity in Cancer" . - . - . - "An ontology to standardize research output of nutritional epidemiologic studies."^^ . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "MarCat" . - . - "^PR[0-9]{6}$"^^ . - . - . - . - "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . - . - . - . - . - . - . -_:N2b596d6f851d445d873ed6f8a3aeda5a "Marc Ciriello" . - . - . - . - "false"^^ . - "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0"^^ . - "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . - . - . - . - . - "https://github.com/carrineblank/MicrO"^^ . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/MAO_$1"^^ . - . - . - . - . - "Web Elements" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . - . - . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "Leigh Carmody" . - . - . - "false"^^ . - . - "http://www.sparontologies.net/ontologies/c4o"^^ . - . - "^(MNXR\\d+|EMPTY)$"^^ . - . - . - . - "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . - . - "http://bis.zju.edu.cn/ricenetdb"^^ . - . - . - . - . - "GOLD genome" . - "false"^^ . - "0002233"^^ . - "^K[0-9]+$"^^ . - . - "false"^^ . - "491187"^^ . - . - . - "Genome Properties" . - "BBA0001"^^ . - . - . - . - . - . - . - . - . - . - . - "DTXSID2021028"^^ . - "0000199"^^ . - "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . - "0000013"^^ . - "false"^^ . - . - . - . - . - "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . - . - . - "false"^^ . - . - "BP100000"^^ . - . - . - "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . - . - . - "International repository of Adverse Outcome Pathways."^^ . - . - "P01116"^^ . - . - . - . - . - . - . - . - . - "grid.225360.0"^^ . - . - . - . - . - "https://www.eionet.europa.eu/gemet/en/themes/"^^ . - . - "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . - . - "Cell line collections"^^ . - . - . - . - . - "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^ . - . - . - "false"^^ . - "^\\w+$"^^ . - "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . - . - . - "Sugar Kelp trait ontology" . - . - "Mouse Developmental Anatomy Ontology" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "true"^^ . - "false"^^ . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "http://rdfs.org/ns/void#$1"^^ . - . - . - . - . - "Xeni Kechagioglou" . - . - . - "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . - "https://github.com/evidenceontology/evidenceontology/"^^ . - . - "false"^^ . - . - . - . - . - "Database of Complete Genome Homologous Genes Families" . - . - . - "false"^^ . - . - . - . - . - "100000000000001"^^ . - . - "The international standard for identifying health measurements, observations, and documents."^^ . - . - . - . - "false"^^ . - . - . - "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . - . - . - "90801"^^ . - "^\\d+$"^^ . - . - . - "CATH superfamily" . - . - . - . - . - . - . - "false"^^ . - "PharmGKB Pathways" . - "^(SMP|PW)\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . - . - . - "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . - "http://www.wormbase.org/get?name=$1"^^ . - "Small Molecule Pathway Database" . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ena/"^^ . - "^\\d+$"^^ . - . - . - . - . - "Dublin Core Metadata Vocabulary" . - "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . - . - "SM00015"^^ . - . - "^\\d{8}$"^^ . - . - . - . - "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . - . - . - . - . - . - . - . - . - . - . - "HPSI0114i-bezi_1"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "false"^^ . - "sov:WRfXPg8dantKVubE3HX8pw"^^ . - . - . - "Clare Pilgrim" . - . - . - . - . - . - "true"^^ . - "Bgee stage" . - . - . - "canal"^^ . - "ChEMBL" . - . - . - . - . - "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . - . - . - . - . - . - . - "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . - "ClinicalTrials.gov" . - . - . - . - "false"^^ . - . - . - "https://smid-db.org/"^^ . - . - . - . - . - . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - . - . - "Shur-Jen Wang" . - . - . - "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . - "false"^^ . - "Cell line collections"^^ . - . - "smp-m3w9hbe"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - . - . - "https://www.disprot.org"^^ . - . - . - . - . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html"^^ . - . - . - . - . - . - "Salk Institute for Biological Studies" . - "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Jesualdo Tomás Fernández-Breis" . - "BioContext" . - . - . - . - . - . - . - . - "Scholarly Contributions and Roles Ontology" . - "https://drugs.ncats.io/drug/$1"^^ . - "false"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "Ontology of Physics for Biology" . - . - "https://identifiers.org" . - . - . - . - . - "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . - . - . - "http://www.w3.org/ns/oa"^^ . - "false"^^ . - . - "FungiDB" . - . - . - "Global Research Identifier Database" . - "http://ecogene.org/"^^ . - . - . - . - . - "Cell line collections"^^ . - "https://oborel.github.io/"^^ . - . - . - . - . - . - "ClinVar Submitter" . - . - . - . - . - . - . - "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . - . - "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . - "^\\d+$"^^ . - . - . - "Terminology of Anatomy of Human Histology" . - . - "https://ssbd.riken.jp/database/dataset/$1"^^ . - . - . - . - . - . - "Gene Ontology Registry" . - . - "^\\w+$"^^ . - . - . - . - . - . - . - "http://www.dukeontologygroup.org/Projects.html"^^ . - . - . - "17:41223048"^^ . - . - . - "https://www.cropontology.org/rdf/CO_336:$1"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . - . - . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . - "^\\d{7}$"^^ . - "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . - . - . - "true"^^ . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . - . - . - . - "Sirarat Sarntivijai" . - "^MIR:001\\d{5}$"^^ . - . - "false"^^ . - . - . - "^[a-zA-Z0-9 +#'*]+$"^^ . - . - . - "0004486"^^ . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"^^ . - . - "https://assets.nemoarchive.org/$1"^^ . - . - . - . - . - . - "https://www.alzforum.org/mutations/$1"^^ . - "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . - "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Xenopus Phenotype Ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - "0002989"^^ . - "ALX-210-175"^^ . - "CAPS-DB" . - . - . - "BioGRID Interactions" . - "false"^^ . - . - . - "Lindsay Cowell" . - "HomoloGene" . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - "Open Data Commons for Traumatic Brain Injury" . - "1038233"^^ . - "Uber Anatomy Ontology" . - . - . - . - . - "false"^^ . - . - . - . - . - "https://www.brenda-enzymes.de/ligand.php"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "http://lipidbank.jp/index.html"^^ . - . - . - . - "https://www.webelements.com/"^^ . - . - . - "MIRIAM Registry collection" . - . - . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - . - . - . - "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^ . - . - "http://www.viprbrc.org/brc/home.do?decorator=vipr"^^ . - . - . - . - "Ada Hamosh" . - "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . - . - . - . - "^[A-Z0-9]{6,7}$"^^ . - "^\\d+$"^^ . - . - . - . - "https://cls.shop/"^^ . - "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^ . - . - "75"^^ . - "Ensembl Plants" . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . - . - . - "Genomics Cohorts Knowledge Ontology" . - . - . - . - . - "Cell line collections"^^ . - . - "false"^^ . - "Human Proteome Map Protein" . - . - "MIR:00100005"^^ . - . - . - . - "has reviewer" . - "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . - . - "151022"^^ . - "Virtual International Authority File" . - . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - . - . - . - . - . - "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . - . - . - . - . -_:N6c812e04ad74486588f1e6182fffbbb9 "Mauno Vihinen" . - "false"^^ . - . - . - . - . - . - . - "Bgee organ" . - . - . - . - . - . - . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . - . - "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . - . - . - "bsu:BSU01340"^^ . - . - . - . - "https://xmetdb.org"^^ . - "false"^^ . - . - . - "RGD Disease_Ontology" . - . - . - . - "http://pkuxxj.pku.edu.cn/UNPD/"^^ . - "Stephen Fisher" . - "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . - . - . - "Regulation of Transcription"^^ . - . - . - . - "Expression"^^ . - . - . - . - . - . - . - . - . - . - . - "O80725"^^ . - "1"^^ . - . - "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . - . - . - . - . - . - . - "0000254"^^ . - "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . - . - . - . - . - . - . - "^[0-9]+:[0-9]+$"^^ . - . - . - . - . - "0000255"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/obophenotype/upheno"^^ . - . - . - "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . - . - "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . - "http://purl.obolibrary.org/obo/ECAO_$1"^^ . - "The Echinoderm Anatomy and Development Ontology" . - . - "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . - "Human Protein Atlas tissue profile information" . - . - . - . - . - "https://schema.org/$1"^^ . - . - "MultiCellDS" . - . - "https://cropontology.org/ontology/CO_337/Groundnut"^^ . - . - . - . - "Korean Cell Line Bank" . - . - . - . - . - . - . - . - . - "Apollo Structured Vocabulary" . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - . - "1"^^ . - . - "https://www.cropontology.org/rdf/CO_322:$1"^^ . - "PIRSF000100"^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . - "2GC4"^^ . - "false"^^ . - . - . - "DrugBank Target v4" . - . - . - . - . - . - . - "http://yetfasco.ccbr.utoronto.ca/"^^ . - . - . - . - . - . - . - "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - "ACYPI000159"^^ . - "https://aftol.umn.edu"^^ . - . - "Glycan Naming and Subsumption Ontology" . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "^\\d{5,}$"^^ . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - . - "false"^^ . - . - . - "SR0000178"^^ . - . - . - "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . - "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . - "9606"^^ . - "977869"^^ . - "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . - "^DDB\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - "TA14985"^^ . - "4000027"^^ . - . - . - . - . - "Anatomical Entity Ontology" . - "false"^^ . - "Confidence Information Ontology" . - . - . - . - "0001079"^^ . - . - . - "false"^^ . - . - . - . - . - "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "https://github.com/obophenotype/zebrafish-phenotype-ontology"^^ . - "http://www.sparontologies.net/ontologies/pwo"^^ . - . - "lang"^^ . - . - . - "None"^^ . - . - . - . - "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . - "CPX-263"^^ . - . - . - "http://scop.mrc-lmb.cam.ac.uk/scop/"^^ . - "Animal Genome Pig QTL" . - . - . - . - . - . - . - . - "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . - . - . - "^EGAS\\d{11}$"^^ . - "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . - . - "GCST000035"^^ . - . - . - . - . - . - . - . - . - "https://www.proteomicsdb.org/#human"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . - "false"^^ . - "true"^^ . - . - . - . - . - . - "^UDB\\d{6}$"^^ . - . - . - . - "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/IAO_$1"^^ . - . - . - . - "false"^^ . - . - . - "SIGNOR Relation" . - . - . - . - . - . - . - "0000550"^^ . - . - . - . - . - . - . - . - . - . - . - "1000"^^ . - "0002959"^^ . - . - . - "DrugBank Salts" . - . - . - . - "false"^^ . - . - . - . - . - "https://identifiers.org/$1:$2" . - . - . - . - . - . - "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . - "M77F7JM"^^ . - . - . - "http://www.informatics.jax.org/accession/MGI:$1"^^ . - "biosimulations" . - "https://mmp.sfb.uit.no/databases/mardb/"^^ . - . - . - . - . - "Gazetteer" . - "false"^^ . - "C00000001"^^ . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . - . - . - . - . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1"^^ . - . - . - "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . - . - . - . - "IntAct protein interaction database" . - . - . - . - . - "true"^^ . - . - . - . - "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . - . - . - "^(C|D)\\d{6,9}$"^^ . - . - . - . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - "Integrated Taxonomic Information System" . - . - "^\\d+$"^^ . - . - "Chemical Information Ontology" . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Global LEI Index" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Benjamin M. Gyori" . - . - . - "0000091"^^ . - . - . - "https://biopragmatics.github.io/providers/sdis/$1"^^ . - . - . - "0000046"^^ . - . - . - . - . - . - "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . - . - . - . - . - . - . - . - . - "http://viaf.org/viaf/$1"^^ . - . - . - . - "0000509"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . - . - . - . - . - "^(MNXM\\d+|BIOMASS|WATER)$"^^ . - . - . - . - "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PPO_$1"^^ . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists"^^ . - . - "false"^^ . - . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . - . - . - . - . - . - "^\\d+$"^^ . - "CTD Disease" . - "PROV Namespace" . - . - "Sue Bello" . - . - . - . - . - . - . - . - "false"^^ . - . - "Agilent Probe" . - "false"^^ . - . - . - . - . - "^[a-z0-9]+$"^^ . - "http://biomodels.net/vocab/idot.rdf"^^ . - "^[A-Z0-9]+$"^^ . - . - "VMH Gene" . - . - "false"^^ . - . - . - "MicrosporidiaDB" . - . - . - . - . - . - "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - "431472"^^ . - . - . - . - . - . - . - . - . - . - "https://www.genedb.org/"^^ . - . - "00000022"^^ . - . - . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^ . - . - . - . - "e999"^^ . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . - . - "Ontology"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . - . - "Monarch Disease Ontology" . - . - "0459895"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . - . - . - "^\\d+$"^^ . - . - . - "1058367"^^ . - . - . - "https://gitlab.com/"^^ . - . - . - . - "ai10e-kctd13b"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - "UniProt Post-Translational Modification" . - . - "https://github.com/EnvironmentOntology/environmental-exposure-ontology"^^ . - . - . - "false"^^ . - . - . - "true"^^ . - . - . - "Evidence ontology" . - . - . - . - . - . - . - "Cell line collections"^^ . - . - . - "https://www.cropontology.org/rdf/CO_360:$1"^^ . - . - . - . - . - . - . - . - . - . - . - "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . - . - . - "https://github.com/Radiobiology-Informatics-Consortium/RBO"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.vmh.life/"^^ . - "https://www.cbioportal.org/study/summary?id=$1"^^ . - . - . - . - "00007294"^^ . - . - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - . - . - . - . - "^\\d+$"^^ . - . - "0000088"^^ . - . - . - . - . - . - "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . - . - . - "P683" . - . - . - . - . - . - . - . - "^(ev\\:)?E\\d+$"^^ . - . - . - . - . - . - "Cell Version Control Repository" . - . - . - . - . - . - . - . - . - . - . - "DataCite Ontology" . - . - . - . - "http://bioportal.bioontology.org/ontologies/LBO"^^ . - . - . - . - . - "4D Nucleome Data Portal Biosource" . - . - . - "false"^^ . - . - . - . - "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . - "63189"^^ . - . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . - . - "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . - "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^ . - . - "^.+$"^^ . - . - . - . - "false"^^ . - "https://icd.who.int/browse10"^^ . - . - "http://www.t3db.org/toxins/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - "ABL1"^^ . - . - . - "Enzo Life Sciences" . - "http://si.washington.edu/projects/fma"^^ . - . - . - . - "M94112"^^ . - "Unified Phenotype Ontology" . - "http://www.p3db.org/"^^ . - . - "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - "^EBI\\-[0-9]+$"^^ . - . - . - . - . - . - . - . - . - "^[a-zA-Z0-9-_]+$"^^ . - . - . - . - "^\\d{4}-\\d{3}[\\dX]$"^^ . - . - . - . - . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi"^^ . - "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . - "H3.03.00.0.00007"^^ . - "COlleCtion of Open Natural ProdUcTs" . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast."^^ . - "http://www.wikipathways.org/instance/$1"^^ . - . - "Olfactory Receptor Database" . - . - . - "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . - . - "Zebrafish developmental stages ontology" . - "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . - "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . - . - . - . - . - . - "Mouse Brain Atlas" . - . - . - . - . - . - . - . - . - . - . - . - "https://www.lji.org/"^^ . - . - "0001927"^^ . - . - "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . - . - "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . - . - . - "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . - . - . - . - . - "https://www.scopus.com"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TO_$1"^^ . - . - . - . - . - . - "https://proteinensemble.org/"^^ . - "The Arabidopsis Information Resource" . - "false"^^ . - "Encyclopedia of Life" . - . - . - . - . - "PeptideAtlas" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . - "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . - . - . - "0000208"^^ . - . - "http://purl.obolibrary.org/obo/OHPI_$1"^^ . - "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . - . - "MIMAT0046872"^^ . - . - "^\\d+$"^^ . - . - . - . - "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^ . - . - "^\\w+$"^^ . - . - . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . - "r3d100010772"^^ . - . - . - "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . - . - . - "false"^^ . - . - . - . - . - . - "http://www.pharmgkb.org/"^^ . - "P00024"^^ . - . - "^\\d+$"^^ . - . - "http://www.maizegdb.org/"^^ . - "http://fdasis.nlm.nih.gov/srs/"^^ . - . - . - . - . - "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . - . - . - . - . - . - . - . - . - . - . - "http://antibodyregistry.org/"^^ . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - . - "https://vega.archive.ensembl.org/index.html"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://gdc.cancer.gov"^^ . - "https://pfam.xfam.org/family/$1"^^ . - . - . - . - . - . - . - . - . - "http://vbrc.org/"^^ . - . - . - "http://peroxibase.toulouse.inra.fr/"^^ . - "http://www.p3db.org/"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . - . - . - . - . - . - . - "Cell line collections"^^ . - . - . - "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . - . - . - . - . - . - . - . - . - . - . - "^NOR\\d+$"^^ . - "http://bigg.ucsd.edu/universal/metabolites"^^ . - . - . - . - "false"^^ . - "Lycalopex_vetulus"^^ . - . - . - "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"^^ . - . - . - . - "FaBiO, the FRBR-aligned Bibliographic Ontology" . - . - "https://www.dsmz.de"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "PRINTS compendium of protein fingerprints" . - . - . - . - "^\\d{6}$"^^ . - . - . - . - . - . - . - "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_340:$1"^^ . - . - . - . - . - "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . - . - "http://www.cellsignal.com/reference/pathway/$1.html"^^ . - . - . - "ArachnoServer" . - . - "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^ . - "https://www.ebi.ac.uk/interpro/genomeproperties/"^^ . - "false"^^ . - . - . - . - . - "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . - . - "Cell Biolabs cell line products" . - "https://gitlab.com/$1"^^ . - . - . - . - "^[A-Za-z 0-9]+$"^^ . - . - . - . - . - "Abdomen"^^ . - . - . - . - . - . - . - "MIPF0000002"^^ . - . - . - "http://gpmdb.thegpm.org/"^^ . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . - "Pseudomonas Genome Database" . - . - . - "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . - . - "https://www.cropontology.org/rdf/CO_347:$1"^^ . - . - . - . - . - "NONHSAT000001"^^ . - . - "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . - "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . - "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . - "http://purl.obolibrary.org/obo/ERO_$1"^^ . - . - . - . - "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . - . - "https://worldwide.espacenet.com/classification"^^ . - . - "https://bioregistry.io/metaregistry/go/$1"^^ . - . - "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . - "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . - . - "http://bacmap.wishartlab.com/"^^ . - "March 2017 version "^^ . - . - . - . - . - "http://www.pharmgkb.org/drug/$1"^^ . - . - . - "^\\d{7}$"^^ . - "UniProt Chain" . - . - . - "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . - . - "WikiGenes" . - . - "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . - . - . - "Animal Genome Chicken QTL" . - . - "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . - . - "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . - "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . - . - . - . - . - "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . - "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "23"^^ . - . - . - "http://tritrypdb.org/tritrypdb/"^^ . - . - . - "Search Tool for Interactions of Chemicals" . - "urn:nbn:fi:tkk-004781"^^ . - . - "C0026339"^^ . - "false"^^ . - "false"^^ . - "false"^^ . - "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . - "false"^^ . - . - . - . - . - . - "^\\w{4}$"^^ . - "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . - . - "595"^^ . - . - "Protein ANalysis THrough Evolutionary Relationships Classification System" . - "https://gen3.biodatacatalyst.nhlbi.nih.gov"^^ . - "EDAM Data" . - "derivatives%2Fthiocyclam%20hydrochloride"^^ . - "^[AEP]-\\w{4}-\\d+$"^^ . - "Mark Engelstad" . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . - . - . - . - . - "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . - . - "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . - . - . - "AS000060"^^ . - . - . - . - . - . - . - . - . - . - . - . - "1004" . - "false"^^ . - . - . - . - . - . - . - "TOKU-E Cell-culture Database" . - . - . - "false"^^ . - "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . - . - "http://dictybase.org/"^^ . - "C023"^^ . - . - . - . - . - . - "SBML RDF Vocabulary" . - . - "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html"^^ . - . - "IHW09326"^^ . - . - "false"^^ . - "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . - "GO Evidence Code" . - . - . - . - . - . - . - . - . - . - "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . - . - "Ontology of Host Pathogen Interactions" . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay"^^ . - . - . - . - "false"^^ . - . - . - "959"^^ . - . - . - . - . - "false"^^ . - . - . - "PANTHER Pathway Component" . - . - . - "International Nucleotide Sequence Database Collaboration (INSDC) Run" . - "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . - . - . - . - "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . - . - . - . - "false"^^ . - . - "0000003"^^ . - . - . - "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Datanator Metabolite" . - . - . - . - . - . - "https://cropontology.org/ontology/CO_325/Banana"^^ . - . - "https://www.ebi.ac.uk/miriam/"^^ . - "Jingshan Huang" . - . - . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . - . - "Aceview Worm" . - . - "^\\d+$"^^ . - "^[A-Za-z0-9]+$"^^ . - . - . - . - . - . - . - . - "nsv3875336"^^ . - . - . - . - . - "Sofia Robb" . - . - . - _:N30ac1120786448ac972d9fafdef5ad63 . - . - . - . - . - . - . - . - . - "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . - . - . - "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . - . - . - . - . - . - . - "http://worfdb.dfci.harvard.edu/"^^ . - "MOL000160"^^ . - . - "243002_at"^^ . - "0000124"^^ . - . - . - . - . - . - "https://www.biorxiv.org/content/10.1101/$1"^^ . - . - . - . - "http://www.phosphosite.org/homeAction.do"^^ . - . - . - . - . - "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . - . - . - . - . - "STUDY1040"^^ . - . - . - . - "false"^^ . - "HGVPM623"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . - . - . - . - . - . - . - . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - . - . - "^\\d+$"^^ . - . - . - . - "https://www.gwascentral.org/phenotype/$1"^^ . - . - "Pathway Commons" . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd"^^ . - . - . - . - "http://purl.uniprot.org/annotation/$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://civicdb.org/"^^ . - "https://www.cropontology.org/rdf/CO_324:$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . - . - . - . - . - "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . - . - . - . - "false"^^ . - . - . - "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1"^^ . - . - . - . - "https://hpscreg.eu/"^^ . - . - . - . - . - "false"^^ . - . - . - "Ontology of Adverse Events" . - "Agronomy Ontology" . - . - "Mike Cherry" . - . - "https://www.jax.org/strain/$1"^^ . - . - "^\\w{1,2}\\d+$"^^ . - . - . - . - . - "J55.713G"^^ . - . - . - . - "An issue in any public repository on GitHub."^^ . - . - . - . - . - "^[0-9a-zA-Z]+$"^^ . - . - . - "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . - . - . - "1"^^ . - . - . - . - . - "ENSG00000169174"^^ . - . - . - . - . - . - . - . - "Linguist" . - . - "false"^^ . - . - . - . - . - . - "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . - . - . - . - . - . - "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . - . - "https://ligandbook.org/package/$1"^^ . - "Clytia hemisphaerica Development and Anatomy Ontology" . - "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . - "RNAcentral" . - . - "0001009"^^ . - . - "^[0-9]+$"^^ . - "http://purl.obolibrary.org/obo/DRON_$1"^^ . - . - "http://purl.obolibrary.org/obo/aero"^^ . - "0000027"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "https://github.com/obi-bcgo/bcgo"^^ . - . - . - . - . - . - . - . - "Workflow"^^ . - . - . - "Erik Segerdell" . - . - . - . - "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"^^ . - . - "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . - . - "HBG004341"^^ . - . - "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . - . - . - "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . - "AD834"^^ . - "0000000"^^ . - . - "ERM00000044"^^ . - . - . - . - "https://www.disprot.org/$1"^^ . - "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . - . - . - "false"^^ . - "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . - . - "PubChem Cell Line" . - . - . - . - . - . - . - "Bloomington Drosophila Stock Center" . - . - "false"^^ . - "UniRule" . - "https://progenetix.org/services/ids/$1"^^ . - . - "false"^^ . - "UCSC Genome Browser" . - "https://pypi.org/project/$1"^^ . - . - "Agronomy Vocabulary" . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "http://www.narcis.nl/publication/RecordID/$1"^^ . - . - . - "VegBank" . - . - . - "UniPathway Reaction" . - . - "false"^^ . - "^[0-9]{10}$"^^ . - . - . - . - "false"^^ . - . - . - "Alejandra Gonzalez-Beltran" . - "Informed Consent Ontology" . - . - . - . - . - . - . - "D00123"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/PubMed/"^^ . - "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . - "PicTar" . - "Zebrafish Phenotype Ontology" . - . - . - "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "^T[A-Z]\\d{7}$"^^ . - "https://www.rebuildingakidney.org/"^^ . - "K00973"^^ . - "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . - . - . - . - "https://github.com/proco-ontology/PROCO"^^ . - "false"^^ . - . - "6200"^^ . - . - . - . - . - "Performance Summary Display Ontology" . - . - . - . - . - . - . - . - . - . - . - "0000086"^^ . - . - . - . - "^A[A-Z]+\\d+$"^^ . - "https://www.atcc.org/products/$1"^^ . - . - . - . - . - . - . - "false"^^ . - "CIP - potato ontology - december 2018"^^ . - . - . - "CPD-10330"^^ . - . - . - . - . - . - "false"^^ . - "Golm Metabolome Database Analyte" . - . - . - . - . - . - . - . - "http://www.chemspider.com/"^^ . - . - . - . - "817732"^^ . - . - "false"^^ . - "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^ . - . - . - . - "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - . - . - "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . - "Orphanet" . - . - . - . - . - . - . - . - "B00162"^^ . - . - . - . - "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . - "4DN"^^ . - "https://www.sigmaaldrich.com"^^ . - . - "https://github.com/jannahastings/emotion-ontology"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "Berkeley Drosophila Genome Project EST database" . - "0001417"^^ . - . - "https://viralzone.expasy.org/$1"^^ . - "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . - . - "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . - . - . - "Tohoku University cell line catalog" . - . - . - "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . - "A registry of commonly used prefixes in the life sciences and linked data" . - "https://github.com/PopulationAndCommunityOntology/pco"^^ . - . - . - . - "Lentil ontology" . - "false"^^ . - "VIRsiRNA" . - . - "lectins/172"^^ . - . - "Process Chemistry Ontology" . - . - . - "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . - . - "false"^^ . - . - "T0599"^^ . - . - . - . - "https://www.cropontology.org/rdf/CO_339:$1"^^ . - "NCT00222573"^^ . - . - . - "^\\d{7}$"^^ . - "0005250"^^ . - "44259"^^ . - . - . - . - "Japan Chemical Substance Dictionary" . - "https://www.drugbank.ca/categories/$1"^^ . - . - . - . - . - . - . - . - "https://biolink.github.io/biolink-model/"^^ . - "RiceNetDB Reaction" . - . - "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/"^^ . - . - "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . - . - "false"^^ . - . - "false"^^ . - "EHDAA:2185"^^ . - "Tissue List" . - "http://geneontology.org/docs/ontology-relations/"^^ . - "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - . - "http://bcrj.org.br/celula/bcrj"^^ . - . - "false"^^ . - "https://sitem.herts.ac.uk/aeru/ppdb/"^^ . -_:Ne0ea286e6e0c4fe3a14b5392c427c8ab "eVOC mailing list" . - . - . - . - . - "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . - . - . - "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . - . - . - . - "International Standard Book Number" . - . - . - "false"^^ . - . - . - . - . - . - "1484"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "http://www.whocc.no/atc_ddd_index/"^^ . - "false"^^ . - . - . - "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . - . - . - . - . - . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - . - "12345"^^ . - "https://datanator.info/"^^ . - . - "0000204"^^ . - . - . - . - "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . - "https://cropontology.org/ontology/CO_365/Fababean"^^ . - . - "LG Chemical Entity Detection Dataset (LGCEDe)" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "030719"^^ . - . - . - . - "1.1.1.1"^^ . - "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . - . - . - . - . - . - "Oryzabase Strain" . - . - "Image Data Resource" . - "false"^^ . - . - "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . - . - "http://www.depod.bioss.uni-freiburg.de"^^ . - . - . - "Cell line databases/resources"^^ . - "00000000"^^ . - . - "13GS"^^ . - "false"^^ . - "OncoTree" . - "http://purl.obolibrary.org/obo/FAO_$1"^^ . - . - . - . - . - . - . - "https://www.xenbase.org/"^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "http://hawaii.eagle-i.net/i/$1"^^ . - . - . - . - . - . - . - . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^ . - "^[0-9][A-Za-z0-9]{3}$"^^ . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . - . - . - . - . - . - . - "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . - . - . - . - . - . - . - . - "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." . - . - . - "1"^^ . - "https://github.com/MIT-LCP/mimic-omop"^^ . - . - . - . - . - . - "e0333"^^ . - . - . - "CiteXplore" . - . - . - . - . - "DG00301"^^ . - . - "BARC-013845-01256"^^ . - . - . - "false"^^ . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . - . - "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . - . - "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . - . - . - "Assists in resolving data across cloud resources."^^ . - . - . - "F-SNP" . - . - "http://ensembl.org/glossary"^^ . - . - . - . - . - . - . - . - . - . - "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . - . - "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . - . - . - "Life cycle stages for Medaka"^^ . - . - . - . - . - . - . - . - . - . -_:N10bcddcc6f3e4cb885115dbe30c41186 "Adrien Coulet" . - . - . - . - . - . - . - . - . - . - "William Hogan" . - "false"^^ . - . - "Kaggle" . - "Database of Genotypes and Phenotypes" . - "Human Proteome Map Peptide" . - . - "Cell line databases/resources"^^ . - . - . - . - . - "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - . - "0000060"^^ . - "TopFind" . - . - "false"^^ . - . - . - . - "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^ . - . - "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . - . - . - . - "1"^^ . - . - "https://metazoa.ensembl.org/id/$1"^^ . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^ . - "AOPWiki (Key Event)" . - . - . - . - . - . - . - . - . - . - . - "0000002"^^ . - . - . - "https://prefixcommons.org"^^ . - . - . - . - "1000290"^^ . - . - . - . - . - "ZINC is not Commercial" . - . - "Woody Plant Ontology ontology" . - . - . - . - . - "false"^^ . - . - . - "BRENDA tissue / enzyme source" . - . - . - . - . - "uBio NameBank" . - . - . - . - . - "^\\d{5}$"^^ . - "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . - . - "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp"^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . - "CNP0171505"^^ . - . - . - "0002066"^^ . - . - . - . - "Bacterial Tyrosine Kinase Database" . - . - . - "00023232"^^ . - "^MIRT\\d{6}$"^^ . - . - . - "false"^^ . - . - "Human Disease Ontology" . - . - . - . - . - "false"^^ . - . - "CLV_MEL_PAP_1"^^ . - . - "https://cancer.sanger.ac.uk/cell_lines/"^^ . - "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . - "PhosphoSite Site Group" . - . - "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . - "false"^^ . - . - "Google Scholar Researcher" . - . - . - . - . - . - . - . - . - . - "true"^^ . - "0000003"^^ . - . - . - . - . - . - . - "X58356"^^ . - . - . - "5601141"^^ . - . - . - . - "Antibody Registry" . - "https://github.com/infectious-disease-ontology-extensions/ido-covid-19"^^ . - . - "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . - . - "AMDEFA"^^ . - "https://scholia.toolforge.org/"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "http://omit.cis.usouthal.edu/"^^ . - . - "Gramene protein" . - . - . - . - . - "false"^^ . - . - "The Prescription of Drugs Ontology" . - . - . - . - . - "false"^^ . - . - "Development Data Object Service" . - "^\\d+$"^^ . - . - . - . - "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . - "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . - "http://purl.obolibrary.org/obo/BFO_$1"^^ . - . - . - "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . - "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . - "Clinical measurement ontology" . - "95-0166C6"^^ . - . - . - . - . - . - . - . - . - . - "http://www.cathdb.info"^^ . - "https://bioregistry.io/schema/#$1"^^ . - . - . - . - . - . - "http://biocyc.org"^^ . - . - . - "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^ . - . - . - "PED00017e001"^^ . - "false"^^ . - . - . - . - . - "International Fungal Working Group Fungal Barcoding." . - "http://msi-ontology.sourceforge.net/"^^ . - . - . - . - "https://bitbucket.org/$1"^^ . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . - . - "https://bgee.org/"^^ . - . - "NLXORG covers organisms."^^ . - . - . - "JCOIN" . - "false"^^ . - "00100037"^^ . - . - "Compositional Dietary Nutrition Ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - "http://www.maizemap.org/"^^ . - . - "Food Interactions with Drugs Evidence Ontology" . - "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . - . - "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . - . - . - "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . - . - . - . - "http://viralzone.expasy.org/"^^ . - . - "false"^^ . - "MNXM1723"^^ . - . - . - . - "Dengue Fever Ontology" . - . - "An anatomical and developmental ontology for cephalopods"^^ . - . - . - "https://prefix.cc/" . - . - "false"^^ . - "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . - . - "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . - . - "false"^^ . - . - "http://www.kazusa.or.jp/huge/"^^ . - "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . - . - . - . - . - . - "Internal OBO and PyOBO Relations" . - "http://www.flybase.org/"^^ . - . - "17186"^^ . - "https://medlineplus.gov/genetics/condition/$1"^^ . - "false"^^ . - . - . - "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . - . - "false"^^ . - . - "http://datf.cbi.pku.edu.cn/"^^ . - . - . - "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "http://www.genome.jp/kegg/disease/"^^ . - "^oai\\:cwi\\.nl\\:\\d+$"^^ . - . - . - . - "Pubmed Central" . - "^[0-9]+$"^^ . - . - . - . - "An ontology for the description of Drosophila melanogaster phenotypes."^^ . - . - . - . - "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/COB_$1"^^ . - "http://hymao.org"^^ . - . - "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . - "false"^^ . - . - . - . - . - "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "PELNAW"^^ . - . - . - "PXD000440"^^ . - . - . - . - . - . - "000000159"^^ . - . - "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . - . - . - . - . - "false"^^ . - "0000144"^^ . - "http://www.phosphosite.org/homeAction.do"^^ . - . - . - . - "50885"^^ . - . - "false"^^ . - . - . - . - . - . - "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . - . - . - . - . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "Identifier for a journal article in the fossilworks website"^^ . - . - . - . - "T01B6.1"^^ . - . - . - "http://bigg.ucsd.edu/universal/reactions"^^ . - "ChEBI Integrated Role Ontology" . - "https://www.storedb.org/"^^ . - . - "https://prefixcommons.org" . - . - . - . - "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . - . - . - "https://www.gwascentral.org/studies"^^ . - . - . - . - . - "Gramene Taxonomy" . - "3546"^^ . - . - . - . - . - "UR000124451"^^ . - . - . - . - . - "0000004"^^ . - . - . - . - . - . - . - . - . - . - "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . - . - . - "Pharmacogenetics and Pharmacogenomics Knowledge Base" . - . - "^\\d+$"^^ . - . - . - . - "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . - . - . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . - . - "https://www.yeastgenome.org/locus/$1"^^ . - . - . - . - . - . - . - "0000390"^^ . - "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en"^^ . - . - . - "^ENSGT\\d+$"^^ . - "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . - . - "^\\d+$"^^ . - . - . - . - "NP_012345"^^ . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - "http://www.genome.jp/kegg/catalog/org_list.html"^^ . - "http://www.proglycprot.org/"^^ . - . - "https://www.cropontology.org/rdf/CO_341:$1"^^ . - "https://github.com/obophenotype/bio-attribute-ontology"^^ . - . - . - . - . - "false"^^ . - . - "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . - . - . - . - . - . - . - . - "http://senselab.med.yale.edu/ModelDB/"^^ . - . - . - . - "false"^^ . - "AB_262044"^^ . - . - "true"^^ . - "false"^^ . - . - . - "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . - "https://biopragmatics.github.io/providers/msigdb/$1"^^ . - . - . - "false"^^ . - . - . - . - "^\\d{8}$"^^ . - . - . - . - . - . - . - . - "Identifiers.org Ontology"^^ . - . - "^\\d{8}$"^^ . - . - "http://jglobal.jst.go.jp/en/"^^ . - . - . - . - . - . - . - . - . - . - . - "A comprehensive compendium of human long non-coding RNAs"^^ . - . - "234"^^ . - . - . - . - "0000055"^^ . - . - . - . - "VCell Published Models" . - "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . - . - . - . - . - . - "K00001"^^ . - . - . - . - . - "^\\d{10}$"^^ . - "^\\d+$"^^ . - . - . - . - "Genomes Online Database" . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . - "false"^^ . - . - . - "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . - "http://www.hgmd.cf.ac.uk/ac/index.php"^^ . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^ . - "https://metabolome.cgfb.u-bordeaux.fr/"^^ . - "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . - . - "Platynereis stage ontology" . - . - . - "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . - . - . - "^\\w+$"^^ . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . - "AOPWiki (Stressor)" . - "false"^^ . - . - "Malaria Ontology" . - "https://github.com/semanticchemistry/semanticchemistry"^^ . - "Sunflower ontology" . - . - . - "ERR436051"^^ . - . - . - . - . - "Elizabeth Arnaud" . - "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . - . - . - . - . - _:Ne436db2047a8466592218d4a04b072df . - . - . - . - "enviPath" . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/ZP_$1"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "HD+118-001"^^ . - . - . - . - . - . - . - . - "S-EPMC6266652"^^ . - . - "0000000"^^ . - "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . - "Zach Landis-Lewis" . - . - . - . - "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . - . - . - "0000983"^^ . - . - . - "^[a-z_A-Z0-9]+$"^^ . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/ADO_$1"^^ . - . - . - "A type for entries in the Bioregistry's metaregistry." . - . - "0000546"^^ . - . - "false"^^ . - "https://www.animalgenome.org/QTLdb"^^ . - "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . - . - . - "Melissa Haendel" . - "ProtoNet Cluster" . - "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . - . - "^PROB_c\\d+$"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . - . - "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . - "0000138"^^ . - . - "true"^^ . - "Collection" . - . - . - . - "false"^^ . - . - "25011"^^ . - . - "http://www.violinet.org/vaccineontology"^^ . - "false"^^ . - "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html"^^ . - . - "^\\d+$"^^ . - . - "false"^^ . - "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . - "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . - . - . - "Drosophila RNAi Screening Center" . - . - "A registry of life science prefxes"^^ . - . - . - . - . - . - . - . - . - "1664"^^ . - . - . - . - "Potato ontology" . - . - . - . - . - . - . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . - . - "An identifier for a resource or metaresource." . - "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . - . - . - "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "^MINT\\-\\d{1,7}$"^^ . - "^[a-z0-9\\-_]+$"^^ . - . - "GCF_000005845.2"^^ . - . - "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . - . - . - . - . - "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . - . - . - . - . - "16793"^^ . - . - . - . - . - . - . - . - "false"^^ . - "0000106"^^ . - . - "false"^^ . - . - . - "Provisional Cell Ontology" . - "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . - "^\\w+$"^^ . - . - . - "http://www.humanproteomemap.org/index.php"^^ . - "XUO" . - . - "0002502"^^ . - "LINCS Small Molecule" . - "Clement Jonquet" . - . - . - "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . - "C2584994"^^ . - . - . - . - . - . - . - . - . - "4"^^ . - "LCL-2085"^^ . - . - . - . - . - "0000632"^^ . - "http://www.fao.org/gsfaonline"^^ . - . - "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . - "https://bioportal.bioontology.org/ontologies/NPO"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . - "^[WAICV]\\d{2,}$"^^ . - . - "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . - . - "https://www.geonames.org/export/codes.html"^^ . - . - . - . - . - . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "http://piroplasmadb.org/"^^ . - . - . - . - . - "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^ . - . - . - . - . - . - "false"^^ . - "Regulation of Gene Expression"^^ . - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . - . - . - . - "Chemistry resources"^^ . - . - "^\\d{3}$"^^ . - . - . - . - "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . - "false"^^ . - "10142"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . - "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . - . - "https://www.kerafast.com/"^^ . - . - . - . - . - . - . - . - . - . - . - "The COVID-19 Infectious Disease Ontology" . - . - . - . - . - "CHEBI" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "10.1101/2022.07.08.499378"^^ . - . - . - . - "https://www.atlassian.com/"^^ . - . - . - "^\\w+$"^^ . - . - "0032571"^^ . - "http://purl.obolibrary.org/obo/GSSO_$1"^^ . - "FlyBase internal citation identifiers"^^ . - . - "1"^^ . - "http://ctdbase.org/"^^ . - . - . - . - . - . - . - . - . - . - "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/SEP_$1"^^ . - "FlyBrain Neuron Database" . - "0000019"^^ . - . - . - . - . - . - "^[A-Z0-9]{6,7}$"^^ . - "Barley ontology" . - . - . - . - . - . - "1000"^^ . - "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . - "http://www.knapsackfamily.com/KNApSAcK/"^^ . - "WiCell Research Institute Cell Collection" . - . - . - "67"^^ . - . - . - "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . - "UniProt Protein" . - . - "https://drs.microbiomedata.org/objects/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "provides for" . - . - "https://vertebrate.genenames.org"^^ . - . - . - . - . - "OTTHUMG00000169812"^^ . - "ZDB-GENE-041118-11"^^ . - . - . - "http://ifomis.org/bfo/"^^ . - "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . - "false"^^ . - "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . - . - . - . - . - . - . - . - "A*01:01:01:01"^^ . - . - . - . - . - "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . - . - "https://genelab-data.ndc.nasa.gov/genelab/"^^ . - "false"^^ . - . - . - . - . - . - . - . - "^[AEP]-\\w{4}-\\d+$"^^ . - . - . - . - . - "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . - . - . - . - "http://neurovault.org"^^ . - . - "DragonDB Allele" . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - "^\\d+\\-\\d+\\-\\d+$"^^ . - . - "false"^^ . - "Assembling the Fungal Tree of Life - Taxonomy" . - . - . - "Bibliometric Data Ontology" . - "Neuronal cell types"^^ . - . - "^A_\\d+_.+$"^^ . - "Platynereis Developmental Stages" . - . - . - . - "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . - . - . - . - "NeuroLex Dysfunction" . - . - . - "^GR\\:\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . - "https://data.bloodpac.org/."^^ . - "false"^^ . - . - "^[0-9]+-[0-9]+$"^^ . - . - "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . - . - "http://swissregulon.unibas.ch/query/$1"^^ . - . - "Database of biopesticides maintained by the University of Hertfordshire "^^ . - . - . - . - . - . - "00000014"^^ . - . - . - . - . - "https://ratmine.mcw.edu/ontology/disease/"^^ . - . - "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . - . - . - . - . - . - . - "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . - . - "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . - . - . - "https://smpdb.ca/"^^ . - . - . - . - . - "https://biocyc.org/gene?id=$1"^^ . - "0000564"^^ . - "false"^^ . - "false"^^ . - "^WP\\d{1,5}(\\_r\\d+)?$"^^ . - . - . - . - . -_:N02c0d5f52cd9416fb3689c022283dd41 "Vivian Lee" . - . - . - . - . - "PDC000351"^^ . - . - "http://purl.obolibrary.org/obo/CLAO_$1"^^ . - "0000404"^^ . - . - "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . - . - . - . - . - . - "^[SED]R[APRSXZ]\\d+$"^^ . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . - . - "https://www.cropontology.org/rdf/CO_327:$1"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - "Complex Portal" . - . - . - "PRIDE Controlled Vocabulary" . - . - . - "^\\w+$"^^ . - . - . - . - . - . - "false"^^ . - . - . - "http://www.snomedbrowser.com/"^^ . - . - . - . - . - . - "Metabolite and Tandem Mass Spectrometry Database" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "https://go.drugbank.com/salts/$1"^^ . - "MMP02954345.1"^^ . - "https://catalog.bcrc.firdi.org.tw"^^ . - . - . - "Virus Pathogen Resource" . - . - . - . - "^\\d+$"^^ . - "KW-1273"^^ . - "BEI Resources" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . - "https://archive.softwareheritage.org/browse/swh:$1"^^ . - "PTN000000026"^^ . - . - "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . - . - . - . - . - . - "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . - . - . - "http://www.vbase2.org/vgene.php?id=$1"^^ . - . - . - . - "https://ontochem.com/"^^ . - "Life cycle stages for Human"^^ . - . - . - . - "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . - . - . - . - . - "https://rapdb.dna.affrc.go.jp/"^^ . - . - . - . - "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . - "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . - . - "false"^^ . - "false"^^ . - . - "Medaka Developmental Stages" . - . - . - "https://omim.org/entry/$1"^^ . - . - "CALIPHO Group Ontology of Human Anatomy" . - . - . - "^10.\\w{4}/\\w{10}$"^^ . - . - "UDB000691"^^ . - "https://www.ebi.ac.uk/imgt/hla/allele.html"^^ . - . - . - . - . - . - "false"^^ . - . - "Ontology for Avida digital evolution platform" . - . - . - . - . - . - . - . - . - . - . - . - "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^ . - "^\\d{7}$"^^ . - . - . - "osa-miR446"^^ . - . - . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - "https://www.addexbio.com/productshow?id=4"^^ . - . - "http://purl.org/vocab/frbr/core#$1"^^ . - . - . - . - . - . - . - "https://portal.bluebrain.epfl.ch"^^ . - "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . - . - . - . - . - . - "https://foodb.ca/foods"^^ . - . - . - "false"^^ . - "false"^^ . - "The International Harmonization of Nomenclature and Diagnostic criteria" . - "false"^^ . - . - . - "A nomenclatural ontology for biological names" . - . - . - . - . - . - . - "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . - "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1"^^ . - "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . - "http://taibnet.sinica.edu.tw/home.php"^^ . - . - . - . - "Ax1"^^ . - "Marie-Angélique Laporte" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/EXO_$1"^^ . - . - "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . - . - . - "https://www.ebi.ac.uk/citexplore/"^^ . - . - . - . - . - "Merck Millipore (EMD Millipore)" . - . - . - . - "false"^^ . - "456789"^^ . - . - . - "0000210"^^ . - . - "http://purl.obolibrary.org/obo/HOM_$1"^^ . - "false"^^ . - "false"^^ . - . - "HomologyRelation"^^ . - . - "^\\d{8}$"^^ . - . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - . - "https://www.gleif.org/"^^ . - "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "https://www.ebi.ac.uk/gxa/"^^ . - . - "090701"^^ . - . - . - . - . - . - . - "http://tables.pseudogene.org/[?species_name]/$1"^^ . - . - "0000190"^^ . - "false"^^ . - . - . - . - "https://www.cellbiolabs.com"^^ . - . - . - . - . - . - . - . - "true"^^ . - . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/IEV_$1"^^ . - . - "NOAA Fisheries Species Directory" . - . - . - . - . - "Cell line collections"^^ . - "LDS-1110"^^ . - . - "Cu.me.I1"^^ . - . - . - "Allyson Lister" . - . - . - . - "BioTools" . - "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . - "0001191"^^ . - "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar"^^ . - . - "false"^^ . - . - . - . - . - "Brachiaria ontology" . - . - . - . - . - "false"^^ . - "KEGG Compound" . - . - . - . - . - "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - . - . - . - . - . - "Ontology of Zebrafish Experimental Conditions"^^ . - . - "Cellosaurus identifeirs for publications, like Pubmed"^^ . - . - "false"^^ . - "^CHEMBL\\d+$"^^ . - . - "false"^^ . - "https://code.google.com/p/craniomaxillofacial-ontology/"^^ . - . - . - . - "https://www.ebi.ac.uk/complexportal"^^ . - . - . - . - "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . - "Integrated Microbial Genomes Gene" . - . - . - . - "label"^^ . - . - . - . - "https://github.com/ontoice/ICEO"^^ . - . - "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . - . - "Ali Syed" . - "^[A-Za-z0-9]+$"^^ . - . - . - "BSU29180"^^ . - . - . - "Dimension"^^ . - "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/ECG"^^ . - "NASC code" . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - "G protein-coupled receptor database" . - "1000"^^ . - . - . - . - . - . - "^MIMAT\\d{7}$"^^ . - . - . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . - "0001021"^^ . - "false"^^ . - . - . - . - "A0A009E7X8"^^ . - . - . - . - "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "^CPX-[0-9]+$"^^ . - . - . - "MCDS_S_0000000001"^^ . - . - . - . - "Fly taxonomy" . - . - . - . - . - . - . - . - . - . - "MEROPS Family" . - . - "https://www.hu-berlin.de/?set_language=en&cl=en"^^ . - "0000015"^^ . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/FLU_$1"^^ . - "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . - . - . - . - . - "Rat Strain Ontology" . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://toxodb.org/toxo/"^^ . - . - . - "http://lincs.hms.harvard.edu/db/proteins/"^^ . - . - . - . - "^[1-9]\\d{0,6}$"^^ . - . - . - . - "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . - . - . - "Paul Fabry" . - . - "http://bigg.ucsd.edu/compartments/$1"^^ . - . - "clinical LABoratory Ontology" . - "TriTrypDB" . - . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . - . - "^[a-z0-9\\-]+$"^^ . - . - . - "Healthcare Common Procedure Coding System" . - "Neuro Behavior Ontology" . - . - . - "false"^^ . - . - . - "true"^^ . - "9781584885658"^^ . - . - "P0DP23"^^ . - . - . - . - . - . - . - "Alan Wood's Pesticides" . - . - . - . - . - . - "https://www.ebi.ac.uk/interpro/entry/$1"^^ . - "https://repeatsdb.org/structure/$1"^^ . - . - . - "0002902"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HAO_$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . - "true"^^ . - . - . - "ASPL0000349247"^^ . - . - . - . - "Documentation of the Phenoscape Curation Workflow"^^ . - "false"^^ . - . - . - "1948"^^ . - "http://www.gramene.org/"^^ . - . - "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . - "http://sed-ml.org/"^^ . - "100000001"^^ . - . - "https://www.ebi.ac.uk/intact/molecule/$1"^^ . - . - . - . - "https://bacteria.ensembl.org/"^^ . - . - "https://sumlineknowledgebase.com/"^^ . - . - . - "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . - . - "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . - "ArrayExpress Platform" . - . - "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . - "false"^^ . - . - "Data Use Ontology" . - "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . - . - . - . - . - . - . - . - "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . - . - . - "NucleaRDB" . - "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . - . - . - "ZINC1084"^^ . - . - . - . - . - . - "National Experimental Cell Resource Sharing Platform" . - . - . - "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . - . - . - . - . - . - "true"^^ . - . - "1000100"^^ . - . - . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . - "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . - . - "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . - . - "https://www.iedb.org/reference/$1"^^ . - . - . - . - "https://www.cancerrxgene.org"^^ . - "Novus Biologicals" . - . - . - "https://web.expasy.org/abcd/"^^ . - . - . - . - . - . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/flu/"^^ . - . - "Information for ligand groups (chemical classes)."^^ . - "S7000002168151102"^^ . - "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes."^^ . - . - "UniProt Cross-ref database" . - "http://www.cazy.org/"^^ . - . - . - . - . - . - "app-d678n-tottori"^^ . - "https://human.brain-map.org"^^ . - . - . - . - "https://fairsharing.org/"^^ . - . - . - . - . - "Cancer Cell Line Encyclopedia Cells" . - . - "http://exac.broadinstitute.org/transcript/$1"^^ . - "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . - . - . - . - . - . - "^cpd\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "Fossilworks Journal" . - "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . - "https://prefix.cc/$1" . - "false"^^ . - . - "Ontology of RNA Sequencing" . - "Global Proteome Machine Database" . - . - "90062901"^^ . - . - . - . - . - "https://www.storedb.org/"^^ . - "Plant Ontology" . - . - . - . - . - . - . - . - . - . - "CIViC Evidence" . - . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"^^ . - . - "ExAC Gene" . - . - . - "http://www.vbase2.org/vbase2.php"^^ . - . - . - . - . - "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^ . - . - . - "http://phylomedb.org/?seqid=$1"^^ . - . - . - . - . - . - . - . - "A hierarchical classification of congenital heart disease "^^ . - . - . - . - . - . - . - "false"^^ . - . - "^(cd)?\\d{5}$"^^ . - . - "Chemical Entities of Biological Interest" . - . - "Ontology for Nutritional Studies" . - . - . - . - "Tom Gillespie" . - "http://www.cbioportal.org"^^ . - . - . - . - "268"^^ . - . - "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . - "false"^^ . - "10531"^^ . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . - . - . - . - . - . - "C. elegans Gross Anatomy Ontology" . - . - "^\\d+$"^^ . - "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . - "false"^^ . - "http://repository.topdownproteomics.org/proteoforms/$1"^^ . - . - . - . - "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . - . - . - "Lynn Schriml" . - . - . - . - . - . - "http://crispr.i2bc.paris-saclay.fr/"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.inoh.org"^^ . - . - "^OSR\\d{4}$"^^ . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . - . - . - "^\\w+$"^^ . - . - . - . - . - "https://github.com/OAE-ontology/OAE/"^^ . - "^\\d+$"^^ . - . - . - "^\\d{7}$"^^ . - "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . - . - . - "DataCollection"^^ . - "https://github.com/SED-ML/KiSAO"^^ . - . - "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_348:$1"^^ . - "FBtr0084214"^^ . - "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^ . - . - . - "An ontology to represent genomics cohort attributes."^^ . - "PTHR12345"^^ . - "STOREDB at University of Cambridge" . - . - . - . - . - . - "MimoDB" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "^\\w+\\_\\w+$"^^ . - . - . - . - . - . - . - . - . - . - "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "^\\d+$"^^ . - . - . - . - "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . - . - . - . - . - . - . - "Livestock Breed Ontology" . - . - "https://www.perkinelmer.com/"^^ . - . - . - . - . - "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . - "false"^^ . - "0000006"^^ . - . - . - "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - "12300"^^ . - . - "^[A-Z]+[0-9]+$"^^ . - "56"^^ . - . - . - . - . - "http://www.evocontology.org/"^^ . - . - . - . - . - . - . - . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "http://www.aphidbase.com/aphidbase"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://ontoneo.com"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . - . - . - . - "Bioregistry Metaregistry" . - . - . - . - "^\\d{6}$"^^ . - "https://github.com/obophenotype/biological-spatial-ontology"^^ . - "https://odc-sci.org/data/$1"^^ . - "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . - . - . - "false"^^ . - "https://www.humanbehaviourchange.org/"^^ . - . - "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . - . - "Robert Hoehndorf" . - "https://github.com/EBISPOT/ancestro"^^ . - "0000780"^^ . - . - . - "https://github.com/AgriculturalSemantics/agro"^^ . - . - "Laboratory of Systems Pharmacology Compound" . - . - "Pathway ontology" . - . - . - . - . - . - . - . - "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - "Metabolome Express" . - . - "false"^^ . - . - "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . - "true"^^ . - . - . - . - "http://foodb.ca/compounds/$1"^^ . - "https://github.com/rsc-ontologies/rsc-cmo"^^ . - . - "0000070"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . - "false"^^ . - . - . - . - . - . - . - "^CE\\d{5}$"^^ . - . - . - . - . - "BioPortal" . - "E-cyanobacterium rule" . - . - . - "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . - . - . - . - . - . - . - . - "http://lsdis.cs.uga.edu/projects/glycomics/propreo/"^^ . - . - "http://www.genome.jp/kegg/reaction/"^^ . - "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . - "http://purl.obolibrary.org/obo/ZFS_$1"^^ . - . - . - "A database-specific registry supporting curation in the Gene Ontology" . - . - . - "Bgee gene" . - "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - "false"^^ . - . - . - . - . - . - . - . - "Feature Annotation Location Description Ontology " . - "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . - . - . - . - . - . - . - . - . - "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . - . - "^(T0\\d+|\\w{3,5})$"^^ . - "Animal Genome Sheep QTL" . - . - . - . - . - . - . - . - . - . - . - "Toxic Process Ontology" . - . - . - . - . - "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "CCDC Number" . - . - . - . - . - . - . - "^PED\\d{5}e\\d{3}$"^^ . - . - "Obstetric and Neonatal Ontology" . - "Yvonne Bradford" . - "AberOWL" . - . - . - . - . - . - . - . - . - "0010034"^^ . - "D001151"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - . - . - "Physical Medicine and Rehabilitation" . - . - . - . - "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . - . - . - . - . - . - "http://www.radiomics.org/RO"^^ . - "bioregistry"^^ . - "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . - "Panorama Public" . - . - "http://www.brenda-enzymes.org"^^ . - "https://covid19.sfb.uit.no/api/records/$1"^^ . - . - "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . - . - . - . - "OpenCitations Corpus" . - . - "^NPC\\d+$"^^ . - . - "Cell line collections"^^ . - . - . - . - . - "false"^^ . - "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt"^^ . - . - . - "ChEBI Data Sources" . - . - "^\\d+$"^^ . - "^[0-9]{15}[0-9X]{1}$"^^ . - "oai:cwi.nl:4725"^^ . - . - "false"^^ . - "8497"^^ . - "https://www.ncbi.nlm.nih.gov/genbank/"^^ . - . - "Pfam Clans" . - . - . - "GeneTree" . - "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . - . - . - "^[1-9]\\d{5}$"^^ . - . - "Liver Cancer Model Repository" . - . - "International Geo Sample Number" . - . - "International Classification of Diseases, 11th Revision" . - . - "false"^^ . - "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . - . - . - . - . - . - . - "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . - . - . - . - . - "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "GlyTouCan" . - . - . - . - "http://www.genenames.org"^^ . - "version Dec 2019"^^ . - . - . - "https://odc-tbi.org"^^ . - "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - . - "MycoBrowser marinum" . - . - "false"^^ . - "^FDB\\d+$"^^ . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1"^^ . - . - . - . - . - . - "1455"^^ . - . - . - "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - . - "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"^^ . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . - "OriDB Saccharomyces" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "http://edamontology.org"^^ . - . - "https://www.uniprot.org"^^ . - "https://nanocommons.github.io/identifiers/"^^ . - . - . - "CONSO00010"^^ . - "Allotrope Merged Ontology Suite" . - . - "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . - "https://sumlineknowledgebase.com/?page_id=$1"^^ . - . - . - . - "David Osumi-Sutherland" . - . - "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . - . - . - . - . - . - "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . - . - . - "false"^^ . - . - . - . - . - "375364"^^ . - "12929"^^ . - . - . - . - . - . - . - . - . - . - "https://www.storedb.org/?$1"^^ . - "Cellosaurus Registry" . - "Animal Trait Ontology for Livestock" . - . - . - . - . - . - . - "https://www.vectorbase.org/ontology-browser"^^ . - "602"^^ . - . - "Publishing Roles Ontology" . - . - "DDB_G0267522"^^ . - . - . - "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR"^^ . - . - . - . - . -_:N6f000779f8e44903be5cab1c005b03a9 "Pantelis Topalis" . - . - . - . - . - . - . - . - "https://knowledge.lonza.com/cell?id=$1"^^ . - "false"^^ . - . - . - "false"^^ . - . - "VGNC:3792"^^ . - . - "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . - . - . - . - . - "Bacterial Diversity Metadatabase" . - . - . - . - "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . - . - . - . - "Transporter Classification Database" . - . - . - "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . - . - "http://vegbank.org/"^^ . - . - . - . - . - . - . - "56305849200"^^ . - . - . - "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . - . - . - . - . - . - . - . - . - . - "http://lincsportal.ccs.miami.edu/datasets/"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - "KEGG Reaction Class" . - "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - "https://www.fisheries.noaa.gov/species/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.receptome.org"^^ . - . - . - . - . - . - "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)"^^ . - . - "Database for Prokaryotic Operons" . - . - "Influenza Ontology" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . - . - . - . - . - "Variation Modelling Collaboration" . - . - . - "https://www.cropontology.org/rdf/CO_338:$1"^^ . - . - . - . - . - . - . - . - . - "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . - . - "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . - . - . - . - . - . - . - . - "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . - . - "REPRODUCE-ME Ontology" . - . - "P10636"^^ . - . - . - . - . - . - . - "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . - . - "false"^^ . - "http://sugarbind.expasy.org/$1"^^ . - "0000108"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - "^bt\\d+$"^^ . - "https://www.gtexportal.org"^^ . - . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . - "J0705A10"^^ . - . - . - . - "http://purl.org/spar/pro/$1"^^ . - . - . - . - "YAL001C"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . - . - . - . - . - . - "Beet Ontology ontology" . - . - . - . - . - . - . - . - "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species."^^ . - . - . - "false"^^ . - "false"^^ . - "Peter Midford" . - . - . - . - . - . - . - . - "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . - . - . - . - . - "false"^^ . - "http://exac.broadinstitute.org/"^^ . - . - . - . - . - . - . - "RCB0002"^^ . - . - "^H\\d+$"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . - "http://www.massbank.jp/RecordDisplay?id=$1"^^ . - . - "MLCommons Association" . - "ala"^^ . - . - "https://www.gbif.org/species/$1"^^ . - "^\\d{7}$"^^ . - . - . - "FR-FCM-ZYGW"^^ . - . - . - . - . - . - . - . - "SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints."^^ . - . - . - . - "GWAS Catalog" . - . - . - . - "648028003"^^ . - . - "ZFA description."^^ . - "GrainGenes" . - . - . - . - . - "false"^^ . - . - . - "Human Dephosphorylation Database" . - . - "Planarian Phenotype Ontology" . - "A type for entries in the Bioregistry's registry." . - . - "INSDC CDS" . - . - . - . - . - . - . - . - . - . - . - "^[0-9a-z]{24,24}$"^^ . - . - . - . - . - . - . - . - . - "Ontology of Vaccine Adverse Events" . - . - . - . - . - . - . -_:Nb1491a26268e498b8b8ee70cd2d648d3 "INOH curators" . - "Vital Sign Ontology" . - "Pierre-Alain Binz" . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . - . - . - "https://www.auckland.ac.nz/en.html"^^ . - . - . - "bt0001"^^ . - . - . - . - "https://cropontology.org/ontology/CO_322/Maize"^^ . - . - "http://www.clo-ontology.org"^^ . - "^\\w+(\\-|\\.|\\w)*$"^^ . - "false"^^ . - "BacMap Map" . - . - "http://substrate.burnham.org/"^^ . - . - "false"^^ . - . - . - . - "false"^^ . - "IPI"^^ . - . - . - . - . - "Ontology of Microbial Phenotypes" . - "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . - . - "FuncBase Fly" . - "false"^^ . - . - . - . - "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . - . - . - "http://xmlns.com/foaf/spec/"^^ . - "000009"^^ . - . - . - "https://www.uniprot.org/unirule/"^^ . - "GXA Expt" . - . - . - "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . - . - . - . - . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - . - . - . - "http://stormo.wustl.edu/ScerTF/details/$1"^^ . - . - . - . - . - . - . - . - . - . - "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . - "http://www.drugbank.ca/drugs/$1"^^ . - . - "https://openalex.org/$1"^^ . - . - "false"^^ . - . - "^PTM-\\d{4}$"^^ . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . - . - . - . - "Biotin_biosynthesis"^^ . - "201022999"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1"^^ . - . - "BioSystems" . - . - "http://www.plantontology.org"^^ . - . - . - . - . - "http://kinase.bioinformatics.tw/"^^ . - . - . - . - . - "https://thebiogrid.org/interaction/$1"^^ . - . - . - "PR00001"^^ . - . - . - . - . - . - . - . - . - . - . - "FlowRepository" . - . - . - . - . - . - . - . - . - "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . - . - . - . - "1000001"^^ . - . - "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . - . - "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . - . - . - . - . - . - "2200934"^^ . - . - "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . - . - "The upper level ontology upon which OBO Foundry ontologies are built."^^ . - . - . - . - . - "Banana ontology" . - "Bioinformatics operations, data types, formats, identifiers and topics" . - . - . - . - . - . - "false"^^ . - "ArrayExpress" . - "^(D|PP|R|T|H|X|AI)?\\d+$"^^ . - . - "https://biorxiv.org"^^ . - "Literature references in Gramene"^^ . - "000000012281955X"^^ . - . - . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . - "https://github.com/insect-morphology/lepao"^^ . - "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . - "^\\d{7}$"^^ . - . - "rateRule"^^ . - . - . - . - . - . - "false"^^ . - . - . - "Curation of Neurodegeneration Supporting Ontology" . - . - . - "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . - "https://cell.brc.riken.jp/en/rcb"^^ . - . - . - . - . - . - . - . - . - "http://jaxmice.jax.org/strain/$1.html"^^ . - . - . - "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . - . - "https://www.nextmovesoftware.com/namerxn.html"^^ . - "CY077097"^^ . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/REX_$1"^^ . - . - . - "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . - . - . - . - . - "0000048"^^ . - . - . - . - . - "MatrixDB" . - . - . - "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . -_:N41d82a5714aa4f9bbd5fea9efb312782 "Schober Daniel" . - . - . - "0001000"^^ . - . - "https://repeatsdb.org/"^^ . - . - "DASHR expression" . - . - "http://www.w3.org/XML/1998/namespace#$1"^^ . - . - . - "false"^^ . - . - "baseDimensionEnumeration"^^ . - . - "http://genepio.org/"^^ . - . - . - "^\\d+$"^^ . - "^\\d{7}$"^^ . - . - "Sequence types and features ontology" . - "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . - "http://purl.obolibrary.org/obo/MONDO_$1"^^ . - . - . - . - "BRENDA Ligand" . - . - "119514"^^ . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - . - . - . - "PubChem Substance ID (SID)" . - . - . - . - . - . - . - . - "true"^^ . - "http://www.expasy.org/viralzone/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/YPO_$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Epilepsy and Seizure Ontology" . - . - "Cell line collections"^^ . - "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . - "Store DB" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "^\\d{7,8}$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/clinvar/"^^ . - . - "5621"^^ . - . -_:Naf58c96bde474ef892cb9e1824f8c4c6 "Stephen Larson" . - . - . - "https://animaldiversity.org/accounts/$1"^^ . - "Benjamin Gyori" . - "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . - . - . - "GWAS Central Study" . - . - "JRC Data Catalogue" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . - . - . - . - . - . - . - . - . - "An application ontology for use with miRNA databases."^^ . - "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . - "https://github.com/phenoscape/teleost-taxonomy-ontology"^^ . - . - . - "https://cropontology.org/ontology/CO_343/Yam"^^ . - . - "00000180"^^ . - . - "https://portal.bluebrain.epfl.ch"^^ . - . - "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . - "false"^^ . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes."^^ . - . - . - "https://github.com/obophenotype/caro/"^^ . - . - . - . - . - . - . - . - "FlyBase Gene" . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - "SASDAX8"^^ . - . - "http://classyfire.wishartlab.com/"^^ . - . - . - . - "300165/p13898_2106T"^^ . - "false"^^ . - . - "Wikidata Property" . - "^\\w.+$"^^ . - . - . - . - . - . - . - . - . - "SEED Reactions" . - "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . - . - "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . - . - . - . - "Gs0000008"^^ . - . - . - . - "^DDB_G\\d+$"^^ . - "0000000"^^ . - . - . - "false"^^ . - . - . - . - "67035"^^ . - . - . - "Imanis Life Sciences cell line products" . - . - . - . - . - "true"^^ . - . - "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology"^^ . - . - . - "CLPUB00496"^^ . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . - . - . - "false"^^ . - . - . - . - "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . - . - . - "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . - . - . - "http://purl.obolibrary.org/obo/TRANS_$1"^^ . - . - "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "AgroPortal" . - . - . - . - . - "https://proteinensemble.org/"^^ . - . - . - . - "PA448710"^^ . - . - . - . - . - "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . - "false"^^ . - . - "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . - "http://www.w3.org/ns/activitystreams#$1"^^ . - "27267"^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - "https://bioregistry.io/schema"^^ . - . - . - . - . - "false"^^ . - . - . - . - "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^ . - "^\\d{7}$"^^ . - "https://www.orthodb.org"^^ . - . - . - . - . - . - . - "http://getentry.ddbj.nig.ac.jp"^^ . - . - . - . - . - . - . - . - "http://www.hprd.org/"^^ . - . - "https://github.com/SpeciesFileGroup/nomen"^^ . - . - . - . - "authoredBy"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://csbl.bmb.uga.edu/DOOR/operon.php"^^ . - "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^ . - "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "https://icd.who.int/"^^ . - . - "false"^^ . - . - "DECIPHER CNV Syndromes" . - "http://www.genome.ad.jp/kegg/docs/upd_ligand.html"^^ . - . - "Ensembl Glossary" . - . - . - "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . - . - . - "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . - . - "https://github.com/allysonlister/swo"^^ . - "http://purl.obolibrary.org/obo/NCRO_$1"^^ . - . - . - . - . - . - . - . - . - . - "Bgee family" . - . - "PF11779"^^ . - . - . - "Plant Growth and Development Stage" . - . - . - . - . - "IA"^^ . - . - . - "Gene Regulation Ontology" . - "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . - . - . - . - . - . - . - . - . - . - "Yeast Intron Database v4.3" . - . - "http://www.metabolomicsworkbench.org/"^^ . - . - . - . - . - . - "^\\d{8}$"^^ . - . - "101775319"^^ . - . - . - . - . - . - . - "https://www.vectorbase.org/"^^ . - "Non-Coding RNA Ontology" . - . - . - "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"^^ . - . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . - "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . - . - "ACM1_HUMAN"^^ . - "false"^^ . - "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . - . - . - . - . - "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . - . - "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . - . - . - "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . - . - "https://github.com/obophenotype/mouse-anatomy-ontology"^^ . - "http://purl.obolibrary.org/obo/AGRO_$1"^^ . - . - . - . - . - "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . - . - "^[0-9\\.]+$"^^ . - . - "Genotype Ontology" . - "101"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "H-InvDb Locus" . - . - "22-46615880-T-C"^^ . - . - "https://www.w3.org/ns/prov"^^ . - "^\\d{7}$"^^ . - "0000001"^^ . - "https://fungidb.org/fungidb/app/record/gene/$1"^^ . - "Selventa Families" . - "MINID Test" . - . - . - . - . - . - . - . - . - "https://www.biocatalogue.org/"^^ . - . - . - . - . - "100101"^^ . - "false"^^ . - "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . - "true"^^ . - . - . - "false"^^ . - . - "false"^^ . - "HIT000195363"^^ . - "18030"^^ . - "617102"^^ . - "^[A-Z_a-z]+$"^^ . - . - . - . - . - _:N4d23b2240e434caa96574a6c1329f620 . - . - . - . - . - . - "G24361QY"^^ . - "^\\d{7}$"^^ . - . - . - "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"^^ . - . - . - "false"^^ . - . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . - "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . - . - . - . - "false"^^ . - "https://aopwiki.org/relationships/$1"^^ . - "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . - . - "http://www.signaling-gateway.org/molecule"^^ . - . - . - "chebi" . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . - . - . - . - "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . - "VMH metabolite" . - . - . - . - . - . - . - "false"^^ . - "Human Cell Atlas Ontology" . - "Leszek Vincent" . - . - "LSM-6306"^^ . - . - "true"^^ . - . - . - . - . - "^A\\d+$"^^ . - . -_:N098fd1bf832348feb0b5bcdc5b7db793 "chEBI" . - . - "Yongqunh He" . - . - . - "^\\d+$"^^ . - . - "Nicole Vasilevsky" . - . - . - . - "Ontology for General Medical Science" . - . - "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . - . - "^(data|topic|operation|format)\\_\\d{4}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "0000001"^^ . - "^G(PL|SM|SE|DS)\\d+$"^^ . - "http://www.treefam.org/family/$1"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1"^^ . - . - . - . - . - . - "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there."^^ . - . - "^\\d{7}$"^^ . - . - . - . - "^ERM[0-9]{8}$"^^ . - . - . - . - . - . - "false"^^ . - "identifier for a scientific journal, in the UniProt database"^^ . - . - "Willy Wong" . - . - . - . - "http://bioinfo.lifl.fr/norine/"^^ . - . - . - "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . - . - "false"^^ . - "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . - . - . - "https://labsyspharm.github.io/lspci/$1"^^ . - . - . - . - . - "Canadian Drug Product Database" . - . - "27106865"^^ . - "http://purl.obolibrary.org/obo/FIX_$1"^^ . - "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"^^ . - . - "Cell Image Library" . - . - . - . - . - "0000685"^^ . - . - . - . - . - "https://www.yeastgenome.org/observable/APO:$1"^^ . - "CRISPRdb" . - . - "http://purl.obolibrary.org/obo/PCO_$1"^^ . - . - . - . - . - . - . - "Assists in resolving data across cloud resources."^^ . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - . - . - . - . - "https://www.clinicaltrialsregister.eu/"^^ . - . - . - "NCBI Gene Expression Omnibus" . - . - . - "^\\d{3}$"^^ . - . - . - "^CNP\\d{7}$"^^ . - "^[0-9a-zA-Z]{8}$"^^ . - . - . - . - . - . - . - "http://www.chemspider.com/"^^ . - . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - . - . - . - . - . - "http://www.pdb.org/"^^ . - . - "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - "https://web.expasy.org/cellosaurus/"^^ . - . - . - _:Nc09f0b1a44ab40779fcac26a35eea2ef . - . - . - . - "has responsible" . - . - . - "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . - . - . - "688"^^ . - . - . - . - "http://purl.obolibrary.org/obo/AERO_$1"^^ . - "784"^^ . - . - . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - . - . - . - . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - . - "Conserved Domain Database at NCBI" . - . - "https://www.ebi.ac.uk/ena/browse/genome-assembly-database"^^ . - . - "Paleobiology Database" . - "https://stemcells.nindsgenetics.org"^^ . - . - . - "false"^^ . - . - . - . - "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . - "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . - . - . - . - . - . - "VMH reaction" . - . - "false"^^ . - "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . - . - . - . - "http://autism.mindspec.org/GeneDetail/$1"^^ . - . - . - "https://casrai.org/credit/"^^ . - "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - "http://aber-owl.net/ontology/$1/#/Browse/" . - . - "http://www.cropontology.org/ontology/CO_347/Castor%20bean"^^ . - . - . - "Information about the C57BL/6J. Includes genetic background and disease data."^^ . - "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . - . - "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . - . - . - "false"^^ . - . - . - "https://www.disprot.org/ontology"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . - . - . - . - . - . - . - . - "LCSCCPN"^^ . - . - . - "false"^^ . - . - . - "Molecular Signatures Database" . - "Cell line collections"^^ . - . - . - . - . - . - . - "Information Artifact Ontology" . - "false"^^ . - . - "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . - . - . - . - "false"^^ . - . - . - "An ontology to describe entities related to prescription of drugs"^^ . - "International Classification of Diseases, 10th Revision" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . - . - . - . - . - "171"^^ . - . - "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . - . - . - . - . - "0000140"^^ . - . - . - "^PASS\\d{5}$"^^ . - . - . - . - . - . - . - . - . - . - "http://europepmc.org/"^^ . - . - . - . - . - . - . - . - . - . - "Lonza" . - . - . - "A0118748"^^ . - . - . - . - . - . - "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . - . - . - "https://civicdb.org/links/evidence/$1"^^ . - "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . - . - . - "http://www.lrg-sequence.org/"^^ . - . - . - "H00076"^^ . - . - . - . - . - "https://code.google.com/archive/p/ontology-for-genetic-interval/"^^ . - "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . - . - . - . - . - . - . - . - . - . - . - . - "^PMC\\d+$"^^ . - . - "http://www.ensembl.org/"^^ . - . - "ESi007-A"^^ . - . - . - . - . - . - "false"^^ . - . - "true"^^ . - . - . - . - . - "http://merops.sanger.ac.uk/index.htm"^^ . - "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . - "http://purl.obolibrary.org/obo/SCDO_$1"^^ . - . - . - . - "Dr. Alpha Tom Kodamullil" . - . - "http://www.fossilworks.org"^^ . - "PSEEN0001"^^ . - . - . - . - . - . - . - . - . - . - "https://www.brenda-enzymes.de/ligand.php"^^ . - . - . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - . - "^\\d+$"^^ . - "NIF Standard Ontology: Chemical" . - . - . - "false"^^ . - "http://www.pharmgkb.org/"^^ . - "^\\d+$"^^ . - "0000050"^^ . - . - . - "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . - . - . - "YeTFasCo" . - . - . - "Amphibian taxonomy" . - "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - . - "Cassava ontology" . - . - . - . - . - "https://pdc.cancer.gov/pdc/study/$1"^^ . - . - . - . - "^AA\\d{4}$"^^ . - . - . - . - "https://www.internationalgenome.org/data-portal/sample/$1"^^ . - . - "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . - "https://gsso.research.cchmc.org/"^^ . - . - . - . - . - . - . - . - . - "00056"^^ . - . - "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . - "ReviewVersion"^^ . - . - "false"^^ . - . - . - . - . - . - "http://www.e-cyanobacterium.org/bcs/rule/"^^ . - . - "http://purl.obolibrary.org/obo/EPO_$1"^^ . - . - . - . - "Database of Quantitative Cellular Signaling: Model" . - . - . - . - . - "^\\d+$"^^ . - . - . - "https://labsyspharm.github.io/lspci/"^^ . - . - . - . - "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . - . - . - "http://www.affymetrix.com/"^^ . - "http://bigg.ucsd.edu/models"^^ . - "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . - . - "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . - "^\\d+$"^^ . - "^\\d{7}$"^^ . - "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "SIDER Side Effect" . - "false"^^ . - . - . - "SIGNOR-C41"^^ . - "^\\w+\\_\\d+(\\.\\d+)?$"^^ . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . - "http://www.sparontologies.net/ontologies/bido"^^ . - . - "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . - "0000046"^^ . - . - . - "0019030"^^ . - . - . - "Vocabulary of Interlinked Datasets" . - . - "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html"^^ . - . - . - "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . - . - . - . - . - "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . - . - . - . - . - "https://www.ebi.ac.uk/chebi/"^^ . - "3771877"^^ . - . - . - . - "false"^^ . - . - . - "OSR0818"^^ . - . - "https://www.lgcstandards-atcc.org"^^ . - . - . - . - . - . - . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/"^^ . - . - . - . - "PGOHUM00000289843"^^ . - . - . - "0000001"^^ . - . - . - "true"^^ . - "HBB"^^ . - . - . - . - . - "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . - . - . - . - . - . - . - . - . - "Compluyeast-2D-DB" . - . - "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . - . - . - . - . - "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . - . - . - "https://ximbio.com"^^ . - "false"^^ . - . - "^([A-Z]+-)?\\d+$"^^ . - "Cell line collections"^^ . - . - . - "http://func.mshri.on.ca/human/"^^ . - . - . - "http://purl.obolibrary.org/obo/ARO_$1"^^ . - . - . - "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . - "NIF Standard Ontology: Cognitive Function" . - . - "Population and Community Ontology" . - "M00002"^^ . - "https://www.biolegend.com"^^ . - . - . - "International Standard Name Identifier" . - . - . - . - "false"^^ . - . - . - . - "Protein Interaction Network Analysis" . - "http://arabidopsis.info/"^^ . - "false"^^ . - . - . - . - . - . - . - "Computational and Informatics Resources for Glycoscience" . - . - "https://n2t.net"^^ . - . - "Metabolic Encyclopedia of metabolic and other pathways" . - . - . - . - . - . - "Melanie Courtot" . - . - "NCBI dbSNP" . - . - . - . - . - "109082"^^ . - "Cell line collections"^^ . - . - . - "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://www.wikidata.org" . - . - . - . - . - "http://purl.obolibrary.org/obo/MF_$1"^^ . - "false"^^ . - . - . - . - . - "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . - . - . - . - . - "Nematode Expression Pattern DataBase" . - "Research Resource Identification" . - "true"^^ . - . - "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . - "ACHN"^^ . - . - "false"^^ . - . - "MatrixDB Association" . - . - . - . - . - . - "Molbase" . - . - . - . - . - . - . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . - . - "Christian-Alexander Dudek" . - . - . - "false"^^ . - . - . - . - . - "SRS086444"^^ . - "^\\d{6}$"^^ . - "Homologous Organ Groups" . - "Europe PMC Preprints" . - . - "18"^^ . - _:Nb989cb7dedee4004a9c97f1355271a9f . - "false"^^ . - . - "https://github.com/information-artifact-ontology/ontology-metadata"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - "https://bacdive.dsmz.de/strain/$1"^^ . - . - . - . - "Mouse gross anatomy and development, timed" . - . - . - . - "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . - "The RNA Modification Database" . - . - . - . - . - . - . - "Frederic Bastian" . - . - "World Wildlife Fund Ecoregion" . - . - . - "true"^^ . - . - . - . - "CIViC Assertion" . - . - . - . - . - . - . - "false"^^ . - "http://www.sasbdb.org/data/$1"^^ . - "http://www.e-cyanobacterium.org/bcs/entity/"^^ . - "http://www.w3.org/2001/XMLSchema#$1"^^ . - . - . - . - . - "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^ . - . - . - . - . - . - "false"^^ . - . - . - "https://dip.doe-mbi.ucla.edu/"^^ . - . - "000140" . - "true"^^ . - . - . - "http://www.candidagenome.org/"^^ . - . - . - . - . - "false"^^ . - . - . - "NameRXN" . - "0107180"^^ . - . - . - "http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1"^^ . - "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . - "Deepak Unni" . - . - . - . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . - . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv"^^ . - "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.protonet.cs.huji.ac.il/"^^ . - . - . - . - . - "Common Access to Biological Resources and Information Project" . - . - . - . - . - "https://github.com/NCI-Thesaurus/thesaurus-obo-edition"^^ . - "Ontology Concept Identifiers" . - . - . - "false"^^ . - "Genitourinary Development Molecular Anatomy Project" . - . - . - . - . - "http://aber-owl.net/ontology/$1" . - . - "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^ . - "false"^^ . - . - . - . - . - "https://github.com/obophenotype/xenopus-phenotype-ontology"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . - . - . - "true"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - "ProteomicsDB Peptide" . - . - . - . - . - . - . - "^S-[A-Z]{4}[A-Z\\d\\-]+$"^^ . - "SL-0002"^^ . - . - "Common Anatomy Reference Ontology" . - . - . - "AT1G01010"^^ . - . - . - "Dublin Core" . - . - . - . - . - . - . - "false"^^ . - . - . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/PLANP_$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . - . - "https://www.pirbright.ac.uk/node/$1"^^ . - "Tom Gillespie" . - "TF101014"^^ . - . - . - . - "http://rhesus.amu.edu.pl/mirnest/copy/"^^ . - "https://envipath.org/"^^ . - . - . - . - . - "http://bactibase.hammamilab.org"^^ . - . - . - . - . - . - . - . - . - "http://www.jcm.riken.go.jp/"^^ . - "FamPlex" . - . - "0000079"^^ . - . - . - . - "false"^^ . - "https://www.cropontology.org/rdf/CO_356:$1"^^ . - . - . - "false"^^ . - . - . - "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . - . - . - "US4145692"^^ . - "https://morpheus.gitlab.io/"^^ . - . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - . - "http://www.pazar.info/"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "http://comgen.pl/mirex/?page=home"^^ . - . - . - . - . - "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . - "^\\d+$"^^ . - "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/"^^ . - . - "PTM-0450"^^ . - . - "https://rnacentral.org/"^^ . - . - . - "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . - . - "https://www.metanetx.org/"^^ . - "0000618"^^ . - . - . - "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . - . - . - "https://www.uniprot.org/unirule/$1"^^ . - . - . - . - "Plant Genome Network" . - "https://www.datanator.info/metabolite/$1"^^ . - . - "false"^^ . - . - . - "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . - . - . - . - . - . - "Selventa Diseases" . - . - . - "Represent chemical entities having particular CHEBI roles"^^ . - . - . - "https://github.com/"^^ . - . - . - "Troy Pells" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "rxn00001"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . - . - "Tom Gillespie" . - . - . - . - . - "R00100"^^ . - . - . - . - . - "http://www.genome.jp/kegg/catalog/org_list3.html"^^ . - . - . - "https://github.com/obophenotype/chiro"^^ . - "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . - "false"^^ . - . - "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . - "https://github.com/"^^ . - "Radiation Biology Ontology" . - "FuncBase Mouse" . - "Golm Metabolome Database Profile" . - . - . - . - "Gene"^^ . - "http://stitch.embl.de/interactions/$1"^^ . - "false"^^ . - . - "1257009"^^ . - . - "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . - . - . - . - . - "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . - "https://sorgerlab.github.io/famplex/"^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"^^ . - . - . - . - "^c\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "1250"^^ . - . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - "International Classification of Diseases, 9th Revision" . - "false"^^ . - . - . - . - . - . - . - "Horizon Discovery cell line collection" . - . - . - . - "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . - . - "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . - . - . - "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . - "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . - . - . - . - "F4521"^^ . - "http://cerevisiae.oridb.org/details.php?id=$1"^^ . - . - . - . - "http://www.arachnoserver.org/"^^ . - . - "United States Patent and Trademark Office" . - "Q2207226"^^ . - "^\\d{7}$"^^ . - "000017"^^ . - . - . - "BRENDA Ligand Group" . - "0000423"^^ . - "false"^^ . - . - . - . - . - "https://rfam.xfam.org/"^^ . - "C063233"^^ . - . - . - "^[a-z]+(\\..*?)?$"^^ . - "https://www.ebi.ac.uk/chembl/entity/$1"^^ . - "Thermo Fisher Scientific" . - . - . - . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . - . - . - "91005"^^ . - . - . - _:N0b6dc46b862b41399ea93d23b5a47653 . - "http://www.cba.ac.cn"^^ . - . - . - . - . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - . - "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^ . - . - "The Ontology of Genes and Genomes" . - . - . - "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . - . - . - "2966"^^ . - . - . - "^SEQF\\d+$"^^ . - . - "^\\d+$"^^ . - . - "1000001"^^ . - . - . - . - . - . - . - "Interaction Network Ontology" . - . - "https://www.metanetx.org/"^^ . - . - . - . - . - . - "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . - . - "Q-2958"^^ . - "ev:E00032"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . + . + "Anatomical Therapeutic Chemical Classification System" . + . + . + . + . + . + . + . + . + . + . + . + . + "1"^^ . + . + . + . + "10194"^^ . + "Karen Eilbeck" . + "https://doulix.com/biomodules/$1"^^ . + . + "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^ . + . + "false"^^ . + . + "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . + . + "http://www.ebi.ac.uk/chebi"^^ . + . + . + . + . + . + . + . + . + . + "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . + . + "false"^^ . + "2gc4"^^ . + . + . + . + . + . + . + "Database of Quantitative Cellular Signaling: Pathway" . + . + "^AT\\d+$"^^ . + "true"^^ . + "https://github.com/INO-ontology/ino"^^ . + . + "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . + . + . + "^\\d{6}$"^^ . + . + . + . + . + . + . + "377550"^^ . + "https://cropontology.org/ontology/CO_326/Coconut"^^ . + "46977"^^ . + "Scientific Evidence and Provenance Information Ontology" . + . + . + . + "false"^^ . + . + "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html"^^ . + . + . + . + . + . + . + . + "http://www.mgc.ac.cn/VFs/"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://bioregistry.io/metaregistry/"^^ . + . + . + . + . + . + "false"^^ . + . + "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . + . + . + "^\\d+$"^^ . + . + "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there."^^ . + . + "http://www.bindingdb.org/compact/$1"^^ . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "false"^^ . + . + . + "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + "KEGG Environ" . + . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + . + "^[-A-Za-z0-9\\_]*$"^^ . + "http://bigg.ucsd.edu/universal/reactions"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "24867"^^ . + . + . + . + . + . + . + . + "https://web.expasy.org/cellosaurus/"^^ . + . + "Human Gene Mutation Database" . + "http://purl.obolibrary.org/obo/TAHH_$1"^^ . + . + "1017"^^ . + . + . + . + . + . + . + "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + . + "Protein covalent bond" . + . + "false"^^ . + "http://vegbank.org/"^^ . + . + . + . + . + "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . + . + . + . + . + "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . + . + . + . + . + . + . + . + . + . + . + "^MMP\\d+.\\d+$"^^ . + . + . + . + . + "http://www.lipidmaps.org"^^ . + "https://www.ebi.ac.uk/biosamples/"^^ . + . + "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . + . + . + "InChI" . + "http://www.evoio.org/wiki/MIAPA"^^ . + . + "T039"^^ . + . + . + "http://flyrnai.org/"^^ . + . + . + . + "false"^^ . + . + "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . + . + "BRENDA tissue / enzyme source" . + . + . + . + . + "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . + "Gazetteer" . + . + "0000078"^^ . + "^\\d{7}$"^^ . + . + . + . + "http://www.nlm.nih.gov/mesh/"^^ . + . + . + "https://www.ebi.ac.uk/interpro/entry/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . + "https://www.ebi.ac.uk/intact/interaction/$1"^^ . + "false"^^ . + . + "y3ax-8bq3-60"^^ . + . + . + . + "Interaction Network Ontology" . + . + . + . + "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . + . + . + . + . + "Study inside StoreDB"^^ . + "hasOpenAccessRating"^^ . + . + . + . + . + "^\\d{6}$"^^ . + . + . + . + . + . + . + . + . + . + "Yeast phenotypes" . + . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . + . + "https://biolink.github.io/biolink-model/"^^ . + . + . + "^\\d{7}$"^^ . + . + "000000341"^^ . + "RXN-14904"^^ . + . + "Anatomical Entity Ontology" . + . + . + "European Bank for induced pluripotent Stem Cells" . + . + . +_:N85c09898c2cc4155934cacdac0abfb35 "Plant Ontology Administrators" . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . . - . - . - . - . - . - "http://www.peptideatlas.org/PASS/$1"^^ . - . - . - . - . - "^\\w+$"^^ . - "^r3d\\d{9,9}$"^^ . - "^\\w+$"^^ . - . - "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . - "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp"^^ . - "YMDB00001"^^ . - . - . - . - "false"^^ . - . - . - "https://licebase.org"^^ . - . - . - "http://purl.obolibrary.org/obo/MCO_$1"^^ . - . - . - . - . - "Illumina Probe Identifier" . - . - . - . - "https://www.ebi.ac.uk/miriam/main/$1"^^ . - . - . - "240-17-488-3-4-12"^^ . - . - "10015919"^^ . - . - . - . - . - "6038"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "24867"^^ . - . - . - . - . - . - "Disease Class" . - "FooDB Compound" . - . - "Virtual Fly Brain" . - . - . - . - "false"^^ . - . - "The Bioinorganic Motif Database" . - . - "1"^^ . - . - . - . - . - . - "040000"^^ . - "Human Pluripotent Stem Cell Registry" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "0101963"^^ . - . - "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . - . - "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "TF0001053"^^ . - . - . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - "^\\d+$"^^ . - . - "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . - . - "false"^^ . - "iNaturalist Taxonomy" . - "Teleost Anatomy Ontology" . - "http://nematode.lab.nig.ac.jp/"^^ . - "AP011135"^^ . - "5HT3Arano"^^ . - "NCI Thesaurus" . - . - . - . - . - . - "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . - . - "^\\S+$"^^ . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . - . - . - "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Habronattus courtship" . + . + . + . + "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . + "https://pk-db.com/data/$1"^^ . + . + "https://ligandbook.org/"^^ . + "true"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "^(Gi|Gc)\\d+$"^^ . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CLO_$1"^^ . + . + . + . + "Human Endogenous Retrovirus Database" . + . + "https://commonchemistry.cas.org/"^^ . + "SubstrateDB" . + "^virsi\\d+$"^^ . + "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . + . + . + "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . + "false"^^ . + . + . + "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . + . + . + . + . + "^[A-Z0-9]{6,7}$"^^ . + . + . + . + "^[1-9]\\d{5}$"^^ . + . + "0000001"^^ . + "Saccharomyces Genome Database" . + . + "https://zenodo.org"^^ . + . + . + "http://browser.planteome.org/amigo"^^ . + "MeSH 2013" . + . + . + "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . + . + . + "Sugar Kelp trait ontology" . + . + . + "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . + . + "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . + "Gene Expression Ontology" . + . + . + . + "false"^^ . + "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . + . + "Ontology"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . + . . - . - . - . - . - . - . - . - . - . - . - . - "TS-0001"^^ . - . - . - . - "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . - . - . - "Pigeonpea ontology" . - "false"^^ . - "https://www.inaturalist.org/taxa"^^ . - "^DRSC\\d+$"^^ . - . - . - "^\\d+$"^^ . - "^\\d{5}$"^^ . - "https://wiki.phenoscape.org/wiki/Curation_workflow"^^ . - . - . - "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . - . - . - "European Collection of Authenticated Cell Culture" . - "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . - "false"^^ . - "https://ximbio.com/reagent/$1"^^ . - "^\\d{8}$"^^ . - . - . + "http://ciliate.org/index.php/feature/details/$1"^^ . + . + . + "http://www2.idac.tohoku.ac.jp/dep/ccr/"^^ . + . + . + . + . + . + . + . + . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + . + . + . + . + "http://www.w3.org/XML/1998/namespace#$1"^^ . + "Fernanda Dorea" . + . + . + . + "https://www.w3.org/ns/prov"^^ . + . + . + "false"^^ . + . + . + . + . + "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . + "https://sumlineknowledgebase.com/"^^ . + . + "http://www.pharmgkb.org/gene/$1"^^ . + . + "^\\d{7}$"^^ . . - . - "Database of Macromolecular Interactions" . - . - "00000001"^^ . - "0000029"^^ . - . - . - . - . - . - . - . - "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . - . - "true"^^ . - . - . - . - . - "https://omabrowser.org/cgi-bin/gateway.pl"^^ . - "^\\d+$"^^ . - "0004828"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - . - "KEGG Disease" . - . - . - . - "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . - "Collembola Anatomy Ontology" . - . - . - . - . - . - . - "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - "https://portal.gdc.cancer.gov/cases/$1"^^ . - . - . - . - . - "Life cycle stages for Mus Musculus"^^ . - "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . - "UniProt journal ID" . - . - "http://www.informatics.jax.org/searches/MP_form.shtml"^^ . + . + . + . + "https://code.google.com/p/craniomaxillofacial-ontology/"^^ . + . + . + "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . + . + . + . + . + . + . + "chebi" . + . + . + "https://pypi.org/project/$1"^^ . + . + . + . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + "http://wodaklab.org/iRefWeb/"^^ . + . + . + . + . + "0000013"^^ . + . + . + . + "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . + "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . + "false"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "^WBRNAi\\d{8}$"^^ . + "mirEX" . + . + . + . + . + "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . + . + "https://bioportal.bioontology.org/ontologies/VSO"^^ . + . + "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . + . + . + "IHW09326"^^ . + . + . + "^\\d{7}$"^^ . + . + "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . + "Cancer Data Standards Registry and Repository" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . + . + "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . + . + . + . + "http://www.pharmgkb.org/disease/$1"^^ . + . + . + "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . + "1"^^ . + . + . + . + . + . + . + "Ontology of Vaccine Adverse Events" . + "http://purl.obolibrary.org/obo/OLATDV_$1"^^ . + . + . + . + "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . + . + . + . + . + "Carrine Blank" . + . + . + . + . + . + . + . + . + . + . + "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . + "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . + . + . + . + . + . + "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . + . + . + . + "DIP-743N"^^ . + "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . + . + . + . + "https://www.ndexbio.org"^^ . + . + . + . + . + . + "https://www.noguchi.or.jp/"^^ . + "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "National Center for Biotechnology Information Registry" . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + "24801"^^ . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv"^^ . + . + "false"^^ . + "false"^^ . + "Drosophila development" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://fair-research.org"^^ . + "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n"^^ . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . + . + . + "https://www.imanislife.com/?s=$1"^^ . + "false"^^ . + "992"^^ . + "Rat Strain Ontology" . + "http://senselab.med.yale.edu/OrDB/"^^ . + . + "false"^^ . + . + "http://bioassayontology.org"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "https://github.com/obophenotype/cephalopod-ontology"^^ . + "https://lncipedia.org"^^ . + . + . + "false"^^ . + . + . + . + . + "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + "Data Object Service" . + . + . + "Dengue Fever Ontology" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/RBO_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "DP00086r013"^^ . + . + . + . + "false"^^ . + "http://www.protonet.cs.huji.ac.il/"^^ . + . + "Semantic Types Ontology" . + "3"^^ . + . + "OpenCitations Corpus" . + . + . + "Ontology for Biobanking" . + "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . + "0000138"^^ . + "^[A-Z]+[0-9]+$"^^ . + . + . + . + "ICEberg family" . + . + . + . + . + . + . + . + . + "Ath_AT1G01030.1"^^ . + . + . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . + . + . + . + . + . + . + . + "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Nematode Expression Pattern DataBase" . + . + "Database of the dielectric properties of biological tissues."^^ . + "Reagent Ontology" . + "https://github.com/rsc-ontologies/rsc-cmo"^^ . + . + . + "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . + . + . + "Taxonomic rank vocabulary" . + . + . +_:N576da71a94704c05bc5e000eaaad71e4 "Jonathan Bard" . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + "Ada Hamosh" . + . + "https://www.disprot.org/ontology"^^ . + "false"^^ . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . + . + . + "0000423"^^ . + . + . + . + "PRJDB3"^^ . + . + . + . + "https://orcid.org"^^ . + . + . + . + . + . + . + "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . + . + "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . + . + . + . + . + . + "3771992"^^ . + . + "UniProt Variants" . + . + . + . + . + "^[0-9a-zA-Z]{8}$"^^ . + . + "0000632"^^ . + . + . + . + "false"^^ . + . + "MIRT000002"^^ . + "LiceBase" . + "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . + "0807.4956v1"^^ . + . + . + "CTD Gene" . + "http://mycobrowser.epfl.ch/leprosy.html"^^ . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Rebuilding a Kidney" . + "RiceNetDB Reaction" . + . + "SEQF1003"^^ . + "false"^^ . + . + . + . + "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . + . + . + . + "http://qudt.org/schema/qudt#$1"^^ . + . + "1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "https://sed-ml.org/urns.html#format:$1"^^ . + . + . + "http://drugcentral.org"^^ . + "95-0166C6"^^ . + . + "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"^^ . + "^\\d{7}$"^^ . + "http://www.ontobee.org/" . + . + . + . + . + . + "^\\d+$"^^ . + . + "http://cell-lines.toku-e.com"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + "http://pantree.org/"^^ . + . + "Drivers of human diseases including environmental, maternal and social exposures."^^ . + . + . + . + . + . + . + "3"^^ . + . + "http://www.antweb.org/specimen.do?name=$1"^^ . + . + . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . + . + . + . + "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . . - . - "^FOOD\\d+$"^^ . - . - . - . - . - . - . - . - . - "http://sabiork.h-its.org/newSearch?q=$1"^^ . - "https://www.uniprot.org/locations/$1"^^ . - "false"^^ . - . - "OMA Protein" . - . - . - . - . - "^\\d+$"^^ . - "^FB\\d{8}$"^^ . - . - . - "0000574"^^ . - . - . - "https://github.com/luis-gonzalez-m/Collembola"^^ . - "false"^^ . - "Gene Expression Ontology" . - . - . - . - . - . + . + . + . + "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . + . + . + . + . + "laml_tcga_pub"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . . - . - . - . - "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . + . + "Ensembl Gene" . + "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO"^^ . + "^\\d+$"^^ . + . + "An ontology designed to support the semantic annotation of epidemiology resources"^^ . + "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . + . + "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . + . + . + "^[0-9]+-[0-9]+$"^^ . + . + . + . + "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . + "Five Stars of Online Research Articles Ontology" . + . + "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . + . + "GlycoNAVI" . + . + . + . + "TVAG_386080"^^ . + . + . + . + . + . + . + . + . + "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "^Rv\\d{4}(A|B|c)?$"^^ . + "^\\w+$"^^ . + . + . + "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.cdc.gov/nchs/icd/icd9.htm"^^ . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + . + . + "http://www.sparontologies.net/ontologies/cito"^^ . + "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . + "false"^^ . + "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . + "GWAS Central Study" . + . + . + . + . + . + . + . + . + "78073"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "http://www.plantontology.org"^^ . + . + . + . + . + "EchoBASE post-genomic database for Escherichia coli" . + . + . + . + . + . + "veNOG12876"^^ . + . + "https://www.vectorbase.org/ontology-browser"^^ . + . + . + . + . + . + . + . + "FCB005"^^ . + . + . + . + "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . + "InChIKey" . + . + "https://github.com/OPL-ontology/OPL"^^ . + . + . + . + . + "^\\w{4}$"^^ . + . + . + "http://www.viprbrc.org/brc/home.do?decorator=vipr"^^ . + . + . + . + . + "CIAT Common bean trait dictionary - version August 2014"^^ . + "http://eawag-bbd.ethz.ch/$1/$1_map.html"^^ . + . + . + "http://aber-owl.net/ontology/$1" . + . + . + . + . + "9"^^ . + . + . + . + "Genome Properties" . + "The Python Package Index (PyPI) is a repository for Python packages."^^ . + "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . + "Unique Ingredient Identifier" . + "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/protein"^^ . + . + "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . + . + . + . "true"^^ . - "https://obophenotype.github.io/cell-ontology/"^^ . - . - "^SIGNOR\\-[A-Z]+\\d+$"^^ . - . - "false"^^ . - . - "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . - . - . - . - . - . - . - . - . - . - "MGnify Sample" . - "Terminology of Anatomy of Human Embryology" . - "false"^^ . - . - . - "http://ciliate.org/index.php/"^^ . - . + . + . + . + . + . + . + . + "http://www.gramene.org/"^^ . + "https://www.flymine.org/come"^^ . + . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + . + . + . + . + . + . + . + "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . + . + . + . + . + . + . + "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . + "http://www.hgmd.cf.ac.uk/ac/index.php"^^ . + . + "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"^^ . + . + "Human developmental anatomy, abstract version" . + . + . + . + . + . + . + . + "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . + . + . + . + . + "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . + . + . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + . + "https://www.ncbi.nlm.nih.gov/books/$1"^^ . + "false"^^ . + . + . + . + . + "https://pharmacodb.ca/tissues/$1"^^ . + "http://purl.obolibrary.org/obo/MIRO_$1"^^ . + . + . + "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . + . + . + "http://viralzone.expasy.org/"^^ . + . + . + . + . + "Tb927.8.620"^^ . + . + "PROV Namespace" . + . + "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . + "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . + . + "^CHEMBL\\d+$"^^ . + . + . + "4"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + "ZDB-GENE-041118-11"^^ . + . + "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "Cellosaurus identifeirs for publications, like Pubmed"^^ . + . + "^[A-Za-z0-9-]+$"^^ . + "https://cropontology.org/ontology/CO_343/Yam"^^ . + . + . + . + . + . + . + "https://icd.who.int/browse10"^^ . + . + . + . + "^[A-Za-z0-9\\-\\_]+$"^^ . + "https://gitlab.com/"^^ . + "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://rnacentral.org/"^^ . + . + "Alliance of Genome Resources Knowledge Base" . + . + . +_:Naf924f5e718d4739a0f29dcc853fb39e "Jonathan Bard" . + "false"^^ . + . + . + "Cell Ontology" . + "NCI Metathesaurus" . + . + . + "false"^^ . + "https://biopragmatics.github.io/providers/schem/$1"^^ . + . + . + . + . + . + . + "https://www.gleif.org/lei/$1"^^ . + . + . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + "canal"^^ . + "NeuroVault Collection" . + "Amphibian gross anatomy" . +_:N26d14ce966cf45029d3aad979df880c7 "John Garavelli" . + . + . + . + . + . + . + . + . + "William Hogan" . + . + "https://github.com/geneontology/unipathway"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + "false"^^ . + . + . + . + . + "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . + . + . + . + . + "57"^^ . + "false"^^ . + "CHEBI" . + "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . + "false"^^ . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . + . + . + . + "10531"^^ . + "false"^^ . + "P00024"^^ . "true"^^ . - . - . - "968"^^ . - "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."^^ . - . - . - "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . - "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . - "http://www.proteinmodelportal.org/"^^ . - . - "^\\w+$"^^ . - . - . - "408"^^ . - "http://bgee.unil.ch/bgee/bgee"^^ . - . - "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . - . - . - . - . - "Basic Formal Ontology" . - . - . - . - . - "Reactome" . - "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . - . - . - . - . - "https://datacite.org"^^ . - "^\\d+$"^^ . - . - . - "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"^^ . - "High-quality Automated and Manual Annotation of microbial Proteomes" . - . - . - "906801"^^ . - . - . - "Terry Hayamizu" . - . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . - "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . - . - . - . - . - "false"^^ . - "Cell line databases/resources"^^ . + . + "identifierPattern"^^ . + "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species."^^ . + . + "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . + . + . + . + "2.1.1"^^ . + . + . + . + . + . + . + . + . + "Fababean ontology" . + . + "Dublin Core Types" . + . + "Chemistry resources"^^ . + . + . +_:N1990af52b5394a07ad7cc002186040f4 "Thorsten Heinrich" . + "BCRC Strain Collection Catalog" . + "https://www.gbif.org/species/$1"^^ . + . + . + . + . + . + . + . + . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + . + . + "Medical Subject Headings" . + . + "http://www.plantontology.org"^^ . + "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . + . + . + . + . + . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . + "http://www.cathdb.info/cathnode/$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/LPT_$1"^^ . + "Daniel Himmelstein" . + "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . + "http://purl.obolibrary.org/obo/AGRO_$1"^^ . + . + . + . + . + . + "NCBI Protein" . + . + . + "false"^^ . + "^\\d+$"^^ . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + . + "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . + . + . + . + "Antibiotic Resistance Genes Database" . + "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . + "^[a-z]+(\\-[a-z]+)*$"^^ . + . + . + . + . + . + . + . + "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . + . + . + . + . + "Continuous Automated Model Evaluation" . + . + "false"^^ . + . + "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . + . + . + . + "268"^^ . + . + . + "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . + . + "Coli Genetic Stock Center" . + "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . + "false"^^ . + "0000187"^^ . + . + . + . + "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^ . + . + . + "http://purl.obolibrary.org/obo/PAO_$1"^^ . + . + "^\\d{8}$"^^ . + . + . + . + "Mungbean ontology" . + "false"^^ . + "https://www.storedb.org/"^^ . + . + . + . + "Cellosaurus Registry" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "MOL000160"^^ . + . + "false"^^ . + "false"^^ . + . + "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . + "^\\d+$"^^ . + "AD834"^^ . + . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . + . + . + . + . + "75"^^ . + . + . + . + . + "cgd7_230"^^ . + . + . + "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . + "GenPept" . + "^\\d{7}$"^^ . + . + . + "^\\d+$"^^ . + . + . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . + . + . + . + . + "ArachnoServer" . + . + "01467"^^ . + . + . + . + . + . + "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . + . + . + . + . + . + . + "ClinGen Allele Registry" . + "false"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "true"^^ . + "https://gen3.theanvil.io"^^ . + . + . + . + . + "https://pictar.mdc-berlin.de/"^^ . + . + . + "^RCV\\d+(\\.\\d+)?$"^^ . + . + . + . + "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . + . + . + "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . + . + "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . + . + . + "https://www.wormbase.org/db/seq/protein"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://biopragmatics.github.io/providers/sdis/$1"^^ . + . + . + . + . + "false"^^ . + . + "https://bioregistry.io/schema/#$1"^^ . + . + _:N743aadb122be4af0923089a9894fc4e9 . + . + . + . + . + . + . + . + . + "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . + . + . + . + . + . + . + "FuncBase Mouse" . + . + . + . + . + . + . + . + . + . + "^\\d{5}$"^^ . + . + . + "https://www.ebi.ac.uk/intact/molecule/$1"^^ . + . + "BG11523"^^ . + . + "Common Access to Biological Resources and Information Project" . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "http://igsn.org/$1"^^ . + "true"^^ . + "http://purl.obolibrary.org/obo/OHD_$1"^^ . + . + . + "http://www.w3.org/2000/01/rdf-schema#$1"^^ . + "Cell line collections"^^ . + . + . + . + . + "FuTRES Ontology of Vertebrate Traits" . + "^\\d+$"^^ . + "MGYA00002270"^^ . + . + "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . + "^\\d{7}$"^^ . + "Scopus Researcher" . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + "2701"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MRO_$1"^^ . + "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . + . + "Documentation of the Phenoscape Curation Workflow"^^ . + . + . + . + . + . + "UniProt Post-Translational Modification" . + . + . + . + "FaceBase Data Repository" . + "ala"^^ . + "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . + "https://thebiogrid.org/"^^ . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . + . + "^\\d{7}$"^^ . + . + . + "46"^^ . + "https://github.com/insect-morphology/lepao"^^ . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "^\\w+$"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + "false"^^ . + "false"^^ . + . + . + . + . + "DTXSID2021028"^^ . + "https://bioregistry.io/collection"^^ . + . + . + . + "PaxDb Protein" . + "The Arabidopsis Information Resource" . + . + "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . + "false"^^ . + . + "PTPN1"^^ . + . + . + . + . + . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + . + . + . + . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . + . + "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . + "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . + . + . + "http://phylomedb.org/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1"^^ . + . + . + . + . + . + "miRNEST" . + "false"^^ . + . + . + . + . + . + "Pearl millet ontology" . + . + . + "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . + "Tree of Life Web Project ID" . + . + . + . + "KEGG Enzyme" . + "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . + "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . + "https://easychair.org/cfp/"^^ . + . + . + . + . + . + . + "Bio-Pesticides DataBase" . + . + "^\\d+$"^^ . + . + . . - . - . - . - "HGNC Gene Group" . - "Simple Modular Architecture Research Tool" . + "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . + "http://comgen.pl/mirex/?page=home"^^ . + "Cellular Phenotypes" . + "4145692"^^ . + . + . + "false"^^ . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home"^^ . + . + . + . + . + . + . + "Cell Version Control Repository" . + "R-BTA-418592"^^ . + . + . +_:N2498f1bbd088495099f68b3ec13de880 "Pantelis Topalis" . + . + "PASS01237"^^ . + . + "Semantic Web Context" . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . + . + . + . + . + . + . + . + . + . + "the FAIR Cookbook" . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . + . . + "Animal TFDB Family" . + . + . + . + "^\\d+$"^^ . + . + . + "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . + "true"^^ . + . + . + . + . + . + . + "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . + . + . + . + "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . + . + . + . + "http://www.pharmgkb.org/"^^ . + . + "CALM1"^^ . + . + "1398574"^^ . + "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . + "http://github.com/seger/aao"^^ . + "false"^^ . + "C. elegans Small Molecule Identifier Database" . + "false"^^ . + . + "http://www.protonet.cs.huji.ac.il/"^^ . + . + . + . + . + "ScerTF" . + . + . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + "https://lhncbc.nlm.nih.gov/semanticnetwork/"^^ . + . + "BibliographicRecord"^^ . + "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . + . + . + . + . + . + . + . + "PSI Extended File Format" . + "Kaggle" . + "ConoServer" . + . + "https://clinicaltrials.gov/ct2/show/$1"^^ . + "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^ . + . + . + . + . + . + . + . + "Ontology for Avida digital evolution platform" . + . + "^\\d+$"^^ . + "American Type Culture Collection" . + "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . + . + "PA146123006"^^ . + "0000003"^^ . + "Monarch Disease Ontology" . + . + "http://www.chemspider.com/"^^ . + . + "false"^^ . + "false"^^ . + "Information for ligands in the BRENDA database."^^ . + "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "Span" . + "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . + "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . + . + "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . + "http://www.w3.org/ns/dcat#$1"^^ . + . + . + "false"^^ . + . + . + . + "c"^^ . + "false"^^ . + . + . + . + . + "A gazetteer constructed on ontological principles"^^ . + "false"^^ . + . + . + "http://psb.kobic.re.kr/STAP/refinement/"^^ . + . + "G00123"^^ . + "Pathway Commons" . + . + . + . + . + "SPIKE Map" . + "false"^^ . + . + . + "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + . + . + "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . + . + . + . + . + . + "T0599"^^ . + "DrugBank" . + . + "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1"^^ . + "0000040"^^ . + . + "GT10"^^ . + . + . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . + . + . + . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view"^^ . + . + "145"^^ . + "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . + . + . + . + "82"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "BioAssay Ontology" . + "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . + . + "^PDC\\d+$"^^ . + . + "http://www.chemspider.com/$1"^^ . + . + "http://merops.sanger.ac.uk/index.htm"^^ . + "Amos Bairoch" . + "051"^^ . + "OriDB Saccharomyces" . + "false"^^ . + "^\\w+$"^^ . + . + . + . + "https://www.uniprot.org/"^^ . + "Datanator Reaction" . + . + . + . + . + . + . + . + . + . + . + "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . + . + . + "http://ecoportal.lifewatch.eu" . + . + . + "National Library of Medicine Catalog" . + . + "Social Behavior in insects"^^ . + . + "cpd15380"^^ . + "https://www.ebi.ac.uk/biomodels/$1"^^ . + . + "^(\\w+)?\\d+$"^^ . + "http://compluyeast2dpage.dacya.ucm.es/"^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + "0110974"^^ . + . + "The cell line vocabulary inside FlyBase"^^ . + . + . + . + . + . + "false"^^ . + "Soybean ontology" . + . + . + . + . + "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . + . + . + . + . + . + "false"^^ . + . + . + "^[a-z][a-zA-Z]+$"^^ . + "https://sorgerlab.github.io/famplex/"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . + . + "false"^^ . + . + "Cell Signaling Technology Antibody" . +_:Nf8cc7561ff47495ca15ab9427619ec89 "WikiData Support" . + "PA131"^^ . + "http://www.amphibanat.org"^^ . + "Cell Biolabs cell line products" . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . + "false"^^ . + "false"^^ . + . + . + . + "https://www.merckmillipore.com/"^^ . + . + "^MMP\\d+.\\d+$"^^ . + "http://bioportal.bioontology.org/ontologies/MEDDRA"^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + "Bilateria anatomy" . + "https://pubchem.ncbi.nlm.nih.gov"^^ . + . + . + . + "0000586"^^ . + . + . + . + . + . + "http://phylomedb.org/?seqid=$1"^^ . + "true"^^ . + . + . + . + . + . + . + . + . + "Chicken Gene Nomenclature Consortium" . + . + . + . + . + "miRNA Target Prediction at EMBL" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . + . + . + . + . + "0000010"^^ . + . + "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^ . + "https://psidev.info/sepcv"^^ . + . + "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . + . + . + . + "false"^^ . + . + "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. "^^ . + . + . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + "http://www.bmrb.wisc.edu/"^^ . + . + "http://www-deletion.stanford.edu/YDPM/"^^ . + . + . + . + "http://viralzone.expasy.org/all_by_protein/$1.html"^^ . + . + . + . + . +_:N41391cbb5278405d824db68dec3c2cad "Thorsten Henrich" . + . + . + "002368"^^ . + . + . + . + "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . + . + . + "http://www.noncode.org/"^^ . + "https://www.insdc.org/"^^ . + "https://go.drugbank.com/categories"^^ . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . + . + "Prefix.cc" . + "^AA\\d{4}$"^^ . + . + "^EGAS\\d{11}$"^^ . + "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . + . + . + "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . + . + "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . + . + . + . + . + . + . + "true"^^ . + . + "Golm Metabolome Database" . + . + . + "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1"^^ . + . + . + "International Classification of Diseases, 10th Revision, Clinical Modification" . + . + "http://www.treefam.org/family/$1"^^ . + . + . + "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/keywords/$1"^^ . + . + . + . + . + . + . + . + "Brachiaria ontology" . + . + . + "Protein ANalysis THrough Evolutionary Relationships Classification System" . + "RSC3"^^ . + . + "Virtual International Authority File" . + . + . + "http://geneontology.org/"^^ . + . + "0002066"^^ . + . + . + . + . + "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "Saccharomyces genome database pathways" . + . + "https://repo.napdi.org/"^^ . + "^\\d+$"^^ . + "https://www.grid.ac/"^^ . + "http://vocab.deri.ie/void"^^ . + . + . + . + . + "^[0-9A-Za-z\\-.]+$"^^ . + "false"^^ . + . + "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . + . + "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . + . + . + . + "^\\d{7}$"^^ . + . + "feature"^^ . + "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . + . + . + "1046"^^ . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/PLANP_$1"^^ . + "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . + "1200"^^ . + "false"^^ . + . + "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . + "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . + . + "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . + . + . + . + . + . + "https://www.w3.org/TR/xml/"^^ . + "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . + . + . + . + . + . + "https://arxiv.org/abs/$1"^^ . + . + . + "false"^^ . + "RF00230"^^ . + . + . + . + "pubmed"^^ . + "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^ . + . "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . - . - . - "http://variationontology.org"^^ . - "^\\d{7}$"^^ . - . - . - "Ecological terms"^^ . - "^\\d{7}$"^^ . - . - . - . - "American Type Culture Collection" . - "false"^^ . - . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page"^^ . - . - "http://purl.obolibrary.org/obo/OAE_$1"^^ . - . - . - . - . - . - . - . - . - "^\\d{4}$"^^ . - . - . - "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . - "false"^^ . - "Index Fungorum" . - . - "26957"^^ . - . - . - "^ST[0-9]{6}$"^^ . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/OGI_$1"^^ . - . - . - . - . - . - . - "1009107926"^^ . - . - . - . - . - . - . + . + . + . + . + "^\\w{14}$"^^ . + "true"^^ . + . + . + . + . + . + . + . + . + "http://www.homd.org/index.php"^^ . + . + "http://www.cellresource.cn"^^ . + "http://smart.embl-heidelberg.de/"^^ . + . + . + . + . + "Ensembl Glossary" . + . + . + "Plant Transcription Factor Database" . + . + "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . + . + . + . + . + "^\\d+$"^^ . + "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^ . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . + "^\\d{7}$"^^ . + "https://github.com/ClinicalTrialOntology/CTO/"^^ . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OMO_$1"^^ . + "false"^^ . + "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . + . + "GeneTree" . + . + "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "^casent\\d+(\\-D\\d+)?$"^^ . + . + "false"^^ . + . + . + "http://www.pharmgkb.org/"^^ . + "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^ . + . + "Gene Expression Ontology"^^ . + "Ligand-Gated Ion Channel database" . + . + . + . + . + . + "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . + . + . + "Protein Affinity Reagents" . + . + . + . + "PeptideAtlas" . + . + . + "http://purl.obolibrary.org/obo/CEPH_$1"^^ . + . + . + . + . + . + "http://umbbd.ethz.ch/"^^ . + . + . + . + . + "KEGG LIGAND" . + "^([A-Z]+-)?\\d+$"^^ . + . + "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . + "false"^^ . + . + . + . + "false"^^ . + "Integrated Microbial Genomes Taxon" . + "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . + . + . + . + . + "Golm Metabolome Database GC-MS spectra" . + . + . + . + . + . + . + . + . + . + . + . + "1"^^ . + . + . + "TAIR Protein" . + "^PRJ[DEN][A-Z]\\d+$"^^ . + . + . + "0000000"^^ . + . + "OBO Metadata Ontology" . + "RepeatsDB Protein" . + . + . + . + . + . + . + "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . + "AT4G01080"^^ . + "Human Dermatological Disease Ontology" . + . + . + "https://archive.softwareheritage.org/browse/swh:$1"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "BioModels Database" . + . + . + . + "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^ . + . + . + . + . + . + "PDB Structure" . + . + . + . + . + "http://www.sasbdb.org/data/$1"^^ . + . + . + . + . + "false"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/"^^ . + "090924"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + _:N2498f1bbd088495099f68b3ec13de880 . + . + . + "false"^^ . + . + . + . + . + . + . + "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . + "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + "Michael Y Galperin" . + "https://www.metanetx.org/"^^ . + . + "MIPF0000002"^^ . + . + . + "Drug Target Ontology" . + "Benjamin M. Gyori" . + "^IS\\w+(\\-\\d)?$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://bacdive.dsmz.de/"^^ . + . . - "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . - . - . - . - "BugBase Protocol" . - . - "^\\d+$"^^ . - . - "Adverse Event Reporting Ontology" . - . - . - . - "Sorghum ontology" . - . - . - . - "true"^^ . - . - . - . - "25782"^^ . - . - . - . - . - "IM-19210-3"^^ . - . - . - . - . - "100"^^ . - . - . - . - . - "false"^^ . - "Cell line databases/resources"^^ . - . - "false"^^ . - "^[0-9]{12}$"^^ . - "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . - _:Naf946fb96f994872abf9bae43a5fa8a3 . - . - . - . - . - . - . - "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . - "A vocabulary and ontology repository for agronomy and related domains." . - . - . - . - "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . - . - . - . - "BQJCRHHNABKAKU"^^ . + "Human Metabolome Database" . + . + . + . + . + "https://www.ebi.ac.uk/imgt/hla/allele.html"^^ . + . + . + . + . + . + . + . + . + "0000171"^^ . + "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . + . + . + "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . + . + "https://e-cyanobacterium.org/models/model/$1"^^ . + . + . + . + "http://www.phosphosite.org/siteAction.do?id=$1"^^ . + . + . + . + "http://purl.obolibrary.org/obo/OARCS_$1"^^ . + "SPAR Ontologies" . + . + "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . + . + . + . + . + "http://www.genome.jp/kegg/genes.html"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . . - . - . - "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . - "https://www.vmh.life/#metabolite/$1"^^ . - . - "http://www.phenol-explorer.eu/foods/"^^ . - . - . - . - . - "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . - . - "G8944"^^ . - "00000105"^^ . - . - "false"^^ . - . - "false"^^ . - . - "Software Package Data Exchange License" . - . - . - . - . - . - . - . - "ChemIDplus" . - . - . - . - . - "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . - . - . + . + . + "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "false"^^ . + . + . + . + "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^ . + . + "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . + . + . + "https://ifaa.unifr.ch/"^^ . + . + . + . + . + . + "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^ . + . + "Bioregistry" . + "0000449"^^ . "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . - . - "Anvil" . - . - . - . - . - "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. "^^ . - "false"^^ . - "182"^^ . - . - . - "Cooperative Patent Classification" . - . - . - . - "true"^^ . - "true"^^ . - "https://www.gwascentral.org/phenotypes"^^ . - . - "SFB_COVID19_MW286762"^^ . - . - . - . - . - . - . - . - . - "0000189"^^ . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - "Animal Genome Cattle QTL" . - "false"^^ . - . - . - . - . - "https://www.inaturalist.org/taxa/$1"^^ . - . - . - . - . - . - "Fungal gross anatomy" . - "http://www.sisuproject.fi/"^^ . - . - "^TS-\\d+$"^^ . - . - "https://www.cropontology.org/rdf/CO_320:$1"^^ . - "https://pbil.univ-lyon1.fr/databases/hovergen.php"^^ . - . - . - "https://easychair.org/cfp/"^^ . - . - . - . - . - . - "GN_G03681DA"^^ . - . - . - . - . - "http://purl.org/spar/c4o/$1"^^ . - . - . - "^\\d+$"^^ . - "0000013"^^ . - "http://www.dpvweb.net/"^^ . - . - . - . - . - . - . - . - "Peroxibase" . - "Agricultural Online Access" . - . - . - . - . - . - . - . - "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "biopragmatics/bioregistry/424"^^ . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "0005067"^^ . - . - . - . - . + . + . + . + . + . + "00000268"^^ . + . + . + . + "false"^^ . + . + . + "https://github.com/evidenceontology/evidenceontology/"^^ . + . + . + . + . + . + . + "PicTar" . + . + . + . + . + "false"^^ . + . + "true"^^ . + . + "false"^^ . + . + "false"^^ . + . + "true"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "HGNC Symbol" . + . + . + . + . + . + . + . + "false"^^ . + . + . + "BCRTi001-A"^^ . + . + . + . + "https://www.doi.org/"^^ . + "false"^^ . + "https://www.eionet.europa.eu/gemet/en/themes/"^^ . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . + . + "GiardiaDB" . + . + . + . + . "false"^^ . - . - . - . - . - . - . - . - . - "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . - . - "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . - . - "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . - . - "^CHEMBL\\d+$"^^ . - . - "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - . - "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . - "FAIRSharing" . - . - "0001707"^^ . - . - "https://cropontology.org/ontology/CO_356/Vitis"^^ . - . - . - . - . - "Germplasm Resources Information Network" . - "virsi1909"^^ . - "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview"^^ . - "^DAP\\d+$"^^ . - . - "Metabolomics Workbench Study" . - . - "ProteomeXchange" . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Web Annotation Ontology" . - . - "false"^^ . - . - . - . - . - "false"^^ . - "This collection contains various brain atlases from the Allen Institute." . - . - "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . - . - . - "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . - . - . - . - . - "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - "0000127"^^ . - . - "Matt Yoder" . - . - . - . - . - . - "Experimental Factor Ontology" . - . - . - "^[0-9]{4}$"^^ . - . - "https://www.alliancegenome.org"^^ . - "10194"^^ . - . - "NMR Shift Database" . - "NeuroNames" . - . - . - . - . - . - "false"^^ . - . - "Taxonomic rank vocabulary" . - . - . - . - . - "sharesAuthorInstitutionWith"^^ . - . - . - . - "eagle-i resource ontology" . - . - . - . - . - . - . - "http://www.receptors.org/nucleardb/"^^ . - . - . - "false"^^ . - . - . - . - . - . - "0000081"^^ . - "false"^^ . - . - . - . - . + . + "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . + . + . + "http://www.genome.jp/kegg/reaction/"^^ . + . + . + "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . + "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . + "1354581"^^ . + . + "false"^^ . + . + . + . + . + . + . + "https://n2t.net/$1:$2" . + . + . + . + "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^ . + . + . + "false"^^ . + . + "Oryzabase Gene" . + . + . + . + "https://gitub.u-bordeaux.fr/erias/fideo"^^ . + . + "https://www.ncbi.nlm.nih.gov/nucest"^^ . + . + "^[0-9\\.]+$"^^ . + . + . + "Chemical Information Ontology" . + . + . + . + . + . + . + . + . + "http://www.cathdb.info"^^ . + . + . + . + . + . + . + "https://scholia.toolforge.org/"^^ . + . + "^RCB\\d+$"^^ . + . + . + . + "false"^^ . + "SBGN Bricks data and ontology" . + . + . + . + "https://github.com/"^^ . + . + . + . + . + . + . + "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + "ProDom" . + "System Science of Biological Dynamics project" . + . + . + . + "https://www.ebi.ac.uk/ipd/estdab/"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + "DragonDB Protein" . + . + . + . + . + "OSC1416"^^ . + . + "https://smpdb.ca/view/$1"^^ . + . + "Current Procedural Terminology" . + "^\\d{4}$"^^ . + . + . + . + "false"^^ . + . + "https://thebiogrid.org/interaction/$1"^^ . + . + . + _:N21a82802cf5d456583ce1c0f121b99bd . + . + . + . + "http://scipion.i2pc.es/ontology/cryoem"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + "https://www.ebi.ac.uk/gxa/"^^ . + . + . + . + . + . + . + . + "E-cyanobacterium entity" . + "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . + "^\\d+$"^^ . + . + "false"^^ . + "false"^^ . + . + . + . + . + "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "ENCSR163RYW"^^ . + "https://prefixcommons.org" . + . + "false"^^ . + . + . + . + . + "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . + . + "Open Data Commons for Spinal Cord Injury" . + . + . + . + . + "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . + . + "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . + . + . + . + . + . + . + "104674"^^ . + . + . + "000912"^^ . + . + . + . + . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . + . + . + . + "Mike Cherry" . + "http://wheat.pw.usda.gov"^^ . + . + . + . + . + . + "https://www.vmh.life/"^^ . + . + . + "https://www.omim.org/phenotypicSeriesTitles/all"^^ . + "0000001"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + "^([hm]\\_)?\\w+Pathway$"^^ . + . + . + "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^ . + . + . + "^S\\d+$"^^ . + . + "http://antibodyregistry.org/AB_$1"^^ . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . + . + . + . + "50-00-0"^^ . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . + . + "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . + . + . + "ST000900"^^ . + . + . + . + . + "Agilent Probe" . + . + . + . + . + "https://www.nlm.nih.gov/research/umls"^^ . + "DICOM Controlled Terminology" . + . + . + . + . + . + . + . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . + . + . + . + . + . + . + "false"^^ . + "GLDS-141"^^ . + . + . + "Database of Genomic Structural Variation - Variant" . + "false"^^ . + . + . + . + . + "https://cropontology.org/ontology/CO_337/Groundnut"^^ . + "^[AMCST][0-9x][0-9]$"^^ . + . + . + "ALX-210-175"^^ . + . + . + . + "false"^^ . + . + "http://sed-ml.org/"^^ . + . + "Charles Ettensohn" . + "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . + "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . + "Eukaryotic Promoter Database" . + . + . + "Rfam database of RNA families" . + . + . + . + . + "https://lotus.naturalproducts.net"^^ . + . + . + . + . + "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . + . + "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . + . + . + "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm"^^ . + . + . + . + . + . + "Description of Plant Viruses" . + . + . + . + . + . + . + . + "false"^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + "http://bigg.ucsd.edu/compartments/$1"^^ . + . + . + . + "0032571"^^ . + "O08709"^^ . + . + . + . + . + "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . + . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe"^^ . + . + "false"^^ . + . + . + "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . + . + "Glycine max Genome Database" . + "Kyoto Encyclopedia of Genes and Genomes" . + "false"^^ . + . + . + . + "https://pharmacodb.ca/cell_lines"^^ . + . + "Wikidata Property" . + . + . + "Livestock Product Trait Ontology" . + . + "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . + . + . + . + . + . + . + "http://www.informatics.jax.org/expression.shtml"^^ . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "0000048"^^ . + . + . + "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . + "false"^^ . + . + "false"^^ . + . + . . - . - "false"^^ . - . - . - . - "Frédéric Bastian" . - "false"^^ . - . - "MolBase" . - . - "https://github.com/BgeeDB/confidence-information-ontology"^^ . - . - "Alpha Tom Kodamullil" . - "AN0097748"^^ . - "https://github.com/information-artifact-ontology/IAO/"^^ . - . - "System Science of Biological Dynamics project" . - "^\\d{7}$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "https://www.gwascentral.org/studies"^^ . + . + . + . + . + . + . + . + . + "^\\d{4,}((_[asx])?_at)$"^^ . + "http://purl.obolibrary.org/obo/MMO_$1"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . + . + . + "18030"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/FIX_$1"^^ . + . + . + . + . + "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . + . + . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/EHDA_$1"^^ . + . + . + . + . + . + "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . + . + "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . + . + . + . + . + . + . + "http://www.genome.jp/dbget-bin/www_bfind?enzyme"^^ . + "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . + "MarDB" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "Plant Growth and Development Stage" . + . + . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + . + "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . + . + . + "false"^^ . + "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^ . + "^\\d+$"^^ . + . + . + . + "Resource Description Framework" . + . + "http://genolist.pasteur.fr/SubtiList/"^^ . + . + . + . + "http://scop.mrc-lmb.cam.ac.uk/scop/"^^ . + "00000000"^^ . + . + "GN_G03681DA"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Vaccine Ontology" . + "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . + . + "https://bioportal.bioontology.org/ontologies/APAONTO"^^ . + "true"^^ . + . + . + . + . + . + . + . + . + . + "https://flybase.org/reports/FBtc$1"^^ . + "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . + . + "false"^^ . + "http://purl.obolibrary.org/obo/BFO_$1"^^ . + "431472"^^ . + . + "http://arabidopsis.org/index.jsp"^^ . + . + "^\\d+$"^^ . + . + "Citlalli Mejía-Almonte" . + . + . + "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . + "^\\d+$"^^ . + . + "^\\w+\\d+$"^^ . + . + . + "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . + . + "0000984"^^ . + . + "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . + "Bacillus subtilis genome sequencing project" . + . + "ECMDB00005"^^ . + "false"^^ . + "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://mouse.brain-map.org"^^ . + "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . + "http://bioportal.bioontology.org/ontologies/LBO"^^ . + . + . + . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + . + "MetaNetX compartment" . + . . - "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . - . - . - . - "false"^^ . - . + "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . + . + . + "Gene Ontology" . + "https://www.cropontology.org/ontology/$1" . + . + . + "http://sabiork.h-its.org/"^^ . + . + . + "2004-2820"^^ . + . + "Document Components Ontology" . + "http://purl.obolibrary.org/obo/MO_$1"^^ . + . + "1a05"^^ . + . + "http://www.evocontology.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + "https://www.gleif.org/"^^ . + . + . + "http://www.aspgd.org/"^^ . + . + "4007166"^^ . + . + . + "^\\d{8}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . + . + . + . + "false"^^ . + "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . + . + . + "false"^^ . + "Geographical Entity Ontology" . + "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . + . + . + "https://toxpilot.nibiohn.go.jp/"^^ . + . + "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . + "https://reactome.org/content/detail/$1"^^ . + "http://www.pocketome.org/sfSearch.cgi?act=browseall"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.cellsignal.com/catalog/index.html"^^ . + . + . + . + "December 2019"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . + . + . + . + . + . + . + "3546"^^ . + . + . + . + "MobiDB is a database of protein disorder and mobility annotations."^^ . + . + . + "http://en.wikipedia.org/wiki/Main_Page"^^ . + "^\\d{7}$"^^ . + . + "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . + . + "ai10e-kctd13b"^^ . + . + "false"^^ . + "http://www.w3.org/ns/activitystreams"^^ . + "http://arabidopsis.org/index.jsp"^^ . + . + . + . + "http://prodom.prabi.fr/prodom/current/html/home.php"^^ . + "false"^^ . + . + "http://substrate.burnham.org/protein/annotation/$1/html"^^ . + . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . + . + "https://www.geonames.org/export/codes.html"^^ . + . + . + . + . + "^\\w+(\\.)?\\d+$"^^ . + . + "215"^^ . + "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . + . + "A web-developer centric archive of prefixes and URI prefixes" . + . + . + . + "false"^^ . + "https://www.cropontology.org/rdf/CO_331:$1"^^ . + . + . + "http://purl.obolibrary.org/obo/ECTO_$1"^^ . + . + . + "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . + . + . + . + . + . + . + "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . + "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/miriam/main/$1"^^ . + _:N4f2eda7bbb674f9cbb7e832185b2d787 . + . + . + . + "Disease Class" . + . +_:Nd12fbbeab1a9458eb8c7cca00c208a7e "Fahim Imam" . + "Human Proteome Map Protein" . + "Cell Lines in PubChem"^^ . + . + "https://omim.org/"^^ . + "false"^^ . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . + . + "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "DP00003"^^ . + . + . +_:N8a87645627bf4c81ac5bd9bdce54e71e "SEP developers via the PSI and MSI mailing lists" . + . + . + . + "https://www.expasy.org/prosite/"^^ . + "PhosphoSite Protein" . + . + "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . + . + . + . + . + "http://getentry.ddbj.nig.ac.jp"^^ . + . + "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . + . + . + . + "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . + . + . + . + "false"^^ . + "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1"^^ . + "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^ . + . + "https://www.cropontology.org/rdf/CO_334:$1"^^ . + "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . + . + . + . + "AddexBio cell line products" . + . + . + . + . + "^\\d{7}$"^^ . + "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . + . + "Allyson Lister" . + "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . + . + "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . + . + . + . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + . + . + . + "European Collection of Authenticated Cell Culture" . + "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . + "FlyBase internal citation identifiers"^^ . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + "KEGG Genes" . + "^Os\\S+t\\d{7}-\\d{2}$"^^ . + . + . + . + . + "https://cellbank.snu.ac.kr/english"^^ . + . + . + . + . + "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . + . + "^[a-z0-9\\_]+$"^^ . + . + . + . + "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . + "hsa-mir-200a"^^ . + . + . + . + . + "0001655"^^ . + "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . + . + "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . + "^PMC\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . + . + . + . + "http://lipidbank.jp/index.html"^^ . + . + . + "true"^^ . + . + . + "COG Categories" . + "http://asap.ahabs.wisc.edu/asap/home.php"^^ . + . + . + "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . + "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . + . + "https://repeatsdb.org/structure/$1"^^ . + . + . + . + . + . + . + "Gramene protein" . + "https://scicrunch.org/resolver/RRID:$1"^^ . + . + . + . + "Mathematical modeling ontology" . + . + . + "34"^^ . + . + . + . + "VegBank" . + "^\\w+(\\.\\d+)$"^^ . + "URS0000759CF4"^^ . + . + "https://odc-tbi.org/data/$1"^^ . + . + . + . + . + . + "Leigh Carmody" . + . + . + "false"^^ . + "AB_262044"^^ . + . + . + "Paragraph"^^ . + . + "SM00015"^^ . + . + . + "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^ . + "SKIP001214"^^ . + . + . + "0000140"^^ . + . + . + . + . + . + "GeneDB" . + . + "https://www.ebi.ac.uk/uniparc/"^^ . + . +_:N6ece56aaa9f040f498b35a7c9283039c "Schober Daniel" . + . + . + "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . + . + . + . + "^\\d{7}$"^^ . + "Wheat ontology" . + . + . + . + . + "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . + . + . + . + . + . + "0000208"^^ . + . + . + "Orientations of Proteins in Membranes Database" . + . + . + . + . + "^\\d+$"^^ . + "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . + . + . + . + . + . + "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . + . + . + . + . + "Metabolomics Standards Initiative Ontology" . + "Vocabulary of Interlinked Datasets" . + . + "0001017"^^ . + . + . + . + "https://www.storedb.org/?$1"^^ . + . + . + . + . + . + . + "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . + . + . + . + . + . + "1257009"^^ . + "http://www.pdb.org/"^^ . + . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + "Arabidopsis Information Portal" . + . + . + . + "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + . + "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . + . + "WormBase database of nematode biology" . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + "Nonribosomal Peptides Database" . + "NeuroMorpho" . + . + "http://cgsc.biology.yale.edu/index.php"^^ . + . + "false"^^ . + . + . + . + . + . + "^EMD-\\d{4}$"^^ . + . + "false"^^ . + . + "ProtClustDB" . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + . + "FuncBase Fly" . + . + . + "https://www.gtexportal.org"^^ . + . + . + . + . + . + . + "PED00017e001"^^ . + . + . + . + "^S\\w+(\\.)?\\w+(\\.)?$"^^ . + . + "false"^^ . + "Current Dental Terminology" . + . + "MatrixDB" . + . + . + . + . + . + . + . + . + "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . + "false"^^ . + . + "false"^^ . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "PhosphoSite Residue" . + . + . + . + . + . + . + "https://omim.org/entry/$1"^^ . + "false"^^ . + "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . + . + "T01B6.1"^^ . + "true"^^ . + "https://www.wikidata.org/"^^ . + . + . + "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . + "http://teddyontology.sourceforge.net/"^^ . + . + . + "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . + . + "false"^^ . + . + . + . + "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . + "CellBank Australia" . + "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^ . + "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/REX_$1"^^ . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^ . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + . + . + . + "^A\\d{4}$"^^ . + "https://github.com/EnvironmentOntology/environmental-exposure-ontology"^^ . + . + . + . + . + "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . + . + . + "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . + . + "^SM\\d{5}$"^^ . + . + "^D\\d{4}$"^^ . + . + . + . + "^[0-9]+$"^^ . + . + . + "^\\w+$"^^ . + "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . + . + . + . + . + "DataCite Ontology" . + . + "HIX0004394"^^ . + . + "1"^^ . + . + . + . + "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . + . + "https://topfind.clip.msl.ubc.ca"^^ . + "false"^^ . + "A registry of commonly used prefixes in the life sciences and linked data" . + . + . + "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . + . + . + "886"^^ . + . + . + . + "https://n2t.net"^^ . + "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . + . + "Dublin Core" . + . + "https://web.expasy.org/cellosaurus/CVCL_$1"^^ . + . + . + . + "^PWY\\w{2}\\-\\d{3}$"^^ . + . + "RAP-DB Transcript" . + . + . + "SWISS-MODEL Repository" . + . + "G00054MO"^^ . + "RDF Schema" . + . + . + . + . + "BugBase Protocol" . + . + "http://patft.uspto.gov/netahtml/PTO/index.html"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "Small Angle Scattering Biological Data Bank" . + "^[0-9]+:[0-9]+$"^^ . + _:Nd62103f69c70456dab389543cbcf9125 . + . + . + "0000066"^^ . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + "https://biopragmatics.github.io/debio"^^ . + . + . + . + . + . + . + "PXD000440"^^ . + . + "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . + "100"^^ . + . + . + "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . + . + "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . + . + "0000198"^^ . + "false"^^ . + . + . + "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . + . + "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . + . + "https://cropontology.org/ontology/CO_348/Brassica"^^ . + . + "SMP0000219"^^ . + "^\\d+$"^^ . + . + . + . + . + "CE28239"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . + . + . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . + . + . + "false"^^ . + . + . + "Human Plasma Membrane Receptome Families" . + . + . + "http://www.maizegdb.org/"^^ . + "G. Thomas Hayman" . + "false"^^ . + . + . + . + "P4355"^^ . + . + "http://github.com/ga4gh/data-object-service-schemas"^^ . + "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . + . + . + . + "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . + "Virtual Fly Brain" . + "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . + . + . + . + . + . + . + . + . + "Circular double stranded DNA sequences composed" . + . + . + . + . + "false"^^ . + "Merck Millipore (EMD Millipore)" . + . + "http://euhcvdb.ibcp.fr"^^ . + . + . + . + "John Graybeal" . + . + . + "false"^^ . + . + "cl3603"^^ . + . + . + . + . + . + . + . + . + . + "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . + . + . + . + . + . + "Electron Microscopy Data Bank" . + . + "^\\d+$"^^ . + "https://disprot.org/$1"^^ . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"^^ . + . + . + . + . + . + "EG10173"^^ . + . + . + . + . + . + . + . + "^[\\w\\-.]{3,}$"^^ . + . + . + "https://github.com/obophenotype/planaria-ontology"^^ . + "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . + "http://piroplasmadb.org/"^^ . + . + . + . + "http://aber-owl.net/ontology/$1/#/Browse/" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "http://dictybase.org"^^ . + . + . + . + "https://metazoa.ensembl.org/id/$1"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/$1" . + . + . + . + . + "http://www.geneontology.org/gocam"^^ . + . + "false"^^ . + . + "0000001"^^ . + . + "Rat Genome Database" . + "false"^^ . + . + "165a"^^ . + . + . + . + . + . + . + . + "Spectra Hash Code" . + . + . + . + "https://ximbio.com/reagent/$1"^^ . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + "0000055"^^ . + "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . + . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . + . + . + "SUM Breast Cancer Cell Line Knowledge Base" . + . + "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . + . + "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Melissa Haendel" . + . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/"^^ . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/Genbank/"^^ . + . + . + "^rs\\d+$"^^ . + . + . + "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . + . + . + . + . + . + . + . + . + . + . + "https://github.com/SCAI-BIO/EpilepsyOntology"^^ . + . + . + . + . + . + "^EG\\d+$"^^ . + . + . + . + . + . + . + "http://pombe.oridb.org/details.php?id=$1"^^ . + . + . + "NIF Standard Ontology: Organisms" . + . + . + . + . + . + . + . + "http://aims.fao.org/aos/agrovoc/c_$1"^^ . + . + . + . + . + . + . + . + . + "17:41223048"^^ . + . + . + . + . + . + . + . + . + . + "Costal and Marine Ecological Classification Standard" . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Metabolomics Workbench Project" . + . + "http://www.expasy.org/viralzone/"^^ . + . + "Search PRINTS-S" . + "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$"^^ . + "http://www.cellsignal.com/pathways/index.html"^^ . + "https://www.nescent.org/phenoscape/Main_Page"^^ . + "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . + . + . + "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . + "45539"^^ . + . + "0000041"^^ . + . + . + "Human Induced Pluripotent Stem Cells Initiative" . + . + "COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1"^^ . + . + "https://www.ebi.ac.uk/miriam/"^^ . + . + . + . + . + "https://www.internationalgenome.org/"^^ . + . + "https://www.ncbi.nlm.nih.gov/protein"^^ . + . + "^\\d+$"^^ . + "http://bgee.unil.ch/bgee/bgee"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + _:Nd12fbbeab1a9458eb8c7cca00c208a7e . + "false"^^ . + "Semanticscience Integrated Ontology" . + "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . + . + . + . + . + . + . + . + . + "Identifier for a journal article in the fossilworks website"^^ . + . + . + . + . + "Application ontology for entities related to insecticide resistance in mosquitos"^^ . + "0000435"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "LG Chemical Entity Detection Dataset (LGCEDe)" . + . + "0002533"^^ . + "0000630"^^ . + . + . + . + . + . + . + . + "false"^^ . + "International Standard Book Number" . + . + . + "false"^^ . + "Cell line collections"^^ . + "false"^^ . + "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . + . + . + . + . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + . + . + . + . + . + . + "https://sitem.herts.ac.uk/aeru/bpdb/index.htm"^^ . + "Carbohydrate Active EnZYmes" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^DB\\d{5}$"^^ . + . + . + . + . + "false"^^ . + . + . + . + "Computational and Informatics Resources for Glycoscience" . + . + "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Bambara groundnut ontology" . + . + . + "http://purl.obolibrary.org/obo/PLO_$1"^^ . + "http://www.cropontology.org/ontology/CO_347/Castor%20bean"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "Psychology Ontology" . + "^\\d+$"^^ . + "^(STUDY|FILE|DATASET)\\d+$"^^ . + "https://aopwiki.org/events/$1"^^ . + . + "false"^^ . + . + . + . + "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . + . + . + . + . + . + "false"^^ . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt"^^ . + . + . + . + . + "http://www-is.biotoul.fr/i"^^ . + . + . + "Metabolites in the Xenobiotics Metabolism Database."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "Apollo Structured Vocabulary" . + . + . + "vcell"^^ . + . + . + . + "https://www.rebuildingakidney.org/id/$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "http://virtualflybrain.org/reports/$1"^^ . + . + . + "http://biomodels.net/rdf/vocabulary.rdf"^^ . + . + . + . + "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . + . + . + . + . + "https://www.gwascentral.org/marker/$1"^^ . + . + "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . + . + . + "https://sitem.herts.ac.uk/aeru/ppdb/"^^ . + . + . + "https://publons.com/researcher"^^ . + . + . + . + "false"^^ . + "00000014"^^ . + . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . + "https://www.brenda-enzymes.de/ligand.php"^^ . + . + "WGS84 Geo Positioning" . + "PharmacoDB Cells" . + "grid.225360.0"^^ . + "true"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/HAO_$1"^^ . + "Vertebrate Skeletal Anatomy Ontology" . + "0000000"^^ . "https://www.nextprot.org/term/FA-$1"^^ . - . - . - "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . - . - . - . - "false"^^ . - . - "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^ . - . - "false"^^ . - "FaceBase Data Repository" . - "^\\d+$"^^ . - "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . - . - . + . + . + "Heather Piwowar" . + . + . + "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . + "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"^^ . + . + "false"^^ . + . + . + . + "Ontology of Genetic Susceptibility Factor" . + "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . + . + "An ontology of physico-chemical methods and properties."^^ . + . + "SMP0000219"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^ . + . + . + . + . + "http://merops.sanger.ac.uk/index.htm"^^ . + "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . + . + . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + "https://www.brenda-enzymes.org/"^^ . + . + . + . + "true"^^ . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/RNAO_$1"^^ . + "Astrophysics Source Code Library" . + . + . + . + "false"^^ . + . + "0002927"^^ . + . + . + . + . + . + . + "^rs[0-9]+$"^^ . + "http://purl.org/spar/bido/$1"^^ . + "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . + . + "Higher order grouping of Pfam families"^^ . + . + . + "http://www.knapsackfamily.com/KNApSAcK/"^^ . + "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^ . + . + "http://opm.phar.umich.edu/"^^ . + "^\\d{7}$"^^ . + "has canonical" . + . + . + . + "^[AEP]-\\w{4}-\\d+$"^^ . + "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . + "NIF Standard Ontology: Cell Types" . + . + . + . + . + . + . + . + "European Registry of Materials" . + . + "false"^^ . + . + "Oryzabase Reference" . + "0000550"^^ . + "false"^^ . + "Fission Yeast Experimental Conditions Ontology" . + . + . + "Pablo Porras Millán" . + "174"^^ . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF"^^ . + "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/WBbt_$1"^^ . + . + . + . + . + "https://www.storedb.org/"^^ . + "^Gm\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "http://swift.cmbi.kun.nl/swift/hssp/"^^ . + . + . + "880798137"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:N05b61d2a477846efa1178c5107d237f1 . + . + . + . + . + . + . + "TTD Target" . + . + . + . + . + . + "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . + . + . + . + . + "^rs\\d+$"^^ . + "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . + "Genomics Cohorts Knowledge Ontology" . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://ardb.cbcb.umd.edu/"^^ . + . + . + "false"^^ . + . + . + "A database-specific registry supporting curation in the Gene Ontology" . + . + "Animal Genome Pig QTL" . + . + "https://doi.org/$1"^^ . + . + "^\\d{7}$"^^ . + "Research Resource Identification" . + "https://loinc.org/"^^ . + . + "false"^^ . + . + . + . + "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . + . + "DiscoverX cell line products" . + "FlowRepository" . + "BioLegend" . + . + "0000460"^^ . + . + . + . + "Biological Expression Language" . + "MSMEG_3769"^^ . + . + . + . + . + . + "https://github.com/SpeciesFileGroup/nomen"^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "https://github.com/cido-ontology/cido"^^ . + . + . + . + . + "Cancer Cell Line Encyclopedia Cells" . + . + "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "1.1.1.1"^^ . + . + "DrugBank Drug Category" . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^ . + . + . + . + "MNEST029358"^^ . + . + . + "http://biobanknetwork.telethon.it/"^^ . + . + . + . + . + . + . + "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + . + . + "http://www.ebi.ac.uk/sbo/"^^ . + . + . + . + . + . + . + . + "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . + "Tom Gillespie" . + "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "https://horizondiscovery.com/"^^ . + . + . + "false"^^ . + "true"^^ . + . +_:Nbe65d6be29854652803f710d26fdc993 "Matthew Brush" . + "EB0170"^^ . + . + . + . + "https://www.encodeproject.org/$1"^^ . + . + . + . + "Phenoscape Publication" . + "https://www.ebi.ac.uk/ega/studies"^^ . + "false"^^ . + . + . + . + . + . + . + . + "An anatomical and developmental ontology for cephalopods"^^ . + . + . + . + . + "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . + "http://www.antirrhinum.net/"^^ . + "Allotrope Merged Ontology Suite"^^ . + "Proteomics data and process provenance" . + . + . + . + . + "https://orcid.org/$1"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DRON_$1"^^ . + . + "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . + "^BSU\\d{5}$"^^ . + "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x"^^ . + "P3DB Protein" . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://repeatsdb.org/protein/$1"^^ . + "false"^^ . + . + "0000487"^^ . + "https://github.com/insect-morphology/aism"^^ . + "Microbial Conditions Ontology" . + . + . + . + . + "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . + . + . + . + "foaf" . + "false"^^ . + . + . + "0000504"^^ . + . + "Aclame" . + "3403"^^ . + . + . + . + "^LSM-\\d+$"^^ . + "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . + . + . + "false"^^ . + . + "Cell Line Ontology [derivative]" . + . + "4D Nucleome Data Portal Experiment Replicate" . + "^\\d{7}$"^^ . + "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . + . + . + "false"^^ . + "https://swissmodel.expasy.org"^^ . + "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "X58356"^^ . + . + "http://www.proteinmodelportal.org/"^^ . + "https://smpdb.ca/"^^ . + . + . + . + . + . + . + . + . + "WBRNAi00086878"^^ . + "BindingDB" . + . + . + . + . + "^\\d{5}$"^^ . + "Vertebrate trait ontology" . + . + "^\\d{7}$"^^ . + . + . + "0278"^^ . + . + . + . + . + . + . + "^\\d{7,8}$"^^ . + . + . + . + "Thermo Fisher Scientific" . + . + . + . + "http://matrixdb.univ-lyon1.fr/"^^ . + "^[0-9]+$"^^ . + "https://www.storedb.org/"^^ . + "AntWeb ID" . + "http://purl.obolibrary.org/obo/ERO_$1"^^ . + . + "Getty Thesaurus of Geographic Names" . + . + . + . + "9781584885658"^^ . + . + . + . + . + . + . + . + "^((HGNC|hgnc):)?\\d{1,5}$"^^ . + . + "http://purl.org/spar/pwo/$1"^^ . + . + "https://datanator.info/reaction/$1"^^ . + . + "^[A-Za-z0-9-]+$"^^ . + "KEGG Drug Group" . + . + . + "https://glycopost.glycosmos.org/entry/$1"^^ . + . + . + . + . + . + . + "Sebastian Koehler" . + "http://nematode.lab.nig.ac.jp/"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "Canadian Drug Product Database" . + . + . + "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "https://icd.codes/icd10cm/$1"^^ . + . + . + . + . + . + "https://www.lji.org/"^^ . + "https://github.com/biobanking/biobanking"^^ . + "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters"^^ . + . + "https://www.disprot.org/$1"^^ . + . + "AHR"^^ . + . + . + . + . + "https://github.com/obophenotype/zebrafish-phenotype-ontology"^^ . + . + . + "http://ccdb.ucsd.edu/CCDBWebSite/sao.html"^^ . + . + "NeuroLex Dysfunction" . + . + . + . + . + . + . + . + "https://dip.doe-mbi.ucla.edu/"^^ . + . + "BacMap Biography" . + . + . + . + . + . + . + . + . + . + . + "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . + . + . + . + "GLIDA GPCR" . + . + . + . + "https://www.webelements.com/"^^ . + . + . + . + . + . + . + "DUO is an ontology which represent data use conditions."^^ . + . + . + "https://purl.obolibrary.org/obo/ohd/home"^^ . + . + . + _:Na1a78a14bd9e496caff9519402ec99ed . + "NMR-instrument specific component of metabolomics investigations" . + "The upper level ontology upon which OBO Foundry ontologies are built."^^ . + . + . + "http://purl.obolibrary.org/obo/ARO_$1"^^ . + . + . + "false"^^ . + . + . + . + . + "Distributed Archives for Neurophysiology Data Integration" . + . + . + . + "https://www.ncbi.nlm.nih.gov/genome"^^ . + . + "0007114"^^ . + "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . + "RA01.0"^^ . + . + "None"^^ . + "https://www.wikidata.org"^^ . + . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/RS_$1"^^ . + "https://www.hivreagentprogram.org/Home.aspx"^^ . + "WikiPathways" . + "Dictyostelium discoideum anatomy" . + . + . + . + . + . + . + . + "^HMDB\\d+$"^^ . + . + . + "https://www.cropontology.org/rdf/CO_347:$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . + . + "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^ . + "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . + "http://www.gpcrdb.org/"^^ . + . + . + . + . + . + . + "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"^^ . + . + . + . + . + . + . + "The International Standard Book Number (ISBN) is for identifying printed books."^^ . + . + . + "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . + . + "false"^^ . + . + "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . + . + "http://drugcentral.org/drugcard/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . +_:Nb300b24511ca48d8a5fffa649e9e6c22 "Jonathan Bard" . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://github.com/ga4gh/data-object-service-schemas"^^ . + "^\\d{7}$"^^ . + . + . + "P0DP23"^^ . + . + "Affymetrix Probeset" . + "^\\d{7}$"^^ . + . + "NA06985"^^ . + . + "MGnify Project" . + "false"^^ . + . + . + "false"^^ . + . + "https://registry.identifiers.org/registry/$1"^^ . + "false"^^ . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . + . + "false"^^ . + "https://github.com/OHPI/ohpi"^^ . + . + . + . + "IPR016380"^^ . + . + . + . + . + "http://www.diseasesdatabase.com/"^^ . + . + "bsu:BSU01340"^^ . + . + . + . + . + "SIDM01262"^^ . + "false"^^ . + "false"^^ . + . + . + . + "http://www.arachnoserver.org/"^^ . + . + "The set of prefixes used in the Cellosaurus resource" . + "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . + . + "https://doulix.com"^^ . + . + . + . + . + "false"^^ . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . + . + . + "Feature Annotation Location Description Ontology " . + . + . + . + "https://datalab.rwth-aachen.de/MINDER"^^ . + . + . + . + . + "Georgeta Bordea" . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . + . + . + . + "A Systematic Annotation Package for Community Analysis of Genomes" . + . + . + "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . + . + . + . + . + . + . + . + . + . + "http://bactibase.hammamilab.org/$1"^^ . + "^\\d+$"^^ . + . + . + "https://repo.napdi.org/study/$1"^^ . + . + "0000519"^^ . + . + . + . + "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . + "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + . + . + "K00973"^^ . + . + . + . + . + . + . + . + _:N4919606696d74b52a536951cba63e0df . + "^B\\d{5}$"^^ . + "^\\d+$"^^ . + "C138986"^^ . + "^ENSGT\\d+$"^^ . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . + . + . + . + . + "https://www.brainspan.org/"^^ . + "http://crispr.i2bc.paris-saclay.fr/"^^ . + . + "MetaNetX reaction" . + . + . + "Cell Image Library" . + . + . + . + "IM-19210-3"^^ . + "false"^^ . + . + "https://registry.identifiers.org/registry?query=\"MIR:$1\""^^ . + "http://www.t3db.org/"^^ . + . + "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . + . + . + . + . + . + . + . + _:N0a566dc9a31d4284b688fc06eb0598c6 . + "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . + . + . + . + . + . + . + . + "12dgr161"^^ . + . + "Polygenic Score Catalog" . + . + . + . + "MultiCellDS Digital Cell Line" . + . + "false"^^ . + . + . + "Ontology for genetic interval" . + . + "International Standard Serial Number" . + . + . + . + . + . + . + . + . + . + "^\\d{6}$"^^ . + "http://aber-owl.net" . + . + . + . + . + . + . + . + "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . + . "http://purl.obolibrary.org/obo/CIDO_$1"^^ . - . - . - . - . - "false"^^ . - "Ontology of Organizational Structures of Trauma centers and Trauma systems" . - "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . - "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . - . - . - . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - . - . - . - . - . - . - . - "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . - . - "Data Object Service" . - "ClinVar Submission" . - . - . - "false"^^ . - . - . - "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . - . - "has resolver formatter" . - "http://www.wikigenes.org/"^^ . - . - . - _:Ndcdd7944f57c41f490bd5019a483aef6 . - "https://www.arraymap.org"^^ . - "Meng LIU" . - . - "https://github.com/aszool/oarcs"^^ . - . - . - . - "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . - . - "Cell line databases/resources"^^ . - "http://www.uniprot.org"^^ . - . - "1-18"^^ . - "https://github.com/OpenLHS/LABO"^^ . - . - . - "004435"^^ . - . - . - . - . - . - . - "Nucleic Acids Phylogenetic Profiling" . - "http://bactibase.hammamilab.org/$1"^^ . - "Dictyostelium discoideum anatomy" . - _:N098fd1bf832348feb0b5bcdc5b7db793 . - "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^ . - "2200950"^^ . - "false"^^ . - "false"^^ . - . - . - "SIGNOR-252737"^^ . - . - . - . - "^[0-9]+$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://biosimulations.org/projects/$1"^^ . - "Systems Biology Ontology" . - . - . - "http://jcggdb.jp/idb/jcggdb/$1"^^ . - . - "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . - . - . - "Ligand-Gated Ion Channel database" . - "http://purl.obolibrary.org/obo/OBI_$1"^^ . - . - "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . - "https://www.ensembl.org/id/$1"^^ . - . - . - "false"^^ . - . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - "EGAD00000000001"^^ . - . - "TarBase" . - . - . - "UniProt Variants" . - "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . - "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . - . - . - . - . - "false"^^ . - . - "https://github.com/AnimalGenome/vertebrate-trait-ontology"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://www.proteomexchange.org/"^^ . - . - . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/gv/mhc/"^^ . - "EcoLexicon" . - . - . - . - . - "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . - . - . - . - "GeneCards" . - . - . - . - . - . - . - . - . - . + . + "PA447218"^^ . + . + . + "https://www.proteomicsdb.org/#peptideSearch"^^ . + . + . + "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . + . + "4900"^^ . + . + . + . + "Minimum Anformation About a Phylogenetic Analysis Ontology" . + "PR00001"^^ . + . + . + . + . + . + "JRBC Cell Bank" . + . + "false"^^ . + . + . + "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . + "http://omia.angis.org.au/$1/"^^ . + . + . + . + . + . + "090701"^^ . + . + . + . + . + . + . + . + . + . + . + . + "4238"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . + . + "https://hpscreg.eu/"^^ . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/CTENO_$1"^^ . + "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . + "^ECMDB\\d+$"^^ . + "ACC-1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . + "http://rebase.neb.com/rebase/enz/$1.html"^^ . + . + . + . + . + . + . + . + "Glyma0021s00410"^^ . + . + . + "0000210"^^ . + "http://purl.obolibrary.org/obo/MOP_$1"^^ . + . + "https://aopwiki.org/"^^ . + . + . + . + "https://portal.bluebrain.epfl.ch"^^ . + . + . + "Nathan Edwards" . + . + . + . + "^\\w+$"^^ . + "http://pax-db.org/#!protein/$1"^^ . + "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . + "http://compbio.soe.ucsc.edu/yeast_introns.html"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Terminologia Histologica" . + "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . + "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . + . + . + . . - "0000171"^^ . - . - "^\\d+$"^^ . - . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . - "Blue Brain Project Topological sampling Knowledge Graph" . - "Colorectal Cancer Atlas" . - "false"^^ . - . - "December 2019"^^ . - "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . - . - . - "http://ccdb.ucsd.edu/CCDBWebSite/sao.html"^^ . -_:Nce7fed9968da4026a9656318875caf42 "Maria Herrero" . - . - "Alex Bateman" . - . - . - . - "^\\d{7}$"^^ . - . - . - "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . - . - . - "http://bigg.ucsd.edu/compartments/"^^ . - "false"^^ . - . - "http://www.human-phenotype-ontology.org/"^^ . - . - . - . - . - "^[a-z0-9\\_]+$"^^ . - "https://www.reactome.org/"^^ . - "https://registry.identifiers.org/registry"^^ . - . - "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . - "false"^^ . - . - . - "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . - . - "Prefix Commons" . - . - . - "MultiCellDS Digital snapshot" . - "http://www.disease-ontology.org"^^ . - . - . - "Drug Target Ontology" . - . - . - "https://www.w3.org/TR/rdf-schema/"^^ . - . - . - . - . - . - . - "https://tripod.nih.gov/bioplanet/"^^ . - "^PKDB[0-9]{5}$"^^ . - . - "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . - "https://biosimulators.org/"^^ . - "1cukA01"^^ . - . - "Reference"^^ . - . - "http://www.sequenceontology.org/"^^ . - "3771992"^^ . - "HGNC gene family" . - . - "http://www.antirrhinum.net/"^^ . - "false"^^ . - . - . - . -_:N6286b2e88eb043c48cb2a7df2ec973b8 "Thorsten Heinrich" . - . - "http://www.nlm.nih.gov/medlineplus/"^^ . - . - . - . - . - . - . - . - "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . - . - "0000001"^^ . - . - "^HIP\\d{9}(\\.\\d+)?$"^^ . - . - "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "PDB Structure" . - "ThermoFisher is a life sciences supply vendor."^^ . - . - "O08709"^^ . - . - . - "Ximbio" . - "KEGG Module" . - . - . - . - . - . - . - . - . - . - "doi"^^ . - . - "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . - "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . - . - "false"^^ . - "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^ . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . - "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . - "Jackson Laboratories Strain" . - "PAp00000009"^^ . - "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^ . - "International repository of Adverse Outcome Pathways."^^ . - . - . - . + . + "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . + . + . + . + . + . + . + . + . + "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . + . + . + "https://w3id.org"^^ . + "false"^^ . + "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . + "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . + "Publons Researcher" . + . + "^(doi\\:)?\\d{2}\\.\\d{4}.*$"^^ . + "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . + "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . + "Matt Yoder" . + . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx"^^ . + "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . + . + . + . + . + . + . + "true"^^ . + . + "false"^^ . + "true"^^ . + . + . + . + "^\\w+$"^^ . + "https://winter.group.shef.ac.uk/molbase/"^^ . + "John Beverly" . + "https://zenodo.org/record/$1"^^ . + . + "http://neurovault.org"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "BioCyc collection of metabolic pathway databases" . + . + "false"^^ . + . + . + . + . + . + . + . + . + "JCOIN" . + . + . + . + "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . + . + . + . + . + "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . + . + . + "The bioRxiv is a preprint server for biology"^^ . + . + . + "Jennifer Smith" . + "false"^^ . + . + . + . . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/ohmi-ontology/ohmi"^^ . - . - "runBioSimulations" . - . - . - . - "false"^^ . - . - "https://gnome.glyomics.org/"^^ . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^ . - "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . - "http://www.pharmgkb.org/pathway/$1"^^ . -_:N5b5cb92149e84d5181fc7daa005ced76 "Jonathan Bard" . - "The SEED;" . - . - . - . - . - . - . + . + . + . + . + . + "false"^^ . + "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . + "^(cl|tum)\\d+$"^^ . + "false"^^ . + . + . + . + "MarFun" . + . + . + "PF11779"^^ . + "Fission Yeast Phenotype Ontology" . + . + . + . + . + . + . + . + "https://www.fisheries.noaa.gov/species/$1"^^ . + "^\\d{7}$"^^ . + . + "00000180"^^ . + . + . + . + "Sequence Read Archive" . + . + "MimoDB" . + . + "https://www.ebisc.org"^^ . + . + "Global Proteome Machine Database" . + "Expression"^^ . + "Gemina Symptom Ontology" . + . + . + . + "true"^^ . + "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . + . + "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . + "https://www.hdruk.ac.uk"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . + . + . + . + . + "true"^^ . + "P00266"^^ . + . + "http://arabidopsis.info/"^^ . + . + . + "false"^^ . + . + . + "HsapDO:0000004"^^ . + . + . + . + . + . + . + "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . + "http://purl.org/spar/scoro/$1"^^ . + "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . + . + . + "https://www.cropontology.org" . + "0000001"^^ . + . + . + . + . + "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . + . + . + . + . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . + . + . + . + . + . + . + "Open Tree of Life" . + . + . + . + . + "40565"^^ . + . +_:Nce37ebacd38849c58605cc273a55adc9 "Pierre Sprumont" . + "63"^^ . + . + . + . + . + . + . + . + . + . + "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . + . + . + . + "Cell line databases/resources"^^ . + . + . + "http://amigo.geneontology.org/amigo/term/GO:$1"^^ . + . + "https://bio.tools/$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "00000443"^^ . + . + "Ontology of units of Measure" . + . + "http://www.sparontologies.net/ontologies/deo"^^ . + . + "false"^^ . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . + . + . + . + . + . + . + . + . + . + . + "5359"^^ . + . + . + . + . + . + . + . + . + . + "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . + "BRAF"^^ . + . + . + "FlyBrain Neuron Database" . + . + . + . + . + . + . + "false"^^ . + . + . + . + "https://w3c-ccg.github.io/did-spec/"^^ . + "M94112"^^ . + . + . + . + . + "false"^^ . + . + "57-27-2"^^ . + "^e\\d+$"^^ . + . + "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^ . + "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . + . + . + . + . + . + "https://bioregistry.io/registry/$1" . + . + . + . + . + . + "https://www.ebi.ac.uk/chembldb"^^ . + . + . + . + "2842"^^ . + . + . + . + "https://publons.com/researcher/$1"^^ . + . + . + "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . + . + "^\\d{7}$"^^ . + "http://id.nlm.nih.gov/mesh/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://matrixdb.univ-lyon1.fr/"^^ . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd"^^ . + "https://www.genedb.org/"^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/HSO_$1"^^ . + . + . + . + . + "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"^^ . + "false"^^ . + "Protein Model Portal" . + "https://worldwide.espacenet.com/classification"^^ . + "0000001"^^ . + "Biolink Model Registry" . + "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . + "false"^^ . + . + . + . + . + . + "https://webbook.nist.gov/chemistry/"^^ . + "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . + . + . + . + . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . + . + . + "https://ligandbook.org/package/$1"^^ . + . + . + . + . + . + . + . + "http://sideeffects.embl.de/se/$1"^^ . + "https://github.com/calipho-sib/controlled-vocabulary"^^ . + . + "Ontology of RNA Sequencing" . + . + . + "https://pdc.cancer.gov/pdc"^^ . + "http://bgee.unil.ch/bgee/bgee"^^ . + . + . + "MTBLS1"^^ . + "false"^^ . + "EGAD00000000001"^^ . + "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + "false"^^ . + . + . + . + "https://www.metanetx.org/"^^ . + "false"^^ . + . + . + . + . + . + . + "Ontology of Microbial Phenotypes" . + . + "TreeBASE" . + "A0118748"^^ . + . . - . - . - "casent0106247"^^ . - "TVAG_386080"^^ . - . - . - . - . - . - . - "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx"^^ . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . + "0000205"^^ . + . + "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . + "Cellosaurus Publication" . + "https://www.metanetx.org/chem_info/$1"^^ . + . + . + . + "http://urgi.versailles.inra.fr/Genefarm/"^^ . + "00023232"^^ . + . + . + . + "58788"^^ . + . + "https://www.w3.org/2003/01/geo/wgs84_pos"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "Coronavirus Infectious Disease Ontology" . + "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . + "^ACH-\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.metabolome-express.org/"^^ . + . + . + . + . + . + . + "An ontology to capture confidence information about annotations."^^ . + . + "false"^^ . + . + . + . + "mKIAA4200"^^ . + . + "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . + "http://purl.obolibrary.org/obo/MCO_$1"^^ . + "Database of Complete Genome Homologous Genes Families" . + "^CCDS\\d+\\.\\d+$"^^ . + . + "false"^^ . + . + . + "https://glytoucan.org"^^ . + "NASA GeneLab" . + "The RNA Modification Database" . + . + . + . + . + . + "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . + "^(R)?PXD\\d{6}$"^^ . + . + . + "^FR\\-FCM\\-\\w{4}$"^^ . + . + "PWY3O-214"^^ . + . + . + . + "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . + "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . + . + "false"^^ . + "false"^^ . + . + . + . + "chebi" . + . + . + "GlycoPOST" . + . + "^EDI_\\d+$"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://aopwiki.org/aops/$1"^^ . + "SED-ML data format" . + . + . + . + "true"^^ . + "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . + . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "Cell line collections"^^ . + "false"^^ . + "Drosophila gross anatomy" . "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - . - . - . - . - . - . - "Analyses of microbiome data within MGnify"^^ . - "http://www.pseudogene.org"^^ . - . - . - . - "false"^^ . - . - "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . - . - . - . - . - . - "false"^^ . - "^casent\\d+(\\-D\\d+)?$"^^ . - "Resource Description Framework" . - . - "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . - . - . - . - . - "Georgeta Bordea" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . + "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . + "false"^^ . + "http://rebase.neb.com/rebase/"^^ . + "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . + . + "^\\d{7}$"^^ . + "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . + . + . + . + . + . + . + . + . + . + "PED00037"^^ . + "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . + "false"^^ . + . + . + . + "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . + . + "Schema for the export of the Bioregistry as RDF"^^ . + "https://horizondiscovery.com/en/search?searchterm=$1"^^ . + . + . + . + "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . + . + . + . + . + . + "47419"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + "https://github.com/infectious-disease-ontology-extensions/ido-covid-19"^^ . + . + . + . + "^T[A-Z]\\d{7}$"^^ . + "false"^^ . + . + . + . + . + . + . + "https://proteinensemble.org/"^^ . + "http://neuinfo.org/"^^ . + . + "true"^^ . + . + . + . + "90801"^^ . + "Selventa legacy disease namespace used with the Biological Expression Language"^^ . + . + "STOREDB at University of Cambridge" . + "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^ . + . + . + . + . + . + . + . + "^G(PL|SM|SE|DS)\\d+$"^^ . + "false"^^ . + . + . + "true"^^ . + "https://www.ncbi.nlm.nih.gov/projects/RefSeq/"^^ . + . + . + "false"^^ . + . + "https://github.com/semanticchemistry/semanticchemistry" . + . + . + "10087"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "true"^^ . + . + . + "https://scicrunch.org/browse/resourcedashboard"^^ . + . + . + "https://github.com/obophenotype/porifera-ontology"^^ . + "^\\w+$"^^ . + . + . + . + . + "false"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "WP732"^^ . + "RoleInTime"^^ . + "false"^^ . + . + . + . + . + . + "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . + . + . + . + . + . + . + "Laboratory of Systems Pharmacology Compound" . + . + . + "false"^^ . + . + . + . + "A person" . + . + . + . + . + "false"^^ . + . + "https://www.uniprot.org/database/$1"^^ . + "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . + "Histopathology Ontology" . + . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . + . + . + "0000400"^^ . + . + "50885"^^ . + "A database for Triticeae and Avena references."^^ . + . + . + "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . + . + "^\\d+$"^^ . + . + . + "Applied Biological Materials cell line products" . + . + . + . + . + . + . + "false"^^ . + . + "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . + . + . + . + . + . + . + "EMD-1001"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "Lindsay Cowell" . + "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . + . + . + . + "https://github.com/OpenLHS/PDRO"^^ . + . + . + . + "^PF\\d{5}$"^^ . + . + "^PAp[0-9]{8}$"^^ . + . + . + "https://omabrowser.org/oma/hog/HOG:$1"^^ . + . + . + . + . + . + . + . + "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"^^ . + . + "Radiomics Ontology" . + "true"^^ . + . + . + "http://www.ubio.org"^^ . + . + "0000001"^^ . + . + "false"^^ . + . + . + . + . + . + . + "Ontology for the Anatomy of the Insect SkeletoMuscular system" . + . + . + . + "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . + . + "http://ecogene.org/"^^ . + . + . + . + . + . + . + . + . + . + "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . + "https://github.com/information-artifact-ontology/ontology-metadata"^^ . + . + . + . + . + "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . + . + . + "AspGD Protein" . + . + . + . + . + . + . + . + "Eukaryotic Linear Motif Resource" . + . + . + . + . + . + . + "EcoCyc" . + . + . + . + "AAA35559"^^ . + . + . + . + . + "0045310"^^ . + . + . + . + "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . + . + . + "https://comptox.epa.gov/dashboard"^^ . + "CY077097"^^ . + "http://lisanwanglab.org/DASHR/entry/$1"^^ . + . + "13GS"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/"^^ . + . + "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . + "EAWAG Biocatalysis/Biodegradation Database" . + "false"^^ . + . + . + . + . + "Evidence ontology" . + . + . + "^M\\d+$"^^ . + . + . + "4447"^^ . + "Gerhard Mayer" . + "UCSC Genome Browser" . + . + "true"^^ . + . + . + "https://bioregistry.io/resolve/github/pull/$1"^^ . + "https://gsso.research.cchmc.org/"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + "ls-c35719-120"^^ . + "C. elegans ORFeome cloning project" . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "BQJCRHHNABKAKU"^^ . + "http://mycobrowser.epfl.ch/smegmalist.html"^^ . + "CHEBI" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "STOREDB at University of Cambridge" . + . + . + "Database of Genotypes and Phenotypes" . + . + . + "Cross-linker reagents ontology" . + . + . + "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . + "https://www.discoverx.com/products-applications/cell-lines"^^ . + . + . + "ForwardStrandPosition"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "https://gdc.cancer.gov"^^ . + . + . + "OMA Protein" . + "false"^^ . + . + . + "NCBI Genome" . + . + "^[a-z]+(\\..*?)?$"^^ . + "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . + . + "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . + . + . + . + . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + . + . + . + . + . + "KEGG Metagenome" . + "A-GEOD-50"^^ . + . + . + . + _:N9e11602ad5f546a9baecf7f5cafd8a92 . + . + . + . + "false"^^ . + . + . + . + . + . . - . + . + . + "http://www.disease-ontology.org"^^ . + . + "false"^^ . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + "^[0-9]+$"^^ . + . + "The Drug Ontology" . + . + . + . + . + . + "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/FYPO_$1"^^ . + "https://www.nextprot.org/db/entry/$1"^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . + . + "^\\d+$"^^ . + "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . + . + . + . + "https://www.cellbankaustralia.com/$1.html"^^ . + "false"^^ . + . + "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . + "http://pax-db.org/"^^ . + "Vocabulary used in the RDF representation of SBML models."^^ . + . + . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + . + "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . + "^\\d+$"^^ . + . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . + . + "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . + . + "000009"^^ . + . + . + "http://scicrunch.org/resolver/SCR_$1"^^ . + . + . + . + . + . + . + . + . + "Golm Metabolome Database Reference Substance" . + . + "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . + . + "https://www.ebi.ac.uk/pdbe/emdb"^^ . + . + . + . + . + "3G6A5W338E"^^ . + . + . + "false"^^ . + "James C. Hu" . + . + . + . + . + "https://github.com/SDG-InterfaceOntology/sdgio"^^ . + . + "http://flybase.org/"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "National Bibliography Number" . + "171"^^ . + "G protein-coupled receptor database" . + . + "http://purl.obolibrary.org/obo/FOBI_$1"^^ . + . + . + . + "00000105"^^ . + . + . + "Probability Distribution Ontology" . + . + . + "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "HBG284870"^^ . + . + . + "https://clinicaltrials.gov/"^^ . + . + "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . + . + . + . + . + . + . + "PK-DB" . + . + . + . + . + . + "http://bigg.ucsd.edu/universal/metabolites"^^ . + "https://www.w3.org/2004/02/skos/"^^ . + . + "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . + . + "Chemical Entities of Biological Interest" . + . + . + . + . + . + . + . + . + "Martin Ramirez" . + . + "http://neurovault.org"^^ . + "COVID-19 Surveillance Ontology" . + . + "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . + . + "^[a-z0-9-]+$"^^ . + . + . + . + . + "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^ . + . + "false"^^ . + . + "http://en.wikipedia.org/wiki/$1"^^ . + . + "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . + . + . + . + . + . + . + . + . + "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . + "4685"^^ . + . + . + "false"^^ . + . + "https://oborel.github.io/"^^ . + . + . + "^\\d+$"^^ . + "UniProt Resource" . + "TarBase" . + . + "Leszek Vincent" . + "Database of homology-derived secondary structure of proteins" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "0000006"^^ . + "Lycalopex_vetulus"^^ . + . + . + "https://github.com/rsc-ontologies/rxno"^^ . + . + . + . + . + . + . + . + . + "MIMIC III Database" . + . + "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . + . + . + "Represent chemical entities having particular CHEBI roles"^^ . + "GitHub is an online host of Git source code repositories."^^ . + . + . + "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . + "Horizon Discovery cell line collection" . + . + . + . + "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . + . + . + . + . + "http://csbl.bmb.uga.edu/DOOR/operon.php"^^ . + . + . + "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . + . + . + . + "https://vcell.org/biomodel-$1"^^ . + "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . + . + "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . + . + . + . + . + . + . + . + "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . + "http://oryzatagline.cirad.fr/"^^ . + . + "ChemSpider" . + "ABL1"^^ . + . + . + "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . + . + . + . + . + . + "https://flybase.org"^^ . + "WormBase RNAi" . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . + "false"^^ . + "The Bioinorganic Motif Database" . + . + "false"^^ . + . + . + . + . + . + . + "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . + "Colorectal Cancer Atlas" . + . + . + . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^ . + "491187"^^ . + "0000485"^^ . + . + . + . + . + . + "0000057"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . + . + . + . + . + . + . + "^PR\\d{5}$"^^ . + "YeTFasCo" . + . + . + . + "https://arxiv.org/"^^ . + "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . + "false"^^ . + "https://www.grid.ac/institutes/$1"^^ . + "http://www.wikigenes.org/"^^ . + . + "false"^^ . + . + . + . + "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . + . + . + . + "https://genome.ucsc.edu/"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "Glycan Naming and Subsumption Ontology" . + . + . + . + "false"^^ . + . + . + "Workflow"^^ . + "^\\d+$"^^ . + . + . + "https://download.nextprot.org/pub/current_release/controlled_vocabularies/"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/"^^ . + "false"^^ . + . + . + . + . + . + . + "KEGG Orthology" . + "https://www.datanator.info/metabolite/$1"^^ . + . + . + . + "5fce9b7300001250"^^ . + . + . + "http://purl.obolibrary.org/obo/PROCO_$1"^^ . + . + "Elizabeth Arnaud" . + "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . + . + "Plant Stress Ontology" . + . + . + . + "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . + . + "61467"^^ . + . + . + . + . + . + "Beet Ontology ontology" . + . + . + "AT1G01010"^^ . + . + . + "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . + . + "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . + "Dublin Core Metadata Vocabulary" . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "https://fairsharing.org/" . + "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . + . + "Rat Genome Database strain" . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "4DN" . + . + "provides for" . + . + . + "http://purl.obolibrary.org/obo/CIO_$1"^^ . + "false"^^ . + . + "https://www.genenames.org/"^^ . + . + . + . + "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . + . + "^XB\\-\\w+\\-\\d+$"^^ . + . + . + . + . + "Akt_PKB"^^ . + . + . + . + . + "DragonDB Allele" . + . + "10020.2"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "811"^^ . + . + . + . + . + "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries."^^ . + . + . + . + . + . + "Curation of Neurodegeneration Supporting Ontology" . + . + . + . + . + . + . + . + . + . + . + "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . + "European Searchable Tumour Line Database" . + . + . + "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . + . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + . + "false"^^ . + "1h68"^^ . + . + . + "false"^^ . + "^\\d{4,}$"^^ . + "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . + . + . + . + . + . + "true"^^ . + . + . + "false"^^ . + . + . + "https://www.auckland.ac.nz/en.html"^^ . + . + . + "https://gudmap.org/id/$1"^^ . + . + . + . + . + . + . + "GO Evidence Code" . + . + . + . + . + . + "CUT"^^ . + . + . + . + . + "false"^^ . + . + . + "https://bams1.org"^^ . + . + "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . + . + "false"^^ . + "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . + . + "csv"^^ . + . + . + "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + . + "HWUPKR0MPOU8FGXBT394"^^ . + . + . + . + . + . + . + . + . + . + "BBA0001"^^ . + . + "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . + . + . + . + . + . + . + "false"^^ . + "true"^^ . + . + "^CPX-[0-9]+$"^^ . + "447860"^^ . + "^\\d{8}$"^^ . + . + . + "false"^^ . + . + . + . + . + "SABIO-RK Compound" . + "Cotton ontology" . + "1"^^ . + . + . + "false"^^ . + "SBML RDF Vocabulary" . + "https://bioregistry.io/metaregistry/scholia/$1"^^ . + "https://www.worldwildlife.org/ecoregions/$1"^^ . + "^[a-z_A-Z0-9]+$"^^ . + . + "0000411"^^ . + "true"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "0101963"^^ . + . + . + . + . + . + . + . + "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . + "https://repeatsdb.org/"^^ . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . + . + . + . + . + . + . + "re3data" . + . + . + "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . + . + . + "https://www.ncbi.nlm.nih.gov/gtr/"^^ . + . + "Observational Medical Outcomes Partnership" . + . + . + . + "^\\w+$"^^ . + . + . + "March 2017 version "^^ . + . + "^[\\w\\-:,]{3,64}$"^^ . + "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . + "https://www.google.com/patents/$1"^^ . + . + "Sweet Potato ontology" . + "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . + . + "false"^^ . + "International repository of Adverse Outcome Pathways."^^ . + "true"^^ . + . + . + "Banco de Celulas do Rio de Janeiro" . + . + "https://reporter.nih.gov/project-details/$1"^^ . "Long Term Ecological Research Controlled Vocabulary" . - "13"^^ . - . - "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . - "^spike\\d{5}$"^^ . - . - . - . - "http://agricola.nal.usda.gov/"^^ . - "MULT_4_VAR1_bovine"^^ . - . - . - _:Ncd6763d843b14d0896f4a430c8c2d0e9 . - . - "https://panoramaweb.org"^^ . - . - . - . - . - "0007807"^^ . - "false"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - "D0001"^^ . - . - . - . - . - "Emotion Ontology" . - . - "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^ . - . - . - . - . - . - "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^ . - . - . - . - . - "^[AMCST][0-9x][0-9]$"^^ . - . - . - "FBgn0011293"^^ . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . - . - "https://cellbank.snu.ac.kr/english"^^ . - "00001234"^^ . - . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . - "false"^^ . - . - . - . - . - "The Bioregistry's meta-registry"^^ . - "http://cellimagelibrary.org/"^^ . - . - . - . - . - "Jonathan Karr" . - . - "http://lincsportal.ccs.miami.edu/cells/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . - . - . - "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . - . - . - . - "false"^^ . - "NeuroMorpho" . - . - "http://www.gramene.org/"^^ . - . - . - . - "^[0-9]+$"^^ . - "false"^^ . - "https://www.metabolome-express.org/"^^ . - . - "U49845"^^ . - . - "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . - . - . - . - . - . - . - "General Standard for Food Additives Online Database" . + "NOAA Fisheries Species Directory" . + . + "0000003"^^ . + "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . + . + . + "false"^^ . + . + "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . + . + "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . + "https://cropontology.org/ontology/CO_336/Soybean"^^ . + . + . + "MIRIAM Registry resource" . + . + . + _:Nc01a0256846c4e64b983e54db9f7673f . + . + . + . + . + . + . + "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ECAO_$1"^^ . + . + . + "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^ . + . + . + . + "https://github.com/PHI-base/phipo"^^ . + . + . + . + . + "https://cropontology.org/ontology/CO_358/Cotton"^^ . + . + "1948"^^ . + "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . + . + . + . + . + . + "VCell Published Models" . + . + . + "Yongqunh He" . + . + . + "http://zfin.org"^^ . + . + "Publishing Roles Ontology" . + . + . + . + . + . + . + . + . + . + . + "068078"^^ . + . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + "https://www.w3.org/TR/owl-features/"^^ . + . + . + . + . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . + . + . + . + . + . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . + . + "KEGG Reaction Class" . + . + "false"^^ . + . + "004435"^^ . + . + . + . + . + "Protein Structural Change Database" . + . + "false"^^ . + . + "Bgee gene" . + . + . + . + "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . + . + . + "RL3R1_HUMAN"^^ . + . + . + . + . + . + . + "Social Insect Behavior Ontology" . + . + "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . + . + . + "false"^^ . + "https://data.4dnucleome.org/biosources"^^ . + . + . + . + . + . + "0000001"^^ . + . + . + . + . + . + . + "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . + "https://www.alzforum.org/mutations"^^ . + "false"^^ . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . + . + . + . + "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . + . + "^[a-zA-Z0-9_\\.]+$"^^ . + "44259"^^ . + . + "false"^^ . + "https://envipath.org/package/$1"^^ . + . + . + . + . + . + . + "https://stemcells.nindsgenetics.org?line=$1"^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . + . + "Human Disease Ontology" . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + "VMH reaction" . + . + . + "https://civicdb.org/"^^ . + "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . + . + . + . + . + . + . + . + . + . + . + "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . + "E-MTAB-2037"^^ . + "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"^^ . + . + "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . + . + . + . + . + . + . + . + "https://www.who.int/classifications/icd/adaptations/oncology/en/"^^ . + . + . + . + "0000088"^^ . + . + "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "http://supfam.org/SUPERFAMILY/"^^ . + "false"^^ . + "http://autism.mindspec.org/autdb/"^^ . + . + . + . + . + . +_:Nc90f569000894c6fab011435dc1a5fcf "Satya S. Sahoo" . + "https://github.com/obophenotype/c-elegans-development-ontology"^^ . + . + . + . + "0000590"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "CAL0003079"^^ . + . + . + . + "http://purl.obolibrary.org/obo/PSO_$1"^^ . + . + . + . + . + "EasyChair Topic" . + . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + "PiroplasmaDB" . + . + . + . . - . - "^\\w+$"^^ . - . - "Cellular Microscopy Phenotype Ontology" . - . - . - "true"^^ . - . - "Database of Quantitative Cellular Signaling: Pathway" . - . - . - . - "^\\d+$"^^ . - . - . - "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . - "Protein Ensemble Database" . - . - "false"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/TXPO_$1"^^ . - . - "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . - "0000215"^^ . - "^[a-z_A-Z0-9]+$"^^ . - . - "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . - . - "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . - . - "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . - . - . - . - "^DG\\d+$"^^ . - . - "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^ . - . - "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . - "^C\\d{4}$"^^ . - "http://www.genoscope.cns.fr/agc/microscope"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "^HMDB\\d+$"^^ . - "PS00001"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . + . + "true"^^ . + . + "https://www.genome.jp/kegg/reaction/"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . + "false"^^ . + . + . + "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . + . + "MCDS_C_0000000001"^^ . + . + . + "UniPathway Compound" . + . + . + . + . + "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . + "false"^^ . + . + . + . + "0000001"^^ . + . + . + . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + . + "http://agroportal.lirmm.fr/ontologies/$1" . + . + "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . + . + "0000389"^^ . + . + . + . + . + . + "SASDAX8"^^ . + . + . + . + . + . + . + "Gene Regulation Ontology" . + . + . + . + . + "BiGG Metabolite" . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "false"^^ . + . + . + "http://www.wikipathways.org/instance/$1"^^ . + "false"^^ . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . + . + "Enzyme Commission Code" . + . + . + "https://www.picb.ac.cn/limore/home"^^ . + "CNBG_0001"^^ . + . + . + . + . + . + . + . + . + . . - "https://bionumbers.hms.harvard.edu"^^ . - . - . - . - . - . - . - "iECABU_c1320"^^ . - . - . - . - "0000044"^^ . - . - "true"^^ . - . - . - . - . - . - . - "https://github.com/biobanking/biobanking"^^ . - . - . - "https://github.com/CTDbase/exposure-ontology"^^ . - "Pier Luigi Buttigieg" . - . - . - "http://www.sparontologies.net/ontologies/frapo"^^ . - "GO Relations" . - . - . - . - . - . - "https://www.uniprot.org/locations/"^^ . - . - . - . - "https://orcid.org"^^ . - . - "GnpIS" . - . - "https://www.encodeproject.org/$1"^^ . - . - "https://pharmacodb.ca/cell_lines/$1"^^ . - . - "NMR Restraints Grid" . - "^[A-Z]+$"^^ . - . - . - . - . - "https://www.ndexbio.org"^^ . - . - . - . - . - . - "https://n2t.net/$1:" . - . - "c0001"^^ . - "https://github.com/EBISPOT/covoc"^^ . - . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - "humIGHV025"^^ . - "EDDA Study Designs Taxonomy" . - . - . - "The LifeWatch ERIC repository of semantic resources for the ecological domain." . - "^CHEMBL\\d+$"^^ . - "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . - "false"^^ . - . - . - "https://commonchemistry.cas.org/"^^ . - . - "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"^^ . - . - . - . - "EST database maintained at the NCBI." . + . + . + . + "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . + "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . + . + . + . + . + . + "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html"^^ . + . + . + . + . + "https://www.arraymap.org"^^ . + . + "https://pharmacodb.ca/datasets"^^ . + . + "^NBK\\d+$"^^ . + "true"^^ . + . + . + . + "^(data|topic|operation|format)\\_\\d{4}$"^^ . + "Gene Ontology Database references" . + . + . + "^NCT\\d{8}$"^^ . + . + . + . + "true"^^ . + . + . + . + "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . + . + . + . + . + "H-InvDb Locus" . + . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . + . + "https://www.cropontology.org/rdf/CO_337:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:Na4af3ac318644462a9bbd1b961827f9d . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . + "http://www.gramene.org/"^^ . + . + "https://datanator.info/"^^ . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . + . + . + . + "Imanis Life Sciences cell line products" . + . + "https://w3id.org/reproduceme/research"^^ . + "false"^^ . + . + . + . + . + . + . + "BiGG Compartment" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.mesquiteproject.org/ontology/Loggerhead/index.html"^^ . + . + "Cell line collections"^^ . + . + . +_:N97795881207843c4bf7f49eb4d0f3011 "Mauno Vihinen" . + . + . + . + . + "9001411"^^ . + . + . + . + "ARP-1513"^^ . + "^FB\\w{2}\\d{7}$"^^ . + . + . + . + . + . + "ClinVar Submission" . + "090803"^^ . + . + "ChEMBL" . + . + . + . + . + . + . + . + . + "https://bioregistry.io/registry/$1"^^ . + . + "https://github.com/echinoderm-ontology/ecao_ontology"^^ . + . + "false"^^ . + . + "Logical Observation Identifiers Names and Codes" . + "Healthcare Common Procedure Coding System" . + . + . + "9008500"^^ . + . + . + . + "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . + . + "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . . - . - . - . - . - . - . - . - . - "Danielle Welter" . - "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . - . - "GeneDB" . - "true"^^ . - . - . - . - . - . - "https://ocid.ontochem.com/prefname?ocid=$1"^^ . - . - . - "PeptideAtlas Dataset" . - . - "false"^^ . - . - . - "PhosphoPoint Kinase" . - "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . - . - "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . - . - . - . - . - "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . - "https://pubchem.ncbi.nlm.nih.gov"^^ . - "EJH014"^^ . - . - . - . - . - . - . - . - . + "0000047"^^ . + . + . + . + "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . + "false"^^ . + . + . + . + "sbml.level-3.version-2"^^ . + . + "http://purl.org/spar/pro/$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "false"^^ . + "NLXORG covers organisms."^^ . + . + "http://purl.obolibrary.org/obo/RO_$1"^^ . + "Unipathway" . + "https://cropontology.org/ontology/CO_341/Pigeonpea"^^ . + . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "false"^^ . + "http://www.humanproteomemap.org/index.php"^^ . + "760050"^^ . + . + . + . + "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . + "http://purl.obolibrary.org/obo/BSPO_$1"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "A database-specific registry supporting curation in the Gene Ontology"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "CGH Data Base" . + . + . + . + "https://www.ebi.ac.uk/metabolights/$1"^^ . + . + . + . + "^[1-9]\\d*$"^^ . + "0100010"^^ . + . + . + . + . + . + . + . + . "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . - . - . - "https://www.ebi.ac.uk/metabolights/$1"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . - "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . - . - . - "BioStudies database" . - "http://purl.obolibrary.org/obo/CTENO_$1"^^ . - . - . - . - . - . - "http://swissregulon.unibas.ch"^^ . - "false"^^ . - . - . - . - "Alayne Cuzick" . - "UniGene" . - . - . - "Scientific Evidence and Provenance Information Ontology" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . - . - . - . - . - . - "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . - . - . - "false"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"^^ . - "false"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . - "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . - . - . - . - . - . - "DisProt" . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - "A Systematic Annotation Package for Community Analysis of Genomes" . - "A database for Triticeae and Avena references."^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://co.mbine.org/specifications/$1"^^ . - . - . - . - . - . - "Henriette Harmse" . - . - "false"^^ . - "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^ . - "^\\d{7}$"^^ . - "Ontology of Arthropod Circulatory Systems" . - . - "Higher order grouping of Pfam families"^^ . - . - . - . - . - "false"^^ . - "https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_$1" . - . - . - . - . - . - "Open Researcher and Contributor" . - "cl3603"^^ . - . - . - . - . - . - "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . - . - "LOC_Os01g49190.1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Bacillus subtilis genome sequencing project" . - . - . - "ANOVA"^^ . - . - . - . - "MedlinePlus Health Topics" . - . - . - "http://www.bioinfo.org/NONCODEv4/"^^ . - "The cell line vocabulary inside FlyBase"^^ . - "https://github.com/Display-Lab/psdo"^^ . - . - . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . + . + . + . + . + "^ENSG\\d{11}$"^^ . + "false"^^ . + . + "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . + "false"^^ . + . + . + . + . + "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . + "Sue Bello" . + "PTM-0450"^^ . + "http://www.fludb.org/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "https://www.thermofisher.com"^^ . + "70"^^ . + . + . + . + "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . + . + . + . + "Open Citation Identifier" . + . + . + "DDB0191090"^^ . + "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . + . + . + . + "ASPL0000349247"^^ . + . + . + "^\\d+$"^^ . + . + . + "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records."^^ . + . + . + . + . + . + . + "https://github.com/obophenotype/fungal-anatomy-ontology/"^^ . + "http://toxodb.org/toxo/"^^ . + . + . + . + . + . + "ITO_01625"^^ . + . + . + . + . + . + . + "16S rRNA gene database" . + . + "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . + . + . + . + . + . + . + . + "IntellectualContribution"^^ . + . + . + . + . + . + "Paul Schofield" . + "^\\d{7}$"^^ . + . + "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . + . + "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . + . + . + . + . + . + . + "0000008"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Mouse Genome Informatics" . + "http://www.jcvi.org/mpidb/about.php"^^ . + . + . + . + "false"^^ . + . + . + . + . + . . - . - . - "false"^^ . - "https://github.com/geneontology/unipathway"^^ . + . + . + . + . + "0000728"^^ . + . + "https://www.uniprot.org/unirule/"^^ . + . + . + . + . + . + . + "http://jcggdb.jp/index_en.html"^^ . + "0000947"^^ . + "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . + . + . + . + "^SCV\\d+(\\.\\d+)?$"^^ . + . + . + . + . + . + . + "SysBioCancer2022"^^ . + . + "false"^^ . + . + . + . + . + . + . + "Animal Genome QTL" . + "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . + . + . + "^KW-\\d{4}$"^^ . + "http://www.pathbase.net"^^ . + . + "true"^^ . + . + . + . + "^[A-Z]+$"^^ . + . + "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . + . + "1000001"^^ . + "false"^^ . + . + . + . + "Daniel C. Berrios" . + . + "Database of Genomic Structural Variation - Study" . + . + . + . + . + . + "PXD000500"^^ . + "false"^^ . + . + . + "0000001"^^ . + . + "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . + . + "^\\d+$"^^ . + . + "https://data.bloodpac.org/."^^ . + . + "Datasets inside StoreDB"^^ . + . + "^\\d+$"^^ . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . + . + . + "PELNAW"^^ . + "false"^^ . + . + "http://sugarbind.expasy.org/$1"^^ . + . + "C0026339"^^ . + . + "221058"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "^\\w+$"^^ . + "http://tuberculist.epfl.ch/"^^ . + . + . + "Trish Whetzel" . + "http://ecmdb.ca/compounds/$1"^^ . + "https://github.com/enpadasi/Ontology-for-Nutritional-Studies"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + "Gene Ontology Causal Assembly Model" . + "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . + . + . + . + . + . + . + . + . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . + . + . + "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . + . + . + . + . + . + . + . + . + . + . + . + "OSR00185W"^^ . + . + . + . + . + "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . + "https://fungi.ensembl.org/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . + . + . + . + "DataONE" . + "^.*?--%3E.*?$"^^ . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . + . + "Zach Landis-Lewis" . + . + . + . + . + . + "^\\w+:[\\w\\d\\.-]*$"^^ . + . + "https://www.biolegend.com"^^ . + . + . + . + . + . + . + "GnpIS" . + "^[EL]D[SG]-\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . + . + "^\\d+$"^^ . + . + . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv"^^ . + . + . + . + . + . + . + "634515043"^^ . + "https://github.com/VEuPathDB-ontology/MIRO"^^ . + "Cancer Staging Terms" . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + "http://opencitations.net"^^ . + "A manually curated resource for the representation and annotation of metabolic pathways"^^ . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^\\d{4}-\\d{3}[\\dX]$"^^ . + "false"^^ . + "https://genelab-data.ndc.nasa.gov/genelab/"^^ . + . + . + "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . + "00000001"^^ . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . + "http://www.uniprot.org/keywords/"^^ . + . + "Drosophila Phenotype Ontology" . + . + . + . + . + . + . + . + . + . + "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . + . + . + . + "https://www.lgresearch.ai"^^ . + . + . + . + . + "https://flybase.org/reports/FBrf$1"^^ . + . + . + "1000"^^ . + . + . + "1"^^ . + . + "https://www.nextprot.org/"^^ . + "NITE Biological Resource Center" . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . + . + . + "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . + . + . + . + . + . + . + "Performance Summary Display Ontology" . + . + . + "false"^^ . + . + . + . + "00007294"^^ . + . + . + . + . + . + "NCATS Drugs" . + . + . + . + . + . + . + . + . + "PROB_c0000005"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Bob Thacker" . + "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . + "false"^^ . + "https://www.ebi.ac.uk/ega/studies/$1"^^ . + . + "http://www.russelllab.org/miRNAs/"^^ . + . + . + "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . + . + . + . + "false"^^ . + "http://xmlns.com/foaf/spec/"^^ . + . + . + . + . + "^.+$"^^ . + . + "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . + . + . + . + . + . + . + . + . + . +_:Ncd8db50360e4497892747d5c5192e44f "Thorsten Heinrich" . + "CH_001923"^^ . + . + . + . + . + . + . + "https://kaggle.com"^^ . + . + . + . + "https://github.com/prefixcommons/biocontext" . + . + . + . + . + "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . + . + . + . + . + . + . + "http://bugs.sgul.ac.uk/E-BUGS"^^ . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + "Genomic Epidemiology Ontology" . + . + . + "http://www.begdb.com"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . "https://www.uniprot.org/diseases/$1"^^ . - . - . - "http://id.nlm.nih.gov/mesh/"^^ . - . - . - . - . - . - . - . - . - . - "0005452"^^ . - . - "http://www.treefam.org/"^^ . - . - "http://www.aspgd.org/"^^ . - . - "http://matrixdb.univ-lyon1.fr/"^^ . - "http://probonto.org"^^ . - . - . - . - . - "The responsible person for a resource" . - "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . - . - . - . - "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^ . - . - "Mouse pathology ontology" . - "http://edamontology.org/topic_$1"^^ . - "DataONE" . - . - "http://www.marinespecies.org/"^^ . - . - "https://herv.img.cas.cz/s/$1"^^ . - "CHEBI" . - . - "PolBase" . - "false"^^ . - "IPR016380"^^ . - . - . - "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . - "false"^^ . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . - "Hector Escriva" . - . - . - . - . - . - "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . - . - "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . - "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . - "http://www.ecogene.org/gene/$1"^^ . - . - . - . - . - . + "LCL-2085"^^ . + . + . + . + . + "http://europepmc.org/articles/$1"^^ . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . + . + . + "false"^^ . + . + "Environmental conditions, treatments and exposures ontology" . + . + "^\\d{7}$"^^ . + . + "http://www.w3.org/2001/XMLSchema#$1"^^ . + "Cell Line Ontology" . + . + . + . + "http://www.proteinatlas.org/$1"^^ . + . + "false"^^ . + . + . + . + . + "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . + . + . + "European Nucleotide Archive" . + . + "false"^^ . + "Oryzabase Strain" . + "false"^^ . + "LOTUS Initiative for Open Natural Products Research" . + "ReviewVersion"^^ . + . + . + . + "0000639"^^ . + "false"^^ . + "https://jjj.bio.vu.nl/models/$1"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . + . + . + "BioContext contains modular JSON-LD contexts for bioinformatics data." . + . + . + "International Medical Device Regulators Forum" . + "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . + . + . + . + . + "^(D|PP|R|T|H|X|AI)?\\d+$"^^ . + "false"^^ . + . + "MeSH 2012" . + . + "https://www.wormbase.org/db/seq/protein?name=$1"^^ . + . + "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . + . + "^CHEMBL\\d+$"^^ . + "GOLD metadata" . + "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . + "^\\d+$"^^ . + "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^ . + . + . + "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^ . + . + "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . + "Image Data Resource" . + . + . + "KC-0979"^^ . + . + . + . + . + "0011140"^^ . + "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . + . + . + . + "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . + "^\\d+$"^^ . + "https://www.kew.org/data/grasses-db/www/$1"^^ . + . + . + "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . + "false"^^ . + "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . + "false"^^ . + . + . + "http://www.guidetopharmacology.org/targets.jsp"^^ . + "ZINC is not Commercial" . + . + . + "0000002"^^ . + . + . + . + . + "false"^^ . + . + . + "T30002"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "0000204"^^ . + "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^ . + . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . + . + "FAIRsharing Subject Ontology" . + . + "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . + . + . + . + . + "http://www.loria.fr/~coulet/sopharm2.0_description.php"^^ . + . + . + . + . + "63189"^^ . + . + "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . + "Cell line databases/resources"^^ . + . + . + . + "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . + . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . + . + . + . + . + . + "Biosapiens Protein Feature Ontology" . + "false"^^ . + . + . + "^[A-Z0-9]{4}$"^^ . + "Database of Macromolecular Interactions" . + "https://omabrowser.org"^^ . + . + . + . + "Molecular Process Ontology" . + . + "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . + . + . + . + "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . + . + . + . + "Terminology of Anatomy of Human Embryology" . + "false"^^ . + "^\\d{7}$"^^ . + "Aspergillus Genome Database" . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "A formal ontology of phenotypes observed in fission yeast."^^ . + "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . + "Terminology of Anatomy of Human Histology" . + . + . + . + . + . + . + . + "CPX-263"^^ . + . + . + . + . + . + . + . + "false"^^ . + "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . + . + . + "627"^^ . + "false"^^ . + . + "^\\d{7}$"^^ . + "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . + . + . + "1250"^^ . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . + . + . + . + . + . + . + . + . + "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . + . + . + "Feature Type Thesaurus" . + . + "^PKDB[0-9]{5}$"^^ . + "UniProt Isoform" . + . + "SABIO Reaction Kinetics" . + . + . + . + "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . + "0000071"^^ . + . + . + . + . + . + . + "http://www.sparontologies.net/ontologies/fr"^^ . + . + "https://www.cancerrxgene.org"^^ . + . + . + . + . + "http://wheat.pw.usda.gov"^^ . + . + . + . + "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . + . + . + . + . + . + "http://edamontology.org/data_$1"^^ . + . + . + . + . + . + . . - . - . - . - "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . - . - . - . - "https://github.com/EBISPOT/DUO"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - "https://www.facebase.org"^^ . - . - . - "http://www.ebi.ac.uk/efo"^^ . - . - . - "A10BA02"^^ . - "50943"^^ . - . - . - . - "http://flyrnai.org/"^^ . - . - . - "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - "http://www.upol.cz/en/"^^ . - "000000024"^^ . - . - . - "http://purl.obolibrary.org/obo/PDRO_$1"^^ . - . - . - . - "http://rebase.neb.com/rebase/"^^ . - . - . - . - . - . - "GrainGenes" . - "C. elegans ORFeome cloning project" . - . - . - . - . - . - "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^ . - "https://neurovault.org/images/$1"^^ . - . - . - "Bioregistry Schema" . - "http://www.kupkb.org/"^^ . - . - . - "9606117"^^ . - "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . - "https://www.ebi.ac.uk/intact/"^^ . - "0000066"^^ . - "Unique Ingredient Identifier" . - . - "https://commonchemistry.cas.org/detail?ref=$1"^^ . - "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. "^^ . - . - . - . - "Chemical Component Dictionary" . - "DBCAT000600"^^ . - . - . - "http://edamontology.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . - . - . - "^\\d+$"^^ . - "https://nci-crdc.datacommons.io/"^^ . - . - . - . - "^\\w+$"^^ . - . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . - . - . - . - . - . - . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://www.yeastgenome.org/observable/APO:$1"^^ . + . + . + "andreadega/systems-biology-compiler"^^ . + . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/database/"^^ . . - . - "M0001"^^ . - "http://arabidopsis.org/index.jsp"^^ . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/XL_$1"^^ . - "false"^^ . - "100"^^ . - . - . + . + . + . + . + . + "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . + . + . + "Cassava ontology" . + "false"^^ . + "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . + . + "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . + . + "^\\d+$"^^ . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . + "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + "Cell line collections"^^ . + "^BG\\d+$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"^^ . + "Cell line collections"^^ . + . + . + . + . + . + . + . + . + . + . + "SRS086444"^^ . + . + . + . + "^\\d+$"^^ . + . + "https://github.com/FAIRsharing/subject-ontology"^^ . + "https://metabolome.cgfb.u-bordeaux.fr/"^^ . + "https://fcs-free.org"^^ . + . + . + "https://w3id.org/biolink/vocab/$1"^^ . + "EAWAG Biocatalysis/Biodegradation Database" . + . + "0003"^^ . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . + "DEF"^^ . + "ISA1083-2"^^ . + "^\\d{7}$"^^ . + . + . + "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . + . + . + "INSDC CDS" . + . + "BARC-013845-01256"^^ . + "false"^^ . + "18"^^ . + . + "false"^^ . + . + "Sol Genomics Network" . + . + "http://purl.obolibrary.org/obo/XPO_$1"^^ . + . + . + "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . + . + . + . + . + . + . + . + . + "microRNA Ontology" . + . + "clinical LABoratory Ontology" . + . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . + "Integrated Genomic Resources of human Cell Lines for Identification" . + . + . + . + . + "Neural ElectroMagnetic Ontology" . + "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . + . + "^\\d+$"^^ . + "^PD\\d+$"^^ . + "true"^^ . + . + . + . + . + . + "Online Mendelian Inheritance in Man" . + "http://sabiork.h-its.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://www.vbase2.org/vbase2.php"^^ . + "https://www.biozol.de/en/product/$1"^^ . + . + . + . + . + "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . + . + . + . + "Enzo Life Sciences is an antibody vendor."^^ . + . + . + . + . + "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . + . + . + . + "307"^^ . + . + . + . + . + "false"^^ . + . + "Q2207226"^^ . + . + . + "http://img.jgi.doe.gov/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . + . + . + . + "Identifier for a species in iNaturalist"^^ . + . + "Person" . + . + . + . + . + "Crop Ontology Curation Tool" . + . + . + "^[a-zA-Z]+.+$"^^ . + . + "^\\d{7}$"^^ . + . + "Ontology of Physics for Biology" . + "https://www.ebi.ac.uk/miriam/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/"^^ . + . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000"^^ . + "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . + "PAR:0116"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes."^^ . + . + "^\\d+$"^^ . + "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . + . + . + . + . + "eagle-i" . + . + "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . + "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . + "^PTN\\d{9}$"^^ . +_:N3e609a1f28e14528b79ba310b0b63dce "INOH curators" . + . + . + . + . + . + "^P\\w+$"^^ . + . + . + . + . + . + . + "1251"^^ . + "false"^^ . + . + . + "https://biocyc.org/gene?id=$1"^^ . + . + . + . + . + . + . + "KEGG Compound" . + . + "https://tree.opentreeoflife.org"^^ . + "true"^^ . + . + "Identifiers.org Ontology"^^ . + . + . + "0000004"^^ . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/FBbi_$1"^^ . + "AMDEFA"^^ . + "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . + . + . + . + . + . + "AT1G01030.1"^^ . + . + . + . + . + "408"^^ . + . + "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . + . + "Encyclopedia of DNA Elements" . + "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . + . + "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . + "http://www.gramene.org/"^^ . + . + . + . + . + "1968"^^ . + . + . + "Hymenoptera Anatomy Ontology" . + "https://www.clinicaltrialsregister.eu/"^^ . + . + . + . + "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^ . + . + . + "^\\d+$"^^ . + . + . + "Anne Thessen" . + . + . + . + "Pesticide Properties DataBase" . + . + . + . + . + "0000001"^^ . + "A type for entries in the Bioregistry's metaregistry." . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "SABIO-RK Reaction" . + . + . + "https://www.cropontology.org/rdf/CO_324:$1"^^ . + "ToxoDB" . + . + "https://medlineplus.gov/genetics/condition/$1"^^ . + . + . + . + . + . + "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut"^^ . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/CDNO_$1"^^ . + . + . + . + "false"^^ . + . + . + "040000"^^ . + . + "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . + "NIF Standard Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "Intrinsically Disordered proteins with Extensive Annotations and Literature" . + . + . + . + . + . + . + "https://github.com/aszool/oarcs"^^ . + "false"^^ . + _:N78c15455a378489a85b18cf5e05504c0 . + . + . + . + "BugBase Expt" . + "https://vertebrate.genenames.org"^^ . + "BioSample" . + . + . + "false"^^ . + . + . + . + . + . + "^[A-Z_]{3}[0-9]{4,}$"^^ . + . . - . - . - . - "^\\d+$"^^ . - "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . - . - . - . - . - . - . - "3000045"^^ . - . - . - "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . - . - "http://modelseed.org/biochem/reactions/$1"^^ . - . - . - "false"^^ . - "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . - . - "https://bioregistry.io/metaregistry/ncbi/$1"^^ . - "MIRT000002"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . - . - . - . - . - "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . - . - . - "https://cropontology.org/ontology/CO_321/Wheat"^^ . - . - "5fde96bdc5f1aa9ff0cce18a"^^ . - . - . - . - . - . - "^\\w+$"^^ . - . - . - "886"^^ . - . - . - . - . - . - . - "ILMN_129894"^^ . - . - "http://purl.obolibrary.org/obo/EV_$1"^^ . - . - . - . - . - "26753"^^ . - "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . - . - . - . - "https://cropontology.org/ontology/CO_341/Pigeonpea"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "75"^^ . - . - "31623"^^ . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . - "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . - "BT20_BREAST"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "A0001"^^ . - "24801"^^ . - "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . - . - . - . - . - . - . - "^SIGNOR-\\d+$"^^ . - . - . - "PhosphoPoint Phosphoprotein" . - . - . - . - "phs000768.v2.p1"^^ . - "http://multicellds.org/MultiCellDB/$1"^^ . - "1915"^^ . - . - "COMBINE specifications" . - . - "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . - . - . - . + "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://rgd.mcw.edu/"^^ . + "^\\d{1,5}$"^^ . + . + "0000062"^^ . + "National Center for Advancing Translation Sciences BioPlanet" . + . + "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . + . + . + "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . + "FungiDB" . + "BioProject" . + "STOREDB at University of Cambridge" . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . + . + . + . + "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + "https://ccg.epfl.ch/snp2tfbs/"^^ . + . + . + . + . + "http://www.yeastgenome.org/"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."^^ . + . + . + _:N8a87645627bf4c81ac5bd9bdce54e71e . + "25512"^^ . + . + . + "BitterDB Compound" . + . + . + . + . + . + "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology"^^ . + "^DBCAT\\d+$"^^ . + "784"^^ . + "http://www.kazusa.or.jp/huge/"^^ . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . + . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . + "Tom Gillespie" . + "Yeast Metabolome Database" . + . + "false"^^ . + "false"^^ . + . + "http://www.iclc.it"^^ . + . + . + . + "https://fair-research.org"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "BP100000"^^ . + . + . + "https://www.proteomicsdb.org/#human"^^ . + "false"^^ . + . + . + . + . + . + . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . + "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . + . + . + . + "Jingshan Huang" . + "5688061"^^ . + . + . + "^[a-zA-Z0-9\\-:#\\.]+$"^^ . + "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . - . - . - "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^ . - . - . - "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . - . - . - . - "CHEBI" . - . - "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. "^^ . - . - . - . - . - . - . - . + "^\\d{7}$"^^ . + . + "RNA ontology" . + . + "false"^^ . + "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt"^^ . + "^\\w+$"^^ . + "false"^^ . + "http://genome.crg.es/datasets/abs2005/"^^ . + . + . + "https://github.com/MPIO-Developers/MPIO"^^ . + "^HGVST\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Cell line databases/resources"^^ . + . + "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . + "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . + . + . + "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . + . + "bt0001"^^ . + "0000079"^^ . + "AP011135"^^ . + "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . + "false"^^ . + "https://github.com/MIT-LCP/mimic-omop"^^ . + "0000000"^^ . + "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . + . + . + . + "http://purl.obolibrary.org/obo/MFMO_$1"^^ . + . + "false"^^ . + . + . + "https://portal.gdc.cancer.gov/cases/$1"^^ . + . + . + . + . + . + . + . + . + "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . + . + . + . + . + . + . + "miRBase pre-miRNA" . + "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . + . + . + . + . + "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . + . + "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . + . + "false"^^ . + . + "0000000"^^ . + . + "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . + "http://purl.obolibrary.org/obo/MONDO_$1"^^ . + . + . + "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . + . + "false"^^ . + "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . + . + . + . + "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . + . + "http://pax-db.org/"^^ . + "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . + "^UCR\\d{5}$"^^ . + "^\\d+$"^^ . + . + . + . + "http://polbase.neb.com/"^^ . + . + "Mosquito insecticide resistance" . + . + "Bgee organ" . + . + "https://www.cropontology.org/rdf/CO_357:$1"^^ . + "David Osumi-Sutherland" . + "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . + "http://www.kupkb.org/"^^ . + . +_:N4919606696d74b52a536951cba63e0df "Daniel Sonenshine" . + . + . + "^MMP\\d+.\\d+$"^^ . + . + "https://flybrain-ndb.virtualflybrain.org"^^ . + . + "4DNSR73BT2A2"^^ . + . + "1351341"^^ . + "https://web.expasy.org/cellosaurus/"^^ . + . + "^\\d+$"^^ . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . + . + "A_24_P98555"^^ . + . + . + . + "Cereal Plant Gross Anatomy" . + "false"^^ . + . + . + . + "https://panoramaweb.org/$1.url"^^ . + "Castor bean ontology" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . + "^\\d+$"^^ . + . + "MultiCellDS Digital snapshot" . + . + "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . + . + . + . + . + . + . + "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/CTO_$1"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ATO_$1"^^ . + . + . + . + . + . + . + . + . + "Chris Stoeckert" . + "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . + . + . + _:N26d14ce966cf45029d3aad979df880c7 . + . + . + . + "Clement Jonquet" . + "false"^^ . + "false"^^ . + "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . + . + "false"^^ . + . + "Nicole Vasilevsky" . + . + . + . + "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . + "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . + "^\\d{8}$"^^ . + "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . + . + . + . + . + . + . + . + . + _:N366873dcfd384ee1821e5facc6adbaeb . + . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Integrated Taxonomic Information System" . + . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + "Barley ontology" . + . + . + . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . + "9-1-1 Complex"^^ . + "GeneFarm" . + "http://func.mshri.on.ca/human/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "UniProt Chain" . + . + . + "^UPC\\d{5}$"^^ . + . + "ab-1-ha"^^ . + "https://www.cbioportal.org/study/summary?id=$1"^^ . + . + . + . + . + "http://www.geosamples.org/"^^ . + "977869"^^ . + . + . + . + . + "0000101"^^ . + "false"^^ . + "https://sorgerlab.github.io/famplex/$1"^^ . + . + . + . + . + . + "^PASS\\d{5}$"^^ . + . + . + . + "http://purl.org/dc/dcmitype/$1"^^ . + . + . + "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . + "false"^^ . + . + "1174"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . + . + "K00001"^^ . + . + "968"^^ . + . + . + "false"^^ . + . + "101"^^ . + . + . + . + . + . + . + . + . + . + "^\\S+$"^^ . + "1868"^^ . + . + . + . + "https://www.python.org/psf/"^^ . + . + . + . + . + . + "https://www.gwascentral.org/phenotype/$1"^^ . + . + . + "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . + . + "true"^^ . + "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . + . + . + . + "https://nmrshiftdb.nmr.uni-koeln.de"^^ . + "https://www.iedb.org/reference/$1"^^ . + . + . + "false"^^ . + "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/"^^ . + "false"^^ . + . + . + . + "Friend of a Friend" . + . + "false"^^ . + . + "http://emouseatlas.org"^^ . + "http://www.dpvweb.net/"^^ . + . + . + "SitEx" . + . + . + . + . + "false"^^ . + "0000032"^^ . + . + . + . + "false"^^ . + "https://dailymed.nlm.nih.gov/dailymed/"^^ . + "^\\d{7}$"^^ . + . + . + "http://isbndb.com/search-all.html?kw=$1"^^ . + . + . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . + "456789"^^ . + "false"^^ . + "^\\d{8}$"^^ . + . + . + . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + "https://www.opengalen.org"^^ . + . + "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . + . + . + . + . + "^[A-Za-z-0-9]+$"^^ . + . + . + . + "http://www.informatics.jax.org/searches/MP_form.shtml"^^ . + . + . + . + "^\\d+$"^^ . + "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "ChemIDplus" . + "Xeni Kechagioglou" . + "http://ciliate.org/index.php/"^^ . + . + . + . + "ECOCYC"^^ . + "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "http://ecoliwiki.net/colipedia/"^^ . + . + . + . + . + . + . + . + . + . + . + "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . + "https://www.cropontology.org/rdf/CO_359:$1"^^ . + "http://www.narcis.nl/publication/RecordID/$1"^^ . + . + . + . + . + "https://dandiarchive.org/"^^ . + . + . + . + "ATL98012"^^ . + "602"^^ . + . + . + "http://purl.obolibrary.org/obo/OBIB_$1"^^ . + "false"^^ . + "GR_tax:013681"^^ . + . + "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^ . + . + "1000100"^^ . + "http://ecocyc.org/"^^ . + . + . + "false"^^ . + . + . + . + "Rhea, the Annotated Reactions Database" . + . + . + "^m\\w+$"^^ . + . + . + "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"^^ . + "CAE46076"^^ . + . + . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . + . + . + . + "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . + "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^ . + . + . + . + "Cotton ontology from CottonGen database - June 2019"^^ . + . + . + "false"^^ . + . + . + "None"^^ . + "^\\d{7}$"^^ . + . + . + . + _:N0a2ecbcf5c914606819960fd17c853ed . . - . - . - . - . - "^\\d{8}$"^^ . - "^PED\\d{5}$"^^ . - . - . - . - . - "false"^^ . - "The coding sequence or protein identifiers as maintained in INSDC."^^ . - . - "2.7.1.1"^^ . - . - . - . - . - . - . - "Plasmodium Life Cycle" . - . - . - "SIDM01262"^^ . - . - . - . - "0000079"^^ . - . - . - . - . - . - "https://www.gwascentral.org/marker/$1"^^ . - . - "00073"^^ . - "http://supfam.org/SUPERFAMILY/"^^ . - . - "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . - . - . - "false"^^ . - . - . - . - . - . - "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^ . - . - "^\\d{7}$"^^ . - . - "Stacia R Engel" . - "2004-2820"^^ . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "InChIKey" . - . - . - "false"^^ . - "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . - "Functional Requirements for Bibliographic Records" . - . - "Open Citation Identifier" . - . - "false"^^ . - "^\\d{1,5}$"^^ . - . - "http://purl.org/dc/terms/$1"^^ . - . - . - . - "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . - "0100010"^^ . - . - "^\\d+$"^^ . - "https://github.com/"^^ . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . - . - . - "hsa-mir-200a"^^ . - . - "^\\d+$"^^ . - "YRC PDR" . - . - . - . - . - "true"^^ . - "Darren Natale" . - . - . - "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . - . - . - . - . - . - . - "https://proteinensemble.org/$1"^^ . - . - . - . - "Ontology for Biomedical Investigations" . - "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . + . + "A001094"^^ . + . + . + . + . + . + . + . + . + . + . + "http://dictybase.org/gene/$1"^^ . + . + . + . + . + . + . + . + "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . + . + . + . + . + . + . + "http://www.3dmet.dna.affrc.go.jp/"^^ . + . + "http://www.pombase.org/"^^ . + . + "https://archive.softwareheritage.org"^^ . + "SPCC13B11.01"^^ . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "1664"^^ . + . + . + "false"^^ . + "https://aopwiki.org/relationships/$1"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"^^ . + . + . + . + . + . + "Comparative Data Analysis Ontology" . + . + "https://www.dsmz.de"^^ . + "http://www.ebi.ac.uk/interpro/index.html"^^ . + . + "true"^^ . + . + . + "^\\d{7}$"^^ . + "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . + . + . + . + "oct 2016"^^ . + . + . + . + "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . + . + . + "Rahuman Sheriff" . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/chebi/"^^ . + . + . + "Development Data Object Service" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://github.com/obophenotype/human-developmental-anatomy-ontology/"^^ . + . + . + "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . + . + "NIF Standard Ontology: External" . + . + . + "https://github.com/Display-Lab/psdo"^^ . + "Alzforum Mutations" . + . + "^FOOD\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "P3DB Site" . + "https://knowledge.lonza.com"^^ . + . + . + . + "ProteomeXchange" . + "numpy"^^ . + "http://www.sequenceontology.org/"^^ . + "true"^^ . + "Wikidata Property" . + "neXtProt family" . + . . - "^\\d{7}$"^^ . - . - . - . - "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . - "AspGD Protein" . - "A pull request in any public repository on GitHub."^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "http://string.embl.de/interactions/$1"^^ . - . - . - . - _:N6f000779f8e44903be5cab1c005b03a9 . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^C\\d+$"^^ . - "https://reactome.org/content/detail/$1"^^ . - . - . - . - . - . - . - "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . - . - . - . - . - "Biological Expression Language" . - . - "Cell Line Ontology" . - . - . - . - . - "LGCEDe-S-000002244"^^ . - "Selventa Chemicals" . - . - . - "https://mlcommons.org/en/"^^ . - "http://purl.obolibrary.org/obo/SIBO_$1"^^ . - . - . - . - . - . - . - . - "http://www-deletion.stanford.edu/YDPM/"^^ . - . - . - . - . - . - . - "https://www.webelements.com/$1"^^ . - . - . - "https://github.com/obophenotype/c-elegans-development-ontology"^^ . - . - "https://eol.org"^^ . - "Datanator Reaction" . - . - . - . - "Mathias Brochhausen" . - "Raymond Lee" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^[A-Za-z]+$"^^ . - . - "true"^^ . - "^GR\\_tax\\:\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . - "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Human Unidentified Gene-Encoded" . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - . - . - "MMAR_2462"^^ . - . - . - "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . - . - . - . - . - "https://psidev.info/sepcv"^^ . - "^PDC\\d+$"^^ . - "http://www.drugbank.ca"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . - . - "false"^^ . - . - . - . - . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - . - "0005147"^^ . - . - . - "true"^^ . - . - "false"^^ . - "^[-A-Za-z0-9\\_]*$"^^ . - "Semantic Types Ontology" . - . + . + "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . + . + . + . + . + "ENSG00000026508"^^ . + "http://purl.obolibrary.org/obo/IAO_$1"^^ . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/SYMP_$1"^^ . + . + . + "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . + . + . + . + . + "https://github.com/OBOFoundry/COB"^^ . + . + "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . + . + . + . + "^r\\d+$"^^ . + . + . + . + . + . + . + "H00076"^^ . + . + "BioStudies database" . + . + . + . + "https://www.ebi.ac.uk/pride/archive/assays/$1"^^ . + . + "^\\d{3}$"^^ . + "Brian Aevermann" . + "false"^^ . + . + . + . + . + . + . + . + . + "0000049"^^ . + . + . + . + . + . + . + . + . + "ProGlycProt" . + . + . + . + "An ontology of human and animal behaviours and behavioural phenotypes"^^ . + . + . + . + "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . + . + . + . + "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . + "T3D0001"^^ . + "Variants in dbVar."^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "http://flypush.imgen.bcm.tmc.edu/pscreen/"^^ . + "^PA\\d+$"^^ . + "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . + "Homologous Organ Groups" . + . + . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . + . + "true"^^ . + . + . + . + "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + . "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . - . - "^\\d+$"^^ . - . - . - "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . - "Oryzabase Gene" . - "E-cyanobacterium model" . - . - . - "Biological Spatial Ontology" . - "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^ . - . - "http://ctdbase.org/"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "CAE46076"^^ . - . - . - . - . - . - . - "https://github.com/obophenotype/c-elegans-phenotype-ontology"^^ . - "https://www.signalingpathways.org/index.jsf"^^ . - . - . - "http://mycobrowser.epfl.ch/marinolist.html"^^ . - . - . + . + . + . + . + "false"^^ . + . + "saddan"^^ . + "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . + . + . + . + . + "https://health.uconn.edu/"^^ . + "https://www.genome.jp/kegg/pathway.html"^^ . + "http://purl.obolibrary.org/obo/PDRO_$1"^^ . + . + "https://hawaii.eagle-i.net"^^ . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/"^^ . + "GrassBase" . + "0011124"^^ . + . + "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . + . + "90000018"^^ . + "^\\d{7}$"^^ . + . + "http://purl.org/spar/datacite/$1"^^ . + "http://tolweb.org/$1"^^ . + . + "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . + . + "http://oncotree.mskcc.org"^^ . + . + "http://www.w3.org/ns/oa#$1"^^ . + "false"^^ . + "^\\d+$"^^ . + "Chen Yang" . + . + "0174" . + . + . + "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . + . + "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + _:Nc88b509b31e8421e99d8edf9afedc0d8 . + . + . + "false"^^ . + . + "https://cropontology.org/ontology/CO_322/Maize"^^ . + . + "^[a-zA-Z0-9 +#'*]+$"^^ . + . + _:N1990af52b5394a07ad7cc002186040f4 . + . + . + "^\\d+$"^^ . + . + "^[A-Za-z0-9]+$"^^ . + "false"^^ . + . + "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . + "HMS LINCS Compound" . + . + "false"^^ . + . + . + "http://www.wormbase.org/get?name=$1"^^ . + . + "true"^^ . + "https://bioregistry.io/schema"^^ . + . + "false"^^ . + "CHEMBL3467"^^ . + . + . + . + . + . + . + "Clair Kronk" . + . + . + "https://www.getty.edu/research/tools/vocabularies/tgn/"^^ . + "true"^^ . + . + "KNApSAcK" . + . + . + "^[A-Z0-9]{6,7}$"^^ . + . + "GitHub Issue" . + . + . + "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . + . + . + . + "true"^^ . + . + . + "https://civicdb.org/links/evidence/$1"^^ . + . + . + "false"^^ . + . + _:Nce37ebacd38849c58605cc273a55adc9 . + "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://github.com/obophenotype/bio-attribute-ontology"^^ . + "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . + . + . + . + "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . + . + "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^ . + . + "0000634"^^ . + . + "NIF Standard Ontology: Brain Regions" . + . + "https://www.cropontology.org/rdf/CO_330:$1"^^ . + . + . + "http://purl.org/spar/c4o/$1"^^ . + . + . + "false"^^ . + . + "Web Ontology Language" . + "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . + "h_aktPathway"^^ . + . + . + . + . + "https://github.com/$1"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . + "false"^^ . + "7499841"^^ . + . + . + . + . + . + . + "https://www.psidev.info/peff"^^ . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + "http://purl.obolibrary.org/obo/IEV_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "latitude"^^ . + . + . + . + . + . + "Japan Collection of Microorganisms" . + "http://4dx.embl.de/platy"^^ . + . + . + . + . + . + . + . + . + "0000108"^^ . + "http://purl.obolibrary.org/obo/MPATH_$1"^^ . + . + . + . + . + "Resource" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . + . + "NucleaRDB" . + . + . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/GECKO_$1"^^ . + "https://www.ebi.ac.uk/intact/"^^ . + "00001234"^^ . + . + "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"^^ . + . + "BN000065"^^ . + "http://img.jgi.doe.gov/"^^ . + "http://mged.sourceforge.net/ontologies/MGEDontology.php"^^ . + . + "^\\d+$"^^ . + . + . + "https://github.com/OGMS/ogms"^^ . + . + . + . + . + . + . + . + "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . + . + "0000000"^^ . + "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . + "https://icahn.mssm.edu/"^^ . + . + "AU124"^^ . + . + "PRIDE Project" . + . + "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . + . + . + . + . + . + "false"^^ . + . + "Japan Chemical Substance Dictionary" . + . + . + . + . + . + "Mosquito gross anatomy ontology" . + . + . + . + . + . + "0000109"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://www.yeastgenome.org/"^^ . + . + "false"^^ . + . + . + "International Geo Sample Number" . + "Cell line collections"^^ . + . + . + "false"^^ . + "Genatlas" . + "10004892"^^ . + . + "https://www.enzolifesciences.com/$1"^^ . + . + . + . + . + . + . + . + . + "https://github.com/obophenotype/ctenophore-ontology"^^ . + . + "Homology Ontology" . + . + . + "false"^^ . + "1.10.8.10"^^ . + . + "false"^^ . + "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://aopwiki.org/"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^ . + . + "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . + . + . + . + . + . + . + . + . + "Troy Pells" . + . + "http://seed-viewer.theseed.org/seedviewer.cgi"^^ . + . + . + "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . + . + "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . + . + . . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . - "http://www.fludb.org/"^^ . - . - "false"^^ . - "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . - "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . - . - "false"^^ . - . - . - "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . - "https://www.kegg.jp/entry/$1"^^ . - . - . - "false"^^ . - . - . - "LTS0004651"^^ . - . - "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.genenames.org"^^ . - . - . - "Rebecca Jackson" . - . - "false"^^ . - . - . - . - . - . - "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . - . - "false"^^ . - . - "https://caninecommons.cancer.gov/#/study/$1"^^ . - . - "RAP-DB Locus" . - . - . - . - . - "false"^^ . - . - . - "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . - . - . - . - . - "GlycoNAVI" . - . - . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^ . - . - . - . - . - . - . - . - "^[a-z_A-Z0-9]+$"^^ . - "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships"^^ . - "^[A-Z]{2}[A-Z0-9][0-9]{5}$"^^ . - "http://viaf.org"^^ . - . - "false"^^ . - . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . - . - . - "Citation Counting and Context Characterisation Ontology" . - . - "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . - "false"^^ . - . - . - "R-BTA-418592"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "https://bgee.org/?page=gene&gene_id=$1"^^ . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . - "false"^^ . - . - "http://lisanwanglab.org/DASHR/entry/$1"^^ . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . - . - . - . + "^[A-Za-z0-9-]+$"^^ . + . + . + "true"^^ . + "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . + "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . + . + . + . + . + . + "Cell line databases/resources"^^ . + . + "false"^^ . + . + "1"^^ . + "https://www.ncbi.nlm.nih.gov/homologene/"^^ . + . + . + . + . + . + . + . + . + . + "PseudoGene" . + . + "false"^^ . + . + "https://cell.brc.riken.jp/en/rcb"^^ . + "NeuroNames" . + . + . + "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "http://genex.hgu.mrc.ac.uk/"^^ . + "false"^^ . + "^\\d{4}$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "^A\\d+$"^^ . + . + "Stephen Fisher" . + . + . + "Cell line collections"^^ . + "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . + . + . + "false"^^ . + . + . + . + "K"^^ . + "0002058"^^ . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + "Reaxys eMolecules" . + "^\\d+$"^^ . + . + "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . + . + . + "0000319"^^ . + . + . + . + . + "8639.1"^^ . + "false"^^ . + "17165"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "0010034"^^ . + . + . + "https://github.com/tis-lab/reagent-ontology"^^ . + . + "2019-08-03_00000089_1"^^ . + . + . + "Mouse pathology ontology" . + "https://github.com/EBISPOT/ancestro"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . + . + . + . + . + . + . + . + . + "NIF Standard Ontology: Qualities" . + . + . + . + . + . + . + "http://pbil.univ-lyon1.fr/databases/hogenom/"^^ . + "http://fdasis.nlm.nih.gov/srs/"^^ . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"^^ . + "MetaCyc Reaction" . + "depends on" . + . + . + . + . + "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . + . + . + "^\\w+$"^^ . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . + "false"^^ . + "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . + . + . + . + "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . + "true"^^ . + . + . + "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . + . + "Assists in resolving data across cloud resources."^^ . + . + . + "An ontology built for representating the organizational components of trauma centers and trauma systems."^^ . + . + . + "false"^^ . + . + "prgr_human"^^ . + . + "GeneCards" . + "International Classification of Diseases, 9th Revision, Clinical Modification" . + . + . + . + . + "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . + "0000086"^^ . + . + . + . + . + . + . + . + . + . + "C023"^^ . + . + "1"^^ . + . + . + "^\\d{7}$"^^ . + "http://jjj.biochem.sun.ac.za/models/"^^ . + . + . + "http://www.receptome.org"^^ . + . + . + . + "true"^^ . + . + . + . + "http://www.gramene.org"^^ . + "G8944"^^ . + . + . + . + "United States Patent and Trademark Office" . + . + "Os01g0883800"^^ . + . + "MNXC15"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . + "^DAP\\d+$"^^ . + "http://purl.obolibrary.org/obo/LABO_$1"^^ . + . + . + . + . + . . - "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . - . - . - . - . - . - . - . - . - "CAS Chemical Registry" . - "true"^^ . - . - . - . - . - . - . - "MIPModDB" . - "NAD%20biosynthesis"^^ . - . - "has provider formatter" . - . - "^PM\\d{7}$"^^ . - "PathBank" . - . - "Nonribosomal Peptides Database" . - "false"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/$1" . - . - "false"^^ . - . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - "Dendritic cell" . - . - . - . - . - . - . - "COVID-19 Surveillance Ontology" . - . - . - . - . - "Cellosaurus Registry" . - . - "BeAn 70563"^^ . - "https://www.wikidata.org/wiki/Property:$1" . - . - . - . - "false"^^ . - . - . - . - . -_:Nac2201223a8747d1a31b9c6dcc856983 "Christipher Baker" . - . + . + . + . + "false"^^ . + . + . + "http://purl.uniprot.org/annotation/$1"^^ . + . + . + . + . + . + . + "https://portal.issn.org"^^ . + . + "Orphanet" . + . + . + . + . + "https://prefixcommons.org"^^ . + . + . . - . - . - . - . - . - . - "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CRO_$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - "^GE\\d+$"^^ . - . - . - . - "SMP0000219"^^ . - . - "false"^^ . - . - . - "hsa-mir-200a"^^ . - "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . - "Liliana Andres Hernandez" . - "http://www.w3.org/ns/oa#$1"^^ . - . - . - . - "^FR\\-FCM\\-\\w{4}$"^^ . - "090924"^^ . - . - "EDI_244000"^^ . + . + . + "https://www.ensembl.org/id/$1"^^ . + . + . + . + . + . + "277.9"^^ . + . + . + . + "DB-0174"^^ . + "0000001"^^ . + . + . + . + . + "https://www.genome.jp/kegg/ligand.html"^^ . + "International Classification of Diseases, 11th Revision" . + . + "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . + "false"^^ . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . + . + . + "false"^^ . + . + "http://bcrj.org.br/celula/bcrj"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . + . + . + . + . + . + "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/intact/"^^ . + . + . + . + . + . + "http://ascl.net/$1"^^ . + "^\\d+$"^^ . + . + "Proteoform Atlas" . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + . + . + "MarCat" . + . + . + . + . + . + "^RC\\d+$"^^ . + "Activity"^^ . + . + . + "21723"^^ . + . + . + . + "^\\d+$"^^ . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "^\\d+$"^^ . + . + "2h6o"^^ . + . + . + _:N58427d5b8fd140d785a13ae0161ee671 . + "^GPST[0-9]{6}$"^^ . + . + "^\\d{7}$"^^ . + "version Dec 2019"^^ . + . + . + "ZFA description."^^ . + . + . + . + . + "https://www.ebi.ac.uk/chembl"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "UCR00226"^^ . + . + . + . + . + . + "https://registry.identifiers.org/registry"^^ . + "https://www.allotrope.org/"^^ . + . + "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology"^^ . + "Bioregistry Collections" . + . + . + . + . + . + . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv"^^ . + . + "urn:nbn:fi:tkk-004781"^^ . + . + . + . + . + . + . + "0002902"^^ . + "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . + . + . + "Sigma Aldrich is a life sciences supply vendor."^^ . + "http://exac.broadinstitute.org/"^^ . + "LGCEDe-S-000002244"^^ . + . + . + . + . + . + . + . + . + . + "http://www.semantic-systems-biology.org/apo"^^ . + "^\\d{7}$"^^ . + . + . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . + . + . + . + "https://www.phenxtoolkit.org/"^^ . + "https://www.aapc.com"^^ . + "uBio NameBank" . + "ERP004492"^^ . + "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . + . + "https://fairsharing.org/$1"^^ . + . + . + . + . + "Ontology Concept Identifiers" . + "Tick Anatomy Ontology" . + "false"^^ . + "https://ontochem.com/"^^ . + . + "2170610"^^ . + "http://browser.planteome.org/amigo"^^ . + "https://github.com/carrineblank/MicrO"^^ . + . + . + "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . + . + . + . + . + . + . + . + . + . + . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . + "https://github.com/obophenotype/xenopus-phenotype-ontology"^^ . + . + . + . + "Reference Sequence Collection" . + "http://purl.obolibrary.org/obo/flu/"^^ . + "^C\\d+$"^^ . + . + . + . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . + . + . + . + "Physical Medicine and Rehabilitation" . + . + "NIH RePORTER" . + . + "https://www.cropontology.org/rdf/CO_358:$1"^^ . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + . + . + "Polymorphism and mutation databases"^^ . + "https://www.biorxiv.org/content/10.1101/$1"^^ . + . + . + . + "MIR:00100005"^^ . + . + . + . + . + "hsa00190"^^ . + . + . + . + . + "http://bigg.ucsd.edu/models"^^ . + . + . + . + "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html"^^ . + "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . + . + . + . + . + . + . + . + . + "00000099"^^ . + "http://dictybase.org/"^^ . + . + . + . + . + . + "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . + . + "Chickpea ontology" . + "false"^^ . + . + "Intelligence Task Ontology" . + . + . + . + . + . + . + "Consensus CDS" . + . + . + "ECOCYC" . + . + "https://www.nlm.nih.gov/research/umls/rxnorm/"^^ . + . + . + . + . + "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . + . + . + . + . + "12345"^^ . + . + "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . + . + "false"^^ . + "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . + . + . + . + . + . + "75"^^ . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/database/" . + . + . + . + . + . + . + "false"^^ . + "doi" . + . + . + . + "http://sugarbind.expasy.org/"^^ . + . + . + . + . + . + . + "https://cls.shop/"^^ . + "^DDB\\d+$"^^ . + . + "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . + "Data Catalog" . + "http://www.cropontology.org/ontology/CO_335/Common%20Bean"^^ . + . + . + . + . + "false"^^ . + . + . + . + "101"^^ . + "^\\d+$"^^ . + . + "^MIR:001\\d{5}$"^^ . + "true"^^ . + . + "^\\d+$"^^ . + "Scholia Registry" . + "^\\d{8}$"^^ . + . + . + . + . + "2679240"^^ . + . + . + . + . + . + . + "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . + . + . + . + . + "https://www.ebi.ac.uk/chebi/"^^ . + . + . + . + "false"^^ . + . + "0001807"^^ . + . + "^\\d+$"^^ . + . + . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . + . + . + "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "GPST000024"^^ . + "http://www.cs.tau.ac.il/~spike/"^^ . + . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + . + "Molbase" . + . + . + . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . + . + "^KIAA\\d{4}$"^^ . + . + . + "false"^^ . + . + "Variation Ontology" . + . + . + "Korean Cell Line Bank" . + "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . + "false"^^ . + "0000000"^^ . + "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . +_:Nc88b509b31e8421e99d8edf9afedc0d8 "Maria Herrero" . + "https://bioregistry.io/metaregistry/go/$1"^^ . + . + "General Standard for Food Additives Online Database" . + . + "O80725"^^ . + "http://purl.obolibrary.org/obo/ONS_$1"^^ . + . + "http://www.ebi.ac.uk/efo/EFO_$1"^^ . + . + . + "false"^^ . + . + "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . + "https://www.cropontology.org/rdf/CO_338:$1"^^ . +_:Nd62103f69c70456dab389543cbcf9125 "Pierre Sprumont" . + . + . + . + . + . + "Animal Genome Sheep QTL" . + "Fetal Calf Serum-Free Database" . + . + "https://mips.helmholtz-muenchen.de/genre/proj/corum/"^^ . + "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . + . + "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "Mathias Brochhausen" . + . + . + . + "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . + . + . + . + . + . + "false"^^ . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + . + . + "false"^^ . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . + . + . + . + . + "false"^^ . + "biopragmatics/bioregistry/424"^^ . + . + . + "IntAct protein interaction database" . + . + . + "^\\d{7}$"^^ . + . + "MatrixDB Association" . + . + . + . + "^[1-9][0-9]{14}$"^^ . + "000000021"^^ . + . + . + . + "^\\w+$"^^ . + . + . + . + . + . + "Meng LIU" . + . + . + . + . + . + . + "false"^^ . + . + "https://www.wormbase.org/get?name=$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "http://bigg.ucsd.edu/models/$1"^^ . + . + . + "^\\d{8}$"^^ . + . + "https://www.uniprot.org/unirule/$1"^^ . + . + . + . + "doi"^^ . + . + . + . + . + . + "http://e-cyanobacterium.org/models/"^^ . + . + . + . + "https://www.addexbio.com/productdetail?pid=$1"^^ . + . + "false"^^ . + "https://europepmc.org"^^ . + . + "https://sitem.herts.ac.uk/aeru/vsdb"^^ . + . + . + . + "MycoBrowser smegmatis" . + . + . + . + . + . + . + . + . + . + "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . + "63250"^^ . + "Yeast Intron Database v3" . + "https://www.vectorbase.org/"^^ . + "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . + . + . + "false"^^ . + . + . + . + "300108/p3934_A-172"^^ . + "NIF Standard Ontology: Molecules" . + . + "AutDB" . + . + . + "http://lincsportal.ccs.miami.edu/datasets/"^^ . + "https://hpscreg.eu/cell-line/$1"^^ . + . + . + . + . + . + . + "false"^^ . + "0000066"^^ . + . + . + . + . + . + "1242"^^ . + . + . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^ . + . + "Asiyah Yu Lin" . + . + "http://www.gabipd.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . + . + . + "CHEBI" . + "https://www.wwpdb.org/"^^ . + "GO Relations" . + . + . + "https://www.facebase.org"^^ . + . + . + "FlyBase Qualifiers" . + . + . + . + . + "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . + . + . + "https://www.uniprot.org/tissues/$1"^^ . + "^\\d{7}$"^^ . + . + . + . + "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . + "Medaka fish anatomy and development" . + "https://glycopost.glycosmos.org"^^ . + . + "http://www.sparontologies.net/ontologies/scoro"^^ . + . + . + "Software Package Data Exchange License" . + . + . + . + . + . + . + . + "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . + . + . + . + "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . + . + . + . + . + . + . + "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . + . + . + . + . + . + "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . + "https://www.ncbi.nlm.nih.gov/assembly/$1"^^ . + . + . + . + . + . + "http://www.jcvi.org/charprotdb"^^ . + . + . + . + "false"^^ . + . + "http://www.antweb.org/"^^ . + . + . + . + . + . + "Tom Gillespie" . + "https://www.wikidata.org/wiki/Property:$1"^^ . + . + . + "false"^^ . + "https://github.com/PopulationAndCommunityOntology/pco"^^ . + . + "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"^^ . + . + . + . + . + . + "Subcellular Anatomy Ontology" . + . + "2649230"^^ . + . + . + . + "CCLE_867"^^ . + "false"^^ . + "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . + "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^ . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . + . + . + "Yuki Yamagata" . + "^WP\\d{1,5}(\\_r\\d+)?$"^^ . + "Experimental condition ontology" . + "http://sideeffects.embl.de/"^^ . + . + . + . + "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . + "351"^^ . + "MHC Restriction Ontology" . + . + . + . + "false"^^ . + "A controlled vocabulary to support the study of transcription in the primate brain"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/MICRO_$1"^^ . + "^\\d{8}$"^^ . + . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . + "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . + . + . + "^MMP\\d+.\\d+$"^^ . + . + "^AS\\d{6}$"^^ . + . + . + . + . + . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000"^^ . + . + . + . + . + "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . + . + . + . + . + . + "http://string.embl.de/"^^ . + . + "https://github.com/linikujp/OGSF"^^ . + . + . + . + . + . + . + . + "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . + . + . + "https://tripod.nih.gov/bioplanet/"^^ . + . + . + . + . + . + . + "Gene Ontology Registry" . + . + . + . + . + . + . + "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . + "https://www.cropontology.org/rdf/CO_323:$1"^^ . + "Loggerhead nesting" . + . + . + . + . + "false"^^ . + . + "http://edamontology.org/topic_$1"^^ . + "PharmGKB Drug" . + . + . + . + . + . + . + . + . + . + "BioPortal Prefixes" . + . + . + . + . + . + . + . + . + . + . + "000140" . + . + "false"^^ . + . + . + . + . + . + . + . + "Ontology about C. elegans and other nematode phenotypes"^^ . + . + . + "^\\d+$"^^ . + . + "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . + "TA14985"^^ . + . + . + . + "0000111"^^ . + "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . + "https://doulix.com/constructs/$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "Anne Morgat" . + . + . + . + . + . + . + . + "Animal Trait Ontology for Livestock" . + . + . + "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . + . + "bioregistry"^^ . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/COLAO_$1"^^ . + . + "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . + "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . + "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . + "https://smid-db.org/smid/$1"^^ . + . + "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . + . + "false"^^ . + . + . + . + . + . + "Danielle Welter" . + . + "http://www.pantherdb.org/"^^ . + "http://www.drugbank.ca"^^ . + . + . + "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . + . + . + "MU9_3181"^^ . + . + . + . + . + . + . + "^C\\d{8}$"^^ . + . + . + "https://github.com/OpenLHS/LABO"^^ . + . + "https://www.humancellatlas.org"^^ . + . + . + "01406"^^ . + . + . + . + . + . + . "http://purl.obolibrary.org/obo/FBdv_$1"^^ . - . - . - . - "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . - . - "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^ . - "https://europepmc.org"^^ . - . - . - . - . - . - . - . - . - "^(E|D|S)RR[0-9]{6,}$"^^ . - . - "AT1G01030.1"^^ . - . - . - . + . + . + . + "https://www.geonames.org"^^ . + . + "https://vectorbase.org/vectorbase/app/record/gene/$1"^^ . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + "Ion Channel Electrophysiology Ontology" . + "https://openalex.org/"^^ . + . + "false"^^ . + . + . + . + . + . + "http://data.jrc.ec.europa.eu/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MAXO_$1"^^ . + . + . + "http://www.oid-info.com/introduction.htm"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . + "046"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + "^NPC\\d+$"^^ . + "Antibiotic resistance genes and mutations"^^ . + . + . + . + . + . + . + . + "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . + . + . + . + . + "http://www.tcdb.org/search/result.php?tc=$1"^^ . + . + . + . + "false"^^ . + . + . + "Database of Quantitative Cellular Signaling: Model" . + . + . + "^\\d+$"^^ . + . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits."^^ . + "A frontend to Wikidata"^^ . + "http://edamontology.org/data_$1" . + "EP0311"^^ . "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . - "https://sitem.herts.ac.uk/aeru/vsdb"^^ . - . - . - . - . - . - . - . - . - "http://sed-ml.org/"^^ . - "MIMIC III Database" . - . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - "false"^^ . - "Semantic Web Context" . - "jrc-eurl-ecvam-chemagora"^^ . - . - "http://purl.obolibrary.org/obo/ZEA_$1"^^ . - . - "https://github.com/jannahastings/mental-functioning-ontology"^^ . - "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . - "http://www.cabri.org/"^^ . - . - . - . - "https://kaggle.com"^^ . - . - "https://www.deciphergenomics.org/"^^ . - . - "A structured controlled vocabulary for the anatomy of fungi."^^ . - . - "https://www.kegg.jp/entry/$1"^^ . - . - . - . - "^KW-\\d{4}$"^^ . - . - . - "Models developed with the Virtual Cell (VCell) software prorgam."^^ . - . - "http://tfclass.bioinf.med.uni-goettingen.de"^^ . - "278"^^ . - . - . - . - . - . - "ECOLI:CYT-D-UBIOX-CPLX"^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + . + "http://agricola.nal.usda.gov/"^^ . + "http://www.hprd.org/"^^ . + . + . + "https://github.com/PRIDE-Utilities/pride-ontology"^^ . + . + "BiGG Model" . + . + . + . + . + . + . + "true"^^ . + . + "Ontology of Organizational Structures of Trauma centers and Trauma systems" . + . + . + "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . + . + . + . + . + "0001021"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "https://pir.georgetown.edu/"^^ . + . + "Virus Pathogen Resource" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "50943"^^ . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + . + . + . + . + "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . + . + . + . + . + . + . + "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . + . + . + . + . + . + . + . + . + . + . . - . - "00001"^^ . - . - "true"^^ . - . - "Genomic Epidemiology Ontology" . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . - "false"^^ . - . - . - "1"^^ . - . - "https://www.ncbi.nlm.nih.gov/projects/gap"^^ . - . - . - . - . - "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + "Orthology Ontology" . + . + . + "Jim Balhoff" . + . + . + "^(MNXR\\d+|EMPTY)$"^^ . + . + . + "false"^^ . + . + "http://www.treefam.org/"^^ . + . + . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/geo/"^^ . + . + "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . + . + . + . + . + "Jackson Laboratories Strain" . + "Gramene Taxonomy" . + "National Drug Code" . + . + . + . + . + "false"^^ . + "http://purl.org/dc/terms/$1"^^ . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . + "Clare Pilgrim" . + . + . + "^\\d{7}(_\\d)?$"^^ . + . + . + "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "Cell line collections"^^ . + "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . + "http://www.alanwood.net/pesticides/$1.html"^^ . + . + . + . + . + "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + "0000081"^^ . + . + . + . + . + "^[A-Za-z]+$"^^ . + "PyPI" . + "C0001"^^ . + . + "Name-to-Thing" . + "PharmacoDB Datasets" . + . + . + "https://www.genome.jp/kegg/glycan/"^^ . + . + . + "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . + "^(C|D)\\d{6,9}$"^^ . + . + . + "http://www.proglycprot.org/"^^ . + . + . + "28"^^ . + "Semantic Web for Earth and Environment Technology Ontology" . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . + . + . + "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . + . + . + . + "KEGG Genome" . + . + . + "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . + . + . + "http://purl.obolibrary.org/obo/PDUMDV_$1"^^ . + . + . + . + . + "false"^^ . + "0000106"^^ . + . + . + "C. elegans phenotype" . + . + . + . + . + . + "PANTHER Pathway Component" . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "^\\w+\\_\\w+$"^^ . + "http://purl.obolibrary.org/obo/VSAO_$1"^^ . + . + . + "https://reporter.nih.gov/"^^ . + "false"^^ . + . + . + . + "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies"^^ . + . + "Life cycle stages for Platynereis dumerilii"^^ . + . + . + . + . + . + . + . + "Hypertension Ontology" . + . + . + . + . + . + . + . + "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . + . + "Vertebrate Gene Nomenclature Committee" . + "Database of Interacting Proteins" . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . + "false"^^ . + . + . + . + . + . + "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . + "false"^^ . + . + . + . + "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . + "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . + . + . + "Porifera Ontology" . + . + "Panorama Public" . + "false"^^ . + . + . + . + "true"^^ . + "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . + . + . + . + . + "^\\d{7}$"^^ . . - . - . - . - . - "0110974"^^ . - . - . - . - . - "ICEberg element" . - "Oral Health and Disease Ontology" . - "false"^^ . - . - . - . - . - . - "snoRNABase" . - . - . + . + . + . + "TIGR protein families" . + . + . + "false"^^ . + . + . + . + . + . + . + "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml"^^ . + . + _:N1618a3940e7f4abf9d8b141e6627e31f . + . + . + "http://www.mirbase.org/"^^ . + . + "Terminology for Description of Dynamics" . + "OpenAlex" . + . + "ClinVar Record" . + . + . + "HBG004341"^^ . + "KEGG Reaction" . + "http://cicblade.dep.usal.es:8080/APID/"^^ . + . + . + . + . + . + . + "http://www.cathdb.info/domain/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^ML\\w+$"^^ . + . + . + . + . + . + . + . + . + . + . + "Bacterial Diversity Metadatabase" . + . + "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . + . + . + . + "http://purl.org/spar/doco/$1"^^ . + "6200"^^ . + . + . + . + . + . + . + "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . + . + . + . + . + . + "National Experimental Cell Resource Sharing Platform" . + . + . + "https://github.com/insect-morphology/colao"^^ . + "DragonDB Locus" . + "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . + . + . + . + . + . + "https://proteinensemble.org/"^^ . + "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . + . + . + "false"^^ . + . + . + "ND50028"^^ . + "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^ . +_:N05b61d2a477846efa1178c5107d237f1 "Marc Ciriello" . + "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . + . + . + "http://pax-db.org/#!species/$1"^^ . + . + . + . + . + "Yongqun Oliver He" . + . + "ModelDB" . + . + "IID00001"^^ . + "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . + . + . + . + . + . + . + . + . + "Genotype Ontology" . + "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/BCGO_$1"^^ . + "eVOC (Expressed Sequence Annotation for Humans)" . + . + . + . + . + . + . + . + . + . + . + . + "https://github.com/OOSTT/OOSTT"^^ . + . + . + . + . + "Bill Duncan" . + . + . + . + . + . + . + "false"^^ . + "2842"^^ . + . + . + . + . + "Mouse Brain Atlas" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . + "19333"^^ . + "http://www.proteomexchange.org/"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . + . + "https://github.com/biolink/biolink-model" . + "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . + "PathBank" . + . + . + "D00001"^^ . + . + . + "false"^^ . + . + . + . + "MIRIAM Registry collection" . + . + . + . + . + "https://github.com/pombase/fypo"^^ . + . + . + . + "true"^^ . + . + . + . + . + . + "Contains information about cells and data sheets related to transfection."^^ . + . + . + . + . + . + . + . + "The Ontology of Genes and Genomes" . + "CIP - potato ontology - december 2018"^^ . + . + . + . + . + . + . + . + . + "74"^^ . + . + . + . + . + "false"^^ . + . + . + "International repository of Adverse Outcome Pathways."^^ . + . + "http://www.enanomapper.net/"^^ . + . + . + "The Echinoderm Anatomy and Development Ontology" . + "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . + . + . + . + . + . + . + . + . + . + "1801.012"^^ . + "http://neuinfo.org/"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.salk.edu/"^^ . + "^[A-Z0-9]{5}\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . + . + . + "^JCGG-STR\\d{6}$"^^ . + . + "https://www.disprot.org/idpo/IDPO:$1"^^ . + . + . + . + . + "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . + "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . + . + . + . + . + "NIF Standard Ontology: Chemical" . + . + "https://fairsharing.org/"^^ . + . + . + . + . + "Cell line collections"^^ . + "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . + "Bioregistry" . + . + . + . + "International Histocompatibility Workshop cell lines" . + . + . + "HUGO Gene Nomenclature Committee" . + . + "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . + . + . + . + . + "^\\w\\d+$"^^ . + "^\\d+$"^^ . + . + "Index Fungorum" . + "true"^^ . + . + "http://purl.obolibrary.org/obo/FBcv_$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://cancer.sanger.ac.uk/cell_lines/"^^ . + "^\\d{7}$"^^ . + "http://www.p3db.org/"^^ . + "https://foodb.ca/foods/$1"^^ . + . + . + "false"^^ . + . + . + . + "00042"^^ . + "Ontology of Arthropod Circulatory Systems" . + "https://www.gwascentral.org/markers"^^ . + . + . + "false"^^ . + . + "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "https://proconsortium.org/app/entry/PR:$1"^^ . + . + . + . + "Signaling Gateway" . + . + "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . + . + "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."^^ . + "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . + . + . + . + . + "SSF57615"^^ . + . + . + . + . + . + . + . + . + . + "http://www.drugbank.ca/targets"^^ . + . + . + . + "https://github.com/micheldumontier/semanticscience"^^ . + . + "https://github.com/AnimalGenome/livestock-product-trait-ontology"^^ . + . + . + . + . + . + . + . + "false"^^ . + "https://www.perkinelmer.com/"^^ . + "https://www.bio.di.uminho.pt/"^^ . + . + "false"^^ . + "LSM-6306"^^ . + "^[a-z_A-Z0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "P01116"^^ . + . + . + . + . + . + . + "Pharmacogenetics and Pharmacogenomics Knowledge Base" . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^cpd\\d+$"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . + . + . + "HGNC Gene Group" . + . + . + "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . + . + . + . + . + "1"^^ . + . + . + . + . + . + "http://www.jstor.org/stable/$1"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + "http://www.fao.org/gsfaonline"^^ . + "Progenetix" . + "https://www.scopus.com"^^ . + . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . + . + . + . + . + . + . + "http://www.pseudomonas.com/"^^ . + . + . + . + "Sustainable Development Goals Interface Ontology" . + . + . + . + "^[a-zA-Z0-9_-]{3,}$"^^ . + . + . + . + "^\\w+\\_\\d+(\\.\\d+)?$"^^ . + . + . + . + "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . + . + . + "0100002"^^ . + . + . + "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "true"^^ . + . + "ENSFM00500000270089"^^ . + . + "MCDS_S_0000000001"^^ . + . + "Datanator Gene" . + . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . + "https://omabrowser.org/cgi-bin/gateway.pl"^^ . + . + "^A[A-Z]+\\d+$"^^ . + . + "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . + . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + _:N00e71c3083a3461584e6c31c9a4d425d . + . + . + . + . + . + "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . . - . - . - "^CAL\\d{7}$"^^ . - "https://dandiarchive.org/"^^ . - . - . - . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . - . - "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . - "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . - . - . - . - . - . + . + "Protein modification" . + . + . + "AP00378"^^ . + "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . + . + "http://www.narcis.nl"^^ . + . + . + . + "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^ . + . + . + "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . + "Ontologized MIABIS" . + "The SEED;" . + . + "^[A-Za-z0-9]+$"^^ . + "Melanoma Molecular Map Project Biomaps" . + "false"^^ . + . + . + . + "http://jaxmice.jax.org/strain/$1.html"^^ . + "false"^^ . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^ . + . + . + "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^ . + . + "true"^^ . + "100000"^^ . + . + . + "false"^^ . "https://qudt.org"^^ . - . - . - . - "http://qudt.org/schema/qudt#$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Cell Lines in PubChem"^^ . - . - "CAA71118.1"^^ . - . - . - "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"^^ . - . - . - "http://umbbd.ethz.ch/"^^ . - . - . - . - "0400109"^^ . - . - "false"^^ . - . - . - "C. elegans development ontology" . - "33607"^^ . - . - . - "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "0000001"^^ . - . - . - . - "false"^^ . - "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . - . - . - "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . - . - . - "National Center for Biotechnology Information Registry" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - "^RCV\\d+(\\.\\d+)?$"^^ . - "BiGG Compartment" . - . - . - . - . - . - . - . - . - . - "^[A-Za-z]+\\d+$"^^ . - "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . - . - . - . - . - "Morpheus model repository" . - . - "bioRxiv" . - . - . - . - . - . - "http://eawag-bbd.ethz.ch/$1/$1_map.html"^^ . - . - "Bill Duncan" . - . - "https://www.glycoepitope.jp/epitopes/"^^ . - "137"^^ . - "^\\d+$"^^ . - "21723"^^ . - . - . - "https://www.discoverx.com/products-applications/cell-lines"^^ . - "Interlab Cell Line Collection" . - . - . + . + . + . + . + "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . + . + "Lynn Schriml" . + . + . + "SED-ML model format" . + "https://drugs.ncats.io/drug/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "2639"^^ . + . + . + "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . + . + "0000006"^^ . + "false"^^ . + . + "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^ . + "10.1621/vwN2g2HaX3"^^ . + "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . + . + . + . + . + "ABC"^^ . + "http://purl.obolibrary.org/obo/GNO_$1"^^ . + . + . +_:Nb25a11001fb94cab8cdd9b93ffb6b0bf "Stephen Larson" . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "humIGHV025"^^ . + . + . + . + . + . + "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . + . + . + "Arabidopsis Small RNA Project" . + "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "https://github.com/ICO-ontology/ICO"^^ . + "An ontology of prokaryotic phenotypic and metabolic characters"^^ . + . + "265"^^ . + "false"^^ . + . + "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . + "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . + "http://cbg.garvan.unsw.edu.au/pina/"^^ . + "http://bactibase.hammamilab.org"^^ . + . + . + "Peroxibase" . + . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^ . + "http://search.sisuproject.fi/#/variant/$1"^^ . + "http://bioportal.bioontology.org/"^^ . + . + "Global LEI Index" . + "iNaturalist Taxonomy" . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^DP\\d{5}$"^^ . + "REPRODUCE-ME Ontology" . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . + . + "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . + "https://bioregistry.io/collection/$1"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "^[0-9]+$"^^ . + . + "11"^^ . + . + "http://pid.nci.nih.gov/"^^ . + . + . + "https://www.yeastgenome.org/locus/$1"^^ . + . + . + "Coleoptera Anatomy Ontology" . + . + . + . + "false"^^ . + "Biological Collections Ontology" . + . + . + . + . + . + . + "551115"^^ . + . + . + "Conserved Domain Database at NCBI" . + . + "http://si.washington.edu/projects/fma"^^ . + . + "^\\d{7}$"^^ . + "false"^^ . + "Mammalian Feeding Muscle Ontology" . + . + . + "false"^^ . + "0005147"^^ . + . + . + . "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . - . - . - "http://geneontology.org/"^^ . - "PomBase" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "https://www.vectorbase.org/ontology-browser"^^ . + "http://purl.obolibrary.org/obo/EPO_$1"^^ . + . + . + "RAP-DB Locus" . + "Regulation of Gene Expression Ontology" . + "^\\d{7}$"^^ . + . + . + . + . + "http://omia.angis.org.au/"^^ . + . + . + . + "http://webapps2.ucalgary.ca/~groupii/"^^ . + . + . + . + . + . + "1915"^^ . + . + "SUPERFAMILY" . + "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . + . + . + "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . + . + . + "http://www.uniprot.org/uniprot/$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "International Classification of Diseases for Oncology" . + . + . + . + . + . + . + "http://purl.org/spar/biro/$1"^^ . + "https://github.com/obi-bcgo/bcgo"^^ . + . + . + . + . + . + "Potato ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "Francesco Vitali" . + . + "17186"^^ . + . + "European Paediatric Cardiac Codes" . + . + . + . + . + . + "http://www.sequenceontology.org/miso/current_release/term/SO:$1"^^ . + "Gmelins Handbuch der anorganischen Chemie" . + . + . + . + "false"^^ . + "sharesAuthorInstitutionWith"^^ . + . + . + . + "Bjoern Peters" . + "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . + "https://www.humanbehaviourchange.org/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "Hilmar Lapp" . + . + "http://modelseed.org/biochem/compounds/$1"^^ . + "0000091"^^ . + "GWAS Central Marker" . + . + . + . + . + . + "Maize ontology" . + . + "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . + . + . + "true"^^ . + . + . + . + . + . + "http://doqcs.ncbs.res.in/"^^ . + "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . + "^(E|D|S)RR[0-9]{6,}$"^^ . + "0019030"^^ . + . + "http://purl.obolibrary.org/obo/CRO_$1"^^ . + . + . + . + . + "https://neurovault.org/images/$1"^^ . + . + . + "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . + . + . + . + "https://www.va.gov/health"^^ . + "https://github.com/AgriculturalSemantics/agro"^^ . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + . + . + . + . + "Linear double stranded DNA sequences" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://ncim.nci.nih.gov/"^^ . + . + . + "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . + . + "miRBase Families" . + . + . + . + "^A\\d+$"^^ . + . + . + "http://xmlns.com/foaf/0.1/$1"^^ . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . + "http://sabiork.h-its.org/newSearch?q=$1"^^ . + . + . . - "GitHub Pull Request" . - . - . - . - . - . - . - "false"^^ . - . - "ProGlycProt" . - . - . - . - . - . - . - "Distributed Archives for Neurophysiology Data Integration" . - . - . - . - . - "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^ . - . - . - . - . - "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - "Os01t0883800-02"^^ . - "TTD Target" . - . - . - "European Genome-phenome Archive Dataset" . - . - . - . - . - "A download link for the given resource" . - . - "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . - "C6155"^^ . - . - "A_24_P98555"^^ . - . - . - "Hypertension Ontology" . - "false"^^ . - "https://biomodels.net/vocab/idot.rdf#$1"^^ . - . - . - "^[a-zA-Z0-9\\-:#\\.]+$"^^ . - "http://asap.ahabs.wisc.edu/asap/home.php"^^ . - . - . - "CE28239"^^ . - . - "EU Clinical Trials" . - "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . - "https://pfam.xfam.org"^^ . - . + . + "false"^^ . + "240-17-488-3-4-12"^^ . + "^\\d+$"^^ . + "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies."^^ . + "ADA"^^ . + "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . + "The International Harmonization of Nomenclature and Diagnostic criteria" . + . "github" . - . - . - "Oryzabase Mutant" . - "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . - "NASA GeneLab" . - . - . - "^JCGG-STR\\d{6}$"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "0000400"^^ . - "http://purl.obolibrary.org/obo/$1"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - "mKIAA4200"^^ . - . - . - "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . - "IntAct Molecule" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "1044544"^^ . - "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . - "false"^^ . - . - . - _:N8ebd69fb45dc4921afb4d7643fbcd91c . - . + "^M\\d{5}$"^^ . + . + "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . + . + "false"^^ . + "0000339"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Illumina Probe Identifier" . + . + . + . + . + . + . + . + . + "Adverse Event Reporting Ontology" . + . + "ACH-000001"^^ . + . + "false"^^ . + . + . + . + "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . + . + "Bacterial Tyrosine Kinase Database" . + "true"^^ . + "J0705A10"^^ . + "Relation Ontology" . + . + . + "HBB"^^ . + . + . + . + . + . + "http://www.orpha.net/ORDO/Orphanet_$1"^^ . + . + "http://purl.obolibrary.org/obo/TAHE_$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Cell Line Database" . + . + . + "00100037"^^ . + "0000070"^^ . + . + "CryptoDB" . + . + . + "Q9UKQ2"^^ . . - "^MSV\\d+$"^^ . - "Human developmental anatomy, abstract" . - . - . - "47419"^^ . - "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/STATO_$1"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "MEROPS Entry" . + "Lonza" . + . + "false"^^ . + "false"^^ . + "Pigeonpea ontology" . + "ANOVA"^^ . + _:N85c09898c2cc4155934cacdac0abfb35 . + . + . + "https://github.com/EBISPOT/clyh_ontology"^^ . + . + . + . + . + "Benchmark Energy & Geometry Database" . + "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . + . + . + . + "3075966"^^ . + . + . + . + . + . + . + . + . + . + "PRINTS compendium of protein fingerprints" . + . + . + . + . + . + . + . + . + . + . + . + "baseDimensionEnumeration"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "4.2.78"^^ . + . + "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . + . + . + . + . + . + . + . + . + "ALIENSPECIES" . + "^\\w+$"^^ . + "false"^^ . + "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . + . + "Viral Bioinformatics Resource Center" . + . + . + "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . + . + "37232"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "NPC139585"^^ . + . + "AphidBase Transcript" . + "0002999"^^ . + "false"^^ . + . + . + . + "Sickle Cell Disease Ontology" . + "http://www.metabolomicsworkbench.org/"^^ . + "false"^^ . + "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1"^^ . + "^Q[A-Z0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + "https://www.genedb.org/gene/$1"^^ . + . + . + . + . + "Vitis ontology" . + . + . + "false"^^ . + "https://gen3.biodatacatalyst.nhlbi.nih.gov"^^ . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + "https://www.nextmovesoftware.com/namerxn.html"^^ . + "Funding, Research Administration and Projects Ontology" . + . + . + . + "Ontology of Host-Microbiome Interactions" . + . + "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . + . + . + . + . + "Ctenophore Ontology" . + "^\\d+\\-\\d+\\-\\d+$"^^ . + "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . + . + "https://www.ohdsi.org/data-standardization/the-common-data-model/"^^ . + "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . + . + . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + "Rv1908c"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "true"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . . - . - . - . - "http://tolweb.org/$1"^^ . - "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . - . - "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . - . - . - "false"^^ . - . - . - . - . - "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . - . - . - . - "CutDB" . - . - . - . - . - "http://www.ncbi.nlm.nih.gov/CCDS/"^^ . - . - . - . - . - "false"^^ . - . - "Ramona Walls" . - . - "51"^^ . - . - . - . - . - "STOREDB at University of Cambridge" . - . - "Japan Consortium for Glycobiology and Glycotechnology Database" . - "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . - . - . - "0000026"^^ . - . - . - "http://purl.obolibrary.org/obo/OGSF_$1"^^ . - . - . - . - "^\\d+$"^^ . - "Mechanism, Annotation and Classification in Enzymes" . - "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ECTO_$1"^^ . - . - . - . - "Application ontology for entities related to insecticide resistance in mosquitos"^^ . - "351"^^ . - . - "false"^^ . - . - "http://bacmap.wishartlab.com/organisms/$1"^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HTN_$1"^^ . - . - . + . + . + . + . + "0221"^^ . + . + . + "https://github.com/ontoice/ICEO"^^ . + . + . + . + . + . + "0000011"^^ . + . + "87"^^ . + . + "2gc4E"^^ . + . + "https://www.jax.org/strain/$1"^^ . + . + . + . + . + . + "http://www.chemspider.com/"^^ . + . + . + "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . + . + "ADM1"^^ . + "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . + . + . + . + . . - "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . - "false"^^ . - . - . - "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . - "^NONHSAT\\d{6}$"^^ . - "Xenbase" . - "Matthew Brush" . - . - . - . - . - . - . - "https://rnacentral.org/rna/$1"^^ . - . - "^\\d{8}$"^^ . - . - "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . - . - "http://elm.eu.org/"^^ . - . - . - . - "false"^^ . - . - . - "http://exac.broadinstitute.org/"^^ . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . - . - "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - "0100002"^^ . - . - "^\\d+$"^^ . - "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^ . - . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . - . - . - "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "BRENDA, The Comprehensive Enzyme Information System" . - . - "false"^^ . - . - . - . - . - "A web-developer centric archive of prefixes and URI prefixes" . - . - "false"^^ . - "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . - . - "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . - . - . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/VT_$1"^^ . - "http://www.bioguo.org/AnimalTFDB/family_index.php"^^ . - "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . - . - . - . - "Python"^^ . - . - "^BSU\\d{5}$"^^ . - "false"^^ . - . - . - . - . - . - . - "1100107"^^ . - . - . - . - . - . - . - "false"^^ . + . + . + . + "Golm Metabolome Database Analyte" . + . + . + "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^ . + . + . + . + . + "https://www.gsea-msigdb.org"^^ . + . + . + "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "https://protists.ensembl.org/id/$1"^^ . + . + "false"^^ . + . + . + "Lutz Fischer" . + "http://lisanwanglab.org/DASHR/"^^ . + . + . + . + . + "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . + . + . + . + . + . + . + . + "https://www.who.int/teams/health-product-and-policy-standards/inn"^^ . + . + . + . + . . - . - . - . - . - "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato"^^ . - "Yeast Intron Database v3" . - . - . - "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . - . - "Protein Model Database" . - . - . - . - . - "2"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "^MMAR\\_\\d+$"^^ . - . - "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^ . - . - "Tick Anatomy Ontology" . - "Software"^^ . - . - . - . - "^\\d{5}$"^^ . - . - . - "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . - . - "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . - . - . - . - "https://www.uniprot.org/keywords/$1"^^ . - . - . - . - . - . - . - . - . - . - "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . - . - . - "Li7"^^ . - "National Drug File - Reference Terminology" . - . - . - . - "00000443"^^ . - "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp"^^ . - "0000005"^^ . - "^[A-Za-z0-9+_.%-:]+$"^^ . - . - . - . - "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . - . - . - . + . + . + "154022"^^ . + . + . + . + . + . + . + "SIGNOR-252737"^^ . + . + "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . + . + . + "^GN_[A-Za-z0-9_:]+$"^^ . + "false"^^ . + "false"^^ . + . + . + . + "http://www.dukeontologygroup.org/Projects.html"^^ . + . + "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules"^^ . + . + . + . + . + . + . + "LCSCCPN"^^ . + . + . + "false"^^ . + . + . + . + _:Nf8cc7561ff47495ca15ab9427619ec89 . + . + . + . + . + . + . + "S1"^^ . + "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . + "KEGG Module" . + "http://taibnet.sinica.edu.tw/home.php"^^ . + . + . + . + "false"^^ . + . + "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . +_:N58427d5b8fd140d785a13ae0161ee671 "chEBI" . + . + "https://stemcells.nindsgenetics.org"^^ . + . + "rs11603840"^^ . + . + "YMDB00001"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/PubMed/"^^ . + . + "The Amphioxus Development and Anatomy Ontology" . + . + . + "http://purl.obolibrary.org/obo/SCDO_$1"^^ . + "GeoNames" . + . + "Decentralized Identifier" . + . + "http://tfclass.bioinf.med.uni-goettingen.de"^^ . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + "A database of fly neurons and pathways with an associated 3D viewer."^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . + . + . + . + . + . + . + "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . + . + "^\\d{7}$"^^ . + . + . + "0000001"^^ . + . + . + . + . + . + . + . + . + "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . + . + "Plant Experimental Conditions Ontology" . + . + . + . + . + . + . + . + "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . + . + "https://nci-crdc.datacommons.io/"^^ . + "https://github.com/Planteome/plant-stress-ontology"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . + . + "http://zinc15.docking.org/"^^ . + . + . + "false"^^ . + . + . + "TrichDB" . + . + . + "C2584994"^^ . + . + "Metabolite and Tandem Mass Spectrometry Database" . + "https://licebase.org/?q=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "UPI000000000A"^^ . + "M00002"^^ . + . + "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . + "false"^^ . + . + . + . + . + "Tetrahymena Genome Database" . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . + "0000009"^^ . + "false"^^ . + . + "Olfactory Receptor Database" . + . + . + . + "MetaboLights Compound" . + . + . + . + "Online Mendelian Inheritance in Animals" . + . + . + . + . + . + . + . + . + . + . + . + . + "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . + . + "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "Kinetic Simulation Algorithm Ontology" . + . + . + "Allen Institute Ontologies" . + . + . + "http://caps.ncbs.res.in/pass2"^^ . + . + . + . + "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . + . + . + "M58335"^^ . + . + . + "https://VirtualFlyBrain.org"^^ . + . + . + . + . + . + "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . + "^ACYPI\\d{6}(-RA)?$"^^ . + "https://bioportal.bioontology.org/ontologies/NPO"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "https://www.imanislife.com/collections/cell-lines/"^^ . + "https://cmecscatalog.org/cmecs"^^ . + . + . + "https://pav-ontology.github.io/pav/"^^ . + . + "http://www.transcriptionfactor.org/"^^ . + . + . + . + "BRENDA Ligand Group" . + . + . + . + "http://www.pharmgkb.org/pathway/$1"^^ . + . + "false"^^ . + . + . + . + "https://web.expasy.org/variant_pages"^^ . + . + "http://ifomis.org/bfo/"^^ . + "https://microbiomedata.org/"^^ . + . + "PR000001"^^ . + . + . + "MedlinePlus Health Topics" . + . + . + "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . + . + "SRX000007"^^ . + . + "https://www.w3.org/ns/dcat"^^ . + . + "false"^^ . + "CHEBI"^^ . + . + . + . + . + . + . + "NONHSAG00001"^^ . + "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html"^^ . + . + "Suzi Aleksander" . + "0376"^^ . + . + . + . + . + . + "false"^^ . + . + "https://w3id.org/oc/corpus"^^ . + "https://bitbucket.org/hegroup/ogg"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . + "https://www.goreni.org/gr3_nomenclature.php"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "ExAC Gene" . + "Foods in FooDB"^^ . + "^[A-Za-z 0-9]+$"^^ . + "false"^^ . + . + . + "false"^^ . + . + . + "http://autism.mindspec.org/GeneDetail/$1"^^ . + "GCA_000155495.1"^^ . + . + . + . + . + . + . + "0007133"^^ . + "MULT_4_VAR1_bovine"^^ . + "false"^^ . + . + . + . + . + . + "2008-005144-16"^^ . + "false"^^ . + . + . + . + . + . + . + "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1"^^ . + . + . + "TreeFam" . + . + . + "^\\d+$"^^ . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + . + "CATH superfamily" . + . + . + . + . + . + . + . + . + "aap-1"^^ . + . + "https://www.wikidata.org" . + . + . + . + . + . + . + . + "^C\\d+$"^^ . + . + "https://github.com/phenoscape/vertebrate-taxonomy-ontology"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/$1"^^ . + . + . + . + "137"^^ . + "https://www.uniprot.org/diseases/"^^ . + . + "derivatives%2Fthiocyclam%20hydrochloride"^^ . + . + . + . + "^(\\w+)?\\d+$"^^ . + . + . + "https://protists.ensembl.org"^^ . + "Wikipedia" . + "https://www.datanator.info/gene/$1"^^ . + . + "1"^^ . + "https://bioportal.bioontology.org/ontologies/BIRNLEX"^^ . + "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . + . + . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . + . + . + . + "Marijane White" . + "PF11_0344"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . + "^[0-9]+$"^^ . + . + . + . + . + "false"^^ . + "http://jcggdb.jp/idb/jcggdb/$1"^^ . + . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . + . + "Selventa Complexes" . + "^\\d+$"^^ . + "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . + . + "NIF Gross Anatomy" . + . + . + . + . + "Molecular Interactions Controlled Vocabulary" . + . + "The Behaviour Change Intervention Ontology" . + . + . + . + . + "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . + . + . + . + . + . + "74"^^ . + . + . + . + . + "uc001rvw.5"^^ . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + "^\\d+(\\w+)?$"^^ . + . + . + . + . + "NIF Dysfunction" . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + . + . + . + . + . + "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . + . + . + "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^ . + . + "^LTS\\d{7}$"^^ . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + . + "^FDB\\d+$"^^ . + "Protein Alignment organised as Structural Superfamily" . + . + "0002233"^^ . + "ClinVar Variation" . + . + "http://purl.obolibrary.org/obo/IMR_$1"^^ . + "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . + . + "Tom Gillespie" . + . + "^\\d+$"^^ . + "^\\w+$"^^ . + "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . + . + . + . + . + "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . + . + "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . + "https://www.ebi.ac.uk/biomodels/"^^ . + . + "OriDB Schizosaccharomyces" . + . + "false"^^ . + . + . + "Rebecca Jackson" . + . + . + . + . + "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1"^^ . + . + "http://www.sparontologies.net/ontologies/doco"^^ . + . + . + . + . + . + . + . + . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . + "http://hawaii.eagle-i.net/i/$1"^^ . + . + . + "12300"^^ . + . + "MLCommons Association" . + "75121530"^^ . + "false"^^ . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . + . + . + "^\\d+$"^^ . + . + . + "Unified Medical Language System Concept Unique Identifier" . + "https://www.yeastgenome.org/"^^ . + "0000144"^^ . + "^CHEMBL\\d+$"^^ . + "NIF Standard Ontology: Investigations" . + . + . + "http://cdb.ics.uci.edu/"^^ . + "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . + . + . + "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . + "0000190"^^ . + . + . + . + "Metabolic Encyclopedia of metabolic and other pathways" . + "true"^^ . + . + . + . + . + . + "HOMD Taxonomy" . + "appears in" . + "Cellosaurus Registry" . + . + . + . + "https://www.internationalgenome.org/data-portal/sample/$1"^^ . + . + . + . + . + "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . + . + "false"^^ . + . + "false"^^ . + "BAMSC981"^^ . + "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . + . + . + . + "nb100-56351"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . + . + . + "^\\d+$"^^ . + . + "http://purl.obolibrary.org/obo/EMAP_$1"^^ . + . + . + . + . + . + . + . + . + . + "A01M1/026"^^ . + . + "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . + . + . + . + . + "10.1101/2022.07.08.499378"^^ . + . + . + . + . + "A nomenclatural ontology for biological names" . + . + . + . + "https://github.com/OPMI/opmi"^^ . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/COB_$1"^^ . + . + _:N3e609a1f28e14528b79ba310b0b63dce . + "UniProt Diseases" . + . + . + . + . + . + . + . + "^GR\\_tax\\:\\d+$"^^ . + . + . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Cephalopod Ontology" . + . + "Donny Winston" . + . + "EBI-366083"^^ . + . + . + "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . + . + . + . + . + . + "http://swissregulon.unibas.ch"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^ . + "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . + "GitLab" . + . + . + "http://www.w3.org/2002/07/owl#$1"^^ . + "SEED Reactions" . + . + . + . + . + . + . + . + "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . + . + . + . + "638309541"^^ . + "Addgene Plasmid Repository" . + . + . + . + . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . + . + . + . + . + "https://bacteria.ensembl.org/id/$1"^^ . + . + . + . + . + . + "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . + "MobiDB" . + "Classification of Transcription Factors in Mammalia" . + . + . + . + . + . + . + . + . + . + "ECU03_0820i"^^ . + "Jonathan Karr" . + . + . + . + "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . + "https://bioportal.bioontology.org/"^^ . + . + . + "https://signor.uniroma2.it"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "^[0-9]{8}$"^^ . + "Ontology for General Medical Science" . + . + . + . + "false"^^ . + "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . + "^[A-Z0-9]+$"^^ . + . + . + "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . + . + . + . + . + . + . + . + . + "EJH014"^^ . + . + . + "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . + "0000000"^^ . + . + . + . + "false"^^ . + . + . + . + "http://topdb.enzim.hu/?m=show&id=$1"^^ . + . + "ASPL0000349247"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + "http://edamontology.org/operation_$1"^^ . + . + . + . + "https://bitbucket.org/$1"^^ . + . + . + "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"^^ . + . + . + . + . +_:N0a2ecbcf5c914606819960fd17c853ed "Onard Mejino" . + . + . + . + . + . + . + "Name-to-Thing" . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "^\\w+$"^^ . + . + . + . + . + "false"^^ . + "chebi" . + . + . + "http://bis.zju.edu.cn/ricenetdb/"^^ . + "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Cell line databases/resources"^^ . + "false"^^ . + "false"^^ . + . + "https://www.eurofir.org"^^ . + . + . + . + "true"^^ . + . + . + "http://www.gramene.org/"^^ . + . + "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . + . + . + "Yeast Deletion and the Mitochondrial Proteomics Project" . + "https://bgee.org/?page=gene&gene_id=$1"^^ . + "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . + . + "false"^^ . + "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . + . + . + . + "http://www.coloncanceratlas.org"^^ . + . + . + . + "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . + . + . + . + . + "Spectral Database for Organic Compounds" . + "false"^^ . + "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . + "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . + . + . + . + . + "http://ecolexicon.ugr.es/en/index.htm"^^ . + . + . + "Topology Data Bank of Transmembrane Proteins" . + . + . + . + . + "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . + "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . + . + . + "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . + . + . + . + . + "false"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . + "https://viralzone.expasy.org/$1"^^ . + . + "^\\d+$"^^ . + . + . + "NONHSAT000001"^^ . + . + . + . + . + "^\\d+$"^^ . + "true"^^ . + "https://www.icd10data.com/ICD10CM"^^ . + . + . + . + . + . + "COG0001"^^ . + . + . + . + . + . + "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . + "http://senselab.med.yale.edu/OdorDB"^^ . + "D001151"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "http://geneontology.org/docs/guide-go-evidence-codes/"^^ . + "https://disprot.org/"^^ . + "false"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . + . + . + "^\\d+$"^^ . + "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines)."^^ . + . + . + . + "https://rfam.xfam.org/"^^ . + "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . + "has reviewer" . + . + "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . + . + "Tissue List" . + "GE86325"^^ . + . + . + . + "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . + "ASRP1423"^^ . + . + . + . + . + . + "Melanie Courtot" . + . + . + . + "ABE-0009634"^^ . + . + . + . + . + "https://github.com/obophenotype/upheno"^^ . + "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + . + . + . + . + . + . + . + . + "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . + . + . + . + "ProtoNet Cluster" . + "http://purl.obolibrary.org/obo/ZECO_$1"^^ . + . + . + . + "Pier Luigi Buttigieg" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "Mental Disease Ontology" . + . + . + . + . + . + "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . + . + . + "http://purl.obolibrary.org/obo/MAT_$1"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . "^\\d{8}$"^^ . - "false"^^ . - . - "Reaxys" . - . - . - . - "false"^^ . - . - . - . - . - . - "Andrew G. McArthur" . - . - . - . - . - . - . - . - . - "BN000065"^^ . - . - "The bioRxiv is a preprint server for biology"^^ . - "http://trace.ddbj.nig.ac.jp/bioproject/"^^ . - . - . - . - . - . - "^IHW\\d+$"^^ . - . - . - . - . - "^[1-9][0-9]{14}$"^^ . - . - . - . - "https://gudmap.org/id/$1"^^ . - . - "https://cropontology.org/ontology/CO_339/Lentil"^^ . - . - _:Naf58c96bde474ef892cb9e1824f8c4c6 . - . - "Yam ontology" . - "Cell line databases/resources"^^ . - "http://www.alanwood.net/pesticides/$1.html"^^ . - . - "^\\w+$"^^ . - . - . - "^\\d+$"^^ . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . - "^\\d+$"^^ . - "https://www.hdruk.ac.uk"^^ . - . - . - . - "JAX Mice" . - . - . - . - "https://github.com/BgeeDB/homology-ontology"^^ . - "true"^^ . - . - . - "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . - . - . - "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . - . - . - "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . - . - . - . - "NIF Gross Anatomy" . - . - "0000040"^^ . - . - "MultiCellDS collection" . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "Minimum Anformation About a Phylogenetic Analysis Ontology" . - . - "http://bioportal.bioontology.org/ontologies/OPB"^^ . - "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . - . - . - "false"^^ . - "https://gitub.u-bordeaux.fr/erias/fideo"^^ . - "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . - . - . - . - "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . - . - . - . - . - "MeSH 2013" . - . - . - "https://www.ebi.ac.uk/metagenomics/"^^ . - . - . - . - . - "http://drugcentral.org/drugcard/$1"^^ . - "http://bis.zju.edu.cn/ricenetdb/"^^ . - . - . - "^\\w+$"^^ . - . - "^CCDS\\d+\\.\\d+$"^^ . - "^DB\\d{5}$"^^ . - "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . - . - "false"^^ . - "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . - . - . + . + . + . + . + . + "0000215"^^ . + "https://www.uniprot.org/docs/ptmlist"^^ . + . + . + . + . + . + . + . + "false"^^ . + "15000"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . + "Berkeley Drosophila Genome Project EST database" . + . + . + . + . + "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . + . + "0004828"^^ . + "https://casrai.org/credit/"^^ . + . + . + "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"^^ . + . + . + . + . + "InTextReferencePointer"^^ . + "NCBI Probe database Public registry of nucleic acid reagents" . + . + . + "https://www.ebi.ac.uk"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "International Classification of Diseases, 10th Revision, Procedure Coding System" . + . + . + . + . + . + "http://www.imgt.org/"^^ . + . + . + . + . + . + . + . + "0001"^^ . + "MMAR_2462"^^ . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "^PGS[0-9]{6}$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^ . + . + . + "2023"^^ . + "https://co.mbine.org/standards/"^^ . + "https://bdsc.indiana.edu/stocks/$1"^^ . + "^\\d+$"^^ . + "0000512"^^ . + "GOLD genome" . + "Intrinsically Disordered Proteins Ontology" . + . + . + "E. coli Metabolite Database" . + "rsk00410"^^ . + . + . . - "^[a-z]+(\\-[a-z]+)*$"^^ . - . - . - "false"^^ . - "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . - . - "4D Nucleome Data Portal Experiment Replicate" . - . - "false"^^ . - . - . - . - . - . - . - "Fernanda Dorea" . - . - "https://www.uniprot.org/database/" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "http://solgenomics.net/"^^ . - "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . - . - . - "UPI000000000A"^^ . - . - "STOREDB at University of Cambridge" . - "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . - . - . - "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^ . - . - "0000080"^^ . - . - . - "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . - "International Histocompatibility Workshop cell lines" . - . - . - . - . - . - . - . - "130502"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - "FBgn0000015"^^ . - "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . - . - . - "Extensible Markup Language" . - "false"^^ . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . - "^EGAD\\d{11}$"^^ . - . - "https://portal.issn.org/resource/ISSN/$1"^^ . - . - "Phenotype And Trait Ontology" . - "^PD\\d+$"^^ . - . - . - "Banco de Celulas do Rio de Janeiro" . - . - "PiroplasmaDB" . - "2673500"^^ . - . - "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . - . - . - . - . - . - . - "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . - . - "Database of Interacting Proteins" . - . - . - . - . - . - . - "A database of fly neurons and pathways with an associated 3D viewer."^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "false"^^ . - "Fission Yeast Phenotype Ontology" . - . - . - "Insertion sequence elements database" . - "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . - . - . - "^\\w+$"^^ . - "http://www.guidetopharmacology.org/targets.jsp"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "File inside StoreDB"^^ . - . - . - "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . - "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^ . - . - . - "Tom Gillespie" . - . - . - "http://www.gramene.org"^^ . - . - . - . - "Epilepsy Ontology" . - . - . - . - . - . - "false"^^ . - . - "NCBI PubChem database of bioassay records" . - . - "false"^^ . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . - . - "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . - . - . - . - . - . - "false"^^ . - . - "^G\\d+$"^^ . - . - . - . - . - "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . - "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . - . - . - . - . - "^[A-Z_0-9]+$"^^ . - "https://cordis.europa.eu/article/id/$1"^^ . - . - . - . - . - . - . - . - . - . - "Simplified molecular-input line-entry system" . - "http://www.isni.org"^^ . - . - . - . - "http://matrixdb.univ-lyon1.fr/"^^ . - "https://w3id.org/faircookbook/$1"^^ . - "https://repo.napdi.org/"^^ . - . - . - . - "E-MTAB-2037"^^ . - . - "false"^^ . - . - "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . - . - . - . - . - "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - . - . - "https://morpheus.gitlab.io/models/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "https://github.com/INO-ontology/ino"^^ . - . - "https://models.physiomeproject.org/exposure/$1"^^ . - . - "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . - . - . - "false"^^ . - . - . - "https://www.geonames.org"^^ . - . + . + . + . + . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . + . + . + "CATH domain" . + . + . + . + "Salk Institute for Biological Studies" . + . + "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . + "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . + . + . + . + . + . + "5277619"^^ . + . + . + . + . + "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html"^^ . + "https://animaldiversity.org/accounts/$1"^^ . + . + . + "Zebrafish Information Network Gene" . + . + . + . + . + . + . + . + . + "https://n2t.net/$1:" . + . + . + . + . . - . - "false"^^ . - "00020134"^^ . - . - . - "^T\\d{3}$"^^ . - . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . - . - . - . - . - "World Register of Marine Species" . - . - . - . - . - . - . - . - . - "http://www.antirrhinum.net/"^^ . - "false"^^ . - "false"^^ . - "https://www.ebi.ac.uk/biosamples/"^^ . - "InterLex" . - "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . - "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . - "Amos Bairoch" . - "TC010103"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "01467"^^ . - . - "90801"^^ . - . - . - . - . - . - "Person"^^ . - "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . - . - . - . - . - "Janna Hastings" . - . - . - . - . - . - . - . - . - . - . - "https://dandiarchive.org/dandiset/$1"^^ . - . - . - . - . - . - . - "603903"^^ . - "^MTBLS\\d+$"^^ . - "PlasmoDB" . - "ProDom" . - . - . - "false"^^ . - . - . - . - "0000091"^^ . - "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^ . - . - . - . - . - "MIR:00000008"^^ . - "false"^^ . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . - . - . - . - "Zoë May Pendlington" . - . - . - . - . - . - . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . + . + "00000022"^^ . + . + . + . + . + . + . + . + . + . + "http://www.sisuproject.fi/"^^ . + . + "^\\d+$"^^ . + "^[0-9]+$"^^ . + "0001000"^^ . + . + . . - . - "saddan"^^ . - "0000504"^^ . - . - . - "^\\d{8}$"^^ . - . - "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . + "^\\d{7}$"^^ . + . + "^SIGNOR-\\d+$"^^ . + . +_:N78c15455a378489a85b18cf5e05504c0 "Matt Berriman" . + "LIPID MAPS" . + . + "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . + "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt"^^ . + . + . + "false"^^ . + "Selventa Diseases" . + "^PA\\d+$"^^ . + . + . + "false"^^ . + . + "LOC_Os01g49190"^^ . + . + "Bill Hogan" . + . + . + "https://github.com/obo-behavior/behavior-ontology/"^^ . + . + . + . + . + "ENSG00000139618"^^ . + "BioNumbers" . + . + "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . + . + "snoRNABase" . + . + . + . + "false"^^ . + . + "00000021"^^ . + . + . + "QJ51RV02"^^ . + "false"^^ . + . + . + "Mark Engelstad" . + . + . + "false"^^ . + . + . + . + . + . + . + "^\\d{8}$"^^ . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . + . + . + "false"^^ . + . + . + "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . + "Integrative and Conjugative Element Ontology" . + . + . + . + "false"^^ . + "false"^^ . + . + "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^ . + . + . + "^PRO_[0-9]{10}$"^^ . + . + . + . + "false"^^ . + "https://www.ebi.ac.uk/arrayexpress/"^^ . + "false"^^ . + . + . + "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^ . + . + . + "http://doqcs.ncbs.res.in/"^^ . + . + . + . + "https://easychair.org/cfp/$1"^^ . + . + "hsa-mir-200a"^^ . + . + . + . + "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . + "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . + . + . + "false"^^ . + . + . + . + "1000290"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . + . + . + . + . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + . + . + "http://www.imgt.org/ligmdb/view?id=$1"^^ . + . + . + . + . + "http://lsdis.cs.uga.edu/projects/glycomics/propreo/"^^ . + . + . + . + "http://sideeffects.embl.de/drugs/$1"^^ . + . + . + . + . + "Cell line collections"^^ . + . + "http://purl.obolibrary.org/obo/BILA_$1"^^ . + . + . + . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . . - . + "^\\d+$"^^ . + . + "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . + . + . + "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . + . + . + . + . + . + "https://rarediseases.info.nih.gov/diseases"^^ . + "E-cyanobacterium rule" . + . + "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . + "Mike Tyers" . + . + . + "Human developmental anatomy, abstract" . + . + . + . + . + "true"^^ . + "C. elegans development ontology" . + "Pathogen Transmission Ontology" . + "https://www.cropontology.org/rdf/CO_341:$1"^^ . + . + . + . + "Michel Dumontier" . + "NIF Standard Ontology: OEN Terms in Neurolex" . + . + . + . + "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . + "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . + "^\\d{4}$"^^ . + . + . + "frim1"^^ . + . + "https://bioregistry.io/resolve/github/issue/$1"^^ . + "false"^^ . + . + . + . + . + . + "International Classifications of Diseases" . + . + . + "Zebrafish Phenotype Ontology" . + . + . + "^\\d+$"^^ . + . + . + "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . + . + "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . + . + . + . + "Ontology for Parasite LifeCycle" . + "000000159"^^ . + . + . + "^[1-9]\\d{0,6}$"^^ . + . + . + "European Genome-phenome Archive Dataset" . + . + "https://www.oclc.org/en/about.html"^^ . + "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . + . + "https://wiki.phenoscape.org/wiki/Curation_workflow"^^ . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + . + "P53350"^^ . + . + . + "true"^^ . + . + . + . + "MassBank" . + . + . + "Information about the C57BL/6J. Includes genetic background and disease data."^^ . + . + "26957"^^ . + "NCI Thesaurus" . + . + . + . + "Drosophila RNAi Screening Center" . + . + . + . + "NX_O00165"^^ . + . + "false"^^ . + . + . + . + . + . + . + "http://plasmodb.org/plasmo/"^^ . + "https://hamap.expasy.org/"^^ . + . + "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + . + . + . + . + . + . + "false"^^ . + . + "ArrayExpress Platform" . + "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . + . + . + . + . + . + . + "Cell line databases/resources"^^ . + . + . + . + "https://biorxiv.org"^^ . + . + "P23298"^^ . + . + "^\\d{7}$"^^ . + . + "^NOR\\d+$"^^ . + "An experimental run, served thrugh the ENA"^^ . + . + . + . + "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . + . + . + . + "false"^^ . + . + . +_:Nafa6b93512254c399bee788072cfcae3 "Christos (Kitsos) Louis" . + . + "https://biological-expression-language.github.io/"^^ . + "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . + . + "27106865"^^ . + . + . + . + . + "Chris Grove" . + . + . + "https://www.metanetx.org/equa_info/$1"^^ . + . + "https://github.com/semanticchemistry/semanticchemistry"^^ . + . + . + "^CONSO\\d{5}$"^^ . + "^[a-z_\\.]+$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . + . + "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . + . + . + "https://pfam.xfam.org/family/$1"^^ . + . + "false"^^ . + "false"^^ . + "CranioMaxilloFacial ontology" . + "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . + "http://purl.obolibrary.org/obo/fbcv"^^ . + "DAP000773"^^ . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "http://www.w3.org/2001/XMLSchema"^^ . + _:Ne459e12c22ae4cd08cc8ca747998c144 . + . + "^\\d+$"^^ . + . + . + . + . + "^[A-Z\\-]+$"^^ . + . + . + . + "http://amoebadb.org/amoeba/"^^ . + . + . + "Aceview Worm" . + . + "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^ . + . + . . - "https://fairsharing.org/$1" . - "50-00-0"^^ . - . - . - . - . - . - . - "0000072"^^ . - "http://purl.obolibrary.org/obo/HSAPDV_$1"^^ . - "^[a-zA-Z0-9_-]{3,}$"^^ . - . - . - "7499841"^^ . - . - . - . - . - "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . - . - "http://seed-viewer.theseed.org/seedviewer.cgi"^^ . - . - . - "https://VirtualFlyBrain.org"^^ . - . - "^\\d{7}$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "PA146123006"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "57"^^ . - . - . - . - . - . - . - "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . - . - "^\\d{4}$"^^ . - "false"^^ . - . - . - . - "http://www.evoio.org/wiki/MIAPA"^^ . - . - . - . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - . - . - "^\\d+$"^^ . - "http://www.mesquiteproject.org/ontology/Loggerhead/index.html"^^ . - . - . - . - . - "Genotype-Tissue Expression" . - . - . - . - . - . - . - . - . - . - "0000005"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "1174"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^DBSALT\\d{6}$"^^ . - . - . - "^\\d+$"^^ . - . - . - "Cell line collections"^^ . - . - . - . - . - . - "Database of Sequence Tagged Sites" . - . - . - "^\\w+$"^^ . - . - . - . - . - "http://purl.org/cerif/frapo/$1"^^ . - . - . - "https://bioportal.bioontology.org/ontologies/VSO"^^ . - . - . - . - . - . - . - . - . - "MNXR101574"^^ . - . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . - . - . - . - "http://www.orpha.net/consor/"^^ . - . - . - . - . - . - . - "https://github.com/obophenotype/ctenophore-ontology"^^ . - . - . - . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . - . + "false"^^ . + . + . + "https://spdx.org/licenses/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/UBERON_$1"^^ . + "false"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "^\\d+$"^^ . + . + "Ruili Huang" . + "An ontology of traits covering vertebrates"^^ . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . + . + . + . + . + "https://reg.clinicalgenome.org"^^ . + "0002989"^^ . + . + . + "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . + "false"^^ . + . + . + . + . + "https://pbil.univ-lyon1.fr/databases/hovergen.php"^^ . + . + . + . + "http://epd.vital-it.ch/"^^ . + "A0001"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\w{2,4}\\d{5}$"^^ . + "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . + . + "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . + . + "Chlamydia"^^ . + . + . + . + . + . + . + . + . + . + "D00123"^^ . + . + "https://portal.bluebrain.epfl.ch"^^ . + "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . + . + . + . + . + . + . + "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . + "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . + . + . + . + . + "5HT3Arano"^^ . + "https://github.com/sparontologies/fabio"^^ . + "GlycomeDB" . + . + . + . + . + . + . + . + . + . + . + "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . + . + "eVOC mouse development stage" . + . + "false"^^ . + . + . + . + . + . + "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . + . + . + . + "5621"^^ . + . + . . - . - "https://www.ebi.ac.uk/GOA/"^^ . - "^WB[A-Z][a-z]+\\d+$"^^ . + . + . + . + "https://www.vmh.life/#metabolite/$1"^^ . + . + . + . + "false"^^ . + "An application ontology built for beta cell genomics studies."^^ . + . + . + . + "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . + . + "false"^^ . + . + . + "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . + . + . + . + . + "KEGG Glycan" . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^ . + . + . + . + . + "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . + "9606117"^^ . + . + . + "^\\d{7}$"^^ . + . + "^\\d{7}$"^^ . + "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "Manually curated collections of resources stored in the bioregistry"^^ . + . + . + . + . + "Resources mentioned in \"Sharing biological data: why, when, and how\"" . + . + . + . + . + "Open Researcher and Contributor" . + . + . + "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . + . + . + . + . + . + "^\\d+$"^^ . + "HOMD Sequence Metainformation" . + . + . + . + "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . + . + . + . + "https://link.springer.com/bookseries/562"^^ . + . + . + . + "ERR436051"^^ . + . + . + . + . + . + . + . + . + "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "Dictyostelium discoideum phenotype ontology" . + . + . + "GL50803_102438"^^ . + "Life cycle stages for Medaka"^^ . + "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . + . + . + . + . + . + . + . + "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . + . + . + . + . + "^PROB_c\\d+$"^^ . + . + . + . + . + "172"^^ . + "FlyBase Reference Report" . + . + "r3d100010772"^^ . + . + . + "https://github.com/phenoscape/teleost-taxonomy-ontology"^^ . + . + . + . + "GLIDA Ligand" . + "^[A-Za-z0-9+_.%-:]+$"^^ . + . + "https://github.com/infectious-disease-ontology-extensions/ido-virus"^^ . + . + . + . + . + . + . + "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato"^^ . + "http://purl.obolibrary.org/obo/AISM_$1"^^ . + . + "Agricultural Online Access" . + . + . + . + . + . + . + . + . + "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . + . + . + . + "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . + "http://www.antirrhinum.net/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "FAIRsharing.62qk8w" . + . + . + . + . + . + . + . + "Selventa Families" . + "Assists in resolving data across cloud resources."^^ . + "0000773"^^ . + "Val Wood" . + . + "1915"^^ . + . + "Cooperative Patent Classification" . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OGI_$1"^^ . + "^\\d{7}$"^^ . + . + . + "E-cyanobacterium model" . + "https://cropontology.org/ontology/CO_339/Lentil"^^ . + . + "^MSV\\d+$"^^ . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "http://pkuxxj.pku.edu.cn/UNPD/"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + . + "PIR Superfamily Classification System" . + . + . + . + . + "false"^^ . + . + "false"^^ . + "https://www.cropontology.org/rdf/CO_325:$1"^^ . + "false"^^ . + . + . + . + "^P\\d{5}$"^^ . + . + . + "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . + . + "https://cellrepo.ico2s.org/repositories/$1"^^ . + . + "false"^^ . + . + . + . + . + "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . + . + . + "false"^^ . + . + . + "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "https://www.cropontology.org/rdf/CO_346:$1"^^ . + . + . + "false"^^ . + . + . + . + "^OSR\\d{4}$"^^ . + "has provider formatter" . + "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . + "^H\\d+$"^^ . + "Metabolomics Workbench Study" . + "Candida Genome Database" . + . + . + . + . + "Rat Genome Database qTL" . + . + . + "false"^^ . + . + "false"^^ . + "http://edamontology.org"^^ . + . + . + . + . + "0000121"^^ . + . + . + "false"^^ . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + . + . + "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . + . + "NINDS Human Cell and Data Repository" . + . + "^r3d\\d{9,9}$"^^ . + . + . + . + . + . + . + . + . + "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . + "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "CLV_MEL_PAP_1"^^ . + . + . + . + "https://www.biocarta.com/"^^ . + . + . + "4349895"^^ . + . + . + . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "EDAM Format" . + . + . + "false"^^ . + . + . + . + "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . + . + "false"^^ . + "https://www.brenda-enzymes.de/ligand.php"^^ . + . + . + "FB00000917"^^ . + . + "^\\d+$"^^ . + . + . + "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . + . + . + . + . + "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + "false"^^ . + "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . + "http://www.aspgd.org/"^^ . + . + "00000001"^^ . + "An ontology to standardize research output of nutritional epidemiologic studies."^^ . + "Provisional Cell Ontology" . + . + . + . + "An ontology for the description of Drosophila melanogaster phenotypes."^^ . + . + . + "Cell line collections"^^ . + . + . + . + . + . + . + . + . + . + . + . + "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . + "https://proteinensemble.org/$1"^^ . + "AGRO" . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "http://zinc15.docking.org/substances/$1"^^ . + "http://korkinlab.org/dommino"^^ . + . + "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . + . + "0000546"^^ . + "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . + . + . + "false"^^ . + . + "0005926"^^ . + "6038"^^ . + . + . + . + "https://www.metanetx.org/"^^ . + . + . + "http://www.fossilworks.org"^^ . + . + . + "000000024"^^ . + . + . + . + . + . + . + . + . + "HPSI0114i-bezi_1"^^ . + . + "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . + . + . + . + . + . + "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . + "https://www.thermofisher.com/antibody/product/$1"^^ . + "^[0-9]*$"^^ . + "https://cropontology.org/ontology/CO_330/Potato"^^ . + . + . + . + . + "CC-BY-1.0"^^ . + . + . + . + . + . + . + . + . + . + . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . + "NONCODE v4 Gene" . + "75"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . + . + "b97957"^^ . + "http://www.e-cyanobacterium.org/bcs/entity/"^^ . + "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . + . + "https://registry.identifiers.org/registry/$1" . + . + . . - . - . - . - . - . - . - . - . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "https://github.com/ApolloDev/apollo-sv"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.genecards.org/"^^ . - "http://www.kegg.jp/"^^ . - . - . - . - . - . - . - . - . - . - . - "https://www.grid.ac/"^^ . - . - . - . - "https://www.storedb.org/"^^ . - . - . - . - "MRA-253"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . - . - . - . - . - . - "Human Brain Atlas" . - . - . - . - . - "true"^^ . - . - . - . - "TAIR Gene" . - "https://www.cdc.gov/nchs/icd/icd9cm.htm"^^ . - "https://protists.ensembl.org/id/$1"^^ . - . - "https://github.com/geneontology/go-ontology/tree/master/contrib"^^ . - . - . - . - . - "false"^^ . - . - . - . - "VB.Ob.3736.GRSM125"^^ . - "false"^^ . - . - . - "K"^^ . - "http://purl.obolibrary.org/obo/OARCS_$1"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "ECOCYC"^^ . - . - . - . - "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . - . - . - "^\\w+$"^^ . - . - . - . - . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/"^^ . - . - "false"^^ . - . - "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . - . - . - "false"^^ . - . - . - . - "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"^^ . - "https://www.google.com/patents/$1"^^ . - . - . - "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^ . - . - . - . - . - . - . - . - . - . - . - "Coriell Institute for Medical Research" . - . - . - "false"^^ . - . - . - . - . - . + "ClinVar Submitter" . + . + "An ontology for dengue fever."^^ . + . + "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . + . + . + . + . + . + . + "Clinical measurement ontology" . + . + . + . + . + "AOPWiki (Key Event)" . + . + . + . + "EBI-2307691"^^ . + "https://biosimulators.org/simulators/$1"^^ . + . + "false"^^ . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . + "Search Tool for Interactions of Chemicals" . + . + . + "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://glytoucan.org/"^^ . + "DASHR expression" . + . + "^\\d{8}$"^^ . + "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . + . + "^\\w+$"^^ . + . + . + . + "https://www.cellbiolabs.com/search?keywords=$1"^^ . + . + "https://prefix.cc/$1" . + . + "785"^^ . + . + . + "^\\d+$"^^ . . - "Ontology for Nutritional Epidemiology" . - "https://bioportal.bioontology.org/ontologies/EDDA"^^ . - . - . - "true"^^ . - "^A\\d+$"^^ . - . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/GEO_$1"^^ . - . - "^\\d{7}$"^^ . - . - "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . - . - . - "Infectious Disease Ontology" . - . - . - "false"^^ . - . - . - "pubmed"^^ . - . - "https://flybase.org"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "miR-1"^^ . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/AISM_$1"^^ . - . - . - . - . - "numpy"^^ . - . - "Search PRINTS-S" . - . - . - . - . - "false"^^ . - "Prefix.cc" . - . - . - "^\\d{7}$"^^ . - . - . - . - "T30002"^^ . - . - "^ACYPI\\d{6}(-RA)?$"^^ . - "http://birdgenenames.org/cgnc/"^^ . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1"^^ . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - "0000000"^^ . - . - . - . - . - . - . - "https://www.ccdc.cam.ac.uk/"^^ . - . - . - . - . - . - "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . - . - "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . - . - "70"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "^DBCAT\\d+$"^^ . - . - "4900"^^ . - . - . - . - . - "^\\d+$"^^ . - "http://github.com/seger/aao"^^ . - . - "SABIO-RK EC Record" . - . - . - "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . - . - . - "https://github.com/MPIO-Developers/MPIO"^^ . - . - "Cotton ontology from CottonGen database - June 2019"^^ . - "S000002493"^^ . - . - . - . - . - . - "Melanoma Molecular Map Project Biomaps" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "http://bioportal.bioontology.org/"^^ . - "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - . - "https://bioportal.bioontology.org/ontologies/$1" . - . - "PF3D7_1328700"^^ . - . - . - "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . - . - . - "992"^^ . - "http://www.nbrc.nite.go.jp/e/index.html"^^ . - . - "0007404"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . - . - "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS"^^ . - . - . - . - . - "https://bioregistry.io/collection"^^ . - "chebi" . - "https://metazoa.ensembl.org/"^^ . - . - . - . - . - . - . - . - . - . - "RepeatsDB Structure" . - . - . - . - "https://github.com/bio-ontology-research-group/unit-ontology"^^ . - . - . - "Community development of interoperable ontologies for the biological sciences"^^ . - "^.*/.*$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Vertebrate Gene Nomenclature Committee" . - . - "https://cropontology.org/ontology/CO_338/Chickpea"^^ . - . - . - . - . - "http://www.mirbase.org/"^^ . - . - "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"^^ . - . - . - . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Andrew G. McArthur" . + . + "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR"^^ . + "ICARDA - TDv5 - Sept 2018"^^ . + . + . + . + . + . + . + "https://molmedb.upol.cz/mol/$1"^^ . + "false"^^ . + "FBtr0084214"^^ . + . + . + . + . + . + . + . + . + "Blue Brain Project Knowledge Graph" . + . + . + "true"^^ . + . + "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^ . + "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . + . + "false"^^ . + . + . + . + . + . + . + "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . + . + "false"^^ . + . + . + "BioGRID" . + . + . + . + . + . + "http://bioinfo.iitk.ac.in/MIPModDB"^^ . + . + . + "00103"^^ . + "485991"^^ . + "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/"^^ . + . + "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^ . + . + . + . + "https://www.ensembl.org/"^^ . + "https://github.com/qfo/OrthologyOntology"^^ . + . + . + . + . + . + . + . + . + "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^ . + "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/SWEET"^^ . + . + . + "^[0-9]{12}$"^^ . + . + "CorrDB" . + . + . + . + "UniProt Cross-ref database" . + "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + . + "375364"^^ . + "http://purl.obolibrary.org/obo/AERO_$1"^^ . + . + . + . + . + . + . + "https://github.com/rsc-ontologies/rxno"^^ . + . + . + . + . + . + . + "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . + "CAA71118.1"^^ . + . + "InterPro" . + . + . + "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^ . + . + "http://www.cazy.org/$1.html"^^ . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + "false"^^ . + "false"^^ . + . + "Electron Microscopy Public Image Archive" . + . + . + . + "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . + "Enzo Life Sciences" . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/"^^ . + "https://proteininformationresource.org/resid/"^^ . + . + . + "Gene Regulation Ontology" . + "http://crdd.osdd.net/servers/virsirnadb"^^ . + . + "Adrien Rougny" . + . + . + . + . + "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . + . + . + "false"^^ . + "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^ . + "Store DB" . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . + . + "^\\d+$"^^ . + . + "ALA"^^ . + . + "^\\d+$"^^ . + . + "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . + . + . + . + . + . + . + "Chemical Methods Ontology" . + . + . + . + "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . + . + . + . + "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . + "http://www.guidetopharmacology.org/"^^ . + . + . + . + . + . + . + . + . + . + "0000404"^^ . + . + "CATH Protein Structural Domain Superfamily" . + . + . + . + . + . + . + . + "true"^^ . + "false"^^ . + "^\\d+$"^^ . + "BDGP insertion DB" . + . + "NONCODE v4 Transcript" . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MAO_$1"^^ . + "AKR"^^ . + . + . + "https://github.com/bgsu-rna/rnao"^^ . + . + . + . + . + . + "false"^^ . + . + "http://www.imdrf.org/"^^ . + . + . + . + "Bgee family" . + "^TF\\w+$"^^ . + "https://github.com/obophenotype/mouse-anatomy-ontology"^^ . + . + "http://purl.obolibrary.org/obo/EPIO_$1"^^ . + . + . + "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . + . + . + . + . + "NIH HIV Reagent Program" . + "^\\d{8}$"^^ . + . + . + . + "false"^^ . + "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . + "false"^^ . + "000204"^^ . + . + "MI0026471"^^ . + "^\\d+$"^^ . + . + "Mass spectrometry ontology" . + . + . + "http://purl.obolibrary.org/obo/FBSP_$1"^^ . + . + . + . + . + "0000025"^^ . + . + "^[A-Z0-9]+$"^^ . + . + . + "https://icahn.mssm.edu/"^^ . + "^\\d+$"^^ . + "^MF_\\d+$"^^ . + . + . + "Unimod protein modification database for mass spectrometry" . + . + . + . + . + . + . + . + . + . + . + "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . + "http://www.cba.ac.cn"^^ . + . + "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . + . + . + . + "0000780"^^ . + . + . + . + . + . + . + "https://cordis.europa.eu/"^^ . + "PubChem CID" . + . + . + . + . + . + "Human Ancestry Ontology" . + . + "Plant Phenology Ontology" . + . + . + . + "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . + "^\\d+$"^^ . + "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . + "false"^^ . + . + . + "is deprecated" . + "http://dictybase.org/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "https://biopragmatics.github.io/debio/$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "Cell line collections"^^ . + . + "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "BT20_BREAST"^^ . + . + . + . + . + "http://mycobrowser.epfl.ch/marinolist.html"^^ . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + "Simplified molecular-input line-entry system" . + . + . + . "^[0-9]+$"^^ . - "100101"^^ . - . - "^TF\\w+$"^^ . - . - . - "frim1"^^ . - "http://purl.org/pav/$1"^^ . - . - . - . - . - . - . - . - "MetaNetX chemical" . - . - "MycoBrowser leprae" . - "^\\d{7}$"^^ . - . - . - "https://github.com/obophenotype/cephalopod-ontology"^^ . - . - . - . - . - "http://www.kazusa.or.jp/rouge/"^^ . - . - "false"^^ . - . - . - . - "10020.2"^^ . - . - . - . - . - . - . - "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . - . - . - . - . - . - "^\\d+$"^^ . - "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . - . - "HBG284870"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "0000071"^^ . - . - . - . - . - . - "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . - "LOC_Os02g13300"^^ . - . - . - . - . - "http://www.hprd.org/protein/$1"^^ . - . - "Environment Ontology" . - . - "https://disprot.org/"^^ . - . - . - . - "Genomic Data Commons Data Portal" . - "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . - "NCBI Taxonomy" . - . - . - . - "eNanoMapper Ontology" . - "https://www.ebi.ac.uk/chembldb"^^ . + "http://modelseed.org/biochem/reactions/"^^ . + "http://www.human-phenotype-ontology.org/"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + "https://github.com/evoinfo/cdao"^^ . + "false"^^ . + . + . + "101775319"^^ . + "false"^^ . + . + . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . + . + . + "Dendritic cell" . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . + "http://microsporidiadb.org/micro/"^^ . + "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . + "Antibody Registry" . + "http://mint.bio.uniroma2.it/mint/"^^ . + . + "false"^^ . + "KG09531"^^ . + . + . + . + . + "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . + "http://purl.obolibrary.org/obo/CARO_$1"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "^MNEST\\d+$"^^ . + . + . + . + . + . + "https://www.deciphergenomics.org/syndrome/$1"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "http://umbbd.ethz.ch/"^^ . + "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "http://aps.unmc.edu/AP/"^^ . + "false"^^ . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + "Molecular Modeling Database" . + "false"^^ . + . + . + . + . + . + . + . + . + "https://schema.org/$1"^^ . + . + . + . + . + . + . + "https://bykdb.ibcp.fr/BYKdb/"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + . + "https://gitlab.com/$1"^^ . + . + . + . + . + "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . + . + . + . + . + . + . + . + "https://www.w3.org/TR/rdf-schema/"^^ . + . +_:Nb146830ea578464c88406af42b4971a7 "Pantelis Topalis" . + "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . +_:N743aadb122be4af0923089a9894fc4e9 "InterPro Help" . + . + "false"^^ . + "false"^^ . + . + . + . + . + "1018"^^ . + . + . + . + . + "dictyBase Expressed Sequence Tag" . + . + . + . + . + "https://www.kerafast.com/"^^ . + "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . + . + "Federica Quaglia" . + . + "^\\d+$"^^ . + . + "Core Ontology for Biology and Biomedicine" . + . + . + "VEuPathDB ontology" . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/merops"^^ . + "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . + . + . + . + . + "PhenX Toolkit" . + . + . + "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . + . + . + _:Nb25a11001fb94cab8cdd9b93ffb6b0bf . + . + . + . + . + . + . + "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^ . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1"^^ . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + "Os01t0883800-02"^^ . + . + . + . + "^\\d+$"^^ . + "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . + . + "Orphanet Rare Disease Ontology" . + . + . + . + "VFDB Genus" . + . + . + "Bioregistry Schema" . + "false"^^ . + . + "http://www.antirrhinum.net/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/FAO_$1"^^ . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . + "^(\\w){3}$"^^ . + . + "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . + "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . + . + . + . + . + . + "Catalogue of Life in Taiwan" . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . + "false"^^ . + . + . + . + . + . + . + "http://www.drugbank.ca/drugs/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . + "TIGR00010"^^ . + . + . + . + . + "Degradome Database" . + . + . + . + . + . + . + . + . + "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . + . + "E-MEXP-1712"^^ . + . + "^\\d+$"^^ . + "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . + "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^ . . - . -_:Nceb4566787ea45869d0bbc6c2b7d5379 "InterPro Help" . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - "http://www.uniprot.org/uniprot/$1"^^ . - . - . - "http://mycobrowser.epfl.ch/smegmalist.html"^^ . - "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . - "0001017"^^ . - "Bjoern Peters" . - "https://github.com/Novartis/hpath"^^ . + . + . + . + . + . + "false"^^ . + . + "8497"^^ . + . + . + . + . + . + . + . + . + "https://github.com/arpcard/aro"^^ . + "Vertebrate Homologous Organ Group Ontology" . + "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "lectins/172"^^ . + . + . + "http://www.isni.org/isni/$1"^^ . + . + "BLL"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . + . + . + "https://reaxys.emolecules.com"^^ . + "^UDB\\d{6}$"^^ . + . + . + . + . + "19803"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://www.wwpdb.org/pdb?id=$1"^^ . + "false"^^ . + . + . + "https://odc-sci.org"^^ . + . + . + "688"^^ . + . + "System Science of Biological Dynamics dataset" . + . + . + . + . + "false"^^ . + . + . + "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology"^^ . + . + . + . + . + . + . + . + "42840"^^ . + . + . + . + . + "http://www.accessdata.fda.gov/scripts/cder/ndc/"^^ . + "An issue in any public repository on GitHub."^^ . + . + "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . + "Digital archive of scholarly articles" . + "Epilepsy Ontology" . + "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . + "DI-04240"^^ . + "http://geneontology.org/" . + . + "A hierarchical classification of congenital heart disease "^^ . + "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^ . + "http://msi-ontology.sourceforge.net/"^^ . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + . + "false"^^ . + . + . + . + . + "https://www.atcc.org/products/$1"^^ . + . + "COMBINE specifications" . + . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^ . + . + . + . + "E-cyanobacterium Experimental Data" . + . + "https://www.ebi.ac.uk/gxa/"^^ . + "false"^^ . + "PjrpzUIAAAAJ"^^ . + . + . + "false"^^ . + . + . + . + "Vertebrate skeletal anatomy ontology."^^ . + . + . + . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + "Ontology of Biological Attributes" . + . + . + "4390079"^^ . + . + . + . + . + . + . + "10142"^^ . + . + . + "^\\d{6}$"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "https://cropontology.org/ontology/CO_356/Vitis"^^ . + . + . + . + "runBioSimulations" . + . + . + . + "HIP000030660"^^ . + . + . + . + . + . . - . - "Wikidata Property" . - . - "^\\d+$"^^ . - "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . - "http://purl.obolibrary.org/obo/fbcv"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . - "https://www.tcdb.org"^^ . - . - . - . - . - . - . - . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . - . - . - . - . - "Gene Expression Ontology"^^ . - "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . - "vcell"^^ . - "https://www.ebisc.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . - . - . - . - . - "https://pharmacome.github.io/conso/$1"^^ . - . - . - . - . - . - "UniProt Archive" . - . - "/12345/fk1234"^^ . - . - . - . - . - "true"^^ . - . - "https://www.ncbi.nlm.nih.gov/projects/RefSeq/"^^ . - "OMA HOGs" . - . - . - . - . - . - . - . - . - . - . - "^ECMDB\\d+$"^^ . - "false"^^ . - "http://arabidopsis.org/index.jsp"^^ . - "Cell line collections"^^ . - "National Microbiome Data Collaborative" . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1"^^ . - . - "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . - "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html"^^ . - . - . - . - "14362"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "ebf69ca24298b28b2361e7d43eb52d6c"^^ . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/books"^^ . - . + . + . + . + . + "Draft version"^^ . + "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . + "http://dictybase.org/"^^ . + . + "https://www.ccdc.cam.ac.uk/"^^ . + . + . + . + . + . + . + . + . + "Li7"^^ . + . + . + "https://pathbank.org"^^ . + . + . + "https://www.inaturalist.org/taxa/$1"^^ . + . + "Pfam" . + . + . + "https://bioportal.bioontology.org/ontologies/IDODEN"^^ . + . + "Plant Ontology" . + . + . + . + . + "true"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings."^^ . + "SAMEA2397676"^^ . + . + "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page"^^ . + . + . + "AT1402"^^ . + . + "5.1"^^ . + "HomoloGene" . + . + "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . + . + . . - . - . - . - . - . - . - . - "Vertebrate Skeletal Anatomy Ontology" . - . - "false"^^ . - "https://github.com/insect-morphology/colao"^^ . - . - . - "http://ciliate.org/index.php/feature/details/$1"^^ . - . - "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . - . - "false"^^ . - "https://www.cropontology.org/rdf/CO_323:$1"^^ . - . - "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . - . - "https://www.ebi.ac.uk/chebi/"^^ . - . - . - . - . - . - "https://www.datanator.info/gene/$1"^^ . - . - "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - . - "URS0000759CF4"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "BioLegend" . - . - "Robert Druzinsky" . - . - "Cell line collections"^^ . - . - "https://github.com/OHPI/ohpi"^^ . - . - . - . - . - . - . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - "^([a-z]{3,5}_)?M\\d{5}$"^^ . - . - . - . - . - "https://github.com/biolink/biolink-model" . - . - . - . - . - "Cell line collections"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/CMF_$1"^^ . - . - . - . - . - . - . - . - . - . - . - "Livestock Product Trait Ontology" . - . - . - . - "true"^^ . - "https://www.uniprot.org/docs/ptmlist"^^ . - . - "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . - "Human Endogenous Retrovirus Database" . - "aap-1"^^ . - "Q13485"^^ . - . - . - . - . - . - . - . - "false"^^ . - "PWY3O-214"^^ . - "Wes Schafer" . - . - "D053716"^^ . - . - "https://bioregistry.io" . - "http://cerevisiae.oridb.org/index.php"^^ . - . - . - "FDB002100"^^ . - . - . - . - . - . - . - "Sigma Aldrich is a life sciences supply vendor."^^ . - . - "false"^^ . - . - . - "^(\\w+)?\\d+$"^^ . - "^Rv\\d{4}(A|B|c)?$"^^ . - . - . - . - "https://pfam.xfam.org/clan/$1"^^ . - "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . - . - "http://purl.obolibrary.org/obo/FYPO_$1"^^ . - . - . - "http://purl.obolibrary.org/obo/OPMI_$1"^^ . - . - . - . - . - . + . + . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + "http://thebiogrid.org/$1"^^ . + "https://glyconavi.org/hub/?id=$1"^^ . + . + . + "^\\d+$"^^ . + . + "http://www.drugbank.ca/biodb/bio_entities/$1"^^ . + "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . + . + . + "10015919"^^ . + . + . + . + . + "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0"^^ . + . + . + "false"^^ . + "Biological Imaging Methods Ontology" . + "http://elm.eu.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://www.glycoepitope.jp/epitopes/$1"^^ . + "^\\d+\\-\\d+\\-\\d+$"^^ . + . + "false"^^ . + . + "chebi" . + . + "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . + "^\\d+$"^^ . + "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"^^ . + . + "Cell line databases/resources"^^ . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + "http://antibodyregistry.org/"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . + . + "eggNOG" . + "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . + . "^\\d{7}$"^^ . - . - . - . - "http://purl.org/spar/cito/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "CCLE_867"^^ . - . - . - . - . - . - . - . - . - . - . - . - "foaf" . + "^P(X|R)D\\d{6}$"^^ . + . + . + . + . + . + . + . + "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . + . + . + . + "https://bioportal.bioontology.org/ontologies/EDDA"^^ . + "true"^^ . + . + . + "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . + . + . + "S-EPMC6266652"^^ . + "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^ . + "Luis González-Montaña" . + "https://www.ncbi.nlm.nih.gov/medgen/"^^ . + . + . + . + "182"^^ . + "^\\d{7}$"^^ . + . + "false"^^ . + "0000080"^^ . + . + . + "BRENDA Ligand" . + "false"^^ . + . + . + . + . . - . - . - . - . - . - "true"^^ . - "TTD Drug" . - "^\\d+$"^^ . - "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . - . - . - . - . - . + . + "^[A-Z0-9*:]+$"^^ . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ADO_$1"^^ . + . + "Anatomical Therapeutic Chemical Vetinary" . + . + . + . + "Xenopus Phenotype Ontology" . + . + . + . + . + "http://www.sparontologies.net/ontologies/frapo"^^ . + . + . + . + . + . + . + "false"^^ . + "^A_\\d+_.+$"^^ . + "^\\d+$"^^ . + "true"^^ . + . + . + . + . + . + "false"^^ . + . + "BRIP1"^^ . + "^\\d{10}$"^^ . + . + . + . + . + "Cryo Electron Microscopy ontology" . + . + . + "false"^^ . + . + . + . + "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . + . + . + . + . + "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . + . + . + . . - "^\\d+$"^^ . - "^TS-\\d{4}$"^^ . - . - . - . - . - . - . - . - "Tom Gillespie" . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "3"^^ . - "Pankaj Jaiswal" . - "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . - . - "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . - . - "0000038"^^ . - "false"^^ . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . - . - . - "0000634"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . - . - . - . - . - . - "false"^^ . - "http://www.cathdb.info/cathnode/$1"^^ . - "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^ . - "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . - . - _:Nefa30c915878425fa1cb9bca02259543 . - "false"^^ . - . - . - "https://github.com/OGMS/ogms"^^ . - . - . - . - . - "Integrated Microbial Genomes Taxon" . - "Bob Thacker" . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - "http://bidd.group/NPASS/"^^ . - . - . - . - "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"^^ . - . + . + "false"^^ . + "https://www.deciphergenomics.org/"^^ . + "An ontology of core ecological entities" . + . + . + . + . + . + . + . + . + "https://web.expasy.org/variant_pages/VAR_$1.html"^^ . + "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . + "^\\d+$"^^ . + . + . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . + "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . + . + . + . + . + . + . + "https://www.glycoepitope.jp/epitopes/"^^ . + . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . + "false"^^ . + "https://glygen.org/glycan/$1"^^ . + . + "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . + . + "false"^^ . + . + . + "F-SNP" . + "false"^^ . + . + . + . + . + . + . + . + . + "^GenProp\\d+$"^^ . + . + . + . + "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^ . + "An ontology of Drosophila melanogaster developmental stages."^^ . + . + . + . + . + . + . + "Pfam Clans" . + . + . + . + . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . + . + "false"^^ . + "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . + . + "false"^^ . + . + . + . + "^MIRT\\d{6}$"^^ . + . + "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . + . + . + . + "http://tolweb.org/tree/"^^ . + . + . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^ . + "^\\d{6,7}$"^^ . + . + . + "https://depmap.org/portal/cell_line/$1"^^ . + "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . + . + . + . + "AA0001"^^ . + . + "Frédéric Bastian" . + "http://modelseed.org/biochem/reactions/$1"^^ . + . + . + . + "false"^^ . + . + "APID Interactomes" . + "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . + . + . + "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait"^^ . + . + . + "Database of small human noncoding RNAs" . + . + . + "Minimal Information About Anatomy ontology" . + . + . + . + "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . + . + "FooDB Food" . + . + . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"^^ . + "UniProt journal ID" . + . + . + "^\\d+$"^^ . + . + "http://exac.broadinstitute.org/gene/$1"^^ . + . + . + . + . + . + . + . + . + "https://github.com/obophenotype/provisional_cell_ontology"^^ . + . + . + . + . + . + . + "A*01:01:01:01"^^ . + "Variation Modelling Collaboration" . + . + "XML Schema Definition" . + . + . + . + . + . + . + . + "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . + "NCI Pathway Interaction Database: Pathway" . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . + . + "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . + . + . + "false"^^ . + . + "http://repository.topdownproteomics.org/proteoforms/$1"^^ . + "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . + "^\\w+(\\.)?(\\d+)?$"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "COSMIC Cell Lines" . + "http://purl.obolibrary.org/obo/CDAO_$1"^^ . + "Matthew Brush" . + . + . + . + . + "^\\d{7}$"^^ . + "UniRef90_P00750"^^ . + "Flora Phenotype Ontology" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . + "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . + . + . + . + "^G[0-9]{5}[A-Z]{2}$"^^ . + . + "http://unite.ut.ee/"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^ . + . + "MultiCellDS" . + "https://signor.uniroma2.it/"^^ . + . + "^EBI\\-[0-9]+$"^^ . + "Amanda Hicks" . + "http://www.sasbdb.org/"^^ . + . + . + . + "^MTBLS\\d+$"^^ . + . + . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . + "false"^^ . + "https://datanator.info/"^^ . + "false"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . + . + . + . + "http://www.genoscope.cns.fr/agc/microscope"^^ . + "false"^^ . + "https://bacteria.ensembl.org/"^^ . + . + . + "W2741809807"^^ . + . + "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . + . + . + . + . + . + "^[\\w\\d\\.-]*$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "http://classyfire.wishartlab.com/"^^ . + "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . + . + "3304"^^ . + . + . + . + . + . + "false"^^ . + . + "MMP02954345.1"^^ . + . + "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "^[\\d.]+$"^^ . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . + . + . + . + . + . + . + . + "^CL\\d+$"^^ . + . + "^(SMP|PW)\\d+$"^^ . + . + . + . + . + . + "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . + . + . + . + . + . + "0000024"^^ . + "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . + "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . + "Structural Classification of Protein" . + . + . + . + . + . + . + . + . + "Human Proteome Map Peptide" . + . + "^C\\d+$"^^ . + . + . + "A Web-based catalog of recommended measurement protocols"^^ . + . + . + . + . + . + . + . + "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . + . + . + . . - . - . - . - . - . - "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . - . - "false"^^ . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Medical Dictionary for Regulatory Activities Terminology" . - . - "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . - . - . - "GCA_000155495.1"^^ . - . - . - "An ontology for dengue fever."^^ . - . - . - "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1"^^ . - . - "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . - . - "Hilmar Lapp" . - . - . - "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . - . - . - . - "0000547"^^ . - . - "H-InvDb Transcript" . - . -_:N3991e431e80949699eef7263bacf932b "Daniel Sonenshine" . - "Dublin Core Types" . - . - . - . - . - "false"^^ . - "false"^^ . - . - "CATH Protein Structural Domain Superfamily" . - "https://pathbank.org"^^ . - "false"^^ . - . - "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . - . - . - . - . - "^AS\\d{6}$"^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^ . - "SUM Breast Cancer Cell Line Knowledge Base" . - . - . - "false"^^ . - "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . - "Fission Yeast Experimental Conditions Ontology" . - "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . - . - . - . - "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . - "Ctenophore Ontology" . - . - . - "https://cropontology.org/ontology/CO_359/Sunflower"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "https://www.bindingdb.org"^^ . + . + . + . + "Ontology of Medically Related Social Entities" . + . + . + "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . + . + . + . + . + . + "^SL-\\d+$"^^ . + "Dictybase Gene" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + "Human developmental anatomy, timed version" . + "^[a-z_A-Z0-9]+$"^^ . + "MCDS_S_0000000001"^^ . + "http://www.w3.org/ns/oa"^^ . + . + "UCR00513"^^ . + . + . + "0000019"^^ . + . + . + . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . + . + "Gene"^^ . + . + . + . + "^\\d{7}$"^^ . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . + . + . + . + . + . + "HGVPM623"^^ . + . + . + . + . + . + "^[a-z0-9]{32,32}$"^^ . + . + . + . + "https://e-cyanobacterium.org/bcs/rule/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + "The coding sequence or protein identifiers as maintained in INSDC."^^ . + . + "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . + "AOPWiki (Stressor)" . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + "NCBI dbSNP" . + . + . + . + . + . + "2404"^^ . + . + . + "http://ctdbase.org/"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "http://cutdb.burnham.org/relation/show/$1"^^ . + . + "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . + "false"^^ . + "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . + "100000001"^^ . + . + "https://cordis.europa.eu/article/id/$1"^^ . + . + . + . + _:Ncd8db50360e4497892747d5c5192e44f . + . + . + . + . + . + "^\\d+$"^^ . + "Sofia Robb" . + . + . + . + . + . + "5"^^ . + . + . + . + . + "osa-miR446"^^ . + "LINCS Protein" . + "2029"^^ . + . + "Bgee stage" . + "uniprotkb"^^ . + "http://purl.bioontology.org/ontology/MEDDRA/$1"^^ . + "https://github.com/obcs/obcs"^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + "^G\\d+$"^^ . + . + . + . + . + . + "^[0-9\\-_]+$"^^ . + . + "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "Locus Reference Genomic" . + . + "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . + . + . + "6VDC956"^^ . + . + . + "https://dgrc.bio.indiana.edu/cells/Catalog"^^ . + "Edison Ong" . + . + "Measurement method ontology" . + "Q5BJF6-3"^^ . + . + . + . + "9861/3"^^ . + "273"^^ . + . + . + "TB2:S1000"^^ . + . + . + . + . + "https://web.expasy.org/cellosaurus/" . + . + . + "131"^^ . + "Cu.me.I1"^^ . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"^^ . + "DailyMed" . + "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . + . + . + "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . + "false"^^ . + . + . + . + . + . + . + . + "PubMed" . + . + . + . + . + . + . + . + . + "The main contact person for a registry" . + "http://www.obofoundry.org/"^^ . + . + . + . + . + . + . + . + . + . + "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . . - . - . - . - . - . - "true"^^ . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . - . - . - . - . - "^rs\\d+$"^^ . - . -_:Ncd6763d843b14d0896f4a430c8c2d0e9 "Satya S. Sahoo" . - "Statistical Torsional Angles Potentials" . - . - . - "Variants in dbVar."^^ . - . - "131392"^^ . - "HEX1"^^ . - . - "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . - "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view"^^ . - . - "http://www2.idac.tohoku.ac.jp/dep/ccr/"^^ . - . - "http://stitch.embl.de/"^^ . - "https://github.com/AnimalGenome/livestock-product-trait-ontology"^^ . - . - . - . - . - "https://cellrepo.ico2s.org/repositories/$1"^^ . - . - . - . - . - "A database-specific registry supporting curation in the Gene Ontology"^^ . - . - . - "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . - . - . - . - . - "https://github.com/obophenotype/human-developmental-anatomy-ontology/"^^ . - . - "http://opencitations.net"^^ . - . - . - . - . - . - . - . - "http://zfin.org"^^ . - . - "^T3D\\d+$"^^ . - "A person" . - . - "https://flybase.org/reports/FBrf$1"^^ . - "^PIRSF\\d{6}$"^^ . - . - . - . - . - . - "4DNSR73BT2A2"^^ . - . - "^\\w+(\\.)?\\d+$"^^ . - . - . - . - . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/ordo"^^ . - . - "https://www.ebi.ac.uk/intenz/"^^ . - "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^ . - "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . - . - . - . - . - "UniRef90_P00750"^^ . - . - . - . - . - . - . - "4685"^^ . + . + "ValidatorDB" . + . + "^\\d+$"^^ . + . + . + . + "CiteXplore" . + . + . + . + . + . + . + "GR:0080039"^^ . + . + . + . + . + "0000080"^^ . + "Genome assembly database" . + . + "Barry Smith" . + "false"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"^^ . + "false"^^ . + "243002_at"^^ . + . + "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . + . + . + . + . + . + "false"^^ . + . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . + . + . + "http://cellimagelibrary.org/"^^ . + "https://n2t.net/$1:"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Za-z0-9+_.%-:]+$"^^ . + "r0001"^^ . + . + . + . + . + " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . + . + . + . + "^\\w+$"^^ . + . + . + . + "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . + "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . + . + . + . + . + "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^ . + . + . + "0000038"^^ . + . + "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . + . + "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "GPIb_IX_V"^^ . + "fluticasone"^^ . + . + "Assembly" . + . + . + "https://sed-ml.org/urns.html#language:$1"^^ . + "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . + "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . + . + . + . + . + . + . + . + "Plant Genome Network" . + "101"^^ . + . + . + "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . + . + . + "^[A-Za-z]+\\/[0-9]+$"^^ . + . + "http://purl.obolibrary.org/obo/VT_$1"^^ . + "^\\d+$"^^ . + . + . + "Paleobiology Database" . + . + . + "GenProp0699"^^ . + . + "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . + "http://ecoportal.lifewatch.eu/ontologies/$1" . + . + "https://www.e-cyanobacterium.org/experiments-repository/"^^ . + . + . + . + . + . + "http://www.obofoundry.org/" . + . + "^[a-z]+(\\..*?)?$"^^ . + . + "^\\w.+$"^^ . + "achcar11"^^ . + . + . + . + . + . + . + . + "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html"^^ . . - . - . - . - . - . - "^\\d\\w+$"^^ . - "PubMed" . - . - "Identifier for a species in iNaturalist"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "http://rgd.mcw.edu/"^^ . - . - . - "Paragraph"^^ . - "false"^^ . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "false"^^ . - "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . - "FuncBase Human" . - . - . - "https://repeatsdb.org/"^^ . - . - . - . - "https://fairsharing.org/$1"^^ . - "ENSFM00500000270089"^^ . - . - . - "UM-BBD Compound" . - . - . - "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . - . - . - "Plant Transcription Factor Database" . - "0000121"^^ . - . - . - . - "Gi07796"^^ . - . - "RDF"^^ . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe"^^ . - "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . - . - . - . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^ . + . + . + "^\\d+$"^^ . + "true"^^ . + . + . + "CPD-10330"^^ . + "^MINT\\-\\d{1,7}$"^^ . + "Obstetric and Neonatal Ontology" . + . + . + . + . + "https://github.com/jannahastings/emotion-ontology"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "https://www.encodeproject.org"^^ . + . + . + "eagle-i resource ontology" . + "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "SNP to Transcription Factor Binding Sites" . + . + . + . + . + . + "false"^^ . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . + "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . + "true"^^ . + . + "Animal Genome Cattle QTL" . + . + "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . + . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT"^^ . + "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + "http://www.xenbase.org/anatomy/xao.do?method=display"^^ . + "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . + . + "https://www.ncbi.nlm.nih.gov/projects/gap"^^ . + . + "false"^^ . + "https://aopwiki.org/"^^ . + . + "0003463"^^ . + "21393"^^ . + . + . + . + . + "614"^^ . + "0000003"^^ . +_:Ne459e12c22ae4cd08cc8ca747998c144 "Christipher Baker" . + . + "SFB_COVID19_MW286762"^^ . + . + . + . + "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . + . + . + . + "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . + . + "^[0-9]{4}$"^^ . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/SIBO_$1"^^ . + "https://europepmc.org/article/CTX/$1"^^ . + . + . + . + "false"^^ . + . + "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . + . + . + . + "Benjamin Gyori" . + . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + "^HGVM\\d+$"^^ . + . + "http://www.pharmgkb.org/drug/$1"^^ . + "https://www.blueprintnhpatlas.org/"^^ . + "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "1000000"^^ . + "http://neuinfo.org/"^^ . + "false"^^ . + . + . + . + . + . + "https://github.com/proco-ontology/PROCO"^^ . + . + "^\\d{3}$"^^ . + "https://caninecommons.cancer.gov/#/"^^ . + . + . + . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + "H-InvDb Protein" . + . + "030719"^^ . + "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . + "false"^^ . + . + "http://stitch.embl.de/interactions/$1"^^ . + "IA"^^ . + . + "RC00001"^^ . + . + . + . + . + . + "1000003"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/EV_$1"^^ . + . + . + "biosimulations" . + . + "^\\d{7}$"^^ . + "Pseudomonas Genome Database" . + "false"^^ . + . + . + "false"^^ . + "rs17852708"^^ . + . + . + . + . + . + "Alejandra Gonzalez-Beltran" . + "AC119"^^ . + . + "false"^^ . + . + . + . + . + . + "Henning Hermjakob" . + . + . + . + . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + . + "Cell line databases/resources"^^ . + . + "https://spdx.org/licenses"^^ . . - . - "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . - "https://fcs-free.org/fcs-database?$1"^^ . - "https://loinc.org/$1"^^ . - . - . - "ExAC Variant" . - "Homologous Vertebrate Genes Database" . - "false"^^ . - . - . - . - . - . - . - . - . + "Amphibian taxonomy" . + . + . + . + . + . + . + . + . + . + "ppr103739"^^ . + "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . + . + "0000609"^^ . + . + . + . + "Dataset"^^ . + . + . + . + . + . + "Liver Cancer Model Repository" . + . + . + "E5.11.2.0.0.0.4"^^ . + . + . + "https://www.orthodb.org"^^ . + . + . + . + "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . + "Entrez Gene" . + . + . + . + . + . + . + "^\\w+$"^^ . + "53504"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "Network of Different Plant Genomic Research Projects" . + . + "http://kinase.bioinformatics.tw/"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "HGNC gene family" . + "Human Cell Atlas Ontology" . + . + "false"^^ . + . + . + "40000617"^^ . + . + "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . + . + "Banana ontology" . + "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . + "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . + "0004486"^^ . + . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + . + "http://www.hipsci.org/lines/#/lines/$1"^^ . + . + . + . + . + "http://www.informatics.jax.org/"^^ . + . + . + . + . + . + . + . + "https://gitlab.com/fortunalab/ontoavida"^^ . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "https://github.com/The-Sequence-Ontology/SO-Ontologies"^^ . + . + . + "https://www.ebi.ac.uk/gwas/studies/$1"^^ . + . + "PTHR12345"^^ . + "^\\d{6}$"^^ . + . + "https://panoramaweb.org"^^ . + "false"^^ . + . + . + "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . + . + . + "https://www.uniprot.org/journals"^^ . + . + "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . + . + . + . + "Alexander Diehl" . + . + "^\\d{7}$"^^ . + . + "TC010103"^^ . + "^\\d{7}$"^^ . + . + "LinJ.20.0070"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . + . + . + . + "http://rdfs.org/ns/void#$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . + . + . + . + "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . + . + . + "http://www.phosphosite.org/homeAction.do"^^ . + . + . + "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . + . + . + . + "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^ . + . + . + . + "Health Data Research Innovation Gateway" . + . + . + . + . + . + "^K\\d+$"^^ . + . + "Reference"^^ . + . + . + . + "National Drug Data File" . + "MassIVE" . + . + . + . + . + . + "false"^^ . + "https://pharmacodb.ca/datasets/$1"^^ . + . + . + . + . + "https://pharmacodb.ca/cell_lines/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . + "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "http://vocab.getty.edu/page/tgn/$1"^^ . + . + . + . + "identifier for a fungus taxon in Index Fungorum"^^ . + . + . + "false"^^ . + . + . + "GXA Gene" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Oryzabase Stage" . + "EHDAA:2185"^^ . + . + "S7000002168151102"^^ . + "0000015"^^ . + . + . + . + "Microbial Conditions Ontology is an ontology..."^^ . + . + . + . + "http://edamontology.org/format_$1"^^ . + . + . + "http://sed-ml.org/"^^ . + . + "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OBA_$1"^^ . + . + . + . + . + . + "true"^^ . + "https://www.wormbase.org/"^^ . + . + . + . + . + "Livestock Breed Ontology" . + . + "false"^^ . + . + "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . + . + _:Nbeeec24cc7c5432f880d13abe1054669 . + "1004" . + . + . + . + . + . + . + . + "141"^^ . + "http://purl.obolibrary.org/obo/ZFS_$1"^^ . + "1"^^ . + . + . + . + . + "The COVID-19 Infectious Disease Ontology" . + . + "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . + . + . + "Genetic Code" . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/"^^ . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/ECG"^^ . + "false"^^ . + "SubtiWiki" . + . + "CHEMBL465070"^^ . + . + . + . + . + . + "UDB000691"^^ . + "^\\d+$"^^ . + "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . + "false"^^ . + "https://cellbank.nibiohn.go.jp"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "cho"^^ . + . + . + "http://cerevisiae.oridb.org/index.php"^^ . + . + . + . + . + "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . + . + "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . + . + "^[a-zA-Z0-9_\\.]+$"^^ . + "Japan Consortium for Glycobiology and Glycotechnology Database" . + "http://arabidopsis.org/index.jsp"^^ . + . + "ILMN_129894"^^ . + . + . + . + . + "Gene Wiki" . + . + . + "VIRsiRNA" . + . + . + . + . + . + "http://www.ymdb.ca"^^ . + "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . + "https://github.com/SED-ML/KiSAO"^^ . + . + . + . + . + . + . + . + . + "http://www.geneontology.org/formats/oboInOwl#$1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . + "iRefWeb" . + . + . + . + "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . + . + . + . + "http://www.affymetrix.com/"^^ . + . + . + . "MarRef" . - . - . - "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . + . + "Tom Gillespie" . + . + . + . + . "Bitbucket" . - . - . - . - . - . - "1018"^^ . - . - . - . - "http://urgi.versailles.inra.fr/Genefarm/"^^ . - . - . - . - . - . - "uniprotkb"^^ . - . - . - . - . - "Protein Alignment organised as Structural Superfamily" . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . - . - . - . - . - . - "146421"^^ . - . - . - . - . - . - . - "^PRJ[DEN][A-Z]\\d+$"^^ . - . - . + . + "0000000"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://phenol-explorer.eu/foods/$1"^^ . + . + . + . + "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . + . + "false"^^ . + . + "CALIPHO Group Ontology of Human Anatomy" . + "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all"^^ . + "PANTHER Node" . + . + "^\\d{7}$"^^ . + "false"^^ . + . + "^[0-9]{10}$"^^ . + . + . + "Tom Gillespie" . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . + . + "Network Data Exchange" . + . + . + . + . + . + "^[0-9]+$"^^ . + . + . + . + . + . + "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . + . + . + . + . + . + . + . + . + "Fungal Nomenclature and Species Bank" . + "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + "Xenbase" . + . + "http://bgee.unil.ch/bgee/bgee"^^ . + . + . + "https://plants.ensembl.org/"^^ . + "0001417"^^ . + . + . + "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . + . + "RepeatsDB Structure" . + . + "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . + . + "http://func.mshri.on.ca/fly"^^ . + . + "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . + . + "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . + . + . + "MaizeGDB Locus" . + "https://www.ebi.ac.uk/chembldb/"^^ . + . + . + "CAA71118.1"^^ . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . + "false"^^ . + . + . + "false"^^ . + "^Y[A-Z]{2}\\d+[CW]$"^^ . + "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . + . + . + . + . + . + . + . + . + "https://biosimulators.org/"^^ . + . + . + . + . + "false"^^ . + . + "Close to 5K Categorizations for drugs, similar to ATCC."^^ . + . + . + . + . + "Add"^^ . + "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . + . + . + . + . + . + "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . + . + "Common Bean ontology" . + . + . + . + "Schema.org" . + "Gene Ontology Annotation Database" . + . + . + . + "ClassyFire" . + . + "90062901"^^ . + . + . + . + . + "Database of Sequence Tagged Sites" . + "^\\d+$"^^ . + "false"^^ . + "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . + . + "YOR172W_571.0"^^ . + . + "^[A-Za-z0-9_-]+$"^^ . + "has pattern" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . + . + . + "M77F7JM"^^ . + . + . + . + "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + . + . + . + . + . + . + "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . + . + . + "false"^^ . + . + . + . + . + . + "SABIO-RK EC Record" . + . + "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^ . + . + . + . + "XUO" . + . + . + "false"^^ . + "DisProt" . + . + "https://www.vmh.life/"^^ . + "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . + . + . + . + . + . + "http://www.uniprot.org"^^ . + . + "LDS-1110"^^ . + . + . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . + "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."^^ . + . + . + . + . + "1038233"^^ . + . + "^TC\\d+$"^^ . + "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "http://geneontology.org/docs/ontology-relations/"^^ . + . + . + . + "false"^^ . + . + "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . + . + "0000001"^^ . + . + "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + "false"^^ . + "^\\d+$"^^ . + "^\\S+$"^^ . + . + . + "https://datacite.org"^^ . + . + . + "/12345/fk1234"^^ . + . + . + . + "http://purl.obolibrary.org/obo/HSAPDV_$1"^^ . + "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . + . + . + . + "Molecule role (INOH Protein name/family name ontology)" . + . + . + "High-quality Automated and Manual Annotation of microbial Proteomes" . + . + . + . + "DisProt region" . + "CutDB" . + . + . + . + "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . + "OMIM Phenotypic Series" . + "http://planttfdb.cbi.pku.edu.cn"^^ . + "false"^^ . + . + . + . + "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . + "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . + . + "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/chembl/entity/$1"^^ . + . + . + . + . + "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . + . + "0001350"^^ . + . + . + . + "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . + "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . + . + "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . + . + . + . + . + "^COG\\d+$"^^ . + "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . + . + . + . + . + . + "false"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . + . + . + "false"^^ . + . + . + "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . + "http://purl.org/spar/deo/$1"^^ . + . + . + "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . + . + . + . + . + . + . + . + "http://www.conoserver.org/"^^ . + "false"^^ . + . + . + . + . + "morpheus.lab/morpheus"^^ . + "false"^^ . + . + . + . + . + . + . + . + _:N53e99c99f37448aabdd75f1ee8077752 . + . + . + . + . + "false"^^ . + "https://www.drugbank.ca/categories/$1"^^ . + "http://bacmap.wishartlab.com/"^^ . + . + . + . + . + . + "^oai\\:cwi\\.nl\\:\\d+$"^^ . + "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . + . + . + . + . + . + "002804"^^ . + . + . + "https://foodb.ca/"^^ . + . + "MolMeDB" . + . + "Jesualdo Tomás Fernández-Breis" . + . + . + . + . + . + . + "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . + . + . + . + . + . + . + "https://www.wicell.org"^^ . + . + "^(ENSFM|ENSGTV:)\\d+$"^^ . + . + . + . + . + . + . + "https://mobidb.org/$1"^^ . + . + . + . + "^\\w+$"^^ . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + . + . + . + . + "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . + . + . + . + . + "0000079"^^ . + "Ax1"^^ . + . + . + "19-T4"^^ . + . + . + "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . + "http://www.snomedbrowser.com/"^^ . + . + . + "https://sumlineknowledgebase.com/?page_id=$1"^^ . + . + . + . + . + . + . + "0000029"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "http://www.genome.ad.jp/kegg/docs/upd_ligand.html"^^ . + "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . + . + "false"^^ . + . + . + . + . + . + "0000054"^^ . + . + . + . + "false"^^ . + . + . + . + "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . + . + "0000062"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/books"^^ . + . + . + . + . + "http://kinase.bioinformatics.tw/"^^ . + . + . + . + "https://github.com/obophenotype/chiro"^^ . + . + . + "^\\d{3}$"^^ . + . + . + "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "0000046"^^ . + . + . + "e999"^^ . + "Adnan Malik" . + "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "0000021"^^ . + . + "https://www.google.com/patents/"^^ . + . + . + . + "60316"^^ . + . + "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . + . + . + "http://www.semantic-systems-biology.org/apo"^^ . + "false"^^ . + . + . + . + . + . + . + "FuncBase Yeast" . + . + "GO Chemicals" . + . + . + . + . + "false"^^ . + "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . + . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + "false"^^ . + "false"^^ . + . + "http://www.radiomics.org/RO"^^ . + . + "https://glygen.org/glycan/"^^ . + "http://www.hprd.org/protein/$1"^^ . + . + . + "false"^^ . + "ENVO" . + . + "^MGYA\\d+$"^^ . + "http://soybase.org/"^^ . + . + "GWAS Catalog" . + . + "https://www.ncbi.nlm.nih.gov/dbEST/index.html"^^ . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^ . + . + . + . + . + "Allergome" . + . + . + "http://www.upol.cz/en/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/OMP_$1"^^ . + . + . + "^M\\d+$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "^\\d{9,9}$"^^ . + . + "Planarian Phenotype Ontology" . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . + "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906"^^ . + . + . + . + . + "SIDER Side Effect" . + "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . + "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . + . + . + . + . + "Mutant Mouse Resource and Research Centers" . + . + . + . + . + . + "hsa-let-7a-2-3p"^^ . + . + "Models developed with the Virtual Cell (VCell) software prorgam."^^ . + . + "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . + "^\\w+$"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://www.sparontologies.net/ontologies/frbr"^^ . + . + . + . + . + . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + . + . + . + . + . + . + . + "436605"^^ . + "Tohoku University cell line catalog" . + "Pol Castellano Escuder" . + . + "Quality"^^ . + "http://purl.obolibrary.org/obo/ICEO_$1"^^ . + "false"^^ . + . + "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . + . + . + "603903"^^ . + "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . + . + "http://purl.obolibrary.org/obo/GEO_$1"^^ . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . + . + . + "ENSG00000169174"^^ . + "true"^^ . + "Toxin and Toxin Target Database" . + "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . + . + . + . + "^\\d+$"^^ . + "https://pfam.xfam.org/clan/$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "1023371"^^ . + . + . + . + . + . + "0000046"^^ . + "https://asrp.danforthcenter.org/"^^ . + . + . + "http://darcsite.genzentrum.lmu.de/darc/index.php"^^ . + . + . + "^PAR:\\d+$"^^ . + . + . + "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^ . + . + "Collection" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "LOC_Os02g13300"^^ . + . + . + "Microarray experimental conditions" . + "https://cordis.europa.eu/"^^ . + . + . + "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . + . + . + . + . + "0000091"^^ . + "0440"^^ . + "Database of Aligned Ribosomal Complexes" . + . + . + . + "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . + . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . + "false"^^ . + . + . + . + . + . + . + "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^ . + "C00000001"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^ . + "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . + "^DB-\\d{4}$"^^ . + . + . + . + . + . + . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . + "contributor"^^ . + . + . + . + "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . + . + . + . +_:N9e11602ad5f546a9baecf7f5cafd8a92 "Pantelis Topalis" . + . + "^\\d{7}$"^^ . + "https://cropontology.org/ontology/CO_320/Rice"^^ . + . + "http://kim.bio.upenn.edu/software/ornaseq.shtml"^^ . + . + . + . + . + . + . + "Identifiers.org Ontology" . + "false"^^ . + "http://www.violinet.org/ovae/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "0000001"^^ . + "^\\d{7}$"^^ . + "U49845"^^ . + . + . + . + . + . + "Sunflower ontology" . + . + . + . + . + . + "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . + . + . + "^\\d+$"^^ . + . + "Selventa legacy complex namespace used with the Biological Expression Language"^^ . + . + . + "http://nbn-resolving.org/resolve_urn.htm"^^ . + . + . + "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . + . + "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . + . + "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "Environment Ontology for Livestock" . + . + . + "https://cellmodelpassports.sanger.ac.uk/"^^ . + . + . + "^\\d{7}$"^^ . + "https://fairsharing.org/$1" . + . + "0010039"^^ . + . + . + . + . + "http://repository.topdownproteomics.org/proteoforms"^^ . + . + . + "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^ . + . + . + "https://www.vectorbase.org/ontology-browser"^^ . + . + "00020134"^^ . + . + . + . + . + . + "false"^^ . + . + "https://www.fdilab.org"^^ . + "true"^^ . + . + . + . + . + "false"^^ . + "^[A-Za-z0-9\\/]+$"^^ . + . + "Robert Druzinsky" . + . + . + . + . + . + . + "Human Developmental Stages" . + . + . + . + . + . + . + . + "0010316"^^ . + . + . + "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . + . + "label"^^ . + . + . + "^[a-z0-9]+$"^^ . + . + "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . + _:Nc9350b7cae1f47468587257ef77de20c . + . + "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "^[0-9]*$"^^ . + . + . + "http://sourceforge.net/p/mamo-ontology/wiki/Home/"^^ . + "false"^^ . + . + "http://www.swisslipids.org/#/"^^ . + . + . + . + "false"^^ . + . + "A download link for the given resource" . + . + . + "false"^^ . + "Cell line collections"^^ . + . + . + "^[a-z0-9\\-]+$"^^ . + "^[A-Z-a-z0-9]+$"^^ . + "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . + . + . + . + . + . + . + . + . + "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . + . + . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + "Ontology from the APA"^^ . + "003070"^^ . + . + . + "https://scicrunch.org/resolver"^^ . + . + "^CE\\d{5}$"^^ . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . + . + . + "SNR17A"^^ . + . + . + . + "0000072"^^ . + . + . + "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . + . + . + . + . + "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . + . + . + . + . + . + _:N41391cbb5278405d824db68dec3c2cad . + "Identifiers.org namespace" . + . + . + . + "^M\\d{4}$"^^ . + . + "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . + . + . + . + "Scholarly Contributions and Roles Ontology" . + . + "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . + . + . + . + "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . + . + . + "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . + . + . + . + . + . + . + . + . + . + "PaxDb Organism" . + . + . + . + "https://uniresolver.io/#did:$1"^^ . + "4DNESWX1J3QU"^^ . + . + "http://variationontology.org"^^ . + . + "https://www.rebuildingakidney.org/"^^ . + "^\\d{7}$"^^ . + . + . + "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . + . + . + "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . + . + . + "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . + . + . + . + "ChEBI Integrated Role Ontology" . +_:N53e99c99f37448aabdd75f1ee8077752 "Fahim Imam" . + "Jennifer C. Giron" . + . + . + . + . + . + . + . + . + . + "^\\d{6}$"^^ . + . + "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . + . + . + "^[0-9]{1,7}$"^^ . + "false"^^ . + . + . + . + . + "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . + "Neuro Behavior Ontology" . + "Oryzabase Mutant" . + . + "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . + . + . + . + "817732"^^ . + "90806"^^ . + . + . + "https://cropontology.org/ontology/CO_365/Fababean"^^ . + . + . + "HGVM15354"^^ . + . + . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + . + . + "https://jcoin.datacommons.io"^^ . + . + . + . + "false"^^ . + "Plant Anatomy Ontology" . + . + "true"^^ . + "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . + . + . + . + . + . + "^\\d{5}$"^^ . + . + . + . + . + . + . + "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . + . + . + . + "true"^^ . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "^CH_\\d+$"^^ . + "http://purl.obolibrary.org/obo/ZFA_$1"^^ . + . + . + . + . + . + . + . + . + "Provenance, Authoring, and Versioning Vocabulary" . + . + "PF3D7_1328700"^^ . + . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . . - . - . - . - . - . - . - . - . - . - . - . - "GPIb_IX_V"^^ . - "Anne Thessen" . - . - . - . - . - "false"^^ . - . - . - . - . - "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . - . - . - "P23298"^^ . - . - "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.noncode.org/"^^ . - "false"^^ . - . - . - . - . - . - . - "https://cls.shop/$1"^^ . - "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . - "SED-ML data format" . - . - "false"^^ . - . - . - . - . - . - "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/XPO_$1"^^ . - "https://www.ncbi.nlm.nih.gov/protein"^^ . - "pgxbs-kftva5zv"^^ . - "PseudoGene" . - . - "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . - . - . - . - . - "https://urgi.versailles.inra.fr/gnpis/"^^ . - "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . - . - . - . - . - . - . - . - . - . - "Orphanet Rare Disease Ontology" . - . - . - "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . - . - . - . - . - . - "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . - . - . - . - "false"^^ . - . - "0000010"^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "https://developingmouse.brain-map.org/"^^ . - . - . - "https://sorgerlab.github.io/famplex/$1"^^ . - "https://run.biosimulations.org/simulations/$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "Rebuilding a Kidney" . - . - "https://ssbd.riken.jp"^^ . - . - "PubChem CID" . - "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . - . - . - . - . - . - . - "https://www.wwpdb.org/"^^ . - . + . + . + . + "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . + . + "https://smid-db.org/"^^ . + . + "false"^^ . + "MMP743597.11"^^ . + . + . + . + . + . + . + . + "EY223054.1"^^ . + . + "0000-0002-5355-2576"^^ . + . + . + . + . + . + . + "https://www.phosphosite.org"^^ . + . + "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . + . + . + . + . + . + "Cell line collections"^^ . + "JCGG-STR008690"^^ . + . + "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . + . + "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . + _:Nb146830ea578464c88406af42b4971a7 . + "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . + . + "130502"^^ . + . + "GDS1234"^^ . + "false"^^ . + . + "Clinical Trials Ontology" . + . + "VB.Ob.3736.GRSM125"^^ . + . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + . + . + . + . + "http://www.gramene.org/db/ontology/search?id=$1"^^ . + "906801"^^ . + . + . + . + . + . + . + . + . + "Gramene Gene" . + . + . + . + . + . + "http://bioinfo.lifl.fr/norine/"^^ . + . + . + . + "ACM1_HUMAN"^^ . + . + "TubercuList knowledge base" . + . + . + . + . + . + "false"^^ . + "European Food Information Resource Network" . + . + . + . + "false"^^ . + . + . + . + "https://www.merckmillipore.com/catalogue/item/$1"^^ . + . + . + . + "https://assets.nemoarchive.org/$1"^^ . + "Egon Willighagen" . + . + . + . + . + . + . + "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . + . + . + . + "https://loinc.org/$1"^^ . + . + "MycoBrowser leprae" . + "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . + . + . + . + "icdom:8500_3"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "OTTHUMG00000169812"^^ . + . + . + . + "^\\d+$"^^ . + . + "Vertebrate Genome Annotation Database" . + . + . + "PIRSF000100"^^ . + . + . + . + . + "Human Protein Atlas tissue profile information" . + . + . + "688"^^ . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . + . + . + . + . + . + . + "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . + . + . + . + "Henriette Harmse" . + . + . + . + . + "A database for Triticeae and Avena gene symbols."^^ . + "br/1"^^ . + . + . + "http://tables.pseudogene.org/[?species_name]/$1"^^ . + . + "https://github.com/Novartis/hpath"^^ . + . + "UniRule" . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + . + . + . + . + "CLPUB00496"^^ . + . + . + . + "http://hymao.org"^^ . + . + . + . + "Database of biopesticides maintained by the University of Hertfordshire "^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . + "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://github.com/EBISPOT/covoc"^^ . + . + . + . + . + . + . + . + . + . + "None"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . + "false"^^ . + "ThermoFisher is a life sciences supply vendor."^^ . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . + "493771"^^ . + "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html"^^ . + . + . + . + . + "35742"^^ . + . + . + "17254"^^ . + . + . + . + . + "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . + . + . + "0000044"^^ . + . + . + "UniGene" . + . + . + . + . + . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/GSSO_$1"^^ . + "^RF\\d{5}$"^^ . + . + . + "Germplasm Resources Information Network" . + . + . + "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^ . + "http://purl.obolibrary.org/obo/FBcv_$1"^^ . + . + . . - . - . - . - . - . - "http://www.plantontology.org"^^ . - . - . - . - . - . - "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . - "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^ . - "A frontend to Wikidata"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "MassBank" . - "false"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . - . - "WP732"^^ . - "Assembly" . + . + . + "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . + "https://www.cropontology.org/rdf/CO_320:$1"^^ . + . + . + . + "Wormpep" . + . + " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . + "EcoLexicon" . + . + "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . + "http://exac.broadinstitute.org/"^^ . + . + "splash10-0zq2000000-77302b0326a418630a84"^^ . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + "^NX_\\w+$"^^ . + . + . + "Complex Portal" . + . + . + . + "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "PR00001"^^ . + . + . + . + . + . + "false"^^ . + "http://edamontology.org"^^ . + "false"^^ . + . + . + . + . + . + . + "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . + "false"^^ . + . + "http://bioportal.bioontology.org/ontologies/OPB"^^ . + . + . + "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . + . + . + "^\\d+$"^^ . + . + . + "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . + . + "casent0106247"^^ . + "GWAS Central Phenotype" . + . + "^\\d{7}$"^^ . + "https://bioregistry.io/metaregistry/ncbi/$1"^^ . + . + "The Food Ontology" . + . + . + . + . + "false"^^ . + . + "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . + . + . + . + "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . + . + "Eschmeyer's Catalog of Fishes" . + "^bsg-[dscp]?\\d{6}$"^^ . + . + "https://www.nextprot.org/"^^ . + . + . + . + "PAp00000009"^^ . + "http://cellimagelibrary.org/"^^ . + "SM_UB-81"^^ . + . + . + "CIViC Assertion" . + . + . + . + . + . + "https://metacyc.org"^^ . + . + . + "http://www.inoh.org"^^ . + "00573"^^ . + . + "ChEMBL" . + . . - . - . - "https://github.com/phenoscape/vertebrate-taxonomy-ontology"^^ . - . - . - "ClinVar Variation" . - "Study inside StoreDB"^^ . - . - . - . - "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . - . - . - _:Nc89477563b5049e28e7ada477bb69e8c . - "Data Catalog" . - . - "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . - . - . - . - . - . - "Carbohydrate Active EnZYmes" . - . - . - "NIF Standard Ontology: Molecules" . - . - "G. Thomas Hayman" . - "https://ssbd.riken.jp"^^ . - . - "http://bugs.sgul.ac.uk/E-BUGS"^^ . - . - . - . - . - . - "Gramene Growth Stage Ontology" . - "^\\d{7}$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - "false"^^ . - . - "^[CD]\\d+$"^^ . - _:Nb1491a26268e498b8b8ee70cd2d648d3 . - . - "false"^^ . - "false"^^ . - . - "65"^^ . - "BDGP insertion DB" . - . - "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . - "Matúš Kalaš" . - "http://www.pombase.org/"^^ . - . - "JRBC Cell Bank" . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "4892"^^ . - . - "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^ . - . - "0000088"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://web.expasy.org/cellosaurus/"^^ . - . - "Open Tree of Life" . - . - . - "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . - . - . - "BE0000048"^^ . - . - . - "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . - "https://winter.group.shef.ac.uk/molbase/"^^ . - "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . - "Selventa Complexes" . - "^\\w+$"^^ . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . - . - . - . - . - . - . - . - . - . - "UPC04349"^^ . - "https://www.omim.org/phenotypicSeriesTitles/all"^^ . - . - . - . - . - . - . - "https://reg.clinicalgenome.org"^^ . -_:N670300cc4f4e45b8a8b3cfa32ce48e3e "Matthew Brush" . - . - . - . - . - . - "https://registry.identifiers.org/registry/$1"^^ . - . - . - . - "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . - . - "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - "http://www.isni.org/isni/$1"^^ . - . + . + "https://odc-sci.org/data/$1"^^ . + "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . + . + . + . + . + "BitterDB Receptor" . + . + . + . + . + "Collembola Anatomy Ontology" . + . + . + "0000253"^^ . + . + . + . + "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . + . + . + . + . + "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^ . + "false"^^ . + "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . + . + . + . + "Q9P0K8"^^ . + . + . + . + . + . + . + . + "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "Sequence types and features ontology" . + . + . + "true"^^ . + "Developmental stages of the Zebrafish"^^ . + . + "http://purl.obolibrary.org/obo/CMO_$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . + . + . + . + . + "virsi1909"^^ . + . + "https://github.com/information-artifact-ontology/IAO/"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay"^^ . + "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . + . + . + . + . + . + "false"^^ . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt"^^ . + . + . + "0001885"^^ . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/PPO_$1"^^ . + "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . + "NCBI Bookshelf" . + . + "^\\d+$"^^ . + "https://gold.jgi.doe.gov/"^^ . + . + . + "false"^^ . + . + "Dimension"^^ . + . + . + . + . + . + "https://nanocommons.github.io/identifiers/registry#$1"^^ . + "A controlled vocabulary to support the study of transcription in the human brain"^^ . + . + . + "false"^^ . + . + . + "D0001"^^ . + . + . + . + . + "100010"^^ . + . + "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . + . + . + . + . + . + "EU Clinical Trials" . + . + . + . + "http://www.wormbase.org/get?name=$1"^^ . + . + . + "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . + . + . + . + . + . + . + "12345"^^ . + . + . + . + . + . + . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/"^^ . + . + "https://www.beiresources.org"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . + . + "https://data.4dnucleome.org/experiment-set-replicates/"^^ . + . + . + "http://purl.obolibrary.org/obo/SEP_$1"^^ . + . + "Coconut ontology" . + . + "Ontology for Biomedical Investigations" . + . + . + "SR0000178"^^ . + . + "https://ssbd.riken.jp"^^ . + . + . + "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . + . + . + "^\\d+$"^^ . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + "nsv3875336"^^ . + . + . + . + "http://purl.obolibrary.org/obo/OHPI_$1"^^ . + "^\\w+$"^^ . + . + . + "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . + "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html"^^ . + . + . + "DrugBank Target v4" . + . + . + . + . + "Q-2958"^^ . + . + . + . + . + . + "Open Data Commons for Traumatic Brain Injury" . + "Chinese Biological Abstracts" . + . + . + "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . + "false"^^ . + "Janna Hastings" . + . + "https://www.fisheries.noaa.gov/species-directory"^^ . + . + . + "http://jglobal.jst.go.jp/en/"^^ . + . + . + "https://fungi.ensembl.org/id/$1"^^ . + "http://www.cbioportal.org"^^ . + . + . + . + . + . + . + . + . + "http://130.88.97.239/dbbrowser/sprint/"^^ . + . + . + . + . + . + "^TS-\\d+$"^^ . + . + . + . + . + "Ontology about the development and life stages of the C. elegans"^^ . + . + . + . + . + . + . + "https://github.com/EBISPOT/amphx_ontology"^^ . + "^[0-9]{15}[0-9X]{1}$"^^ . + . + . + . + . + . + . + . + . + "https://www.vmh.life/#reaction/$1"^^ . + "false"^^ . + "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + "https://github.com/BgeeDB/homology-ontology"^^ . + . + . + . + . + . + "RNAcentral" . + . + "HMDB00001"^^ . + . + . + "http://purl.obolibrary.org/obo/DUO_$1"^^ . + . + . + . + . + "true"^^ . + . + "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . + "false"^^ . + "http://foodb.ca/compounds/$1"^^ . + . + . + "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . + "Annotated Regulatory Binding Sites" . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + "false"^^ . + . + . + . + . + . + "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . + "^\\d+$"^^ . + . + . + . + . + "SCC111"^^ . + "false"^^ . + . + . + . + . + "SciCrunch Registry" . + . + . + . + . + . + . + . + . + . + . + "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . + . + . + . + . + . + . + . + . + . + . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + . + "190000021540"^^ . + "0000027"^^ . + . + . + "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^ . + . + "^\\w+$"^^ . + . + . + . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . + "https://github.com/allysonlister/swo"^^ . + . + . + . + "false"^^ . + "http://ontoneo.com"^^ . + "Protein Data Bank Ligand" . + . + . + . + . + . + . + "3966782"^^ . + . + . . - . - . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - . - . - . - "false"^^ . - . - . - . - . - "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . - . - "^[A-Za-z_0-9]+$"^^ . - "Publishing Workflow Ontology" . - "Ontology for Parasite LifeCycle" . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "17254"^^ . - "SAMEA2397676"^^ . - "Database of Genomic Structural Variation - Study" . - "false"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://purl.obolibrary.org/obo/PSO_$1"^^ . - . - . - . - . - . - . - . - "Genetics Home Reference" . - . - "1"^^ . - . - . - "http://biohackathon.org/resource/faldo#$1"^^ . - . - . - . - . - "2h6o"^^ . - . - . - "false"^^ . - . - "https://lincs.hms.harvard.edu/db/sm/$1"^^ . - "PGS000018"^^ . - . - . - . - . - . - . - "436605"^^ . - . - "^\\w+$"^^ . - . - . - . - . - "L000001"^^ . - "identifier for a fungus taxon in Index Fungorum"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "SugarBind" . - "The Python Package Index (PyPI) is a repository for Python packages."^^ . - . - . - "National Bibliography Number" . - . - . - "^\\d+$"^^ . - "Henning Hermjakob" . - . - . - "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . - . - . - "P53350"^^ . - "28789"^^ . - "^\\w+$"^^ . - "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . - . - . - "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . - "http://purl.obolibrary.org/obo/MFMO_$1"^^ . - . - . - "ArrayGroup"^^ . - . - . - . - "^[a-z]+(\\..*?)?$"^^ . - . - "85163"^^ . - . - . - . + . + "https://www.biocatalogue.org/services/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/XL_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "MM00040"^^ . + "^\\d\\w+$"^^ . + . + . + . + "false"^^ . + . + "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . + . + . + . + . + "http://www.kegg.jp/kegg/module.html"^^ . + . + . + . + "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . + . + . + . + . + . + . + . + . + . + . + . + "Homologous Vertebrate Genes Database" . + . + . . - "false"^^ . - . - . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . - . - "^\\d+$"^^ . - "http://pombe.oridb.org/index.php"^^ . - . - . - "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . - . - . - . - . - . - "false"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/interpro/genomeproperties/"^^ . + . + "Ontology of Zebrafish Experimental Conditions"^^ . + . + . + . + . + "ECOLI:CYT-D-UBIOX-CPLX"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "NONCODE v3" . + "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . + "3355"^^ . + . + . + . + . + . + . + . + . + "27267"^^ . + "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . + . + "^MI\\d{7}$"^^ . + "long-finned-pilot-whale"^^ . + . + . + . + "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . + "Influenza Ontology" . + "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . + . + . + "https://cropontology.org/ontology/CO_340/Cowpea"^^ . + . + . + . + . + . + . + "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . + "^ERM[0-9]{8}$"^^ . + . + "26753"^^ . + . + "C12345"^^ . + . + . + "^\\d{5}$"^^ . + . + "http://modelseed.org/"^^ . + "http://purl.obolibrary.org/obo/MPIO_$1"^^ . + . + . + "miR-1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "https://www.genome.jp/kegg/drug/"^^ . + . + . + . + . + "false"^^ . + "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . + "CA981206459"^^ . + . + . + . + "false"^^ . + . + . + . + "http://stato-ontology.org/"^^ . + . + "https://www.ebi.ac.uk/ols" . + . + . + "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology"^^ . + "https://nanocommons.github.io/identifiers/"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "http://degradome.uniovi.es/"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "0000010"^^ . + . + . + . + "Human Unidentified Gene-Encoded" . + . + "bioRxiv" . + "Physico-chemical process" . + "false"^^ . + "BindingDB is the first public database of protein-small molecule affinity data."^^ . + . + "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . + . + . + "https://github.com/rdruzinsky/feedontology"^^ . + "https://mmp.sfb.uit.no/databases/mardb/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^ . + "false"^^ . + . + . + . + "WikiGenes" . + . + . + . + . + . + . + . + "Fossilworks Taxon" . + . + . + "https://schema.org"^^ . + . + . + . + "false"^^ . + "LigandBook" . + "1100107"^^ . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . + . + "https://www.cropontology.org/rdf/CO_360:$1"^^ . +_:N1618a3940e7f4abf9d8b141e6627e31f "eVOC mailing list" . + . + "278"^^ . + . + . + . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . + . + . + . + "http://purl.obolibrary.org/obo/MF_$1"^^ . + . + "UniRef" . + . + . + . + "1050"^^ . + . + "true"^^ . + . + "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "EcoPortal" . + . + . + . + "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . + . + . + "Online Computer Library Center WorldCat" . + . + . + . + . + "Anvil" . + . + "Human Dephosphorylation Database" . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/OGMS_$1"^^ . + . + . + . + . + "false"^^ . + . + . + "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . + . + . + . + . + . + . + . + . + . + . + "Human Brain Atlas" . + . + . + "C0020004/4992"^^ . + . + . + . + "NIST Chemistry WebBook" . + "false"^^ . + . + . + . + . + . + . + "ebf69ca24298b28b2361e7d43eb52d6c"^^ . + "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . + . + . + "iECABU_c1320"^^ . + . + "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . + "false"^^ . + . + . + "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . + "https://www.enzolifesciences.com"^^ . + . + . + . + . + . + "https://www.ada.org/publications/CDT"^^ . + . + . + . + . + . + "ProtoNet ProteinCard" . + . + "FDB002100"^^ . + . + . + "false"^^ . + "http://greengenes.lbl.gov/"^^ . + "Experimental Factor Ontology" . + . + . + . + . + . + . + . + "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . + . + . + "http://www.informatics.jax.org/accession/MGI:$1"^^ . + . + . + . + . + . + . + . + . + . + . + "Pathway ontology" . + "https://github.com/futres/fovt"^^ . + "2000191"^^ . + . + . + "^(MNXM\\d+|BIOMASS|WATER)$"^^ . + . + "22-46615880-T-C"^^ . + "http://www.bioguo.org/AnimalTFDB/family_index.php"^^ . + . + "http://purl.obolibrary.org/obo/$1_$2" . + . + . + . + . + . + "MIR:00000008"^^ . + "A10BA02"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "Alpha Tom Kodamullil" . + "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . + . + . + . + "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . + . + . + "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . + . + "Rosa2"^^ . + . + . + . + . + . + "^[A-Z]C\\d{1,3}$"^^ . + . + . + . + "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . + . + "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . + . + . + . + "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + "UR000124451"^^ . + . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . + "http://purl.obolibrary.org/obo/TTO_$1"^^ . + . + . + "https://rapdb.dna.affrc.go.jp/"^^ . + . + "Fungal gross anatomy" . + "http://www.cellsignal.com/reference/pathway/$1.html"^^ . + "http://worfdb.dfci.harvard.edu/"^^ . + "false"^^ . + "PKDB00198"^^ . + . + "Suggested Ontology for Pharmacogenomics" . + . + "An ontology of phenotypes covering microbes"^^ . + . + "^\\d{7}$"^^ . + "false"^^ . + . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "1009107926"^^ . + "false"^^ . + . + . + "0001009"^^ . + "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . + . + "false"^^ . + . + . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . + "MNXM1723"^^ . + . + "Chris Mungall" . + . + . + . + . + "http://www.clo-ontology.org"^^ . + . + . + "MIPModDB" . + . + . + . + . + . + . + . + "https://civicdb.org/links/assertions/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "1433C_TOBAC_1_252"^^ . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + "6472"^^ . + . + . + . + . + . + "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . + . + . + "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . + . + . + "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . + . + . + . + . + . + "KYinno cell lines" . + "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . + "^((VGNC|vgnc):)?\\d{1,9}$"^^ . + . + . + . + . + "EDI_244000"^^ . + . + . + "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . + . + "31623"^^ . + "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . + "G-Rich Sequences Database" . + "Damion Dooley" . + . + "^\\d+$"^^ . + . + . + "^\\d+$"^^ . + . + "false"^^ . + "Developing Human Brain Atlas" . + "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . + . + . + "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . + "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . + . + . + . + "Robert Hoehndorf" . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . + . + . + . + . + "The international standard for identifying health measurements, observations, and documents."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "https://www.ebi.ac.uk/complexportal"^^ . + . + . + . + . + . . - . - "false"^^ . - . - . - . - . - "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . - "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . - "false"^^ . - . - . - . - . - "Higher-level classifications of COG Pathways"^^ . - . - . - . - . - . - . - . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/dbvar"^^ . + . + "https://cropontology.org/ontology/CO_350/Oat"^^ . + "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . + "PRIDE Controlled Vocabulary" . + . + "http://rna.rega.kuleuven.be/rnamods/"^^ . + "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . + "Meghan Balk" . + . + "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . + . + . + . + "https://plants.ensembl.org/id/$1"^^ . + . + "http://www.genome.jp/kegg/ko.html"^^ . + . + "http://biohackathon.org/resource/faldo"^^ . + "false"^^ . + "http://www.whocc.no/atc_ddd_index/"^^ . + . + . + . + "https://www.nemoarchive.org"^^ . + . + "https://cropontology.org/ontology/CO_324/Sorghum"^^ . + . + . + "0002959"^^ . + "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . + "OID Repository" . + . + "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . + "^\\d+$"^^ . + . + "false"^^ . + "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . + . + "false"^^ . + . + . + "Archival Resource Key" . + . + . + . + . + . + . + . + . + "lang"^^ . + . + . + "P29894"^^ . + . + "Michelle Giglio" . + . + . + . + . + . + . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + . + . + "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/fbbt"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + "https://europepmc.org/article/ppr/$1"^^ . + . + "has responsible" . + "Emotion Ontology" . + "false"^^ . + . + . + . + . + . + . + . + "https://www.sigmaaldrich.com"^^ . + "A comprehensive compendium of human long non-coding RNAs"^^ . + . + . + "http://research.nhgri.nih.gov/apps/homeodomain/web/"^^ . + . + "http://www.marinespecies.org/"^^ . + . + "^\\d+$"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." . + . + . + . + . + "false"^^ . + . + "International repository of Adverse Outcome Pathways."^^ . + "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . + "false"^^ . + "Event (INOH pathway ontology)" . + . + . + "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . + . + "1044544"^^ . + . + . + "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships"^^ . + "^\\d+$"^^ . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"^^ . + . + . + "https://flowrepository.org/"^^ . + . + . + "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + . + . + "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . + . + "100101"^^ . + "SIGNOR-C41"^^ . + . + . + "^\\d{7}$"^^ . + "http://www.kazusa.or.jp/rouge/"^^ . + . + . + . + "1000"^^ . + . + . + "https://envipath.org/"^^ . + . + . + . + "Bioregistry Metaregistry" . + . + . + "Ontology of Biological and Clinical Statistics" . + "false"^^ . + . + . + . + . + . + "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp"^^ . + . + . + . + . + . + "Community development of interoperable ontologies for the biological sciences"^^ . + . + . + . + "https://bioportal.bioontology.org/" . + "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . + . + . + . + . + "0000031"^^ . + "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^ . + . + . + . + . + . + . + . + "https://fungidb.org/fungidb/app/record/gene/$1"^^ . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . + . + "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . + . + . + . + . + "Food-Biomarker Ontology" . + . + . + . + . + . + "Environment Ontology" . + . + "http://www.drugbank.ca"^^ . + "728"^^ . + . + . + . + . + "0000712_1"^^ . + . + . + . + "TA_H3"^^ . + . + . + . + . + . + . + "SwissRegulon" . + . + . + . + . + . + . + "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . + . + . + "^\\d{7}$"^^ . + . + "The Prescription of Drugs Ontology" . + "^\\d{7}$"^^ . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . + . + . + . + . + "Tom Gillespie" . + . + . + . + "false"^^ . + . + "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . + . + . + "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . + "http://exac.broadinstitute.org/variant/$1"^^ . + . + "284196006"^^ . + "true"^^ . + . + "0000001"^^ . + "^CNP\\d{7}$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/OBCS_$1"^^ . + . + "http://www.boldsystems.org/"^^ . + . + . + . + . + . + . + . + . + . + "VFG2154"^^ . + . + . + . + . + . + . + . + . + . + . + . + "F4521"^^ . + "4776"^^ . + "Rice ontology" . + . + . + . + . + . + . + . + . + "Veterans Health Administration (VHA) unique identifier" . + . + . + . + "http://research.amnh.org/atol/files/"^^ . + "AKR-270"^^ . + . + "https://cls.shop/$1"^^ . + . + "http://ccr.coriell.org/"^^ . + "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . + . + . + . + "09200010"^^ . + . + "false"^^ . + . + "http://www.sparontologies.net/ontologies/fivestars"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "false"^^ . + "Call for paper topics in EasyChair"^^ . + . + . + . + . + "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . + "https://amzn.com/$1"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_356:$1"^^ . + . + . + . + "NAD%20biosynthesis"^^ . + "0000125"^^ . + "0000088"^^ . + . + . + . + . + . + "false"^^ . + . + "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . + . + . + . + _:Nafa6b93512254c399bee788072cfcae3 . + . + . + . + . + . + "https://github.com/Radiobiology-Informatics-Consortium/RBO"^^ . + . + . + . + . + . + . + "false"^^ . + "Luis A. Gonzalez-Montana" . + . + . + "false"^^ . + "^\\d+$"^^ . + "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . + . + "^\\d+$"^^ . + "https://omabrowser.org/cgi-bin/gateway.pl"^^ . + "BacMap Map" . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + . + . + . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ArrayExpress" . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/unigene"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "^\\w+$"^^ . + . + "https://www.cropontology.org/rdf/CO_321:$1"^^ . + . + . + . + . + . + "http://data.europa.eu/89h/$1"^^ . + "http://www.genome.jp/kegg/reaction/"^^ . + . + "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + "Xenobiotics Metabolism Database" . + . + . + . + . + . + "false"^^ . + . + . + . + . + "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . + "http://purl.obolibrary.org/obo/SWO_$1"^^ . + "http://agroportal.lirmm.fr" . + "Sigma Aldrich" . + . + . + . + "Nucleotide" . + "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . + . + . + "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . + . + . + . + . + "Human Medical Genetics" . + "http://purl.obolibrary.org/obo/OAE_$1"^^ . + "https://cropontology.org/ontology/CO_359/Sunflower"^^ . + "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^ . + "https://open.med.harvard.edu/wiki/display/eaglei/Ontology"^^ . + "Python"^^ . + . + . + "GCST000035"^^ . + "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . + . + . + . + . + . + . + . + "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . + "https://web.www.healthdatagateway.org/dataset/$1"^^ . + . + "NameRXN" . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + "0000041"^^ . + "MMP3888430"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.flybase.org/"^^ . + "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . + "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . + . + . + "CategorialBibliometricData"^^ . + . + . + "https://hamap.expasy.org/unirule/$1"^^ . + . + "^FB\\d{8}$"^^ . + . + "https://bdsc.indiana.edu/about/mission.html"^^ . + . + "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . + . + . + . + . + . + . + "false"^^ . + "https://prosite.expasy.org/$1"^^ . + . + "false"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1"^^ . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + . + . + . + "http://edamontology.org"^^ . + . + "Chemical Information Ontology" . + . + "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . + . + . + . + . + . + "4DN"^^ . + . + . + . + . + . + . . - . - . - . - "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . - . - . - . - . - . - . - "100010"^^ . - "^\\d+$"^^ . -_:Nb10cfdfe8ec745368a2e70a3b46283ad "Bill Hogan" . - "CC-BY-1.0"^^ . - . - . - . - "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . - . - . - . - . - "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . - . - . - "false"^^ . - . - . - "https://metacyc.org"^^ . - . - "0000000"^^ . - "Biological Magnetic Resonance Data Bank" . - . - . + . + "false"^^ . + . + . + "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . + . + . + . + . + "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . + . + . + . + "Plant Trait Ontology" . + . + "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . + . + "false"^^ . + . + . + "false"^^ . + "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page"^^ . + "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . + . + "^[A-Z]+[A-Z-0-9]{2,}$"^^ . + . + . + . + . + "https://www.cellbiolabs.com"^^ . + . + "false"^^ . + . + . + . + . + . + "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . + "false"^^ . + . + . + "BioCarta Pathway" . + . + "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . + "ExAC Variant" . + . + . + . + . + . + "^HGVPM\\d+$"^^ . + "false"^^ . + . + . + . + . + "151022"^^ . + . + . + . + . + . + . + "http://string.embl.de/interactions/$1"^^ . + "^HIT\\d{9}(\\.\\d+)?$"^^ . + "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . + . + . + . + "1-18"^^ . + . + . + . + . + . + . + . + . + "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . + . + . + . + . + . + . + "https://co.mbine.org/specifications/$1"^^ . + . + "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . + . + . + . + . + . + . + . + . + "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "NanoParticle Ontology" . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "GitHub Pull Request" . + "https://www.vmh.life/#gene/$1"^^ . + "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . + "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . + . + "false"^^ . + "^.*/.*$"^^ . + . + . + . + . + "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . + . + . + . + "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . + . + "EDAM Ontology" . + . + . + . + . + . + . + . + . + . + . + "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . + "PA448710"^^ . + . + . + . + . + "0004"^^ . + "Richard Cyganiak" . + "http://bacmap.wishartlab.com/"^^ . + . + "00001"^^ . + . + "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . + "^[A-Za-z]+$"^^ . + "false"^^ . + . + . + . + "^PA\\w+$"^^ . + . + . + "Petra Fey" . + "^TA\\d+$"^^ . + . + "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . + . + "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . + . + "7123"^^ . + "01N50ZZ"^^ . + . + . + "109082"^^ . + . + . + . + . + "TriTrypDB" . + . + . + "^[A-Z0-9]+$"^^ . + "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en"^^ . + "http://www.jcm.riken.go.jp/"^^ . + "https://www.disprot.org"^^ . . - . - "Genetic Testing Registry" . - . - . - . - . - . - . - "Xenobiotics Metabolism Database" . - . - . - "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . - . - . - . - . - . - "Vertebrate Homologous Organ Group Ontology" . - . - . - . - . - "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . - . - . - . - . - "^DP\\d{5}$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/$1_$2" . - "false"^^ . - . - . - . - . - . - . - . - . - "https://github.com/rsc-ontologies/rxno"^^ . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . - "^\\d+$"^^ . - . - "National Drug Data File" . - . - "spike00001"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://glyconavi.org/hub/?id=$1"^^ . - . - . - . - . - "UCR00513"^^ . - . - "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . - "1251"^^ . - . - . - . - "https://www.getty.edu/research/tools/vocabularies/tgn/"^^ . - "false"^^ . - . - . - . - "MEROPS Entry" . - . - "developed by ICARDA - Dec 2018"^^ . - "^\\d+$"^^ . - . - . - . - . - "^\\d+\\-\\d+\\-\\d+$"^^ . - "^\\w+_COVID19_[-\\w]+$"^^ . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . - . - . - . - . - . - "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . - "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . - . - "https://clinicaltrials.gov/"^^ . - "https://bioportal.bioontology.org/"^^ . - . - . - . - "microRNA Ontology" . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology"^^ . - . - . - "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^ . - "^[a-z][a-z]/[0-9]+$"^^ . - . - . - "LigandBook" . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - . - "634515043"^^ . - "SEQF1003"^^ . - . - . - "^SAM[NED](\\w)?\\d+$"^^ . - "Karen Eilbeck" . - . - . - "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . - . - . - . - "true"^^ . - . - "0278"^^ . + . + . + "Phenotype And Trait Ontology" . + . + . + "BEI Resources" . + "Ensembl Protists" . + . + . + "false"^^ . + . + "Biological Magnetic Resonance Data Bank" . + . + . + . + . + . + . + . + . + "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . + . + "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"^^ . + "https://www.xenbase.org/"^^ . + . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . + "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . + . + "http://vbrc.org/"^^ . + "5fde96bdc5f1aa9ff0cce18a"^^ . + "0000252"^^ . + "http://www.phenol-explorer.eu/foods/"^^ . + "http://isbndb.com/"^^ . + "http://www.molbase.com/"^^ . + . + . + "false"^^ . + . + "Colin Batchelor" . + . + . + "Bactibase" . + . + . + . + . +_:N4f2eda7bbb674f9cbb7e832185b2d787 "Julie Thompson" . + . + "Epidemiology Ontology" . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk"^^ . + "false"^^ . + . + "RIKEN Bioresource Center Cell Bank" . + . + . + . + . + . + . + . + . + "PS214100"^^ . + . + . + . + "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . + "MINID Test" . + . + . + "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . + . + . + "^\\d+$"^^ . + . + "biopragmatics/bioregistry"^^ . + "https://gpcrdb.org/protein/$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + _:N6ece56aaa9f040f498b35a7c9283039c . + . + . + . + "RiceNetDB Compound" . + . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/AAO_$1"^^ . + . + . + . + . + . + . + . + . + . + . + " http://edamontology.org" . . - . - "false"^^ . - . - . - . - . - "0000858"^^ . - . - "^\\w{14}$"^^ . - . - "SPCC13B11.01"^^ . - . - . - "^\\w+$"^^ . - "https://europepmc.org/article/CBA/$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . - "http://www.antirrhinum.net/"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . - . - . - . - "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . - "^(ENSFM|ENSGTV:)\\d+$"^^ . - "0011140"^^ . - . - _:Ne83bc53683cc401c8d9aa32085d472b2 . - "false"^^ . - "^\\d{7}$"^^ . - . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - . - "Coleoptera Anatomy Ontology" . - . - . - "https://www.eurofir.org"^^ . - . - . - . - . - . - . - . - "2224"^^ . - . - "^[A-Z]\\d+(\\.[-\\d+])?$"^^ . - . - . - . - . - "^\\d+$"^^ . - "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . - . - . - . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . - . - . - "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . - . - . - . + "CQG5"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "true"^^ . + "https://www.cropontology.org/rdf/CO_327:$1"^^ . + "Woody Plant Ontology ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "Medical Action Ontology" . + "Frederic Bastian" . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + . + . + . + . + "http://solgenomics.net/"^^ . + . + . + "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . + "Jennifer C. Girón" . + . + "https://w3id.org/faircookbook/$1"^^ . + . + "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^ . + . + "TopFind" . + "^\\d+$"^^ . + "OMA HOGs" . + "Biotin_biosynthesis"^^ . + . + . + . + "PharmGKB Pathways" . + "https://www.geonames.org/$1"^^ . + . + "https://bgee.org/"^^ . + . + "2.7.1.1"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/TAO_$1"^^ . + . + "PMC3084216"^^ . + . + . + . + . + "^[A-Z]{2}\\d+$"^^ . + . + . + "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . + . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . + . + . + . + . + . + "pgxbs-kftva5zv"^^ . + "http://www.kegg.jp/entry/$1"^^ . + "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . + . + . + . + . + "Transporter Classification Database" . + "false"^^ . + "false"^^ . + . + . + . + "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . + . + . + "RDF"^^ . + . + . + . + . + . + "false"^^ . + "https://drs.microbiomedata.org/objects/$1"^^ . + . + . + . + . + "JRC Data Catalogue" . + "Google Patents" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . + . + . + . + . + . + . + . + "SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints."^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . + . + "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . + . + . + . + . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt"^^ . + . + . + "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology."^^ . + "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"^^ . + "false"^^ . . - . - "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . - . - . - . - . - . - . - . - . - . - "NIF Standard Ontology: Investigations" . - . - "^Os\\S+g\\d{7}$"^^ . + . + . + "http://www.alanwood.net/pesticides"^^ . + "AN0097748"^^ . + . + . + . + . + . + . + . + . + "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . + . + . + . + "01001"^^ . + . + . + . + . + "false"^^ . + "Primate Brain Atlas" . + . + "AICARTRANSIMPCYCLO-CPLX"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "LRG_1"^^ . + . + . + . + . + . + "Bloomington Drosophila Stock Center" . + "http://purl.obolibrary.org/obo/NCRO_$1"^^ . + "I31.952"^^ . + . + "false"^^ . + . + . + . + . + . + . + . +_:N17601d69c183488abe17f5b23143ef61 "Plant Ontology Administrators" . + "PS00001"^^ . + . + . + . + "14362"^^ . + "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . + "0745-4570"^^ . + . + . + "false"^^ . + "The responsible person for a resource" . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ZP_$1"^^ . + . + . + . + . + "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . + . + . + "app-d678n-tottori"^^ . + . + "false"^^ . + . + "A formal represention for drug-drug interactions knowledge."^^ . + "false"^^ . + . + "100101"^^ . + "http://www.receptors.org/nucleardb/"^^ . + . + . + . + "false"^^ . + . + . + "CHEMBL4303805"^^ . + . + . + . + "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . + "Snapshot" . + . + . + . + . + . + "^(ZINC)?\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + "Discourse Elements Ontology" . + "false"^^ . + "Wikidata" . + . + . + "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . + . + "Genitourinary Development Molecular Anatomy Project" . + . + . + . + "3"^^ . + . + . + . + . + . + . + "J55.713G"^^ . + . + "http://stormo.wustl.edu/ScerTF/"^^ . + . + "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . + . + "^\\w{1,3}$"^^ . + . + "EDDA Study Designs Taxonomy" . + "http://www.wikidata.org/entity/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . + "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^ . + "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . + . + . + "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^ . + . + . + "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . + . + "http://purl.obolibrary.org/obo/CVDO_$1"^^ . + . + . + . + "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . + . + . + . + . + "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_333:$1"^^ . + . + . + . + "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . + "false"^^ . + . + . + . + "CIViC Evidence" . + . + . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/snp/"^^ . + "Laurel Cooper" . + . + . + . + . + "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . + "PharmGKB Disease" . + . + . + "Pankaj Jaiswal" . + . + "false"^^ . + "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + "Nucleotide Sequence Database" . + "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . + . + . + "https://dandiarchive.org/dandiset/$1"^^ . + . + "http://www-bionet.sscc.ru/sitex/"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ICO_$1"^^ . + "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . + . + . + . + . + . + "Identifier for an entity in open tree of life"^^ . + . + . + . + . + . + . + "https://icd.who.int/"^^ . + . + . + . + . + . + . + . + "https://icahn.mssm.edu/"^^ . + "https://github.com/obophenotype/biological-spatial-ontology"^^ . + "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . + . + . + . + . + . + . + . + "GenBank" . + . + . + "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . + . + . + . + _:N97795881207843c4bf7f49eb4d0f3011 . + . + . + . + . + . + . + "Tom Gillespie" . + . + . + "European Genome-phenome Archive Study" . + . + . + "Contributor Role Ontology" . + . + . + . + . + . + . + "false"^^ . + . + . + "http://planteome.org/"^^ . + "http://genatlas.medecine.univ-paris5.fr/"^^ . + . + . + . + . + . + . + "Sanger Cell Model Passports" . + . + . + . + . + . + . + . + . + "102l"^^ . + "https://drugs.ncats.io/"^^ . + . + . + . + . + . + . + . + . + "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . + . + "false"^^ . + "http://www.gramene.org/"^^ . + . + "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . + "https://www.ebi.ac.uk/ols/ontologies/ordo"^^ . + . + . + . + "Ontology about the gross anatomy of the C. elegans"^^ . + . + "4544"^^ . + . + . + . + . + . + . + . + "DICOM Controlled Terminology"^^ . + . + . + "false"^^ . + "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . + . + "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . + . + "https://medlineplus.gov/genetics/condition"^^ . + . + . + . + . + . + . + . + . + . + "https://github.com/obophenotype/sibo"^^ . + "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . + "false"^^ . + . + "false"^^ . + "^C\\d+$"^^ . + "0058"^^ . + . + "SIGNOR Relation" . + "Ali Syed" . + "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . + . + "0000194"^^ . + . + "128796-39-4"^^ . + . + "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"^^ . + . + "false"^^ . + . + "https://www.wikidata.org/wiki/Property:$1" . + "Comprehensive Resource of Mammalian protein complexes" . + "ArrayMap" . + . + . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . + . + . + . + . + . + "Higher-level classifications of COG Pathways"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "Zebrafish Experimental Conditions Ontology" . + . + . + . + "Integrated Canine Data Commons" . + . + "COlleCtion of Open Natural ProdUcTs" . + . + "false"^^ . + "https://www.kegg.jp/entry/$1"^^ . + "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . + "^\\d+$"^^ . + . + "https://www.genenames.org"^^ . + "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . + . + "Ontology of rat strains"^^ . + . . - "Reference Sequence Collection" . - . - . - . - . - . - . - "PM0012345"^^ . - "https://github.com/insect-morphology/aism"^^ . - . - "Francesco Vitali" . - . - . - . - . - "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . - "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - "false"^^ . - "265"^^ . - . - . - . - . - . - . - "https://www.alliancegenome.org/accession/$1"^^ . - . - "false"^^ . - . - . - . - "false"^^ . - . - "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . - . - . - "http://sugarbind.expasy.org/"^^ . - "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "NIF Standard Ontology: Cell Types" . - . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . - "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . - . - . - . - . - "The Amphioxus Development and Anatomy Ontology" . - . - . - "miRBase mature miRNA" . - . - "^\\d{7}$"^^ . - "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . - . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . - . - "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "MSV000082131"^^ . - . - . - "Small Angle Scattering Biological Data Bank" . - . - . - "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . - . - . - . - . - . - . - . - . - . - . - "^virsi\\d+$"^^ . - "http://repository.topdownproteomics.org/proteoforms"^^ . - "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . - "ls-c35719-120"^^ . - . - "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Annotated Regulatory Binding Sites" . - "false"^^ . - . - "https://bdsc.indiana.edu/stocks/$1"^^ . - . - . - . - . - . - "RDF Schema" . - . - . - "Spectral Database for Organic Compounds" . - . - . - . - _:N6c812e04ad74486588f1e6182fffbbb9 . - "MetaNetX reaction" . - "Gene Ontology" . - . - . - . - . - . - . - . - "true"^^ . - . - "Sugar Kelp trait ontology"^^ . - "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . - . - . - . - . - "https://molmedb.upol.cz/mol/$1"^^ . - . - . - . - . - . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . - . - . - "BG11523"^^ . - "Bill Hogan" . - . - . - "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . - "FuTRES Ontology of Vertebrate Traits" . - . - "DBSALT001211"^^ . - . - . - . - "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt"^^ . - "https://www.ebi.ac.uk/pdbe/emdb"^^ . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . - "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . - . - "^DP\\d{5}r\\d{3}$"^^ . - "^\\d+$"^^ . - . - . - "^NONHSAG\\d{5}$"^^ . - . - . - . - "^\\d{7}(_\\d)?$"^^ . - . - "^ENST\\d{11}$"^^ . - "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . - . - "false"^^ . - "Rfam database of RNA families" . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "https://github.com/jannahastings/mental-functioning-ontology"^^ . - . - "^\\d+$"^^ . - . - . - "Sigma Aldrich" . - . - "277.9"^^ . - . - "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^ . - . - . - . + . + . + . + . + . + . + . + . + "RxNorm" . + . + . + . + "0001290"^^ . + "0000690"^^ . + . + . + . + . + . + "https://github.com/BiodiversityOntologies/bco"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Sierra Moxon" . + . + . + . + "http://purl.obolibrary.org/obo/fbcv"^^ . + . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . + . + . + "Mouse gross anatomy and development, timed" . + . + . + "false"^^ . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . + . + . + "true"^^ . + . + "NMR Shift Database" . + . + . + . + "Gm00047"^^ . + . + . + "1cukA01"^^ . + . + "Lepidoptera Anatomy Ontology" . + . + "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . + . + "Deepak Unni" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + "LL379-9"^^ . + "false"^^ . + . + . + . + . + . + . + . . - . - . - . - . - . - . - . - . - "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . - . - . - "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . - . - . - "EBI-2307691"^^ . - . - . - . - . - "https://odc-sci.org"^^ . - . - . - . - . - . - . - . - . - . - . - "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^ . - . - . - . - . - "^\\d+$"^^ . - . - "17165"^^ . - "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . - . - . - . - . - . - "MicrobeamManipulation"^^ . - "Microarray experimental conditions" . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/MIRO_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "1.10.8.10"^^ . - . - . - "ModelDB" . - . - . - "The Virus Infectious Disease Ontology" . - . - "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . - . - . - . - . - "http://doqcs.ncbs.res.in/"^^ . - . - "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - "Jie Zheng" . - . - . - "true"^^ . - "Mosquito gross anatomy ontology" . - "false"^^ . - . - . - "false"^^ . - "Adrien Rougny" . - . - . - . - . - . - . - "Kinetic Simulation Algorithm Ontology" . - "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . - "https://www.ncbi.nlm.nih.gov/"^^ . + . + "^R\\d+$"^^ . + "http://purl.obolibrary.org/obo/OPMI_$1"^^ . + "Cell line collections"^^ . + . + . + "http://purl.obolibrary.org/obo/ONE_$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "false"^^ . + "false"^^ . + "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . + "false"^^ . + "false"^^ . + . + "false"^^ . + "http://purl.obolibrary.org/obo/$1"^^ . + . + . + . + . + . + "https://github.com/monarch-initiative/SEPIO-ontology"^^ . + "http://purl.obolibrary.org/obo/VARIO_$1"^^ . + "^PM\\d{7}$"^^ . + . + . + . + . + . + . + . + "false"^^ . + "MagnitudeValueType"^^ . + . + . + . + . + . + "http://uberon.org"^^ . + . + "^\\d{8}$"^^ . + . + "http://www.pharmgkb.org/"^^ . + . + "false"^^ . + . + "false"^^ . + . + "https://github.com/AnimalGenome/vertebrate-trait-ontology"^^ . + . + . + . + "https://github.com/DiseaseOntology/PathogenTransmissionOntology"^^ . + . + . + . + . + . + . + "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . + . + . + "http://www.ebi.ac.uk/cmpo"^^ . + . + . + . + . + "1.1.1.1"^^ . + . + . + . + "Amazon Standard Identification Number" . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "Hazardous Substances Data Bank" . + . + "^rxn\\d+$"^^ . + . + . + "false"^^ . + "Analyses of microbiome data within MGnify"^^ . + "http://exac.broadinstitute.org/"^^ . + . + . + "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . + "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . + . + . + . + "https://www.aepc.org/european-paediatric-cardiac-coding"^^ . + . + . + . + "CORDIS Project" . + . + . + . + . + . + . + . + "Genomic Data Commons Data Portal" . + . + . + . + . + "0001157"^^ . + . + . + "S000002493"^^ . + "^\\d{7}$"^^ . + . + "A registry of life science prefxes"^^ . + . + . + . + . + "http://topdb.enzim.hu/"^^ . + "http://www.genome.jp/kegg/catalog/org_list3.html"^^ . + . + "false"^^ . + . + "EcoliWiki from EcoliHub" . + . + . + . + . + . + . + . + "https://cryptodb.org/cryptodb/"^^ . + "https://licebase.org"^^ . + . + . + . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "TS-0285"^^ . + "^DTXSID\\d+$"^^ . + "Stacia R Engel" . + "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . + "false"^^ . + . + . + "^[0-9]*$"^^ . + . + "The Drug-Drug Interactions Ontology" . + . + "http://purl.obolibrary.org/obo/PECO_$1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/PCO_$1"^^ . + . + . + . + "https://portal.issn.org/resource/ISSN/$1"^^ . + . + . + . + . + . + "RiceNetDB miRNA" . + . + "1466"^^ . + "http://trace.ddbj.nig.ac.jp/bioproject/"^^ . + . + . + . + . + . + "^[SED]R[APRSXZ]\\d+$"^^ . + "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . + "1"^^ . + . + . + "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . + "Maize gross anatomy" . + . + . + . + . + . + . + . + "https://dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + . + . + . + . + "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp"^^ . + "STUDY1040"^^ . + . + . + "5.A.1.1.1"^^ . + . + "An ontology covering the taxonomy of teleosts (bony fish)"^^ . + . + . + "90801"^^ . + . + . + . + . + . + . + "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology"^^ . + . + "false"^^ . + . . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . - "http://arabidopsis.org/index.jsp"^^ . - . - "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^ . - "Tetrahymena Genome Database" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . - "Wormpep" . - . - . - "^\\d{5}$"^^ . - . - "Ontology of units of Measure" . + "BIOMD0000000048"^^ . + . + "false"^^ . + "PhosphoPoint Kinase" . + . + . + . + . + . + . + "http://www.snomedbrowser.com/Codes/Details/$1"^^ . + "false"^^ . + . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/sra"^^ . + "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . + . + . + "Agronomy Ontology" . + "Ascomycete phenotype ontology" . + . + . + . + . + "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . + . + . + . + . + . + . + "https://github.com/IEDB/MRO"^^ . + "Catalytic Site Atlas" . + "0001"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "PhylomeDB" . + . + "false"^^ . + . + . + . + . + . + . + "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . + "https://www.vmh.life/"^^ . + . + . + . + "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . + . + "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . + . + "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . + "http://mona.fiehnlab.ucdavis.edu/"^^ . + . + . + . + "https://scdontology.h3abionet.org/"^^ . + . + "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^ . + . + . + . + "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . + . + . + "Genetic and Rare Diseases Information Center" . + "http://trichdb.org/trichdb/"^^ . + . + . + . + "^[A-Z]\\d+(\\.[-\\d+])?$"^^ . + . + . + "0290"^^ . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/STATO_$1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . + "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "^BAMSC\\d+$"^^ . + . + "false"^^ . + "0000111"^^ . + . + . + "^\\d{7}$"^^ . + "67035"^^ . + . + . + "Guide to Pharmacology Target" . + "2244"^^ . + . + . + "false"^^ . + "DragonDB DNA" . + . + "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo"^^ . + "^MIMAT\\d{7}$"^^ . + . + . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi"^^ . + "^\\d+$"^^ . + "http://geneontology.org/"^^ . + "3SBPLMKKVEVR"^^ . + . + . + . + "ENSGT00550000074763"^^ . + . + . + . + . + "NMR Restraints Grid" . + "^spike\\d{5}$"^^ . + "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . + "ProteomicsDB Peptide" . + . + . + "false"^^ . + . + . + . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . + . + . + . + . + . + . + . + "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . + "^\\w+$"^^ . + "Integrated Microbial Genomes Gene" . + "Software Heritage is the universal archive of software source code."^^ . + "http://www.peptideatlas.org/PASS/$1"^^ . + "https://www.uniprot.org"^^ . + "http://purl.obolibrary.org/obo/BCO_$1"^^ . + . + . + "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . + . + . + . + . + . + . + "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . + . + . + . + . + . + . + . + "nstd102"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . + . + "^\\d+$"^^ . + "^SIGNOR\\-[A-Z]+\\d+$"^^ . + . + . + "https://pharmacome.github.io/conso/$1"^^ . + . + . + . + . + "http://www.york.ac.uk/"^^ . + "National Academic Research and Collaborations Information System" . + "https://www.rhea-db.org/"^^ . + "JCRB1355"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "https://github.com/HajoRijgersberg/OM"^^ . + "000410"^^ . + . + . + . + . + . + . + . + "The cBioPortal for Cancer Genomics" . + "Biological Spatial Ontology" . + "http://edamontology.org"^^ . + . + "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . + "https://cropontology.org/ontology/CO_334/Cassava"^^ . + . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + "1058367"^^ . + . + . + "^\\d{7}$"^^ . + "TAIR Gene" . + . + . + . + . + "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . + . + . + "false"^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/TO_$1"^^ . + . + "http://purl.obolibrary.org/obo/NBO_$1"^^ . + . + . + . + "UniProt Keywords" . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . + . + . + . + . + . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology"^^ . + "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . + . + . + . + . + "http://www.antirrhinum.net/"^^ . + . + . + "Unified Medical Language System Atomic Unique Identifier" . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "^\\d{7}$"^^ . + "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . + . + "SIDER Drug" . + . + . + "FlyBase Controlled Vocabulary" . + "PharmacoDB Tissues" . + . + . + . + . + . + "false"^^ . + . + . + . + . + "MIMAT0046872"^^ . + "Stemcell Knowledge and Information Portal" . + . + "Ecological terms"^^ . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . + . + "M0001"^^ . + . + . + . + . + . + "Genetic Testing Registry" . + . + . + "^F\\d{4}$"^^ . + "70"^^ . + . + . + "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . + . + . + . + "Bibliometric Data Ontology" . + . + . + . + . + "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . + . + "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . + . + "Sorghum TDv5 - Oct 2019"^^ . + . + . + . + "http://zfin.org/$1"^^ . + "^[A-Za-z0-9]+$"^^ . + . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "UniProt Archive" . + . + . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . + . + "false"^^ . + . + . + . + . + . + "A vocabulary and ontology repository for agronomy and related domains." . + . + . + . + "false"^^ . + "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . + . + . + . + . + "0001191"^^ . + "https://www.ebi.ac.uk/metagenomics/"^^ . + . + . + . + "Gramene Growth Stage Ontology" . . - . - . - . - . - "http://www.ebi.ac.uk/sbo/"^^ . - . - "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MPIO_$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - "https://www.kerafast.com/Search?SearchTerm="$1""^^ . - "false"^^ . - . - "true"^^ . - "0000031"^^ . - . - . - "http://addgene.org/"^^ . - "https://registry.identifiers.org/registry/$1" . - . - . - . - "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . - "^\\d{7}$"^^ . - "false"^^ . - "Cellosaurus Publication" . - "Flybase Cell Line" . - . - . - . - . - . - . - "Medical Subject Headings" . - . - . - . - "https://www.genome.jp/kegg/pathway.html"^^ . - . - . - . - . - . -_:N4d23b2240e434caa96574a6c1329f620 "John Garavelli" . - . - . - "11303"^^ . - . - "https://easychair.org/cfp/$1"^^ . - "PK-DB" . - . - "https://www.uniprot.org/"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - "Suzi Aleksander" . - . - . - "^[A-Z-_0-9]+$"^^ . - . - . - . - . + . + . + . + . + "Disease Drivers Ontology" . + . + "^\\d+$"^^ . + . + "^\\d+$"^^ . + . + . + "NP_012345"^^ . + . + . + "^BE\\d{7}$"^^ . + . + . + "http://thebiogrid.org/"^^ . + "UniPathway Reaction" . + . + "http://www.psidev.info/MOD"^^ . + . + "chromium"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^ . + . + . + . + . + . + . + "http://www.cellsignal.com/products/$1.html"^^ . + "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . + . + "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . + . + "http://prism.case.edu/prism/index.php/EpilepsyOntology"^^ . + . + . + "https://ratmine.mcw.edu/ontology/disease/"^^ . + . + "false"^^ . + . + "MicrosporidiaDB" . + . + . + . + . + . + "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . + . + . + . + . + . + . + "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^ . + "25011"^^ . + . + . + "false"^^ . + "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . + "^IID\\d+$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . + . + . + . + "https://github.com/OAE-ontology/OAE/"^^ . + "https://github.com/monarch-initiative/GENO-ontology/"^^ . + . + "https://ifaa.unifr.ch/"^^ . + . + "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . + "EDAM Data" . + . + "Medical Dictionary for Regulatory Activities Terminology" . + . + . + . + "^\\d+$"^^ . + . + "http://www.ebi.ac.uk/efo"^^ . + . + . + . + "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . + . + . + . + . + . + . + . + "NCBI Gene Expression Omnibus" . + . + "https://civicdb.org/"^^ . + . + . + . + . + "3000887619"^^ . + . + . + "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . + . + . + "http://purl.obolibrary.org/obo/OVAE_$1"^^ . + "Pocketome" . + . + . + "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . + "false"^^ . + . + . + "^[1-9]\\d{0,5}$"^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/gv/mhc/"^^ . + . + "CL0192"^^ . + . + "CNP0171505"^^ . + . + . + "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm"^^ . + . + . + . + "Prefix Commons" . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . + . + . + . + "SNHG3"^^ . + . + . + "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . + "http://www.sparontologies.net/ontologies/bido"^^ . + . + . + . + . + "Interlab Cell Line Collection" . + . + . + "http://ligand-depot.rutgers.edu/index.html"^^ . + . + . + . + . + "NeuroVault Image" . + . + . + "1199"^^ . + . + . + . + "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . + . + . + "Cell line databases/resources"^^ . + . + "Oryza Tag Line" . + . + . + "http://www.pseudogene.org"^^ . + . + "^EBI\\-[0-9]+$"^^ . + . + . + . + . + . + . + . + "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . + . + . + . + . + . + . + . + . + . + "RGD Disease_Ontology" . + . + . + "http://purl.org/dc/terms/$1"^^ . + "GCF_000005845.2"^^ . + "false"^^ . + . + . + "^\\d{7}$"^^ . + "0000072"^^ . + "https://cropontology.org/ontology/CO_325/Banana"^^ . + . + . + . + . + "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . + . + . + . + . + . + "http://func.mshri.on.ca/yeast"^^ . + . + . + . + . . - . - . - . - "dictyBase Expressed Sequence Tag" . - "false"^^ . - . - . - "^C?\\d+$"^^ . - . - "mirEX" . - . - "https://github.com/IEDB/MRO"^^ . - . - . - . - "0003"^^ . - . - . - . - . - "AmoebaDB" . - . - "false"^^ . - . - . - "^CL\\d+$"^^ . - . - "Jennifer C. Giron" . - "false"^^ . - . - . - . - . - . - . - "CALM1"^^ . - . - "https://prefixcommons.org/?q=$1" . - . - "CH_001923"^^ . - . - . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/BILA_$1"^^ . + "InterLex" . + . + . + . + "1868"^^ . + "false"^^ . + . + . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^ . + "https://github.com/IHCC-cohorts/GECKO"^^ . + "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . + . + . + . + "A controlled vocabulary to describe phenotypic traits in plants."^^ . + "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . + . + . + . + . + . + . + . + . + "Antimicrobial Peptide Database" . + "https://www.storedb.org/"^^ . + "http://www.ncbi.nlm.nih.gov/CCDS/"^^ . + . + "https://kidsfirstdrc.org"^^ . + . + . + . + "ChEBI"^^ . + . + . + . + . + . + "G77500AY"^^ . + . + . + "false"^^ . + . + "https://pathbank.org/view/$1"^^ . + . + . + . + "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . + "true"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "https://www.kaggle.com/$1"^^ . + . + . + "false"^^ . + "https://www.cropontology.org/rdf/CO_366:$1"^^ . + "false"^^ . + . + . + . + . + . + "1"^^ . + . + . + . + . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^ . + . + . + "false"^^ . + . + "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . + . + "http://purl.obolibrary.org/obo/TRANS_$1"^^ . + . + . + . + . + . + . + . + . + . + . + "1000001"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "NCBI Registry" . + . + . + "http://purl.obolibrary.org/obo/PLANA_$1"^^ . + . + . + . + . + . + . + . + "^PR[0-9]{6}$"^^ . + "http://www.peptideatlas.org/"^^ . + . + . + . + . + . + . + "Open Data for Access and Mining" . + . + "3905431"^^ . + "false"^^ . + . + "false"^^ . + "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"^^ . + . + . + . + . + . + . + . + . + "A0014"^^ . + "OMA Group" . + "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . + "^\\d+$"^^ . + "^UPI[A-F0-9]{10}$"^^ . + "https://www.ccdc.cam.ac.uk/"^^ . + "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . + . + . + . + . + . + . + . + . + . + . + "https://bioregistry.io/$1:$2" . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + . + "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . + . + . + . + . + . + "eNanoMapper Ontology" . + . + . + . + . + . + . + "http://www.lrg-sequence.org/"^^ . + . + . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . + . + . + "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . + . + "ev:E00032"^^ . + "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . + "https://ximbio.com"^^ . + "^\\d+$"^^ . + . + "http://www.mirbase.org/"^^ . + . + . + "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"^^ . + . + . + . + . + "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . + . + . + . + . + . + . + . + "https://www.reactome.org/"^^ . + . + . + . + "Extensible Markup Language" . + . + "https://mmp.sfb.uit.no/databases/marcat/"^^ . + . + . + . + "Allotrope Merged Ontology Suite" . + . + . + . + "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . + . + . + . + . + "Information Artifact Ontology" . + . + . + . + "https://www.cropontology.org/rdf/CO_343:$1"^^ . + . + "0002502"^^ . + "^\\d+$"^^ . + "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . + . + . + . + . + . + . + . + . + . + . + . + "TF0001053"^^ . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + "DepMap Cell Lines" . + . + . + . + . + . + . + . + . + "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . + . + . + "http://addgene.org/$1"^^ . + "false"^^ . + . + "1000"^^ . + . + . + "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . + "An ontology to represent genomics cohort attributes."^^ . + "http://birdgenenames.org/cgnc/"^^ . + . + "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . + . + "https://www.cropontology.org/rdf/CO_339:$1"^^ . + "0000095"^^ . + . + "R00100"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . + . + "http://www.semantic-systems-biology.org/apo"^^ . + . + . + "false"^^ . + . + "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + "https://gold.jgi.doe.gov/resolver?id=$1"^^ . + . + . + . + . + . + "^\\w{1,2}\\d+$"^^ . + . + . + "^EB\\d+$"^^ . + . + . + . + . + . + . + . + "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . + . + . + . + . + . + . + . + . + . + "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . + "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes."^^ . + . + "^TIGR\\d+$"^^ . + . + "http://bugs.sgul.ac.uk/E-BUGS"^^ . + . + . + . + . + "false"^^ . + . + "https://www.signalingpathways.org/index.jsf"^^ . + . + "Web Elements" . + "http://purl.obolibrary.org/obo/HOM_$1"^^ . + "false"^^ . + . + . + . + "false"^^ . + "https://run.biosimulations.org/simulations/$1"^^ . + . + "N0000001662"^^ . + . + "https://xmetdb.org"^^ . + "Pierre-Alain Binz" . + "^\\w+$"^^ . + "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . + "http://www.hmdb.ca/metabolites/$1"^^ . + . + "RiceNetDB Protein" . + . + "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . + "false"^^ . + . + "Protein Ensemble Database ensemble" . + . + . + . + . + "2"^^ . + . + . + . + "false"^^ . + "Cell line collections"^^ . + . + . + . + "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . + . + . + "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . + . + . + "2022.07.08.499378"^^ . + . + . + "http://www.hipsci.org"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "349124"^^ . + . + "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . + . + "false"^^ . + . + "65"^^ . + "false"^^ . + . + "Cell line databases/resources"^^ . + . + "NIF Standard Ontology: Digital Resources" . + . + "false"^^ . + "Universal Spectrum Identifier" . + "^D\\d+$"^^ . + "http://intron.ucsc.edu/yeast4.3/"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . +_:N0a566dc9a31d4284b688fc06eb0598c6 "David Blackburn" . + . + . + . + "https://www.novusbio.com"^^ . + . + . + "false"^^ . + . + "US4145692"^^ . + . + . + "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . + "false"^^ . + "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . + . + "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . + . + . + . + . + "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "BIOZIL" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . + "FuncBase Human" . + . + . + "true"^^ . + . + "^\\d{7}$"^^ . + "https://biosimulations.org/projects/$1"^^ . + . + . + . + . + . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . + "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . + . + "PROSITE" . + . + . + "BiGG Reaction" . + . + "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . + . + . + . + . + "6b1"^^ . + "false"^^ . + . + . + "false"^^ . . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^ . - . - "LOC_Os01g49190"^^ . - "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^ . - "AP00378"^^ . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . - . - . - . - "^\\w{2,4}\\d{5}$"^^ . - "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . - . - . - "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . - . - . - . - . - "551115"^^ . - . - "https://www.fisheries.noaa.gov/species-directory"^^ . - . - "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . - "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . - "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . - . - . - . - "false"^^ . - "Amphibian gross anatomy" . - . - . - . - . - . - . - "https://scicrunch.org/browse/resourcedashboard"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "MGYA00002270"^^ . - "0019171"^^ . - "https://zenodo.org/record/$1"^^ . - . - "https://jjj.bio.vu.nl/models/$1"^^ . - . - . - . + "Genotype-Tissue Expression" . + . + "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . + . + . + . + . + . + . + . + "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . + . + "^\\d{7}$"^^ . + . + . + "Medical Data Models" . + . + . + "Identifiers.org Terms" . + . + . + "Teleost taxonomy ontology" . + "http://www.indexfungorum.org"^^ . + "Common Anatomy Reference Ontology" . + . . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . - "http://www.whocc.no/atcvet/atcvet_index/"^^ . - . - . - . - "KEGG Environ" . - . - . - . - "false"^^ . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - "https://www.ccdc.cam.ac.uk/"^^ . - . - "true"^^ . - "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . - "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . - . - . - . - . - "https://purl.obolibrary.org/obo/ohd/home"^^ . - "Pearl millet ontology" . - . - . - . - . - . - . - "Minimal Information About Anatomy ontology" . - . - . - . - . - . - . - "Primate Brain Atlas" . - "Allotrope Merged Ontology Suite"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^MIR:000\\d{5}$"^^ . - "^[a-z_\\.]+$"^^ . - . - . - . - . - . - "^[EL]D[SG]-\\d+$"^^ . - . - . - . - . - . - . - "98"^^ . - . - "https://plants.ensembl.org/id/$1"^^ . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . - . - . - . - "GitHub Issue" . - "http://www.cathdb.info/domain/$1"^^ . - . - . - "http://www.mirbase.org/"^^ . - . - "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . - "false"^^ . - "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html"^^ . - "The Behaviour Change Intervention Ontology" . - "Progenetix" . - . - . - . - . - . - . - . - "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . - "EB0170"^^ . - "W2741809807"^^ . - . - . - . - . - "true"^^ . - "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . - . - . - . - . - "^\\d+$"^^ . - "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - "https://proteinensemble.org/$1"^^ . - . - . - "https://smid-db.org/smid/$1"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "^\\d{6}$"^^ . - . - . - "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "A controlled vocabulary to support the study of transcription in the primate brain"^^ . - . - . - . + "PhosphoSite Site Group" . + . + . + . + . + . + "0000093"^^ . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . + . + "Phy000CLXM_RAT"^^ . + "22RV1_12_2019"^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . + . + . + . + "^c\\d+$"^^ . + "^10.\\w{4}/\\w{10}$"^^ . + . + . + . + "FunderRegistry" . + "http://substrate.burnham.org/"^^ . + "31"^^ . + . + . + "^[A-Z]{2}[A-Z0-9][0-9]{5}$"^^ . + . + . + "PolBase" . + . + . + "MCDS_L_0000000001"^^ . + . + . + . + . + "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/genbank/"^^ . + . + "KEGG Disease" . + . + "^\\d{7}$"^^ . + "28789"^^ . + "COSMIC Gene" . + . + . + . + . + "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . + . + . + . + "https://www.novusbio.com/products/$1"^^ . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + . + . + . + . + . + . + "Protein Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "https://depmap.org/portal"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + "false"^^ . + . + "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Terry Hayamizu" . + . + . + "Tom Gillespie" . + . + "Software Heritage" . + "^\\d{7}$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . + . + "sourceDateStart"^^ . + . + "^S-[A-Z]{4}[A-Z\\d\\-]+$"^^ . + . + . + . + . + . + "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . + . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "miriam"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.wormbase.org/"^^ . + "National Drug File - Reference Terminology" . + . + "1755"^^ . + . + . + "http://purl.obolibrary.org/obo/OGG_$1"^^ . + "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . + "Pazar Transcription Factor" . + . + . + . + "Morpheus model repository" . + "false"^^ . + . + . + "false"^^ . + . + "http://sideeffects.embl.de/"^^ . + "EST database maintained at the NCBI." . + . . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . - . - . - . - . + "arXiv" . + . + "false"^^ . + "Bio-MINDER Tissue Database" . + . + . + . + "MNXR101574"^^ . + "http://purl.obolibrary.org/obo/XAO_$1"^^ . + . + . + . + "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . + . + . + . + . + "AgroPortal" . + . + . + . + "NCBI Taxonomy" . + . + . + . + . + . + . + "https://catalog.bcrc.firdi.org.tw"^^ . + . + . + . + "https://github.com/phenoscape/taxrank"^^ . + "http://www.genome.jp/kegg/drug/environ.html"^^ . + "false"^^ . + . + "rateRule"^^ . + . + . + "BioLegend is a life sciences supply vendor."^^ . + "false"^^ . + . + "^\\d{7}$"^^ . + "dictyBase" . + "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + "Novus Biologicals" . + "https://ssbd.riken.jp/database/project/$1"^^ . + "Google Scholar Researcher" . + "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . + . + . + "Publishing Workflow Ontology" . + . + . + . + . + "^([a-z]{3,5}_)?M\\d{5}$"^^ . + . + . + . + "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . + . + . + . + "PB000166"^^ . + . + "false"^^ . + "prefLabel"^^ . + . + . + "^\\d{5}$"^^ . + . + "false"^^ . + . + . + . + "DRSC05221"^^ . + . + . + . + . + . + . + . + . + . + "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^ . + . + . + . + . + "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . + "https://foodon.org/"^^ . + . + . + . + . + . + "false"^^ . + "001"^^ . + . + "0000199"^^ . + . + . + . + . + . + . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . + . + . + . + . + . + . + "Epilepsy and Seizure Ontology" . + . + . + . + . + "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . + . + "000017"^^ . + . + . + . + . + . + "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . + . + . + . + "https://github.com/aellenhicks/htn_owl"^^ . + . + "http://www.metabolomicsworkbench.org/"^^ . + . + . + "^[0-9]+$"^^ . + "http://purl.obolibrary.org/obo/MMUSDV_$1"^^ . + "false"^^ . + . . - . - . - "https://www.vmh.life/#gene/$1"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/protein"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Activity Streams" . - "^\\d+$"^^ . - . - . - . - "0000984"^^ . - . - . - . - . - . - . - . - . - "https://www.itis.gov/"^^ . - . - "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . - . - . - . - . - "International Classification of Diseases for Oncology" . - "^\\d+(\\w+)?$"^^ . - . - . - "https://www.mmrrc.org"^^ . - "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . - . - . - . - . - "HPA000698"^^ . - . - "false"^^ . - . - "OSC1416"^^ . - . - . - "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "Protein Structural Change Database" . - . - . - . - . - "https://www.cropontology.org/rdf/CO_335:$1"^^ . - . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT"^^ . -_:N81701af170f54963a1109ab1bda92df0 "Matt Berriman" . - . - . - "63"^^ . - "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . - . - "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . - . - . - . - "Q5BJF6-3"^^ . - . - "false"^^ . - . - . - . - . - "^\\d{8}$"^^ . - . - . - "Ontology of standardized units"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . - "Ensembl Bacteria" . - . - . - . - . - "Martin Ramirez" . - . - "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . - "Charles Tapley Hoyt" . - "^[A-Za-z0-9-]+$"^^ . - . - "RNA ontology" . - "ASRP1423"^^ . - . - . - . - . - . - . - "https://github.com/data2health/contributor-role-ontology"^^ . - . - "http://www.orpha.net/ORDO/Orphanet_$1"^^ . - . - . - . - "0000609"^^ . - . - "200282"^^ . - "141"^^ . - . - . - . - . - . - "https://github.com/pombase/fypo"^^ . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "^[1-9]\\d*$"^^ . - . - . - . - . - "false"^^ . - "http://obi-ontology.org"^^ . - . - "EchoBASE post-genomic database for Escherichia coli" . - . - "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . - . - . - . - . - "https://www.ebi.ac.uk/biostudies/"^^ . - "Rodent Unidentified Gene-Encoded Large Proteins" . - . - . - "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . - "false"^^ . - . - "http://cutdb.burnham.org"^^ . - "QJ51RV02"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/snp/"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . - "false"^^ . - . - . - "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . - . - "http://kim.bio.upenn.edu/software/ornaseq.shtml"^^ . - . - "http://www.cs.tau.ac.il/~spike/"^^ . - . - . - . + . + . + . + "http://www.chemspider.com/inchikey=$1"^^ . + . + "Cell line collections"^^ . + . + . + "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . + . + . + "Insect Resistance Ontology" . + . + "Encyclopedia of Life" . + . + . + "https://skip.stemcellinformatics.org/en/"^^ . + "false"^^ . + "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"^^ . + . + "Internal OBO and PyOBO Relations" . + . + . + "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . + . + . + . + . + . + "http://www.maizemap.org/"^^ . + . + . + . + "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . + "^\\d+$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1"^^ . + . + . + . + . + "false"^^ . + . + "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "OBO in OWL" . + . + . + . + . + . + . + . + . + . + . + . + . + . . - "false"^^ . - "https://github.com/HUPO-PSI/psi-mi-CV"^^ . - . - . - "NCI Metathesaurus" . - . - . - . - . - "^\\d+$"^^ . - . - "http://pathway.yeastgenome.org/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . - . - . - . - . - "0000-0002-5355-2576"^^ . - . - "MarFun" . - . - . - . - . - . - . - . + . + . + . + . + "false"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . + "http://www.jstor.org/"^^ . + . + . + "National Microbiome Data Collaborative" . + "http://en.wikipedia.org/wiki/Gene_Wiki"^^ . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . + "Functional Requirements for Bibliographic Records" . + . + . + "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. "^^ . + . + . + . + . + "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . + "http://ctdbase.org/"^^ . + . + "FamPlex" . + . + "A structured controlled vocabulary for the anatomy of fungi."^^ . + . + "^GR\\:\\d+$"^^ . + . + . + . + . + "Fly taxonomy" . + . + . + "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . + "International Fungal Working Group Fungal Barcoding." . + . + "^CAL\\d{7}$"^^ . + . + "5282"^^ . + "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . + . + . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^ . + . + . + . + . + . + . + "http://www.massbank.jp/RecordDisplay?id=$1"^^ . + "false"^^ . + "^\\d+$"^^ . + "OntoBee" . + "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^ . + "A type for entries in the Bioregistry's collections" . + "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ACYPI000159"^^ . + "spike00001"^^ . + . + "^\\d{7}$"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF"^^ . + "false"^^ . + "Flybase Cell Line" . + . + . + . + . + . + . + "HD+118-001"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "rs121909098"^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + "https://github.com/BgeeDB/confidence-information-ontology"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . + . + . + . + "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . + . + . + . + "http://www.pharmgkb.org/"^^ . + . + . + "http://environmentontology.org/"^^ . + . + "^[A-Z_0-9]+$"^^ . + . + . + "KW-1273"^^ . + "LMPR0102010012"^^ . + . + . + "http://www.wikipathways.org/"^^ . + "LINCS Small Molecule" . + . + . + . + "https://vocab.lternet.edu/vocab/vocab/index.php"^^ . + "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^ . + . + "smp-m3w9hbe"^^ . + . + "false"^^ . + "^TTHERM\\_\\d+$"^^ . + . + . + "GeoNames Feature Code" . + . + . + . + "false"^^ . + "http://www.nlm.nih.gov/medlineplus/"^^ . + . + . + . + . + . + . + . + . + "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . + . + "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182"^^ . + . + "595"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "NASC code" . + . + . + . + "https://www.cameo3d.org/sp/targets/target/$1"^^ . + . + "false"^^ . + . + . + . + . + "FAIRsharing" . + . + "^GLDS-\\d+$"^^ . + "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^ . + "CORDIS Article" . + . + . + . + "http://purl.obolibrary.org/obo/TXPO_$1"^^ . + . + . + . + . + . + "https://cropontology.org/ontology/CO_338/Chickpea"^^ . + "117"^^ . + . + . + . + . + . + . + . + . + . + "https://morpheus.gitlab.io/"^^ . + . "https://www.cbioportal.org/study/summary?id=ccle_broad_2019"^^ . - . - . - . - . - "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . - . - . - . - . - . - . - . - . - . - . - "Federica Quaglia" . - "https://www.thermofisher.com"^^ . - "C0001"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "false"^^ . - . - . - "FOOD00020"^^ . - "http://isbndb.com/search-all.html?kw=$1"^^ . - . - . - . - "MINT-10000"^^ . - . - "^S\\d+$"^^ . - . - . - . - . - . - "http://www.chemspider.com/"^^ . - "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . - "16941567"^^ . - . - . - . - "https://w3id.org/oc/corpus/$1"^^ . - . - "0000000"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/OGG_$1"^^ . - "1801.012"^^ . - . - . - "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . + "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . + . + . + . + . + "BE0000048"^^ . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + . + . + "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv"^^ . + . + . + . + . + . + . + . + . + . + . + "2555646"^^ . + "^\\d{7}$"^^ . + "http://www.violinet.org/vaccineontology"^^ . + . + "Literature references in Gramene"^^ . + . + . + "M1"^^ . + . + . + . + . + . + "0002005"^^ . + "http://jaxmice.jax.org/"^^ . + "https://data.apps.fao.org/catalog/organization/agrovoc"^^ . + . + . + "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . + "false"^^ . + . + . + . + . + . + . + . + "https://www.swisslipids.org/#/entity/SLM:$1"^^ . + "https://www.ebi.ac.uk/sbo/main/SBO:$1"^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_322:$1"^^ . + "false"^^ . + "International Molecular Exchange" . + . + . + . + . + . + . + "https://rnacentral.org/rna/$1"^^ . + . + . + . + . + . + . + . + . + "TOKU-E Cell-culture Database" . + . + "false"^^ . + . + . + . + . + . + . + "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . + "^\\d{6}$"^^ . + "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . + . + "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . + . + "^\\d+$"^^ . + "https://code.google.com/archive/p/ontology-for-genetic-interval/"^^ . + . + . + . + . + "false"^^ . + "Units of measurement ontology" . + . + "https://n2t.net" . + . + . + "BSU29180"^^ . + . + . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . + . + . + . + . + . + . + . + . + "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "http://www.genecards.org/"^^ . + . + "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . + . + . + "^\\w+$"^^ . + . + "^P\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . + "CONSO00010"^^ . + . + . + . + "false"^^ . + . + "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . + . + . + . + . + . + . + "128011350"^^ . + "98"^^ . + . + "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . + "0000026"^^ . + . + "https://mlcommons.org/en/"^^ . + "https://www.uniprot.org/uniref/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "http://www.whocc.no/atcvet/atcvet_index/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "GXA Expt" . + . + . + "https://github.com/obophenotype/c-elegans-phenotype-ontology"^^ . + "^[a-z_A-Z]+$"^^ . + "https://herv.img.cas.cz/s/$1"^^ . + "false"^^ . + "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . + "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "98034"^^ . + . + . + "^bt\\d+$"^^ . + . + . + "HGVST1828"^^ . + . + "https://web.expasy.org/cellosaurus/"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + "PANTHER Pathway" . + . + "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . + "1829126"^^ . + "http://swissregulon.unibas.ch/query/$1"^^ . + . + "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "OncoTree" . + "2200950"^^ . + "https://www.gwascentral.org/study/$1"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . + . + . + . + . + . + . + . + "^IHW\\d+$"^^ . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . + "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . + . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . + . + . + "^\\d+$"^^ . + . + . + "^DBSALT\\d{6}$"^^ . + . + "c0001"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "http://www.orpha.net/consor/"^^ . + "DAPK1"^^ . + . + . + . + . + . + "^C?\\d+$"^^ . + "http://paleodb.org/"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "Alex Bateman" . + "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . + . + . + . + "Willy Wong" . + . + . + . + . + . + . + "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . + . + "Studies in dbVar."^^ . + "^MMAR\\_\\d+$"^^ . + . + . + . + . + . + "HOSAPI0399"^^ . + . + . + . + . + . + . + "^OSC\\d{4}$"^^ . + "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . + . + "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + . + . + "https://eol.org/pages/$1"^^ . + "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . + "Regulation of Transcription"^^ . + . + "http://biocyc.org"^^ . + . + "https://github.com/OpenLHS/CVDO"^^ . + . + "^\\d{7}$"^^ . + . + "https://www.kyinno.com/"^^ . + . + . + "CL070"^^ . + "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . + "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . + "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . + . + . + "http://yetfasco.ccbr.utoronto.ca/"^^ . + "DECIPHER CNV Syndromes" . + "AgentIdentifierScheme"^^ . + . + "false"^^ . + "https://www.ndexbio.org/viewer/networks/$1"^^ . + "http://www.sparontologies.net/ontologies/datacite"^^ . + . + . + . + "https://cdno.info/"^^ . + . + "Citation Counting and Context Characterisation Ontology" . + . + "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . + . + . + "http://datf.cbi.pku.edu.cn/"^^ . + "^DI-\\d{5}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://www.pocketome.org/files/$1.html"^^ . + . + "14"^^ . + . + . + . + . + "OrthoDB" . . - . - . - "0000253"^^ . - . - . - . - . - . - "NCBI Registry" . - . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . - . - . - . - "COSMIC Gene" . - "https://www.nemoarchive.org"^^ . - . - "http://www.cghtmd.jp/CGHDatabase/index_e.jsp"^^ . - . - . - . - . - . - . - . + "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . + . + "^\\d{7}$"^^ . + . + "http://www.animaldiversity.org"^^ . + . + . + . + "Database of Escherichia coli Sequence and Function" . + . + . + . + . + "http://fishbase.org"^^ . + . + "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . +_:Na4af3ac318644462a9bbd1b961827f9d "Burke Squires" . + "http://lincsportal.ccs.miami.edu/cells/"^^ . + . + "^A\\d{6}$"^^ . + "false"^^ . + . + . + . + . + . + . + "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . + "00000098"^^ . + . + . + "Non-Coding RNA Ontology" . + . + . . - . - . - . -_:Nfac200ed2c064af48ed9910ac7785fc4 "Christos (Kitsos) Louis" . - "https://www.ohdsi.org/data-standardization/the-common-data-model/"^^ . - . - . - . - . - . - . - . - . - "International Classification of Diseases, 9th Revision, Clinical Modification" . - . - . - "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . - . - . - . - . - . - . - . - . - "Gramene QTL" . - . - "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - . + . + . + . + "false"^^ . + "false"^^ . + "http://senselab.med.yale.edu/ModelDB/"^^ . + "http://purl.obolibrary.org/obo/TGMA_$1"^^ . + . + "IntAct Molecule" . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://www.pgscatalog.org/pgs/$1"^^ . + . + "^DRSC\\d+$"^^ . + . + "^C\\d+$"^^ . + "https://www.arraymap.org/pgx:$1"^^ . + "https://medical-data-models.org/"^^ . + . + "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^ . + . + . + . + . + "https://pharmacome.github.io/conso/"^^ . + . + . + . + . + "https://bio.tools/"^^ . + . + . + . + "EMLSAT00000003403"^^ . + . + . + . + "0000008"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\d{8}$"^^ . + . + "Toxic Process Ontology" . + . + . + "https://lincs.hms.harvard.edu/db/sm/$1"^^ . + . + . + . + . + . + _:N576da71a94704c05bc5e000eaaad71e4 . + . + . + . + . + . + . + . + . + . + "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . + . + . + . + . + "0000069"^^ . + . + "1784"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "Confidence Information Ontology" . + . + "false"^^ . + . + . + "true"^^ . + "General Multilingual Environmental Thesaurus" . + . + "2966"^^ . + . + . + . + "false"^^ . + "false"^^ . + "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license."^^ . + . + . + "Ontology for MicroRNA Target" . + "Human Pluripotent Stem Cell Registry" . + "health_care_quality_assessment"^^ . + . + . + . + . + "Ligand Expo" . + . + . + . + . + . + "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "https://github.com/data2health/contributor-role-ontology"^^ . + . + . + . + "http://fossilworks.org"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + "http://stormo.wustl.edu/ScerTF/details/$1"^^ . + . + "^\\d{7}$"^^ . + . + . + "XB-GENE-922462"^^ . + . + . + . + "false"^^ . + . + "http://pgscatalog.org"^^ . + . + . + "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . + . + . + . + . + . + . + . + . + . + "^(Q|P)\\d+$"^^ . + . + . "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . - "true"^^ . - . - . - "^FCB\\d{3}$"^^ . - "Cotton ontology" . - "0000400"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . - . - . - "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . - "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . - "false"^^ . - . - . - . - . - "Viral Bioinformatics Resource Center" . - . - "KEGG LIGAND" . - "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^ . - . - . - "false"^^ . - . - . - . - "SubtiWiki" . - . - . - . - . - . - "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . - "https://www.cropontology.org/rdf/CO_337:$1"^^ . - . - "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . - . - "Plant Anatomy Ontology" . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - . - "http://www.sasbdb.org/"^^ . - . - "http://purl.obolibrary.org/obo/MRO_$1"^^ . - "MNEST029358"^^ . - "Classification of Transcription Factors in Mammalia" . - . - "https://github.com/The-Sequence-Ontology/SO-Ontologies"^^ . - . - . - . - . - . - . - . - "^\\d{4}$"^^ . - . - . - . - . + . + . + . + . + "https://biopragmatics.github.io/providers/sfam/$1"^^ . + "http://viaf.org"^^ . + "005012"^^ . + . + "NIF Standard Ontology: Subcellular Entities" . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/GAZ_$1"^^ . + . + . + . + . + . + . + . + "https://www.cropontology.org/rdf/CO_350:$1"^^ . + . + . + . + . + "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology"^^ . + . + "Telethon Network of Genetic Biobanks" . + . + "https://ssbd.riken.jp/database/dataset/$1"^^ . + . + "http://pombe.oridb.org/index.php"^^ . + . + "false"^^ . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.unimod.org/"^^ . + . + "648028003"^^ . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "http://www.depod.bioss.uni-freiburg.de"^^ . + "http://www.mirbase.org/"^^ . + "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . + . + . + . + . + "0000060"^^ . + "false"^^ . + . + . + . + . + . + "https://medical-data-models.org/forms/$1"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + "00073"^^ . + . + . + . + "^[CD]\\d+$"^^ . + . + "MetaNetX chemical" . + . + . + "aaeA"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . + "^[A-Z-_0-9]+$"^^ . + "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "3000045"^^ . + "2200934"^^ . + "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "85163"^^ . + "false"^^ . + . + "UM-BBD Compound" . + "^\\d+$"^^ . + . + "https://www.pirbright.ac.uk/node/$1"^^ . + . + . + . + . + . + "https://code.google.com/p/epidemiology-ontology/"^^ . + . + "13"^^ . + "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . + . + "Guide to Pharmacology Ligand" . + "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . + . + . + . + . + "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . + . + . + "http://www.e-cyanobacterium.org/bcs/rule/"^^ . + . + . + . + "false"^^ . + "^HIP\\d{9}(\\.\\d+)?$"^^ . + "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . + . + "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . + "Bioinformatics operations, data types, formats, identifiers and topics" . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "146421"^^ . + "BioContext" . + . + . + "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/INO_$1"^^ . + "false"^^ . + . + "false"^^ . + . + "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . + . + "Database for Prokaryotic Operons" . + . + . + "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"^^ . + "00005254"^^ . + . + "false"^^ . + . + "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . + . + . + "CHEBI" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://www.addexbio.com/productshow?id=4"^^ . + . + . + . + "Mouse Developmental Stages" . + "false"^^ . + "false"^^ . + "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . + "false"^^ . + . + . + "https://www-snorna.biotoul.fr/"^^ . + . + "false"^^ . + "^PR\\d{5}$"^^ . + "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . + . + . + . + "https://www.re3data.org/repository/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/VTO_$1"^^ . + . + . + . + . + . + . + "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . + "Zebrafish developmental stages ontology" . + . + . + "http://proconsortium.org"^^ . + . + "^\\d{5}$"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://developingmouse.brain-map.org/"^^ . + "PTN000000026"^^ . + . + . + "https://neurovault.org/collections/$1"^^ . + . + . + "https://vega.archive.ensembl.org/index.html"^^ . + "ProteomicsDB Protein" . + . + . + . + . + "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . + . + . + "Global Research Identifier Database" . + . + . + "Agronomy Vocabulary" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "9606"^^ . + . + "http://www.chemspider.com/"^^ . + "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . + . + . + . + "Protein Ensemble Database" . + "^(G|P|U|C|S)\\d{5}$"^^ . + . + "https://polbase.neb.com/polymerases/$1#sequences"^^ . + "http://ensembl.org/glossary"^^ . + . + . + "ClinicalTrials.gov" . + . + . + . + . + "false"^^ . + . + "AOPWiki" . + . + . + . + . + "^[0-9]+$"^^ . + . + . + "https://github.com/jannahastings/mental-functioning-ontology"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . + . + . + . + . + "^\\d{8}$"^^ . + . + . + "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . + . + . + "CharProt" . + "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + . + . + "Hector Escriva" . + . + "https://progenetix.org/services/ids/$1"^^ . + "^\\d+$"^^ . + "^[A-Za-z-0-9_]+$"^^ . + "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. "^^ . + . + . + "Sorghum ontology" . + . + . + . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/OBI_$1"^^ . + . + . + . + "MicrobeamManipulation"^^ . + . + . + . + "NOR00681"^^ . + . + "false"^^ . + "http://biocyc.org/getid?id=$1"^^ . + "90901"^^ . + "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . + . + . + . + "false"^^ . + _:Naf924f5e718d4739a0f29dcc853fb39e . + . + . + . + . + . + . + . + . + . + "Transcription Factor Database" . + "false"^^ . + "Metabolome Express" . + . + . + . + "ExAC Transcript" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "0107180"^^ . + "false"^^ . + . + . + "Rodent Unidentified Gene-Encoded Large Proteins" . + "^L\\d+$"^^ . + "https://github.com/DIDEO/DIDEO"^^ . + . + . + . + "https://www.cdc.gov/nchs/icd/icd9cm.htm"^^ . + . + . + . + . + . + . + "http://www.nlm.nih.gov/mesh/"^^ . + . + "http://purl.obolibrary.org/obo/CLAO_$1"^^ . + "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . + . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast."^^ . + . + . + "Drosophila Genomics Resource Center" . + . + "BioData Catalyst" . + . + . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "0002350"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_$1" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . + . + . + . + . + . + "https://labsyspharm.github.io/lspci/"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + "NIA Mouse cDNA Project" . + . . - . - . - . - . - . - . - . - . - . - "8639.1"^^ . - "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . - . - . - . - . - . - . - . - . - . - . - . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . - . - "^BE\\d{7}$"^^ . - . - . - "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . - . - . - . - . - . - . - . - . - . - . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - . - . - . - . - . - . - "1"^^ . - . - "http://www.ontobee.org/" . - "^D\\d+$"^^ . - . - . - "KYinno cell lines" . - . - . - . - . - . - . - "Terminology for Description of Dynamics" . - "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . - . - "^[A-Za-z0-9\\-\\/]+$"^^ . - . - . - "M1"^^ . - . - . - . - . - . - "^[0-9]+$"^^ . - "false"^^ . - "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . - . - . - "Medical Action Ontology" . - "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - . - "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . - . - "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF"^^ . - . - . - "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - . - . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . - . - . - . - "GT10"^^ . - "https://www.imexconsortium.org/"^^ . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . - . - . + . + "http://www.pantherdb.org/"^^ . + "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^ . + "^[A-Z0-9]+$"^^ . + . + . + . + "https://metacyc.org/compound?orgid=META&id=$1"^^ . + "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . + . + "false"^^ . + . + . + . + . + . + "MRA-253"^^ . + "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . + "^\\d{7}$"^^ . + . + . + . + "GPM32310002988"^^ . + "false"^^ . + . + "FaBiO, the FRBR-aligned Bibliographic Ontology" . + . + . + . + . + . + . + . + . + . + "^[1-9]\\d{0,5}$"^^ . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d{9}$"^^ . + . + . + . + "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi"^^ . + "131392"^^ . + . + "^\\d{7}$"^^ . + "http://bacmap.wishartlab.com/organisms/$1"^^ . + . + . + "Q-2958"^^ . + "https://biopragmatics.github.io/providers/scomp/$1"^^ . + . + . + "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . + "http://exac.broadinstitute.org/transcript/$1"^^ . + "https://repeatsdb.org/"^^ . + . + . + . + . + . + . + "http://microbialphenotypes.org"^^ . + . + "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . . - . - . - . - . - . - . - . - . - "TrichDB" . - "^KIAA\\d{4}$"^^ . - "false"^^ . - . - . - . - "35742"^^ . - "0000025"^^ . - . - . - "Epidemiology Ontology" . - . + "Systems Biology Ontology" . + . + . + . + "F0001"^^ . + "https://lincs.hms.harvard.edu/db/sm/"^^ . + . + . + . + "https://obophenotype.github.io/cell-ontology/"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/TADS_$1"^^ . + . + . + . + . + "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . + "false"^^ . + . + . + . + "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . + "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . + . + . + "World Wildlife Fund Ecoregion" . + . + . + "false"^^ . + . + . + . + . + . + . + "d4e2515"^^ . + . + . + "CTD Chemical" . + . + "false"^^ . + "234"^^ . + . + . + . + . + . + . + "false"^^ . + "https://github.com/obophenotype/ncbitaxon"^^ . + . + . + . + . + "false"^^ . + . + . + . + "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . + "91005"^^ . + "1001"^^ . + . + . + . + . + . + . + . + . + "0001927"^^ . + . + . + . + . + "false"^^ . + "H-InvDb Transcript" . + "0009089"^^ . + . + "^[A-Z]+[0-9]+$"^^ . + "^[0-9a-zA-Z]+$"^^ . + . + . + . + "C6155"^^ . + "http://www.w3.org/2004/02/skos/core#$1"^^ . + . + . + "https://www.gwascentral.org/phenotypes"^^ . + . + "0005452"^^ . + "http://rgd.mcw.edu/"^^ . + . + "Genomes Online Database" . + . + "https://www.biozol.de/en"^^ . + . + . + . + "International repository of Adverse Outcome Pathways."^^ . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "false"^^ . + . + "JWS Online" . + . + . + . + . + . + "false"^^ . + . + . + . + "https://morpheus.gitlab.io/models/$1"^^ . + "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . + . + "Oral Health and Disease Ontology" . + . + . + "56586"^^ . + "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . + "^\\d+$"^^ . + . + . + . + "https://cropontology.org/ontology/CO_346/Mungbean"^^ . + "true"^^ . + . + . + "L000001"^^ . + . + . + "Molecular database for the identification of fungi" . + . + "Diseases Database" . + . + . + "Small Molecule Pathway Database" . + . + . + . + . + "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . + . + "http://probonto.org"^^ . + "Human Protein Reference Database" . + "Bibliographic Reference Ontology" . + . + . + "^PS\\d{5}$"^^ . + . + "REBASE restriction enzyme database" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFO_$1"^^ . + . + "002678"^^ . + "http://purl.obolibrary.org/obo/AEO_$1"^^ . + . + . + "https://www.cropontology.org/rdf/CO_336:$1"^^ . + . + . + "^\\w+_COVID19_[-\\w]+$"^^ . + "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "John Kunze" . + . + "http://www.aphidbase.com/aphidbase"^^ . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . + . + . + "Abdomen"^^ . + . + . + . + . + . + . + . + . + "Gramene Reference" . + . + . + . + "MEROPS Clan" . + . + "http://purl.obolibrary.org/obo/FOVT_$1"^^ . + "^\\d+$"^^ . + . + . + . + . + "Teleost Anatomy Ontology" . + . + . + . + . + "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/OPL_$1"^^ . + . + . + . + . + . + "http://proteomecentral.proteomexchange.org/"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/aero"^^ . + . + . + "WiCell Research Institute Cell Collection" . + "LOC_Os01g49190.1"^^ . + "^[0-9]+$"^^ . + . + . + . + . + "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . + . + . + . + "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . + . + "https://knowledge.lonza.com/cell?id=$1"^^ . + "http://www.cathdb.info/cathnode/$1"^^ . + . + "https://www.biomodels.net/kisao/KISAO#KISAO_$1"^^ . + . + "https://www.jax.org/strain"^^ . + . + . + . + . + . + . + . + "Animal Genome Chicken QTL" . + . + "P10636"^^ . + . + . + . + . + "https://www.itis.gov/"^^ . + "^EP\\d{4}$"^^ . + . + "589462"^^ . + . + . + . + . + "dsmz_mutz-id:ACC 291"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://pfam.xfam.org"^^ . + . + "Universal Natural Products Database" . + . + . + . + "https://bioportal.bioontology.org/ontologies/$1" . + . + . + . + . + . + "SEED Compound" . + . + . + "false"^^ . + . + "^TTDS\\d+$"^^ . + . + . + . + . + . + "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . + "Ontology of Adverse Events" . + . + "https://www.ebi.ac.uk/biostudies/"^^ . + . + "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . + "^\\d{7}$"^^ . + "The allele registry provides and maintains identifiers for genetic variants"^^ . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . + . + . + "false"^^ . + "https://aftol.umn.edu"^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_340:$1"^^ . + . + "^\\d+$"^^ . + "true"^^ . + . + . + . + "^\\d+$"^^ . + . + "http://www.cazy.org/"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "Ontology for Nutritional Epidemiology" . + . + "Barcode of Life database" . + "miRTarBase" . + "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^ . + . + "https://prefix.cc/" . + . + . + . + . + "July 2018"^^ . + . + . + . + . + . + . + . + . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . + "FxnI151FMs"^^ . + . + . + "false"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + "false"^^ . + . + . + . + . + "^PIRSF\\d{6}$"^^ . + . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/database/DB-$1" . + "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + "^[A-Za-z]+\\d+$"^^ . + . + . + . + . + "Tom Gillespie" . + "Developing Mouse Brain Atlas" . + . + . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "37"^^ . + . + . + "https://github.com/HUPO-PSI/psi-mi-CV"^^ . + . + "https://github.com/NCI-Thesaurus/thesaurus-obo-edition"^^ . + . + "https://www.tcdb.org"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://identifiers.org/$1:$2" . + . + . + . + . + . + . + "https://bioregistry.io/metaregistry/biocontext/$1" . + . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . + . + "http://purl.obolibrary.org/obo/ZEA_$1"^^ . + . + . + . + "100"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1"^^ . + . + . + . + . + "http://neuromorpho.org/index.jsp"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + "DrugBank Salts" . + . + . + "An application ontology for use with miRNA databases."^^ . + . + "Genetics Home Reference" . + "C0017565"^^ . + . + . + "^\\d+$"^^ . + . + "Cell line collections"^^ . + "Mouse adult gross anatomy" . + . + . + . + "^PA\\d+$"^^ . + "^\\d+$"^^ . + . + "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^ . + . + . + "false"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + . + . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + "https://www.ncbi.nlm.nih.gov/clinvar/"^^ . + "http://purl.obolibrary.org/obo/PSDO_$1"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "1"^^ . + . + . + . . - . - . - . - "https://bioportal.bioontology.org/ontologies/APAONTO"^^ . - . - . - . - "Developing Human Brain Atlas" . - . - . - . - . - "false"^^ . - . - . - . - . - . - "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . - . - . - . - . - . - . - "Zenodo" . - . - . - . - . - . - . - . - . - "UniProt Isoform" . - "BLL"^^ . - "^HBG\\d+$"^^ . - . - . - . - . - "Foundational Model of Anatomy" . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - "BCRC Strain Collection Catalog" . - . - . - "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . - . - . - . - . - . - . - "false"^^ . - "Intrinsically Disordered proteins with Extensive Annotations and Literature" . - . - . - "http://www.wikigenes.org/e/gene/e/$1.html"^^ . - "https://co.mbine.org/standards/"^^ . - "^\\w+$"^^ . - "Vertebrate Taxonomy Ontology" . - . - . - . - . - . - . - . - "Geographical Entity Ontology" . - "false"^^ . - "http://purl.obolibrary.org/obo/ONE_$1"^^ . - . - . - . - . + . + . + . + . + . + . + "051"^^ . + . + . + "Yeast Intron Database v4.3" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + . + . + . + . + . + "https://mmp.sfb.uit.no/databases/marfun"^^ . + "Legacy disease classes that later became MONDO"^^ . + "Cell line collections"^^ . + . + . + . + . + . + . + . + . + . + . + . + "MSV000082131"^^ . + . + . + . + "https://mmp.sfb.uit.no/databases/marref/"^^ . + . + . + . + . + "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . + . + "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . + . + . + "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . + . + . + . + . + . + . + . + . + . + "imp10873"^^ . + . + . + "^\\d{7}$"^^ . + "https://www.alliancegenome.org/accession/$1"^^ . + "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^ . + . + . + . + . + "CASRAI Contributor Roles Taxonomy" . + . + "Terminologia Embryologica" . + . + . + . + . + . + . + "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . + . + . + . + . + . + . + . + . + . + . + "0000983"^^ . + "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^ . +_:Nbeeec24cc7c5432f880d13abe1054669 "Adrien Coulet" . + . + "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . + . + . + . + . + . + "https://www.aapc.com/codes/cpt-codes/$1"^^ . + . + . + . + . + "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . + . + . + "MMP3312982.2"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . + "P12345"^^ . + . + . + . + . + . + . + . + "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . + "http://purl.obolibrary.org/obo/fbdv"^^ . + "BioSimulators" . + . + "http://bioportal.bioontology.org/ontologies/$1"^^ . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + "https://w3id.org/hso"^^ . + "http://senselab.med.yale.edu/NeuronDB/"^^ . + . + . + "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . + . + . + . + "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . + "LigandBox" . + . + . + . + "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . + "https://cellrepo.ico2s.org/"^^ . + . + . + . + . + . + . + . + "BloodPAC" . + . + . + "TR0000001"^^ . + "LNCipedia" . + "^IPR\\d{6}$"^^ . + "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . + "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . + "http://purl.obolibrary.org/obo/CMF_$1"^^ . + "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . + . + "ISCW007415"^^ . + "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . + . + . + . + . + . + . + "PubChem Classification" . + "https://www.ncbi.nlm.nih.gov/research/cog/pathways"^^ . + . + . + "100810"^^ . + . + . + "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "https://www.kew.org/data/grasses-syn/index.htm"^^ . + . + . + . + . + . + . + . + "Ontology of Host Pathogen Interactions" . + "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . + . + . + . + "https://rapdb.dna.affrc.go.jp/"^^ . + . + . + . + . + "Microbial Protein Interaction Database" . + . + . + . + . + . + . + "Erik Segerdell" . + "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . + "TF101014"^^ . + . + "4019477"^^ . + . "false"^^ . - . - . - . - . - . - . - "Regulation of Gene Expression Ontology" . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - "decimal"^^ . - . - . - . - . - . - . - . - . - "https://www.nlm.nih.gov/research/umls"^^ . - . - . - "DB-0174"^^ . - "false"^^ . - . - . - "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . - . - . - . + . + . + . + "^\\d{7}$"^^ . + "Gramene QTL" . + . + . + . + . + "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . + . + "false"^^ . + . + . + . + "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . + . + "Tribolium Genome Database -- Insertion" . + "0000001"^^ . + "false"^^ . + . + "An ontology of Drosophila melanogaster anatomy."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . . - . - "false"^^ . - "http://www.homd.org/index.php"^^ . - . - . - . - . - . - . - . - "A Web-based catalog of recommended measurement protocols"^^ . - "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^ . - "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "SABIO Reaction Kinetics" . - . - . - . - "^G[0-9]{5}[A-Z]{2}$"^^ . - . - . - . - . - . - . - . - . - "csv"^^ . - . - . - . - . - . - "false"^^ . - . - "https://biopragmatics.github.io/providers/schem/$1"^^ . - "2649230"^^ . - . - "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . - "Allen Institute Ontologies" . - . - . - . - "http://planteome.org/"^^ . - . - "1868"^^ . - "https://www.rhea-db.org/"^^ . - "Chicken Gene Nomenclature Consortium" . - . - . - "^[A-Z0-9]{5}\\d+$"^^ . + . + "Name Reaction Ontology" . + . + . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . + . + . + "http://purl.org/cerif/frapo/$1"^^ . + . + "https://www.lgcstandards-atcc.org"^^ . + . + "https://github.com/github/linguist"^^ . + "Christian-Alexander Dudek" . + . + "http://www.sbgnbricks.org/"^^ . + . + . + "false"^^ . + "Hepatitis C Virus Database" . + . + . + . + . + "Sirarat Sarntivijai" . + . + . + . + . + "^\\d+$"^^ . + . + . + "https://cordis.europa.eu/project/id/$1"^^ . + . + . + . + . + . + . + . + "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . + . + "Quantities, Units, Dimensions, and Types Ontology" . + . + . + . + . + . + . + . + . + "http://genepio.org/"^^ . + "^D\\d+$"^^ . + . + . + . + "https://urgi.versailles.inra.fr/gnpis/"^^ . + "https://openalex.org/$1"^^ . + . + "false"^^ . + . + . + . + . + "https://rfam.xfam.org/family/$1"^^ . + . + "http://www.ontobee.org/ontology/$1" . + "^\\d{7}$"^^ . + "H3.03.00.0.00007"^^ . + . + "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . + "Redistributor of bilogics and biomedical supplies"^^ . + . + . + . + . + "Neuronal cell types"^^ . + . + . + . + . + "false"^^ . + "MicroScope" . + "false"^^ . + "false"^^ . + . + . + . + "https://github.com/OMIABIS/omiabis-dev"^^ . + . + . + "Catalog of purchasable reagents and building blocks"^^ . + "HPA000698"^^ . + "COG Pathways" . + . + . + . + . + . + "NCI Data Commons Framework Services" . + "^\\w+$"^^ . + . + . + "AT1G73965"^^ . + . + "https://github.com/EcologicalSemantics/ecocore"^^ . + . + . + . + "TTHERM_00648910"^^ . + . + . + "Proteomic Data Commons" . + "^\\w+$"^^ . + "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"^^ . + . + . + . + "0000003"^^ . + . + . + "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . + . + . + . + . + "Lucas Leclere" . + . + . + "false"^^ . + "5601141"^^ . + . + . + "https://github.com/pato-ontology/pato/"^^ . + . + . + . + . + . + . + . + . + . + "4D Nucleome Data Portal Biosource" . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + "Oat ontology" . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + "https://fungidb.org/fungidb"^^ . + . + "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . + . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + . + "Golm Metabolome Database Profile" . + . + . + . + . + "Gs0000008"^^ . + "Kerafast cell lines" . + . + . + . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + "^\\w+$"^^ . + . + . + "NCBI PubChem database of bioassay records" . + . + . + . + "http://www.w3.org/ns/prov#$1"^^ . + "Data Use Ontology" . + . + "Computer Retrieval of Information on Science Projects Thesaurus" . + . + . + . + . + "Biolink Model" . + . + . + "PRO_0000016681"^^ . + "Ceri Van Slyke" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "Carissa Park" . + . + . + . + . + "^LGCEDe-S-\\d{9}$"^^ . + "ZINC1084"^^ . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/locations/$1"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . + . + "false"^^ . + . + . + "^PED\\d{5}e\\d{3}$"^^ . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + "LK99"^^ . + "Genomics of Drug Sensitivity in Cancer" . + "http://n2t.net/ark:$1"^^ . + . + "false"^^ . + . + . + "SCV000151292"^^ . + . + . + . + . + . + "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . + "AntiBodies Chemically Defined database" . + . + "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . + . + . + . + . + . + . + "MultiCellDS collection" . + "DG00301"^^ . + . + . + . + . + . + . + "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . + . + "ArrayGroup"^^ . + "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . + . + "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . + . + "1-FEH+w3"^^ . + . + . + . + . + "GrainGenes" . + "https://caninecommons.cancer.gov/#/study/$1"^^ . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . + . + "^[0-9]+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/PORO_$1"^^ . + . + . + "RCB0002"^^ . + . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . + "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . + . + . + . + . + . + . + . + . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . + . + . + "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . + . + . + . + . + "http://www.mgc.ac.cn/VFs/"^^ . + "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . + . + "https://bionumbers.hms.harvard.edu"^^ . + . + . + "^[0-9a-z]{24,24}$"^^ . + "0000005"^^ . + . + . + . + "16333295"^^ . + "GrainGenes" . + "^(imp|gen)\\d{5}$"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + "PubChem Substance ID (SID)" . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . + "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)"^^ . + "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . + . + "https://go.drugbank.com/salts/$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . + . + "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . + . + "FBgn0000015"^^ . + . + _:Nb300b24511ca48d8a5fffa649e9e6c22 . + . + . + . + . + . + "phs000768.v2.p1"^^ . + . + . + . + . + . + "https://www.crossref.org/"^^ . + "true"^^ . + . + . + . + "^EGAD\\d{11}$"^^ . + . + . + "Search Tool for Retrieval of Interacting Genes/Proteins" . + "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . + "VGNC:3792"^^ . + . + "LINCS Cell" . + . + . + "http://www.massbank.jp"^^ . + "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^ . + . + . + . + . + "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . + . + . + "http://www.bioinfo.org/NONCODEv4/"^^ . + . + "https://bioinformatics.cineca.it/PMDB/"^^ . + " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + . + . + "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . + . + . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . + . + . + "CHEMBL3307800"^^ . + . + . + . + "http://www.genome.jp/kegg/disease/"^^ . + . + "https://gnome.glyomics.org/"^^ . + . + "https://www.ebi.ac.uk/metagenomics"^^ . + . + . + . + . + . + . + . . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "M0001"^^ . - "Datasets inside StoreDB"^^ . - "false"^^ . - . - . - . - . - . - "Tom Gillespie" . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . - "1.10.10.200"^^ . - "RepeatsDB Protein" . - "false"^^ . - . - "http://flypush.imgen.bcm.tmc.edu/pscreen/"^^ . - . - "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html"^^ . - . - "false"^^ . - . - . - . - . - . - "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology"^^ . - "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . - "Akt_PKB"^^ . - . - . - . - . - . - . - "Foods in FooDB"^^ . - "MaizeGDB Locus" . - "https://foodb.ca/"^^ . - . - "Reagent Ontology" . - . - . - "Beta Cell Genomics Ontology" . - "false"^^ . - . - "https://github.com/OpenLHS/CVDO"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/RO_$1"^^ . - . - "^[0-9]+$"^^ . - "Guide to Pharmacology Ligand" . - "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . - . - . - "^\\d{7}$"^^ . - "75"^^ . - . - . - . - . - "^[a-z_A-Z]+$"^^ . - "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . - . - "false"^^ . - . - "false"^^ . - . - . - "https://github.com/prefixcommons/biocontext" . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . - . - . - "5fce9b7300001250"^^ . - . - . - "ADA"^^ . - . - . - . - . - "false"^^ . - . - "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . - "true"^^ . - . - . - "Neural ElectroMagnetic Ontology" . - . - . - . - . - "hsa-let-7a"^^ . - . - . - . - "0000001"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "AT4G01080"^^ . - . - . - . - . - . - . - . - . - "100810"^^ . - . - . - "Measurement method ontology" . - . - . - "^ENSG\\d{11}$"^^ . - . - . - . - . - . - "https://drugs.ncats.io/"^^ . - . - "http://cellimagelibrary.org/images/$1"^^ . - . - "Marijane White" . - . - . - "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . - . - . - "H-InvDb Protein" . - "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://github.com/FAIRsharing/subject-ontology"^^ . - "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . - . - . - "Human Plasma Membrane Receptome Families" . - . - . - . - . - . - . - . - . - "https://aopwiki.org/events/$1"^^ . - . - . - . - . - . - "CQG5"^^ . - "Logical Observation Identifiers Names and Codes" . - . - "1784"^^ . - . - . - . - . + "false"^^ . + "^[A-Za-z0-9\\-\\/]+$"^^ . + . + . + . + "http://lgsun.grc.nia.nih.gov/cDNA/"^^ . + "https://www.ebi.ac.uk/ena/data/view/$1"^^ . + "1"^^ . + . + . + . + "http://www.genenames.org"^^ . + . + . + . + . + . + "CoVoc Coronavirus Vocabulary" . + . + . + . + . + . + "UniProt Subcellular Locations" . + . + . + . + "Wasila Dahdul" . + . + . + . + "Ontology for Nutritional Studies" . + "https://metazoa.ensembl.org/"^^ . + . + . + . + . + "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . + "https://www.animalgenome.org/QTLdb"^^ . + "false"^^ . + . + "^\\d{8}$"^^ . + "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . + "Life cycle stages for Mus Musculus"^^ . + . + "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . + . + . + "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . + "FAIRSharing" . + . + "^\\d+$"^^ . + . + . + . + . + "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . + . + . + . + "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . + . + . + . + "VMH Gene" . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . + . + . + . + "^[CN]*\\d{4,7}$"^^ . + "^\\d+$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . + . + . + "http://www.geneontology.org/cgi-bin/references.cgi"^^ . + "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + "http://sabiork.h-its.org/"^^ . + "00000000"^^ . + . + . + "The set of prefixes used in the Cellosaurus resource"^^ . + "^MSMEG\\w+$"^^ . + "NCT00222573"^^ . + "false"^^ . + "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . + . + . + . + "https://pharmacodb.ca/tissues"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . . - "false"^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . - . - . - . - . - . - . - "Cellosaurus" . - . - "Anne Morgat" . - . - "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . - . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - "Chen Yang" . - "61467"^^ . - "http://purl.obolibrary.org/obo/BCO_$1"^^ . - . - . - "http://www.ymdb.ca/compounds/$1"^^ . - "^M\\d{5}$"^^ . - . - . - . - "^HIT\\d{9}(\\.\\d+)?$"^^ . - . - . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . - "^\\d{7}$"^^ . - "http://www.inoh.org"^^ . - . - . - . - . - . - . - . - "http://github.com/ga4gh/data-object-service-schemas"^^ . - . - "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . + . + . + "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . + . + . + . + . + . + . + . + "Charles Tapley Hoyt" . + . + "Veterans Administration National Drug File" . + . + . + "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . + "^SMP\\d+$"^^ . + . + . + . + . + "https://github.com/obophenotype/caro/"^^ . + "false"^^ . + . + "Alayne Cuzick" . + . + . + . + . + "Malaria Ontology" . + "^\\d{7}$"^^ . + . + "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . + "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . + . + . + . + . + "0000066"^^ . + "YAL001C"^^ . + . + "false"^^ . + . + . + . + . + . + "https://github.com/geneontology/go-ontology"^^ . + . + . + "^\\w+(\\-|\\.|\\w)*$"^^ . + . + . + . + . + . + . + "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . + . + . + "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . + . + . + . + . + . + . + "P683" . + . + "^[A-Z]{6}(\\d{2})?$"^^ . + "http://cerevisiae.oridb.org/details.php?id=$1"^^ . + . + "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . + "ViralZone" . + "Matúš Kalaš" . + . + . + . + . + . + . + . + "Multum MediSource Lexicon" . + "0000184"^^ . + . + . + . + . + "false"^^ . + "00620027"^^ . + "https://github.com/PlantPhenoOntology/PPO"^^ . + "Collection of European paediatric cardiac coding files"^^ . + "Life cycle stages for Human"^^ . + . + "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . + "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html"^^ . + . + "true"^^ . + . + "0000005"^^ . + . + . + . + "WGS-95-1333"^^ . + . + . + "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . + . + "http://purl.obolibrary.org/obo/CHMO_$1"^^ . + . + . + "1484"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . +_:Na1a78a14bd9e496caff9519402ec99ed "David Blackburn" . + . + "037727"^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "^GCST\\d{6}\\d*$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "GlyTouCan" . + . + . + . + . + . + "Identifiers.org" . + . + . + . . - . - "false"^^ . - . - "https://www.gleif.org/lei/$1"^^ . - . - "^\\d{6}$"^^ . - "^\\d{7}$"^^ . - . - "MGnify Analysis" . - "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . - . - "has download URL" . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . - . - . - . - . - . - . - . - "https://e-cyanobacterium.org/bcs/rule/$1"^^ . - . - "78073"^^ . - "C138986"^^ . - . - "Terminologia Histologica" . - "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . - . - . - . - "4005"^^ . - "S1"^^ . - . - . - . - . - . - . - . - "http://environmentontology.org/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/GENO_$1"^^ . - "NCI Pathway Interaction Database: Pathway" . - "false"^^ . - "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"^^ . - . - . - . - . - . - . - "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . - "Rhea, the Annotated Reactions Database" . - . - "2244"^^ . - "false"^^ . - . - . - . - "1968"^^ . - . - . - . - . - . - "GeoNames" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "50018"^^ . - . - . - . - "Transport Systems Tracker" . - . - "9008500"^^ . - "Aspergillus Genome Database" . - . - "false"^^ . - . - . - . - "A manually curated resource for the representation and annotation of metabolic pathways"^^ . - . - . - . - "C0020004/4992"^^ . - . - "http://en.wikipedia.org/wiki/Main_Page"^^ . - "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . - . - . - . - . - . - . - . - . - "https://scholar.google.com/"^^ . - . - . - . + . + . + . + . + . + . + . + "^\\d{5,}$"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + "Miguel A. Fortuna" . + "^\\d{8}$"^^ . + . + . + "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . + "enviPath" . + . + "false"^^ . + . + "^SAM[NED](\\w)?\\d+$"^^ . + "false"^^ . + . + "Signaling Network Open Resource" . + . + "http://n2t.net/"^^ . + . + "0187632"^^ . + "Cellular Microscopy Phenotype Ontology" . + . + . + . + "^YMDB\\d+$"^^ . + . + . + "0000001"^^ . + . + . + . + . + . + . + . + "25782"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "PeptideAtlas Dataset" . + "http://www.mycobank.org/"^^ . + "^\\d+$"^^ . + "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^ . + . + . + . + . + "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . + . + . + . + . + . + . + "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . + . + "NeuronDB" . + "https://progenetix.org/"^^ . + . + . + . + . + "Infectious Disease Ontology" . + . + . + . + "identifier for a scientific journal, in the UniProt database"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ena/"^^ . + . + "G24361QY"^^ . + . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^ . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + . + "http://masspec.scripps.edu/"^^ . + . + . + "http://tritrypdb.org/tritrypdb/"^^ . + "WBGene00000001"^^ . + "false"^^ . + . + . + "100000000000001"^^ . + "300165/p13898_2106T"^^ . + . + . + . + . + . + "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology"^^ . + "false"^^ . + . + . + . + . + . + "https://www.imexconsortium.org/"^^ . + . + . + "https://web.expasy.org/abcd/ABCD_$1"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "nasa/kepler-exoplanet-search-results"^^ . + . + . + . + "Assembling the Fungal Tree of Life - Taxonomy" . + . + . + "https://www.cropontology.org/rdf/CO_345:$1"^^ . + . + . + . + "Signaling Pathways Project" . + "https://www.ebi.ac.uk/metagenomics"^^ . + . + . + . + "CTD Disease" . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . + "0000022"^^ . + "false"^^ . + "00056"^^ . + . + . + . + "false"^^ . + "A pull request in any public repository on GitHub."^^ . + "^[A-Z0-9]+$"^^ . + . + . + "https://ocid.ontochem.com/prefname?ocid=$1"^^ . + . + . + "2005080"^^ . + . + . + "Sequencing Initiative Suomi" . + . + . + "1731"^^ . + "0000564"^^ . + . + . + . + . + . + . + . + "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . + "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . + . + . + . + "http://www.nbrc.nite.go.jp/e/index.html"^^ . + . + . + . + . + . + . + "0007807"^^ . + . + "^DG\\d+$"^^ . + "false"^^ . + . + "PerkinElmer cell line collection" . + "https://coconut.naturalproducts.net"^^ . + "Vital Sign Ontology" . + . + . + . + . + . + . + . + . + "https://w3id.org/oc/oci/$1"^^ . + . + "https://www.ebi.ac.uk/GOA/"^^ . + . + . + "Tick Cell Biobank" . + . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "0005067"^^ . + . + . + . + "FBgn0011293"^^ . + . + . + "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1"^^ . + . + . + . + "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . + . + . + "^ST[0-9]{6}$"^^ . + "CCDC Number" . + . + . + . + "ChemDB" . + . + . + . + "https://www.alliancegenome.org"^^ . + . + "^[0-9]+$"^^ . + "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . + . + . + . + . + . + "BeAn 70563"^^ . + . + . + "ViralZone" . + . + . + . + . + "^\\d{7}$"^^ . + . + "NLXCELL conatins cell types with a focus on neuron types."^^ . + . + . + . + . + . + . + "Mouse Developmental Anatomy Ontology" . + . + "false"^^ . + . + . + "Tom Gillespie" . + . + "Q0VCA6"^^ . + "Grant"^^ . + "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . + "false"^^ . + "^\\w+$"^^ . + "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . + "^\\d+$"^^ . + "A modeling paradigm-specific registry of prefixes and their URL expansions" . + . + "3532759"^^ . + . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . + "0001410"^^ . + . + "https://cameo3d.org"^^ . + "Cowpea ontology" . + . + "TGME49_053730"^^ . + "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . + . + "^\\d+$"^^ . + . + "Zenodo" . + . + . + . + "https://www.ebi.ac.uk/citexplore/"^^ . + "false"^^ . + . + . + . + . + "https://aopwiki.org/stressors/$1"^^ . + . + . + "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . + . + . + . + . + . + . + "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . + . + . + . + . + . + "http://www.genome.jp/kegg/catalog/org_list.html"^^ . + . + . + . + . . - . - "^L\\d+$"^^ . - . - . - . - . + . + . + . + . + "https://pdc.cancer.gov/pdc/study/$1"^^ . + . + . + "false"^^ . + . + . + . + "https://cells.ebisc.org/$1"^^ . + . + . + "false"^^ . + . . - . - . - . - . - . - . - . - "http://www.sparontologies.net/ontologies/fivestars"^^ . - . - . - . - "http://senselab.med.yale.edu/NeuronDB/"^^ . - . - "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . - "false"^^ . - . - "http://edamontology.org"^^ . - "http://proteomecentral.proteomexchange.org/"^^ . - . - . - . - . - . -_:Naf946fb96f994872abf9bae43a5fa8a3 "Fahim Imam" . - . - . - . - . - "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . - "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . - "Unipathway" . - "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"^^ . - . - . - . - "http://darcsite.genzentrum.lmu.de/darc/index.php"^^ . - . - . - . - . - "false"^^ . - . - "^GenProp\\d+$"^^ . - "Proteomics data and process provenance" . - . - . - . - . - . - . - . + "0000124"^^ . + . + . + . + "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . + . + . + . + . + . + "78"^^ . + . + . + "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . + . + . + . + . + . + "Multiple alignment" . + "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . + "Mechanism, Annotation and Classification in Enzymes" . + "http://hpc-bioinformatics.cineca.it/fusion/main"^^ . + . + "16941567"^^ . + "2673500"^^ . + . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . + . + "SCC111"^^ . + . + . + . + "0007404"^^ . + . + . + . + . + "false"^^ . + "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . + . + . + "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . + "None"^^ . + "http://purl.obolibrary.org/obo/SPD_$1"^^ . + "false"^^ . + . + . + . + . + "NBK331"^^ . + . + "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "^\\d{6}$"^^ . + . + "false"^^ . + . + . + "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1"^^ . + . + . + "https://bacdive.dsmz.de/strain/$1"^^ . + . + "http://www.humanproteomemap.org/index.php"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "00020007"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "Coriell Institute for Medical Research" . + . + "The pattern for identifiers in the given resource" . + "http://purl.obolibrary.org/obo/VO_$1"^^ . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . + . + "false"^^ . + . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . + . + . + . + . + . + . + . + . + "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . + . + "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . + . + . + . + . + "Identifiers.org Registry" . + . + . + "0000030"^^ . + "http://bis.zju.edu.cn/ricenetdb/"^^ . + . + . + . + . + . + "^\\d{4}$"^^ . + "1000560"^^ . + . + . + . + . + "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . + . + . + . + . + "DataCollection"^^ . + . + . + . + . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . + "Gi07796"^^ . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^ . + "false"^^ . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . + . + . + . + "https://www.ebi.ac.uk/pdbe/emdb/"^^ . + . + . + . + "http://bidd.group/NPASS/"^^ . + . + "Dr. Alpha Tom Kodamullil" . + . + "SugarBind" . + . + . + . + . + . + . + . + . + . + "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . + . + . + . + . + . + . + . + "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^K[0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Yam ontology" . + . + . + "false"^^ . + . + . + "http://planteome.org/"^^ . + . + . + . + . + "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . + . + . + . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "Foundational Model of Anatomy" . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + . + "Uberon Property" . + . + . + . + "Cell line collections"^^ . + . + . + . + "^\\d+$"^^ . + . + "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . + . + . + "ChEMBL target" . + "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . + . + . + . + "http://www.isni.org"^^ . + "https://ega-archive.org/"^^ . + "http://purl.bioontology.org/ontology/STY/$1"^^ . + "false"^^ . + "https://github.com/ohmi-ontology/ohmi"^^ . + . + "Jie Zheng" . + . + . + . + . + . + . + . + . + . + "HUMAN16963"^^ . + "FR-FCM-ZYGW"^^ . + . + "PM0012345"^^ . + . + . + . + . + "http://www.kegg.jp/"^^ . + . + . + . + . + "http://www.hmdb.ca/"^^ . + . + "false"^^ . + "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . + "Groundnut ontology" . + . + . + . + "83088"^^ . + . + "10343835"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://doulix.com"^^ . + "false"^^ . + "http://code.google.com/p/mirna-ontology/"^^ . + . + . + . + "0000685"^^ . + . + . + . + . + . + . + "false"^^ . + . + "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . + "^WB[A-Z][a-z]+\\d+$"^^ . + . + "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . + . + . + . + "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . + . + . + . + . + . + "^DP\\d{5}r\\d{3}$"^^ . + "https://biopragmatics.github.io/providers/msigdb/$1"^^ . + . + . + . + . + . + . + "AmoebaDB" . + "23"^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_365:$1"^^ . + . + "^GE\\d+$"^^ . + "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . + . + . + . + "http://rgd.mcw.edu/rgdweb/search/strains.html"^^ . + . + "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . + "http://bcrj.org.br/celula/$1"^^ . + . + . + . + . + . + . + . + . + . + "http://elm.eu.org/elms/elmPages/$1.html"^^ . + . + "http://www.allergome.org/"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . + . + "false"^^ . + "NIF Standard Ontology: Neurolex" . + . + "false"^^ . + . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . + . + . + . + "^(T0\\d+|\\w{3,5})$"^^ . + . + "https://w3id.org/oc/corpus/$1"^^ . + . + . + . + . + . + "0000288"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "KIAA0001"^^ . + . + . + . + . + . + . + "Antibiotic Resistance Ontology" . + "^PTM-\\d{4}$"^^ . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "https://www.ebi.ac.uk/metabolights/"^^ . + . + "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . + . + "http://www.proteinatlas.org/"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . + . + "https://www.atlassian.com/"^^ . + "http://dictybase.org/"^^ . + . + . + . + . + . + . + "Darren Natale" . + . + . + . + . + "https://www.abmgood.com/Cell-Biology.html"^^ . + . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . + . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . + . + . + . + . + "KEGG Drug" . + . + "TRQ"^^ . + . + . + . + . + . + . + . + . + . + . + "T06648"^^ . + "Web Annotation Ontology" . + "Cancer cell LInes GEne fusions portAl" . + . + "^\\w+$"^^ . + . + "Marie-Angélique Laporte" . + . + "false"^^ . + . + . + . + . + "MINT-10000"^^ . + "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . + . + . + "https://www.ebi.ac.uk/pride/"^^ . + . + "^[A-Z][a-z][0-9]+$"^^ . "false"^^ . - . - . - . - "https://cordis.europa.eu/"^^ . - . - . - . - . - . -_:Nc89477563b5049e28e7ada477bb69e8c "Plant Ontology Administrators" . - . - . - . - . - . - . - . - "0000487"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^EP\\d{4}$"^^ . - . - . - . - . - "doi" . - "^bsg-[dscp]?\\d{6}$"^^ . - "^\\d{6}$"^^ . - . - . - "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - "^\\d{9,9}$"^^ . - "miriam"^^ . - . - "NCI Data Commons Framework Services" . - . - . - . - . - . - . - . - . - . - "Database of Genomic Structural Variation - Variant" . - . - . - . - . - . - . - . - . - . - "Tom Gillespie" . - "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "The cBioPortal for Cancer Genomics" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . - "^NBK\\d+$"^^ . - "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/merops"^^ . - "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/"^^ . - . - "Aclame" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Cell line collections"^^ . - . - . - . - . - . - . - . - "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . - . - . - . - . - . + "HomologyRelation"^^ . + "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . + . + . + . + "^[8-9]\\d{3}(/[0-3])?$"^^ . + . + "https://web.expasy.org/abcd/"^^ . + . + "http://www.bioinfo.org/NONCODEv4/"^^ . + . + "https://www.rhea-db.org/rhea/$1"^^ . + . + . + . + . + . + . + "true"^^ . + "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.alzforum.org/mutations/$1"^^ . + . + . + . + . + . + . + . + . + "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . +_:N21a82802cf5d456583ce1c0f121b99bd "GenBank Support" . + "false"^^ . + . + . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . + . + . + . + . + . + . + . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + . + . + . + "Peter Midford" . + . + . + "JAX Mice" . + "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . + . + "Cell line databases/resources"^^ . "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en"^^ . - . - "CHEBI" . - . - . - . - . - . - . - . - . - . - "Five Stars of Online Research Articles Ontology" . - . - "Ath_AT1G01030.1"^^ . - . - . - "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . - . - "GitHub is an online host of Git source code repositories."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - "^\\d{7}$"^^ . - . - "300108/p3934_A-172"^^ . - . - "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . - . - . - . - . - "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . - "http://mobidb.bio.unipd.it"^^ . - . - "Database of Aligned Ribosomal Complexes" . - "false"^^ . - . - . - . - "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . - . - "http://purl.org/spar/doco/$1"^^ . - . - "0001"^^ . - . - . - "AURKA"^^ . - . - . - . - . - "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/intact/"^^ . - "Spider Ontology" . - . - . - "6017782"^^ . - . - . - . - . - . - . - "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . - . - "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . - . - "16333295"^^ . - . - . - . - "Ontologized MIABIS" . - "https://www.beiresources.org"^^ . - "https://www.enzolifesciences.com"^^ . - . - . - . - . - . - . - . - "BioPortal Prefixes" . - . - . - "https://www.storedb.org/?STOREDB:DATASET$1"^^ . - "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . - . + . + . + "Europe PMC Preprints" . + . + "http://umbbd.ethz.ch/"^^ . + . + . + . + . + "An identifier for a resource or metaresource." . + . + . + . + . + "http://purl.obolibrary.org/obo/VHOG_$1"^^ . + . + . + "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . + . + "http://www.phytozome.net/"^^ . + "http://www.signaling-gateway.org/molecule"^^ . + . + . + . + "false"^^ . + "http://cellimagelibrary.org/images/$1"^^ . + "false"^^ . + . + . + "A representation of the variety of methods used to make clinical and phenotype measurements. "^^ . + . + . + . +_:Nc9350b7cae1f47468587257ef77de20c "Nathan Baker" . + . + "CAS Chemical Registry" . + . + . + . + . + . + "https://covid19.sfb.uit.no"^^ . + . + "false"^^ . + . + "http://linkedlifedata.com/resource/umls/id/$1"^^ . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + . + . + "^\\d+$"^^ . + "^[a-zA-Z0-9-_]+$"^^ . + . + . + . + . + "36"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "0001707"^^ . + "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.mmrrc.org"^^ . + . + . + . + "false"^^ . + "https://cropontology.org/ontology/CO_345/Brachiaria"^^ . + "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes."^^ . + . + "PGS000018"^^ . + . + . + . + "Reactome" . + . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . + . + "A0A009E7X8"^^ . + _:N0e2e1708baa4480894a453ecfdaa90ab . + . + . + . + . + . + . + . + "http://www.pantherdb.org/"^^ . + "http://mobidb.bio.unipd.it"^^ . + . + . + . + . + "https://fcs-free.org/fcs-database?$1"^^ . + "FooDB Compound" . + . + "^HIX\\d{7}(\\.\\d+)?$"^^ . + . + "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . + . + . + "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . + . + "https://www.nlm.nih.gov/research/umls"^^ . + "^\\d{7}$"^^ . + "0001011"^^ . + . + . + "false"^^ . + "http://purl.org/vocab/frbr/core#$1"^^ . + . + . + . + . + . + "Raymond Lee" . + . + . + "ERM00000044"^^ . + . + . + . + . + . + . + "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . + "false"^^ . + . + . + "http://cutdb.burnham.org"^^ . + . + . + "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^ . + . + . + "^[1-9][0-9]*$"^^ . + . + . + . + "Cell line collections"^^ . + . + . + "https://proteinensemble.org/$1"^^ . + "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . + . + . + . + . + . + "https://github.com/monarch-initiative/MAxO"^^ . + . + . + "^ILMN_\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "4685"^^ . + . + . + . + . + "has download URL" . + "Cell Cycle Ontology" . + . + . + "Rice Genome Annotation Project" . + "decimal"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . + . + . + "https://github.com/ufbmi/dron"^^ . + . + . + "^\\d+$"^^ . + "Selventa Chemicals" . + . + . + . + . + . + "false"^^ . + "chebi"^^ . + . + . + "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . + . + . + "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . + . + . + . + . + . + . + . + "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . + . + "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure"^^ . + "http://purl.obolibrary.org/obo/GENO_$1"^^ . + . + . + . "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1"^^ . - . - . - . - "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . - . - "http://www.pocketome.org/files/$1.html"^^ . - . - . - . - . - "DisProt region" . - . - . - . - "00042"^^ . - . - "https://www.wormbase.org/db/seq/protein"^^ . - "SRX000007"^^ . - . - "https://licebase.org/?q=$1"^^ . - . - "false"^^ . - "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . - . - . - . - "https://depmap.org/portal"^^ . - . - . - . - "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . - "^[A-Z]{2}\\d+$"^^ . - "0005926"^^ . - "http://prodom.prabi.fr/prodom/current/html/home.php"^^ . - "RiceNetDB Protein" . - "HIX0004394"^^ . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - "false"^^ . - "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . - . - "Astrophysics Source Code Library" . - "false"^^ . - . - . - "https://bacdive.dsmz.de/"^^ . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . - "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . - . - . - . - . - . - . - . - "http://pantree.org/"^^ . - . - . - . - . - . - "https://www.metanetx.org/comp_info/$1"^^ . - . - . - "19333"^^ . - . - . - . - . - . - . + . + "https://aopwiki.org/"^^ . + "false"^^ . + . + . + . + "^[a-z0-9\\-_]+$"^^ . + . + . + . + . + . + . + . + . + . + . + "The reviewer of a prefix" . + "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . + . + . + . + . + . + . + "Process Chemistry Ontology" . + . + . + "0000128"^^ . + . + . + . + _:N17601d69c183488abe17f5b23143ef61 . + . + . + "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . + . + . + . + . + "https://github.com/luis-gonzalez-m/Collembola"^^ . + . + . + . + . + "AADB12"^^ . + "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . + "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . + . + . + "true"^^ . + "PD10000"^^ . + . + . + . + "https://labsyspharm.github.io/lspci/$1"^^ . + . + "LTS0004651"^^ . + "https://www.worldcat.org/oclc/$1"^^ . + . + . + . + "PubChem Element" . + . + "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . + . + "false"^^ . + "false"^^ . + . + . + "^\\d+$"^^ . + . + "Gender, Sex, and Sexual Orientation Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . + . + "Activity Streams" . + . + "ChEBI Data Sources" . + . + "0001079"^^ . + "false"^^ . + . + . + "https://github.com/"^^ . + . + . + "An ontology of minimum information regarding potential drug-drug interaction information."^^ . + . + . + . + . + . + . + "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . + . + "288"^^ . + "Nico Matentzoglu" . + . + "false"^^ . + . + . + . + . + . + . + "http://stitch.embl.de/"^^ . + . + . + . + . + . + . + . + "Mental Functioning Ontology" . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + "nextProt" . + "Wes Schafer" . + "^T\\d{3}$"^^ . + . + . + . + . + . + "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . + . + . + . + . + . + . + . + . + "http://www.atol-ontology.com"^^ . + "10153"^^ . + . + . + "20090303"^^ . + . + "https://github.com/CTDbase/exposure-ontology"^^ . + "https://scholar.google.com/"^^ . + . + "IRD Segment Sequence" . + "Mammalian Phenotype Ontology" . + . + "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . + "53504"^^ . + . + . + . + . + . + "sov:WRfXPg8dantKVubE3HX8pw"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + "http://www.homd.org/index.php"^^ . + . + . + "Ximbio" . + "http://www.sanger.ac.uk/Users/mb4/PLO/"^^ . + . + "false"^^ . + . + . + . + . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS"^^ . + . + "^(cd)?\\d{5}$"^^ . + "AberOWL" . + . + . + . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . + "PDC000351"^^ . + "The Virus Infectious Disease Ontology" . + "10595"^^ . + . + . + . + "An ontology to describe entities related to cardiovascular diseases"^^ . + . + . + "https://ssbd.riken.jp"^^ . + "Minimum PDDI Information Ontology" . + . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . + "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . + . + "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . + "http://www.atol-ontology.com"^^ . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^ . + . + . + . + . + . + . + "100"^^ . + . + "https://www.ncbi.nlm.nih.gov/gene"^^ . + . + . + . + . + "101"^^ . + . + . + "http://www.fungalbarcoding.org/"^^ . + "HEX1"^^ . + . + . + "false"^^ . + . + "ML0224"^^ . + "https://flybase.org/reports/$1"^^ . + "https://www.worldwildlife.org/biomes"^^ . + "959"^^ . + . + . + . + "Ensembl Plants" . + . + "http://dictybase.org/gene/$1"^^ . + "MolBase" . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . + . + "http://www.t3db.org/toxins/$1"^^ . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + . + . + . + . + . + . + "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^ . + . + "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . + . + . + . + . + . + "0000574"^^ . + . + . + . + "Fossilworks Journal" . + . +_:N366873dcfd384ee1821e5facc6adbaeb "Animal Diversity Web technical staff" . + . + . + "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . + . + . + . + "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . + "^\\d{7}$"^^ . + . + . + . + . + "^TS-\\d{4}$"^^ . + . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + . + "^\\d+$"^^ . + "PlasmoDB" . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + "IPI"^^ . + "false"^^ . + . + . + . + "MycoBrowser marinum" . + . + . + "Chemical Component Dictionary" . + "Protein Model Database" . + . + . + . + "AS000060"^^ . + . + "^\\d+$"^^ . + . + "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . + . + "https://flybase.org"^^ . + . + . + . + . + . + . + "0000029"^^ . + "PhosphoPoint Phosphoprotein" . + "12929"^^ . + . + . + . + . + "https://github.com/ufbmi/geographical-entity-ontology/wiki"^^ . + "Ramona Walls" . + "0000127"^^ . + . + "NeuroLex Anatomy" . + . + . + . + "https://data.4dnucleome.org/biosources/$1"^^ . + "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . + . + . + . + . + . + . + "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . + "https://github.com/"^^ . + "Physico-chemical methods and properties" . + . + "https://cropontology.org/ontology/CO_321/Wheat"^^ . + . + "^M[0-9]{4,}$"^^ . + . + . + . + . + . + . + . + . + . + . + "617102"^^ . + . + . + . + . + . + . + . + "0001998"^^ . + . + . + . + . + . + "OBO Foundry" . + "https://github.com/ApolloDev/apollo-sv"^^ . + . + "Cell line databases/resources"^^ . + . + . + "MEROPS Family" . + . + "^\\d{6}$"^^ . "3D Metabolites" . - "eVOC (Expressed Sequence Annotation for Humans)" . - . - . - "http://purl.obolibrary.org/obo/OBCS_$1"^^ . - . - . - "http://purl.obolibrary.org/obo/GECKO_$1"^^ . - . - "^m\\w+$"^^ . - "GALEN" . - . - . - . - "ENSG00000139618"^^ . - "^[0-9]+$"^^ . - "http://purl.obolibrary.org/obo/IMR_$1"^^ . - "SCC111"^^ . - . - . - "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . - . - . - "false"^^ . - . - "01N50ZZ"^^ . - "http://www.gramene.org/"^^ . - . - . - . - . - "false"^^ . - . - . - "165a"^^ . - . - . - "https://rapdb.dna.affrc.go.jp/"^^ . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - "https://reaxys.emolecules.com"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "An experimental run, served thrugh the ENA"^^ . - . - . - "HMS LINCS Compound" . - "^TC\\d+$"^^ . - . - . - . - . - "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . - . - . - "https://www.cropontology.org/rdf/CO_334:$1"^^ . - "1023371"^^ . - . - "HGVM15354"^^ . - . - . - . - . - "^PA\\d+$"^^ . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . - . - . - . - "728"^^ . - . - . - "4349895"^^ . - . - . - "EBI-366083"^^ . - . - . - . - "false"^^ . - "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . - . - . - "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://merops.sanger.ac.uk/index.htm"^^ . - . - . - "false"^^ . - "http://oryzatagline.cirad.fr/"^^ . - . + "M0001"^^ . + . + . + . + . + . + . + "https://www.metanetx.org/comp_info/$1"^^ . + . + . + . + . + . + . + . + "https://metacyc.org"^^ . + . + . + . + . + "http://www.ensembl.org/"^^ . + "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp"^^ . + . + . + . + "CCDS13573.1"^^ . + . + . + . + . + . + . + "https://bioregistry.io" . + . + "false"^^ . + "true"^^ . + "false"^^ . + . + . + . + . + . + "https://www.araport.org/"^^ . + . + . + . + . + . + "1.10.10.200"^^ . + . + . + . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . + . + "AURKA"^^ . + . + . + . + "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . + "https://identifiers.org" . + . + "http://www.sparontologies.net/ontologies/pwo"^^ . + "http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1"^^ . + . + . + . + . + "false"^^ . + . + "Health Surveillance Ontology" . + "0000139"^^ . + "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "CADAFLAT00006211"^^ . + "false"^^ . + "false"^^ . + . + . + "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . + . + . + . + "rxn00001"^^ . + "http://purl.obolibrary.org/obo/PCL_$1"^^ . + . + . + . + . + "http://ctdbase.org/"^^ . + . + . + "0000000"^^ . + . + . + . + "YRC PDR" . + . + "false"^^ . + "false"^^ . + . + "Liliana Andres Hernandez" . + "OSR0818"^^ . + "authoredBy"^^ . + . + . + "00000001"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^Os\\S+g\\d{7}$"^^ . + . + "jrc-eurl-ecvam-chemagora"^^ . + . + . + . + "http://www.w3.org/ns/activitystreams#$1"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + . + "^\\d+$"^^ . + "https://www.gtexportal.org/home/gene/$1"^^ . + . + "67"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "Phenol-Explorer" . + . + . + . + . + "Collection"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://www.ymdb.ca/compounds/$1"^^ . + . + . + "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . + . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . + . + "false"^^ . + . + . + . + . + . + . + "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . + . + . + "Terms from the source appear in the target resource" . + . + "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . + . + . + "has responsible" . + . + . + . + . + . + "SNR17A"^^ . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "GlycoEpitope" . + "http://peroxibase.toulouse.inra.fr/"^^ . + . + . + . + "https://ecmdb.ca"^^ . + . + . + . + . + . + "2224"^^ . + "5046"^^ . + . + . + . + . + . + "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^ . + . + "^[0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . + . + . + . + . + "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . + . + . + . + "false"^^ . + . + . + "^\\d{6}$"^^ . + "0000509"^^ . + . + . + . + . + . + . + . + . + "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . + . + . + . + . + . + "biopragmatics/bioregistry/416"^^ . + . + "Prefix Commons" . + . + . + . + "https://www.uniprot.org/journals/$1"^^ . + "https://monarch-initiative.github.io/mondo"^^ . + . + "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . + "MGnify Analysis" . + "MGnify Sample" . + . + . + "http://bigg.ucsd.edu/compartments/"^^ . + "http://biomodels.net/vocab/idot.rdf"^^ . + . + . + "Decentralized Biomedical Ontology" . + . + . + . + "http://purl.obolibrary.org/obo/OGSF_$1"^^ . + . + . + . + "https://www.webelements.com/$1"^^ . + . + "http://www.yeastrc.org/pdr/"^^ . + . + "https://pfam.xfam.org/"^^ . + . + . + . + . + . + . + . + . + "^\\d{5}$"^^ . + . + . + . + "3618"^^ . + . + . + . + "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^ . + . + . + "Platynereis stage ontology" . + "^\\d+$"^^ . + "^\\d+$"^^ . + "0002-1975-61"^^ . + "Lentil ontology" . + "^\\d{7}$"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "http://treebase.org/"^^ . + "https://bioregistry.io"^^ . + "https://human.brain-map.org"^^ . + . + . + . + "Immune Epitope Database" . + "http://europepmc.org/"^^ . + . + . + . + . + "false"^^ . + . + . + "56305849200"^^ . + . + . + "false"^^ . + . + "Medaka Developmental Stages" . + "Database of human Major Histocompatibility Complex" . + "Natural Product-Drug Interaction Research Data Repository" . + . + "false"^^ . + "4892"^^ . + "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . + . + "0000052"^^ . + "http://www.sparontologies.net/ontologies/biro"^^ . + "3hB06"^^ . + "false"^^ . + . + . + "Compositional Dietary Nutrition Ontology" . + . + . + "0000189"^^ . + . + . + "33607"^^ . + . + "81944ba1-81d0-436e-8552-33d77a27834b"^^ . + . + . + "0000012b-5661-2f63-2f73-b43980000000"^^ . + "Nucleic Acids Phylogenetic Profiling" . + . + "false"^^ . + "chebi" . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "false"^^ . + "https://idr.openmicroscopy.org"^^ . + . + . + . + . + . + . + "0019171"^^ . + . + . + . + . + "Shur-Jen Wang" . + . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + . + . + . + "false"^^ . + "Unified Phenotype Ontology" . + . + "Pubmed Central" . + . + . + . + . + "0459895"^^ . + . + . + . + . + . + . + "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . + . + "http://eggnog.embl.de/version_3.0/"^^ . + . + "Molecular Signatures Database" . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + . + . + . + "Odor Molecules DataBase" . + "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . + . + "false"^^ . + "false"^^ . + . + "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . + . + . + . + "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . + . + "PGOHUM00000289843"^^ . + . + . + . + . + . + . + . + "51"^^ . + . + . +_:N00e71c3083a3461584e6c31c9a4d425d "Jonathan Bard" . + . + "http://rgd.mcw.edu/"^^ . + "Ontology of standardized units"^^ . + . + "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto"^^ . + . + . + . + "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . + "CRISPRdb" . + . + . + . + "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . + . + . + . + . + . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + "http://gpmdb.thegpm.org/"^^ . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "Fyler" . + . + . + "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . + "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . + . + . + . + "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . + "3305"^^ . + "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . + . + . + . + . + . + . + "LipidBank" . + . + . + . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . + . + . + . + . + . + "0.7-123"^^ . + . + . . - . - "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . - . - "1046"^^ . - . - "http://immunet.cn/bdb/"^^ . - . - . - . - "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "National Drug Code" . - . - "284196006"^^ . - "false"^^ . + . + "oai:cwi.nl:4725"^^ . + . +_:Nc01a0256846c4e64b983e54db9f7673f "Fahim Imam" . + . + . + . + . + "SNOMED CT (International Edition)" . + "0000295"^^ . + . + "C34"^^ . + . + . + . + . + . + . + "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . + . + . + . + . + . + "title"^^ . + . + "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . + . + "has resolver formatter" . + . + . + . + . + . + "0400109"^^ . + "false"^^ . + "false"^^ . + . + "false"^^ . + . + "Molecular Interaction Database" . + "^\\d+$"^^ . + . + "https://odc-tbi.org"^^ . + . + "MF_01400"^^ . + . + . + . + "^\\d{8}$"^^ . + "https://cropontology.org/ontology/CO_323/Barley"^^ . + "false"^^ . + . + "^\\d+$"^^ . + . + "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . + . + . + . + "03307879"^^ . + "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . + . + . + . + "DDB_G0267522"^^ . + "IUPHAR family" . + . + "false"^^ . + . + "false"^^ . + . + "false"^^ . + "bsg-000052"^^ . + . + . + . + "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^ . + . + . + "sbgn.er.level-1.version-1.2"^^ . + "^[1-9][0-9]*$"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + "true"^^ . + . + . + . + . + . + . . - "^[0-9]+\\.[0-9]+$"^^ . - . - . - "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . - "^[SCTAGMNU]\\d+$"^^ . - . - "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "IID00001"^^ . - . - "http://purl.obolibrary.org/obo/RNAO_$1"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . - . - . - . - "International Nonproprietary Names" . - "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings."^^ . - . - "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . - . - . - . - . - . - . - . - . - . - "GLIDA GPCR" . - . - . - "false"^^ . - . - . - "FB00000917"^^ . - . - "0000049"^^ . - . - . - "https://cdno.info/"^^ . - . - "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . - . - "Structural Classification of Protein" . - "https://www.animalgenome.org/QTLdb"^^ . - "false"^^ . - . - . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - . - . - "https://github.com/DrugTargetOntology/DTO"^^ . - "^\\d+$"^^ . - "false"^^ . - . - . - "Tb927.8.620"^^ . - . - . - . - "0000072"^^ . - . - "false"^^ . - "https://github.com/rdruzinsky/feedontology"^^ . - . - . - "RiceNetDB miRNA" . - "NCATS Drugs" . - . - . - "Rv1908c"^^ . - . - . - . - "false"^^ . - . - . - . - . - "http://ecoliwiki.net/colipedia/"^^ . - . - . - . - . - "PA131"^^ . - "22RV1_12_2019"^^ . - . - . - . - . - . - . - "http://www.nlm.nih.gov/mesh/"^^ . - "https://www.cropontology.org/rdf/CO_345:$1"^^ . - . - "Mungbean ontology" . - . - "https://clinicaltrials.gov/ct2/show/$1"^^ . - . - . - . - . - . - . - . - . - . - . + . + . + "Transport Systems Tracker" . + "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . + "SL-0002"^^ . + . + "false"^^ . + "Software"^^ . + . + "http://aclame.ulb.ac.be/"^^ . + . + "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . + . + . + . + . + . . - . - . - . - "http://www.molbase.com/"^^ . - . - . - . - . - "128796-39-4"^^ . - . - "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . - . - . - "false"^^ . - "Database of homology-derived secondary structure of proteins" . - . - . - . - . - . - . - . - . - . - . - . - . - "http://dictybase.org/"^^ . - . - . - "Vertebrate Genome Annotation Database" . - . - "2842"^^ . - . - . - . - "215"^^ . - . - "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - . - . - . - . - . - "Drivers of human diseases including environmental, maternal and social exposures."^^ . - "https://github.com/tis-lab/reagent-ontology"^^ . - "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - . - "https://web.expasy.org/cellosaurus/CVCL_$1"^^ . - "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . - "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . - . - "http://www.psidev.info/MOD"^^ . - . - . - . - . - . - . - . - . - . - "https://omabrowser.org/cgi-bin/gateway.pl"^^ . - . - . - . - . - . - . - "0007114"^^ . - "000204"^^ . - . - "Adnan Malik" . - . - . - "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^ . - . - . - . - . - . - "Collection of European paediatric cardiac coding files"^^ . - . - . - . + . + . + . + . + . +_:N0e2e1708baa4480894a453ecfdaa90ab "Vivian Lee" . + . + . + . + . + . + "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . + "https://www.reaxys.com"^^ . + . + . + . + "false"^^ . + "Xenopus Anatomy Ontology" . + . + . + . + "C. elegans Gross Anatomy Ontology" . + "Insertion sequence elements database" . + . + "http://www.cropontology.org/ontology/CO_327/Pearl%20millet"^^ . + . + . + . + "Contains entries for various database identifiers" . + . + "PubChem Cell Line" . + "GALEN" . + . + . + . + . + . + . + . + . + . + . + "^GPM\\d+$"^^ . + . + . + . + "Homeodomain Research" . + . + "https://omim.org/phenotypicSeries/$1"^^ . + . + "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . + . + "false"^^ . + . + . + "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . + . + "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . + "hsa-let-7a"^^ . + . + "090201"^^ . + . + . + "^(ev\\:)?E\\d+$"^^ . + . + "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://github.com/pcastellanoescuder/FoodBiomarkerOntology"^^ . + . + . + . + "http://www.uniprot.org/"^^ . + . + . + "https://bioregistry.io/metaregistry/$1"^^ . + . + "hasDbXref"^^ . + . + . + . + . + . + . + . + . + "^[WAICV]\\d{2,}$"^^ . + . + . + . + . + . + . + . + . + . + "http://www.cathdb.info/"^^ . + . + "has example" . + . + "false"^^ . + "^ENSG\\d{11}$"^^ . + . + . + . + . + . + . + "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . + . + . + . + . + . + . + "Reaxys" . + . + . + . + . + "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . + . + "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . + . + . + "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . + . + "http://napp.u-psud.fr/"^^ . + . + . + "http://www.sparontologies.net/ontologies/c4o"^^ . + "http://ascl.net/"^^ . + . + . + _:Nbe65d6be29854652803f710d26fdc993 . + . + . + . + "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . + . + . + "Plant Environment Ontology" . + "4005"^^ . + "VMH metabolite" . + . + . + . + . + . + . + . + "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . + . + . + . + "http://purl.uniprot.org/uniprot/$1"^^ . + . + . + . + . + "false"^^ . + "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . + "http://purl.org/pav/$1"^^ . + . + . + . + . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + . + . + . + . + . + . + . + "Brassica ontology" . + . + . + "false"^^ . + . + . + . + "cd00400"^^ . + . + "true"^^ . + . + "https://github.com/pombase/fypo"^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . + . + . + "http://www.cghtmd.jp/CGHDatabase/index_e.jsp"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + "Electrocardiogram Ontology" . + . + . + . + . + . + "AURKA"^^ . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/EXO_$1"^^ . + . + "false"^^ . + "NLXFUNC covers terms for cognitive function."^^ . + . + "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . + . + . + . + . + . + . + . + . + . + "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . + . + . + . + . + "http://cancer.sanger.ac.uk/cosmic/"^^ . + . + "4214"^^ . + "false"^^ . + "A type for entries in the Bioregistry's registry." . + . + . + . + . + . + . + . + . + . + "BioCatalogue Service" . + "http://www.gramene.org/plant_ontology/"^^ . + . + . + "http://func.mshri.on.ca/mouse/"^^ . + . + "false"^^ . + . + . + . + . + "4201PAT-CCTCC00348"^^ . + . + "^\\d+$"^^ . + . + . + "Pathogen Host Interaction Phenotype Ontology" . + . + "https://flowrepository.org/id/$1"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "false"^^ . + . + . + "RCV000033555.3"^^ . + "^[A-Za-z0-9]+$"^^ . + . + "http://www.obofoundry.org/ontology/$1" . + "http://addgene.org/"^^ . + . + "CompTox Chemistry Dashboard" . + "^C\\d{4}$"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^IM-\\d+(-?)(\\d+?)$"^^ . + . + "version 2019 - pvs"^^ . + "http://purl.obolibrary.org/obo/FLU_$1"^^ . + . + . + . + . + . + . + . + . + . + "Registry" . + . + "https://foodb.ca/foods"^^ . + . + "http://purl.obolibrary.org/obo/HTN_$1"^^ . + . + . + . + . + . + . + "Cellosaurus" . + "http://edamontology.org"^^ . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + "http://obi-ontology.org"^^ . + "D053716"^^ . + "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + . + "http://omit.cis.usouthal.edu/"^^ . + "Symptom Ontology" . + . + . + . + . + "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . + . + "false"^^ . + . + "^T3D\\d+$"^^ . + . + . + . + . + . + "http://sabiork.h-its.org/"^^ . + . + . + "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^ . + . + "Beta Cell Genomics Ontology" . + . + . + "Veterinary Substances DataBase" . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "^PS\\d+$"^^ . + . + "Software ontology" . + . + . + . + "http://purl.obolibrary.org/obo/RXNO_$1"^^ . + "^T3\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.storedb.org/?STOREDB:DATASET$1"^^ . + . + . + . + . + "000000012281955X"^^ . + . + "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . + . + . + . + . + "https://comptox.epa.gov/dashboard/$1"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + "data_1664"^^ . + "false"^^ . + . + . + . + . + "https://www.ebi.ac.uk/chembldb/"^^ . + "^\\d+$"^^ . + . + "16793"^^ . + "^.+$"^^ . + . + . + "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . + "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . + . + . + . + . + . + . + "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . + "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^ . + . + . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/DINTO_$1"^^ . + . + "Basic Formal Ontology" . + . + "TTDS00056"^^ . + . + "International Standard Name Identifier" . + . + "1000160"^^ . + . + "^\\w+$"^^ . + . + "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . + . + . + "CO_010" . + . + "NIF Standard Ontology: Cognitive Function" . + . + "https://www.flymine.org/come/entry?gn=$1"^^ . + . + . + "201022999"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . + "0000618"^^ . + "^\\d+$"^^ . + "https://www.cancerrxgene.org/translation/Drug/$1"^^ . + "http://www.semantic-systems-biology.org/apo"^^ . + "^\\w+$"^^ . + "Cell Lines Service" . + "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . + . + "11303"^^ . + . + . + . + "Gene Ontology Registry" . + . + . + "http://www.cabri.org/"^^ . + . + . + "0471491039"^^ . + . + . + . + "http://compbio.cs.queensu.ca/F-SNP/"^^ . + "Biomedical Informatics Research Network Lexicon" . + . + . + . + "Linguist" . + . + . + . + . + . + . + . + . + "BRENDA, The Comprehensive Enzyme Information System" . + . + . + "Adriano Rutz" . + . + "https://hpo.jax.org/app/browse/term/HP:$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + "Food Interactions with Drugs Evidence Ontology" . + "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . + . + . + "https://biomodels.net/vocab/idot.rdf#$1"^^ . + . + "Regulation of Gene Expression"^^ . + . + . + . + . + . + . + . + . + "0000050"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . + "^\\d{7}$"^^ . + . + . + . + "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . + . + . + "International Nonproprietary Names" . + . + "https://europepmc.org/article/CBA/$1"^^ . + . + . + . + . + . + . + "9002859"^^ . + . + . + . + . + . + "P00747__P07355"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d{8}$"^^ . + "Paul Fabry" . + . + . + . + "https://www.xenbase.org/entry/$1"^^ . + . + . + "Uber Anatomy Ontology" . + "Vertebrate Taxonomy Ontology" . + . + . + . + . + "false"^^ . + "http://www.brenda-enzymes.org"^^ . + "http://umbbd.ethz.ch/"^^ . + . + "false"^^ . + . + . + . + . + . + . +_:Nb2194da6bc9f4b059c88b94a4cf764cd "Jonathan Bard" . + . + . + "^NONHSAT\\d{6}$"^^ . + . + "https://github.com/jannahastings/mental-functioning-ontology"^^ . + . + "PSEEN0001"^^ . + . + "false"^^ . + . + "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . + . + . + . + . + "DB14938"^^ . + . + . + . + "TTD Drug" . + "Q13485"^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . + . + . + . + "false"^^ . + . + "false"^^ . + "8000221"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . + . + . + "2.16.840"^^ . + "AB0"^^ . + . + "Platynereis Developmental Stages" . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . + "0000598"^^ . + . + "VFDB Gene" . + . + . + . + . + "Sugar Kelp trait ontology"^^ . + . + . + "https://www.ebi.ac.uk/ena/browse/genome-assembly-database"^^ . + . + . + . + . + . + . + . + . + . + "BioSystems" . + . + "false"^^ . + . + "International Classification of Diseases, 9th Revision" . + "Simple Modular Architecture Research Tool" . + . + . + "PomBase" . + . + . + . + "false"^^ . + . + "LINCS Data" . + . + "false"^^ . + . + . + . + "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . + . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . + . + . + "http://www.ecogene.org/gene/$1"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "http://beetlebase.org/"^^ . + "^[SCTAGMNU]\\d+$"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . + . + "1455"^^ . + . + . + . + . + "B00162"^^ . + "File inside StoreDB"^^ . + . + . + "Protein Interaction Network Analysis" . + . + . + "Lipid Ontology" . + . + "Alzheimer's Disease Ontology" . + . + . + . + . + . + . + "false"^^ . + . + "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . + . + "true"^^ . + . + . + . + . + . + . + "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . + . + . + "Natural Product Activity and Species Source Database" . + . + "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^ . + "This collection contains various brain atlases from the Allen Institute." . + . + . + . + . + "http://purl.obolibrary.org/obo/OHMI_$1"^^ . + . + . + . + "false"^^ . + . + . + "http://www.wikigenes.org/e/gene/e/$1.html"^^ . + . + . + "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . + . + . + . + "false"^^ . + . + . + "http://www.pombase.org/spombe/result/$1"^^ . + . + . + "10001-101"^^ . + . + . + "false"^^ . + "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . + "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . + . + . + . + . + . + "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^ . + . + "6017782"^^ . + . + . + "^ENST\\d{11}$"^^ . + . + . + . + "http://www.genenames.org"^^ . + . + . + . + . + "^NONHSAG\\d{5}$"^^ . + "ACHN"^^ . + . + . + . + . + . . - . + . + . + . + . + . + . + "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . + . + "BioPortal" . + . + . + "Plasmodium Life Cycle" . + . + . + . + "https://www.cropontology.org/rdf/CO_348:$1"^^ . + "EDAM Operation" . + "Blue Brain Project Topological sampling Knowledge Graph" . + "^[0-9]+\\.[0-9]+$"^^ . + . + . + . + . + "International Genome Sample Resource" . + . + . + . + "false"^^ . + . + . + "false"^^ . + "http://www.pathwaycommons.org/pc/"^^ . + "http://www.sparontologies.net/ontologies/pro"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://herv.img.cas.cz/"^^ . + . + . + "http://www.vbase2.org/vgene.php?id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.biocatalogue.org/"^^ . + . + "Kidney and Urinary Pathway Ontology" . + . + "0000255"^^ . + . + . + . + . + . + "RNA Modification Database" . + . + . + . + . + . + . + . + . + "DBCAT000600"^^ . + . + . + . + . + "EDAM Topic" . + . + . + . + . + . + . + "56"^^ . + . + . + . + . + . + . + . + "true"^^ . + . + . + "Animal natural history and life history" . + . + . + . + . + . + "DBG2 Introns" . + . + . + "Tom Gillespie" . + . + . + "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . + "miRBase mature miRNA" . + "false"^^ . + "TS-0001"^^ . + "An ontology to describe entities related to prescription of drugs"^^ . + . + "00050"^^ . + . . - "http://www.hmdb.ca/metabolites/$1"^^ . - . - "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . - . - "false"^^ . - . - "https://webbook.nist.gov/chemistry/"^^ . - . - . - . - . - . - . - . - . - "http://bacmap.wishartlab.com/"^^ . - . - . - . - . - . - . - "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/OPL_$1"^^ . - . - "Current Procedural Terminology" . - . - . - "00620027"^^ . - . - "Broad Fungal Genome Initiative" . - . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "D00001"^^ . - "0000339"^^ . - . - . - . - . - . - . - "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . - . - . - . - . - "http://rgd.mcw.edu/"^^ . - . - . - "Os01g0883800"^^ . - . - "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "OSR00185W"^^ . - "http://genolist.pasteur.fr/SubtiList/"^^ . - . - "57-27-2"^^ . - "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . - . - . - . - "false"^^ . - "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . - . - . - . - "Metabolites in the Xenobiotics Metabolism Database."^^ . - . - "OBO Foundry" . - . - . - . - . - . - "false"^^ . - . - . + . + "Statistical Torsional Angles Potentials" . + . + . + . + . + . + . + . + . + . + "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . + "Cluster of orthologous genes" . + "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . + . + "https://github.com/flora-phenotype-ontology/flopoontology"^^ . + . + "false"^^ . . - "false"^^ . - "^[0-9\\-_]+$"^^ . - . - . - . - . - . - "false"^^ . - "false"^^ . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . - "^\\d+$"^^ . - . - "https://cropontology.org/ontology/CO_334/Cassava"^^ . - "Wikipedia" . - . - . - . - . - . - . - . - . - "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm"^^ . - . - . - . - . - . - "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . - "^\\d{7}$"^^ . - "An ontology of Drosophila melanogaster anatomy."^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . - . - . - "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . - . - . - . - . - . - . - "https://www.e-cyanobacterium.org/experiments-repository/"^^ . - "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . - "MMP743597.11"^^ . - "false"^^ . - . - . - . - . - . - "http://www.yeastrc.org/pdr/"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "https://loinc.org/"^^ . - . - "BioCarta Pathway" . - . + . + . + . + . + "https://github.com/obophenotype/planarian-phenotype-ontology"^^ . + . + . + . + "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + "https://giardiadb.org/giardiadb/"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "^[A-Z_a-z]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000400"^^ . + "Regulation of Transcription Ontology" . + . + . + . + . + . + . + . + . + . + . + _:Nc90f569000894c6fab011435dc1a5fcf . + . + . + . + . + "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . + . + . + . + . + . + . + . + . + . + . + . + "1a24"^^ . + . + "false"^^ . + "The Statistical Methods Ontology" . + . + "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + "Citation Typing Ontology" . + . + . + . + . + . + "http://mirtarbase.mbc.nctu.edu.tw/"^^ . + . + . + . + "Exposure ontology" . + . + . + . + "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . + . + "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "h2o"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . + . + . + "Fernanda Farinelli" . + . + . + . + . + . + . + "^\\d+$"^^ . + "0000013"^^ . + . + "false"^^ . + . + "BioTools" . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + . + . + "Radiation Biology Ontology" . + . + . + . + . + "Jade Hotchkiss" . + . + "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . + . + "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . + "UPC04349"^^ . + . + "false"^^ . + . + "EGAS00000000001"^^ . + "World Register of Marine Species" . + "https://covid19.sfb.uit.no/api/records/$1"^^ . + "Population and Community Ontology" . + "DBSALT001211"^^ . + . + . + "CHEBI" . + "https://www.kerafast.com/Search?SearchTerm="$1""^^ . + . + "http://biohackathon.org/resource/faldo#$1"^^ . + . + . + "false"^^ . + . + . + . + "N1899"^^ . + . + . + . + . + . + . + . + "SwissLipid" . + . + . + . + . + . + . + "BAC045"^^ . + . + . + "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . + "^\\d+$"^^ . + "^FCB\\d{3}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . + . + _:Nb2194da6bc9f4b059c88b94a4cf764cd . + "Datanator Metabolite" . + "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . + "IMGT/HLA human major histocompatibility complex sequence database" . + . + "https://www.inaturalist.org/taxa"^^ . + . + . + . + "Human Phenotype Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "AY109603"^^ . + . + . + "^HBG\\d+$"^^ . + . + "http://www.gudmap.org/"^^ . + . + . + "false"^^ . + . + . + . + . + "https://www.ebi.ac.uk/intenz/"^^ . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + . + "true"^^ . + . + . + "https://www.hu-berlin.de/?set_language=en&cl=en"^^ . + . + . + "C063233"^^ . + "false"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . + "https://github.com/geneontology/go-ontology/tree/master/contrib"^^ . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . + . + . + "http://www.p3db.org/"^^ . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . + . + . + . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . + . + "https://github.com/bio-ontology-research-group/unit-ontology"^^ . + . + . + . + . + "4000027"^^ . + . + "https://eol.org"^^ . + . "false"^^ . - . - "false"^^ . - . - . - . - "false"^^ . - "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . - . - "BioSimulators" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://www.lipidmaps.org"^^ . - "AA0001"^^ . - "Selventa legacy complex namespace used with the Biological Expression Language"^^ . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/MICRO_$1"^^ . - . - "G00123"^^ . - . - . - "^\\d+$"^^ . - . - "00000021"^^ . - "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . - . - . - . - . - . - "MMP3888430"^^ . - . - "http://cancer.sanger.ac.uk/cosmic/"^^ . - . - "^PF\\d{5}$"^^ . - "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . - . - . - . - "0000586"^^ . - . - . - "http://purl.bioontology.org/ontology/STY/$1"^^ . - "3355"^^ . - . - . - "http://zfin.org/$1"^^ . - . - . - . - "https://bio.tools/$1"^^ . + . + . + . + . + . + "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . + . + "^\\d{7}$"^^ . + "0000547"^^ . + "^\\d{4}$"^^ . + . + . + . + . + . + . + . + . + "0000390"^^ . + . + . + "https://models.physiomeproject.org/exposure/$1"^^ . + . + . + . + . + "Conferences in EasyChair"^^ . + . + . + "http://www.cathdb.info/"^^ . + . + "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . + "George Gkoutos" . + . + . + . + . + "ICEberg element" . + . + . + . + "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . + . + . + "HIT000195363"^^ . + "THE1B"^^ . + . + "http://www.candidagenome.org/"^^ . + . + . + "FOOD00020"^^ . + "0000254"^^ . + . + . + . + "e0333"^^ . + . + . + . + . + . + . + "http://www.phosphosite.org/homeAction.do"^^ . + "Ontology Lookup Service" . + . + "Kids First" . + . + "https://www.ebi.ac.uk/ega/datasets/$1"^^ . + "Database portal containing replicate experiments of different assays and samples"^^ . + . + . + "CAPS-DB" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "FlyBase Gene" . + . + . + "26"^^ . + . + . + "2GC4"^^ . + . + "Sample processing and separation techniques" . + . + . + . + . + "Zoë May Pendlington" . + . + "https://www.ebi.ac.uk/gxa/genes/$1"^^ . + "http://www.inoh.org"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/dbvar"^^ . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Cardiovascular Disease Ontology" . + . + . + "false"^^ . + . + . + "Informed Consent Ontology" . + "false"^^ . + . + "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . + . + . + "https://commonchemistry.cas.org/detail?ref=$1"^^ . + . + "http://www.pazar.info/"^^ . + . + . + "Cube db" . + . + . + . + . + . + . + . + "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . + "^SEQF\\d+$"^^ . + "Global Biodiversity Information Facility" . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + "Tom Gillespie" . + . + "^[1-9][0-9]{3,6}$"^^ . + . + . + . + . + . + "false"^^ . + . + "Zebrafish anatomy and development ontology" . + . + "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . + "https://www.uniprot.org/docs/tisslist.txt"^^ . + "0001114"^^ . + . + "434"^^ . + . + . + "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . + "http://braininfo.rprc.washington.edu/"^^ . + "false"^^ . + . + "Cambridge Structural Database" . + . + . + . + "Ensembl Bacteria" . + . + . + . + "^[0-9]+$"^^ . + . + . + . + "Browser for the periodic table of the elements"^^ . + . + . + "UniProt Protein" . + . + "https://www.phenxtoolkit.org/protocols/view/$1"^^ . + . + "^\\d+$"^^ . + . + "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . + . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + . + "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . + . + . + . + . + "Yvonne Bradford" . + "http://purl.obolibrary.org/obo/CLYH_$1"^^ . + "^PED\\d{5}$"^^ . + "https://www.dataone.org"^^ . + . + . . - . - "0000000"^^ . - . - . - "https://www.rebuildingakidney.org/id/$1"^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . - . - "Q9P0K8"^^ . - "http://wodaklab.org/iRefWeb/"^^ . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . - "DI-04240"^^ . - . - . - . - . - . - . - . - . - . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . - . - . - . - . - . - "Bio-MINDER Tissue Database" . - . - . - "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . - . - . - "http://www.homd.org/index.php"^^ . - "KEGG Enzyme" . + . + "Information for ligand groups (chemical classes)."^^ . + . + "50018"^^ . + "Simple Knowledge Organization System" . + "Compluyeast-2D-DB" . + . + . + . + . + "false"^^ . + "119514"^^ . + "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed."^^ . + "^MIR:000\\d{5}$"^^ . + . + . + "AOPWiki (Key Event Relationship)" . + . + . + . + . + . + . + . + . + . + . + . + "GM17027"^^ . + . + "familyName"^^ . + "^\\w+$"^^ . + . + "false"^^ . + "0000858"^^ . + . + . + "^LRG_\\d+$"^^ . + "true"^^ . + . + "https://easychair.org/cfp/"^^ . + . + . + . + . + . + "https://www.animalgenome.org"^^ . + . + . + "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^ . + . + . + . + . + . + "http://www.disease-ontology.org"^^ . + . + . + . + "false"^^ . + "FishBase" . + "Database of Arabidopsis Transcription Factors" . + . + . + "Broad Fungal Genome Initiative" . + . + . + . + . + . + . + . + . + "Digital Object Identifier" . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + "https://prefixcommons.org/?q=$1" . + "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . + . + "Minimal Viable Identifier" . + . + . + . + . + . + "http://4dx.embl.de/4DXpress"^^ . + . + . + "A vendor of antibodies and other biologics"^^ . + "^\\d{7}$"^^ . + . + "^DDB_G\\d+$"^^ . + "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . + . + . + "developed by ICARDA - Dec 2018"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://immunet.cn/bdb/"^^ . + . + . + . + "FAIR* Reviews Ontology" . + . + . + . + . + . + . + . + . + . + "https://www.mlcommons.org/mlc-id/$1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "The Bioregistry's meta-registry"^^ . + . + "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . + . + "^[A-Z-_0-9]+$"^^ . + . + . + . + . + . + "http://vegbank.org/cite/$1"^^ . + "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . + . + "https://www.gbif.org/species"^^ . + . + . + . + "https://github.com/EBISPOT/DUO"^^ . + "International Classification of Diseases, 10th Revision" . + . + . + . + . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + . + "KEGG Pathways Database" . + . + . + . + . + "International Nucleotide Sequence Database Collaboration (INSDC) Run" . + . + . + . + . . - . - "^SL-\\d+$"^^ . - . - "https://go.drugbank.com/categories"^^ . - . - . - "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - . - . - . - "false"^^ . - "Veterinary Substances DataBase" . - "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO"^^ . - "MGnify Project" . - . - "false"^^ . - "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . - . - "http://www.boldsystems.org/"^^ . - . - . - "6b1"^^ . - "^\\w+$"^^ . - . - . - "EDAM Topic" . - . - . - . - . - "RoleInTime"^^ . - "andreadega/systems-biology-compiler"^^ . - . - . - "6VDC956"^^ . - . - . - . - . - "http://bioportal.bioontology.org/ontologies/$1"^^ . - . - . - "^NX_\\w+$"^^ . - "https://cellbank.nibiohn.go.jp"^^ . - "Miguel A. Fortuna" . - . - . - . - "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . - "http://cdb.ics.uci.edu/"^^ . - . - . - . - . - "false"^^ . - "BAC045"^^ . - . - . + "https://github.com/DrugTargetOntology/DTO"^^ . + . + . + "48439"^^ . + . + . + "^\\d+$"^^ . + "https://www.cropontology.org/rdf/CO_335:$1"^^ . + . + . + . + . + "Clytia hemisphaerica Development and Anatomy Ontology" . + "^\\d{7}$"^^ . + "The LifeWatch ERIC repository of semantic resources for the ecological domain." . + "false"^^ . + . + . + . + . + . + "ENST00000407236"^^ . + . + . + . + . + . + "http://viaf.org/viaf/$1"^^ . + "DDB0016567"^^ . + . + . + "^\\d{7}$"^^ . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + "0005250"^^ . + . + . + . + "false"^^ . + . + . + "200282"^^ . + . + . + . + . + "EasyChair Call for Paper" . + . + . + "Alan Wood's Pesticides" . + . + . + "Spider Ontology" . + . + . + . + "http://www.receptors.org/nucleardb/proteins/$1"^^ . + "https://www.uniprot.org/locations/"^^ . + . + "BioGRID Interactions" . + . + . + . + . + "3771877"^^ . + "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . + . + "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . + . + . + . + . + . + "http://lincs.hms.harvard.edu/db/proteins/"^^ . + "true"^^ . + . + . + . + . + . + . + . + "Drug Central" . + . + "true"^^ . + . + . + . + "Identifier for a species on the noaa fisheries website"^^ . + "false"^^ . + "http://www.w3.org/1999/02/22-rdf-syntax-ns"^^ . + . + "1981638"^^ . + "http://pathway.yeastgenome.org/"^^ . + . + . + "http://purl.org/spar/cito/$1"^^ . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + . + . + . + "Minimal Anatomical Terminology" . . - "EcoCyc" . - "false"^^ . - . - . - "https://github.com/OpenLHS/PDRO"^^ . - "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . - . - . - . - . - . - . - "KEGG Orthology" . - "https://ifaa.unifr.ch/"^^ . - . - "Electrocardiogram Ontology" . - "https://polbase.neb.com/polymerases/$1#sequences"^^ . - . - . - "http://purl.obolibrary.org/obo/CMO_$1"^^ . - "https://covid19.sfb.uit.no"^^ . + "https://www.ideal-db.org"^^ . + . + "false"^^ . + "ESi007-A"^^ . + "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . + . + "^\\d{6}$"^^ . + . + "Person"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . + . + "^[a-z][a-z]/[0-9]+$"^^ . + "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . + . + . + . + . + . + . + . + . + "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "http://environmentontology.github.io/gaz/"^^ . + . + . + . + . + "NIF Cell" . + . + "Ontology of Precision Medicine and Investigation" . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + "RiceNetDB Gene" . + . + . + . + . + . + . + . + . + . diff --git a/exports/rdf/bioregistry.ttl b/exports/rdf/bioregistry.ttl index 9bbdcd42b..99403e2e7 100644 --- a/exports/rdf/bioregistry.ttl +++ b/exports/rdf/bioregistry.ttl @@ -11,7 +11,6 @@ @prefix cheminf: . @prefix cropoct: . @prefix dc: . -@prefix dcterms: . @prefix ecoportal: . @prefix edam.data: . @prefix fairsharing: . @@ -20,7 +19,8 @@ @prefix miriam: . @prefix n2t: . @prefix ncbi.resource: . -@prefix ns1: . +@prefix ns1: . +@prefix ns2: . @prefix obofoundry: . @prefix ols: . @prefix ontobee: . @@ -34,25 +34,25 @@ bioregistry.schema:0000001 a rdfs:Class ; rdfs:label "Resource" ; - dcterms:description "A type for entries in the Bioregistry's registry." . + ns1:description "A type for entries in the Bioregistry's registry." . bioregistry.schema:0000002 a rdfs:Class ; rdfs:label "Registry" ; - dcterms:description "A type for entries in the Bioregistry's metaregistry." . + ns1:description "A type for entries in the Bioregistry's metaregistry." . bioregistry.schema:0000003 a rdfs:Class ; rdfs:label "Collection" ; - dcterms:description "A type for entries in the Bioregistry's collections" . + ns1:description "A type for entries in the Bioregistry's collections" . bioregistry.schema:0000020 a rdfs:Class ; rdfs:label "Person" ; - dcterms:description "A person" . + ns1:description "A person" . bioregistry.collection:0000001 a bioregistry.schema:0000003 ; rdfs:label "Resources mentioned in \"Sharing biological data: why, when, and how\"" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." ; - dcterms:hasPart bioregistry:biostudies, + ns1:hasPart bioregistry:biostudies, bioregistry:bmrb, bioregistry:cellimage, bioregistry:ega.dataset, @@ -75,7 +75,7 @@ bioregistry.collection:0000002 a bioregistry.schema:0000003 ; rdfs:label "Semantic Web Context" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." ; - dcterms:hasPart bioregistry:ac, + ns1:hasPart bioregistry:ac, bioregistry:dc, bioregistry:dcat, bioregistry:dcterms, @@ -97,7 +97,7 @@ bioregistry.collection:0000003 a bioregistry.schema:0000003 ; rdfs:label "ChEBI Data Sources" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." ; - dcterms:hasPart bioregistry:chebi, + ns1:hasPart bioregistry:chebi, bioregistry:chemidplus, bioregistry:come, bioregistry:drugbank, @@ -126,7 +126,7 @@ bioregistry.collection:0000004 a bioregistry.schema:0000003 ; rdfs:label "International Classifications of Diseases" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." ; - dcterms:hasPart bioregistry:icd10, + ns1:hasPart bioregistry:icd10, bioregistry:icd10cm, bioregistry:icd10pcs, bioregistry:icd11, @@ -138,7 +138,7 @@ bioregistry.collection:0000005 a bioregistry.schema:0000003 ; rdfs:label "Allen Institute Ontologies" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "This collection contains various brain atlases from the Allen Institute." ; - dcterms:hasPart bioregistry:dhba, + ns1:hasPart bioregistry:dhba, bioregistry:dmba, bioregistry:hba, bioregistry:mba, @@ -148,7 +148,7 @@ bioregistry.collection:0000006 a bioregistry.schema:0000003 ; rdfs:label "SPAR Ontologies" ; dc:creator orcid:0000-0003-4423-4370 ; dc:description "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." ; - dcterms:hasPart bioregistry:bido, + ns1:hasPart bioregistry:bido, bioregistry:biro, bioregistry:c4o, bioregistry:cito, @@ -172,85 +172,85 @@ bioregistry.metaresource:prefixcc a bioregistry.schema:0000002 ; bioregistry.schema:0000005 a rdf:Property ; rdfs:label "has example" ; - dcterms:description "An identifier for a resource or metaresource." ; + ns1:description "An identifier for a resource or metaresource." ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range xsd:string . bioregistry.schema:0000006 a rdf:Property ; rdfs:label "has provider formatter" ; - dcterms:description "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." ; + ns1:description "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range xsd:string . bioregistry.schema:0000007 a rdf:Property ; rdfs:label "has resolver formatter" ; - dcterms:description "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." ; + ns1:description "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." ; rdfs:domain bioregistry.schema:0000002 ; rdfs:range xsd:string . bioregistry.schema:0000008 a rdf:Property ; rdfs:label "has pattern" ; - dcterms:description "The pattern for identifiers in the given resource" ; + ns1:description "The pattern for identifiers in the given resource" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range xsd:string . bioregistry.schema:0000010 a rdf:Property ; rdfs:label "has download URL" ; - dcterms:description "A download link for the given resource" ; + ns1:description "A download link for the given resource" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range xsd:string . bioregistry.schema:0000011 a rdf:Property ; rdfs:label "provides for" ; - dcterms:description "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." ; + ns1:description "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000001 . bioregistry.schema:0000012 a rdf:Property ; rdfs:label "is deprecated" ; - dcterms:description "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." ; + ns1:description "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range xsd:boolean . bioregistry.schema:0000016 a rdf:Property ; rdfs:label "has canonical" ; - dcterms:description "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" ; + ns1:description "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000001 . bioregistry.schema:0000017 a rdf:Property ; rdfs:label "depends on" ; - dcterms:description "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" ; + ns1:description "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000001 . bioregistry.schema:0000018 a rdf:Property ; rdfs:label "appears in" ; - dcterms:description "Terms from the source appear in the target resource" ; + ns1:description "Terms from the source appear in the target resource" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000001 . bioregistry.schema:0000019 a rdf:Property ; rdfs:label "has responsible" ; - dcterms:description "The responsible person for a resource" ; + ns1:description "The responsible person for a resource" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000020 . bioregistry.schema:0000021 a rdf:Property ; rdfs:label "has reviewer" ; - dcterms:description "The reviewer of a prefix" ; + ns1:description "The reviewer of a prefix" ; rdfs:domain bioregistry.schema:0000001 ; rdfs:range bioregistry.schema:0000020 . bioregistry.schema:0000022 a rdf:Property ; rdfs:label "has responsible" ; - dcterms:description "The main contact person for a registry" ; + ns1:description "The main contact person for a registry" ; rdfs:domain bioregistry.schema:0000002 ; rdfs:range bioregistry.schema:0000020 . orcid:0000-0001-9439-5346 rdfs:label "Benjamin Gyori", "Benjamin M. Gyori" ; - dcterms:contributor bioregistry:bko, + ns1:contributor bioregistry:bko, bioregistry:casspc, bioregistry:cordis.project, bioregistry:nihreporter.project, @@ -260,21 +260,21 @@ orcid:0000-0001-9439-5346 rdfs:label "Benjamin Gyori", bioregistry:zenodo.record . orcid:0000-0002-3012-7446 rdfs:label "Daniel Himmelstein" ; - dcterms:contributor bioregistry:openalex . + ns1:contributor bioregistry:openalex . orcid:0000-0002-7356-1779 rdfs:label "Nico Matentzoglu" ; - dcterms:contributor bioregistry:pav . + ns1:contributor bioregistry:pav . orcid:0000-0002-8719-7760 rdfs:label "Sierra Moxon" ; - dcterms:contributor bioregistry:agrkb, + ns1:contributor bioregistry:agrkb, bioregistry:cpt, bioregistry:ncats.bioplanet . bioregistry:3dmet a bioregistry.schema:0000001 ; rdfs:label "3D Metabolites" ; dc:description "3DMET is a database collecting three-dimensional structures of natural metabolites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2635, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2635, biocontext:3DMET, n2t:3dmet, fairsharing:FAIRsharing.5ab0n7, @@ -290,8 +290,8 @@ bioregistry:3dmet a bioregistry.schema:0000001 ; bioregistry:4dn.biosource a bioregistry.schema:0000001 ; rdfs:label "4D Nucleome Data Portal Biosource" ; dc:description "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:4DN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:4DN, fairsharing:FAIRsharing.CugtbQ, prefixcommons:4dn, miriam:4dn ; @@ -304,8 +304,8 @@ bioregistry:4dn.biosource a bioregistry.schema:0000001 ; bioregistry:aao a bioregistry.schema:0000001 ; rdfs:label "Amphibian gross anatomy" ; dc:description "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:AAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:aao, biocontext:AAO, fairsharing:FAIRsharing.mxx5rp, prefixcommons:aao ; @@ -317,8 +317,8 @@ bioregistry:aao a bioregistry.schema:0000001 ; bioregistry:abcd a bioregistry.schema:0000001 ; rdfs:label "AntiBodies Chemically Defined database" ; dc:description "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ABCD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ABCD, fairsharing:FAIRsharing.Z8OKi5, uniprot.resource:ABCD ; foaf:homepage "https://web.expasy.org/abcd/"^^xsd:string ; @@ -329,8 +329,8 @@ bioregistry:abcd a bioregistry.schema:0000001 ; bioregistry:abm a bioregistry.schema:0000001 ; rdfs:label "Applied Biological Materials cell line products" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ABM ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ABM ; foaf:homepage "https://www.abmgood.com/Cell-Biology.html"^^xsd:string ; bioregistry.schema:0000005 "T0599"^^xsd:string ; bioregistry.schema:0000006 "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^xsd:string ; @@ -339,8 +339,8 @@ bioregistry:abm a bioregistry.schema:0000001 ; bioregistry:abs a bioregistry.schema:0000001 ; rdfs:label "Annotated Regulatory Binding Sites" ; dc:description "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2741, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2741, biocontext:ABS, n2t:abs, fairsharing:FAIRsharing.7mnebr, @@ -355,8 +355,8 @@ bioregistry:abs a bioregistry.schema:0000001 ; bioregistry:aceview.worm a bioregistry.schema:0000001 ; rdfs:label "Aceview Worm" ; dc:description "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ACEVIEW.WORM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ACEVIEW.WORM, n2t:aceview.worm, prefixcommons:aceview.worm, miriam:aceview.worm ; @@ -369,8 +369,8 @@ bioregistry:aceview.worm a bioregistry.schema:0000001 ; bioregistry:addexbio a bioregistry.schema:0000001 ; rdfs:label "AddexBio cell line products" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:AddexBio ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:AddexBio ; foaf:homepage "https://www.addexbio.com/productshow?id=4"^^xsd:string ; bioregistry.schema:0000005 "C0020004/4992"^^xsd:string ; bioregistry.schema:0000006 "https://www.addexbio.com/productdetail?pid=$1"^^xsd:string ; @@ -379,8 +379,8 @@ bioregistry:addexbio a bioregistry.schema:0000001 ; bioregistry:addgene a bioregistry.schema:0000001 ; rdfs:label "Addgene Plasmid Repository" ; dc:description "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:addgene, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:addgene, fairsharing:FAIRsharing.8hcczk, prefixcommons:addgene, miriam:addgene ; @@ -393,9 +393,9 @@ bioregistry:addgene a bioregistry.schema:0000001 ; bioregistry:adw a bioregistry.schema:0000001 ; rdfs:label "Animal natural history and life history" ; dc:description "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ADW, - obofoundry:ADW, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ADW, + obofoundry:adw, bioportal:ADW, biocontext:ADW, n2t:adw, @@ -411,9 +411,9 @@ bioregistry:adw a bioregistry.schema:0000001 ; bioregistry:aero a bioregistry.schema:0000001 ; rdfs:label "Adverse Event Reporting Ontology" ; dc:description "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AERO, - obofoundry:AERO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AERO, + obofoundry:aero, bioportal:AERO, biocontext:AERO, fairsharing:FAIRsharing.rycy2x ; @@ -427,8 +427,8 @@ bioregistry:aero a bioregistry.schema:0000001 ; bioregistry:affy.probeset a bioregistry.schema:0000001 ; rdfs:label "Affymetrix Probeset" ; dc:description "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AFFY.PROBESET, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AFFY.PROBESET, n2t:affy.probeset, miriam:affy.probeset ; foaf:homepage "http://www.affymetrix.com/"^^xsd:string ; @@ -440,8 +440,8 @@ bioregistry:affy.probeset a bioregistry.schema:0000001 ; bioregistry:afo a bioregistry.schema:0000001 ; rdfs:label "Allotrope Merged Ontology Suite" ; dc:description "Allotrope Merged Ontology Suite"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AFO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AFO, bioportal:AFO, fairsharing:FAIRsharing.595710, ols:afo ; @@ -451,8 +451,8 @@ bioregistry:afo a bioregistry.schema:0000001 ; bioregistry:aftol.taxonomy a bioregistry.schema:0000001 ; rdfs:label "Assembling the Fungal Tree of Life - Taxonomy" ; dc:description "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AFTOL.TAXONOMY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AFTOL.TAXONOMY, n2t:aftol.taxonomy, miriam:aftol.taxonomy ; foaf:homepage "https://aftol.umn.edu"^^xsd:string ; @@ -464,8 +464,8 @@ bioregistry:aftol.taxonomy a bioregistry.schema:0000001 ; bioregistry:agricola a bioregistry.schema:0000001 ; rdfs:label "Agricultural Online Access" ; dc:description "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AGRICOLA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AGRICOLA, go.resource:AGRICOLA_ID, n2t:agricola, miriam:agricola ; @@ -478,8 +478,8 @@ bioregistry:agricola a bioregistry.schema:0000001 ; bioregistry:agrovoc a bioregistry.schema:0000001 ; rdfs:label "Agronomy Vocabulary" ; dc:description "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:AGROVOC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:AGROVOC, ecoportal:AGROVOC, fairsharing:FAIRsharing.anpj91 ; foaf:homepage "https://data.apps.fao.org/catalog/organization/agrovoc"^^xsd:string ; @@ -491,8 +491,8 @@ bioregistry:agrovoc a bioregistry.schema:0000001 ; bioregistry:allergome a bioregistry.schema:0000001 ; rdfs:label "Allergome" ; dc:description "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ALLERGOME, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ALLERGOME, n2t:allergome, fairsharing:FAIRsharing.w6cxgb, prefixcommons:allergome, @@ -507,8 +507,8 @@ bioregistry:allergome a bioregistry.schema:0000001 ; bioregistry:amoebadb a bioregistry.schema:0000001 ; rdfs:label "AmoebaDB" ; dc:description "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AMOEBADB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AMOEBADB, n2t:amoebadb, fairsharing:FAIRsharing.swbypy, prefixcommons:amoebadb, @@ -522,8 +522,8 @@ bioregistry:amoebadb a bioregistry.schema:0000001 ; bioregistry:antibodyregistry a bioregistry.schema:0000001 ; rdfs:label "Antibody Registry" ; dc:description "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ANTIBODYREGISTRY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ANTIBODYREGISTRY, n2t:antibodyregistry, miriam:antibodyregistry ; foaf:homepage "http://antibodyregistry.org/"^^xsd:string ; @@ -535,8 +535,8 @@ bioregistry:antibodyregistry a bioregistry.schema:0000001 ; bioregistry:antweb a bioregistry.schema:0000001 ; rdfs:label "AntWeb ID" ; dc:description "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ANTWEB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ANTWEB, n2t:antweb, ncbi.resource:AntWeb, fairsharing:FAIRsharing.yk38tw, @@ -552,8 +552,8 @@ bioregistry:antweb a bioregistry.schema:0000001 ; bioregistry:aop a bioregistry.schema:0000001 ; rdfs:label "AOPWiki" ; dc:description "International repository of Adverse Outcome Pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AOP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AOP, n2t:aop, miriam:aop ; foaf:homepage "https://aopwiki.org/"^^xsd:string ; @@ -565,8 +565,8 @@ bioregistry:aop a bioregistry.schema:0000001 ; bioregistry:aop.events a bioregistry.schema:0000001 ; rdfs:label "AOPWiki (Key Event)" ; dc:description "International repository of Adverse Outcome Pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AOP.EVENTS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AOP.EVENTS, n2t:aop.events, miriam:aop.events ; foaf:homepage "https://aopwiki.org/"^^xsd:string ; @@ -578,8 +578,8 @@ bioregistry:aop.events a bioregistry.schema:0000001 ; bioregistry:aop.relationships a bioregistry.schema:0000001 ; rdfs:label "AOPWiki (Key Event Relationship)" ; dc:description "International repository of Adverse Outcome Pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AOP.RELATIONSHIPS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AOP.RELATIONSHIPS, n2t:aop.relationships, miriam:aop.relationships ; foaf:homepage "https://aopwiki.org/"^^xsd:string ; @@ -591,8 +591,8 @@ bioregistry:aop.relationships a bioregistry.schema:0000001 ; bioregistry:aop.stressor a bioregistry.schema:0000001 ; rdfs:label "AOPWiki (Stressor)" ; dc:description "International repository of Adverse Outcome Pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AOP.STRESSOR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AOP.STRESSOR, n2t:aop.stressor, miriam:aop.stressor ; foaf:homepage "https://aopwiki.org/"^^xsd:string ; @@ -604,8 +604,8 @@ bioregistry:aop.stressor a bioregistry.schema:0000001 ; bioregistry:apaonto a bioregistry.schema:0000001 ; rdfs:label "Psychology Ontology" ; dc:description "Ontology from the APA"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:APAONTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:APAONTO, bioportal:APAONTO, fairsharing:FAIRsharing.gkw1w8 ; foaf:homepage "https://bioportal.bioontology.org/ontologies/APAONTO"^^xsd:string ; @@ -616,8 +616,8 @@ bioregistry:apaonto a bioregistry.schema:0000001 ; bioregistry:apd a bioregistry.schema:0000001 ; rdfs:label "Antimicrobial Peptide Database" ; dc:description "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:APD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:APD, n2t:apd, fairsharing:FAIRsharing.ctwd7b, prefixcommons:apd, @@ -631,8 +631,8 @@ bioregistry:apd a bioregistry.schema:0000001 ; bioregistry:aphidbase.transcript a bioregistry.schema:0000001 ; rdfs:label "AphidBase Transcript" ; dc:description "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:APHIDBASE.TRANSCRIPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:APHIDBASE.TRANSCRIPT, n2t:aphidbase.transcript, miriam:aphidbase.transcript ; foaf:homepage "http://www.aphidbase.com/aphidbase"^^xsd:string ; @@ -644,8 +644,8 @@ bioregistry:aphidbase.transcript a bioregistry.schema:0000001 ; bioregistry:apid.interactions a bioregistry.schema:0000001 ; rdfs:label "APID Interactomes" ; dc:description "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:APID.INTERACTIONS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:APID.INTERACTIONS, n2t:apid.interactions, miriam:apid.interactions ; foaf:homepage "http://cicblade.dep.usal.es:8080/APID/"^^xsd:string ; @@ -658,9 +658,9 @@ bioregistry:apid.interactions a bioregistry.schema:0000001 ; bioregistry:apo a bioregistry.schema:0000001 ; rdfs:label "Ascomycete phenotype ontology" ; dc:description "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:APO, - obofoundry:APO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:APO, + obofoundry:apo, ontobee:APO, bioportal:APO, biocontext:YPO, @@ -676,8 +676,8 @@ bioregistry:apo a bioregistry.schema:0000001 ; bioregistry:arachnoserver a bioregistry.schema:0000001 ; rdfs:label "ArachnoServer" ; dc:description "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2578, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2578, biocontext:ARACHNOSERVER, n2t:arachnoserver, fairsharing:FAIRsharing.c54ywe, @@ -693,8 +693,8 @@ bioregistry:arachnoserver a bioregistry.schema:0000001 ; bioregistry:araport a bioregistry.schema:0000001 ; rdfs:label "Arabidopsis Information Portal" ; dc:description "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ncbi.resource:Araport, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ncbi.resource:Araport, uniprot.resource:Araport ; foaf:homepage "https://www.araport.org/"^^xsd:string ; bioregistry.schema:0000005 "AT1G01010"^^xsd:string ; @@ -704,8 +704,8 @@ bioregistry:araport a bioregistry.schema:0000001 ; bioregistry:ardb a bioregistry.schema:0000001 ; rdfs:label "Antibiotic Resistance Genes Database" ; dc:description "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARDB, n2t:ardb, miriam:ardb ; foaf:homepage "http://ardb.cbcb.umd.edu/"^^xsd:string ; @@ -717,8 +717,8 @@ bioregistry:ardb a bioregistry.schema:0000001 ; bioregistry:ark a bioregistry.schema:0000001 ; rdfs:label "Archival Resource Key" ; dc:description "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARK, n2t:ark, miriam:ark ; foaf:homepage "http://n2t.net/"^^xsd:string ; @@ -730,8 +730,8 @@ bioregistry:ark a bioregistry.schema:0000001 ; bioregistry:arrayexpress a bioregistry.schema:0000001 ; rdfs:label "ArrayExpress" ; dc:description "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARRAYEXPRESS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARRAYEXPRESS, cellosaurus.resource:ArrayExpress, n2t:arrayexpress, fairsharing:FAIRsharing.6k0kwd, @@ -746,8 +746,8 @@ bioregistry:arrayexpress a bioregistry.schema:0000001 ; bioregistry:arrayexpress.platform a bioregistry.schema:0000001 ; rdfs:label "ArrayExpress Platform" ; dc:description "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARRAYEXPRESS.PLATFORM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARRAYEXPRESS.PLATFORM, n2t:arrayexpress.platform, miriam:arrayexpress.platform ; foaf:homepage "https://www.ebi.ac.uk/arrayexpress/"^^xsd:string ; @@ -759,8 +759,8 @@ bioregistry:arrayexpress.platform a bioregistry.schema:0000001 ; bioregistry:arraymap a bioregistry.schema:0000001 ; rdfs:label "ArrayMap" ; dc:description "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARRAYMAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARRAYMAP, n2t:arraymap, fairsharing:FAIRsharing.1fbc5y, miriam:arraymap ; @@ -773,8 +773,8 @@ bioregistry:arraymap a bioregistry.schema:0000001 ; bioregistry:arxiv a bioregistry.schema:0000001 ; rdfs:label "arXiv" ; dc:description "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ARXIV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ARXIV, n2t:arxiv, prefixcommons:arxiv, miriam:arxiv ; @@ -787,8 +787,8 @@ bioregistry:arxiv a bioregistry.schema:0000001 ; bioregistry:asap a bioregistry.schema:0000001 ; rdfs:label "A Systematic Annotation Package for Community Analysis of Genomes" ; dc:description "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ASAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ASAP, go.resource:ASAP, n2t:asap, ncbi.resource:ASAP, @@ -804,8 +804,8 @@ bioregistry:asap a bioregistry.schema:0000001 ; bioregistry:ascl a bioregistry.schema:0000001 ; rdfs:label "Astrophysics Source Code Library" ; dc:description "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ASCL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ASCL, n2t:ascl, fairsharing:FAIRsharing.wb0txg, miriam:ascl ; @@ -818,8 +818,8 @@ bioregistry:ascl a bioregistry.schema:0000001 ; bioregistry:asin a bioregistry.schema:0000001 ; rdfs:label "Amazon Standard Identification Number" ; dc:description "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ASIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ASIN, n2t:asin, miriam:asin ; foaf:homepage "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182"^^xsd:string ; @@ -831,8 +831,8 @@ bioregistry:asin a bioregistry.schema:0000001 ; bioregistry:aspgd.locus a bioregistry.schema:0000001 ; rdfs:label "Aspergillus Genome Database" ; dc:description "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ASPGD.LOCUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ASPGD.LOCUS, go.resource:AspGD_LOCUS, n2t:aspgd.locus, miriam:aspgd.locus ; @@ -845,8 +845,8 @@ bioregistry:aspgd.locus a bioregistry.schema:0000001 ; bioregistry:aspgd.protein a bioregistry.schema:0000001 ; rdfs:label "AspGD Protein" ; dc:description "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ASPGD.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ASPGD.PROTEIN, n2t:aspgd.protein, miriam:aspgd.protein ; foaf:homepage "http://www.aspgd.org/"^^xsd:string ; @@ -858,8 +858,8 @@ bioregistry:aspgd.protein a bioregistry.schema:0000001 ; bioregistry:atc a bioregistry.schema:0000001 ; rdfs:label "Anatomical Therapeutic Chemical Classification System" ; dc:description "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ATC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ATC, edam.data:3103, bioportal:ATC, biocontext:ATC, @@ -877,8 +877,8 @@ bioregistry:atc a bioregistry.schema:0000001 ; bioregistry:atcc a bioregistry.schema:0000001 ; rdfs:label "American Type Culture Collection" ; dc:description "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ATCC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ATCC, cellosaurus.resource:ATCC, n2t:atcc, ncbi.resource:ATCC, @@ -893,8 +893,8 @@ bioregistry:atcc a bioregistry.schema:0000001 ; bioregistry:atcvet a bioregistry.schema:0000001 ; rdfs:label "Anatomical Therapeutic Chemical Vetinary" ; dc:description "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ATCVET, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ATCVET, n2t:atcvet, miriam:atcvet ; foaf:homepage "http://www.whocc.no/atcvet/atcvet_index/"^^xsd:string ; @@ -906,8 +906,8 @@ bioregistry:atcvet a bioregistry.schema:0000001 ; bioregistry:atfdb.family a bioregistry.schema:0000001 ; rdfs:label "Animal TFDB Family" ; dc:description "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ATFDB.FAMILY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ATFDB.FAMILY, n2t:atfdb.family, miriam:atfdb.family ; foaf:homepage "http://www.bioguo.org/AnimalTFDB/family_index.php"^^xsd:string ; @@ -919,9 +919,9 @@ bioregistry:atfdb.family a bioregistry.schema:0000001 ; bioregistry:ato a bioregistry.schema:0000001 ; rdfs:label "Amphibian taxonomy" ; dc:description "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ATO, - obofoundry:ATO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ATO, + obofoundry:ato, bioportal:ATO, biocontext:ATO, fairsharing:FAIRsharing.ayjdsm ; @@ -935,8 +935,8 @@ bioregistry:ato a bioregistry.schema:0000001 ; bioregistry:atol a bioregistry.schema:0000001 ; rdfs:label "Animal Trait Ontology for Livestock" ; dc:description "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ATOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ATOL, agroportal:ATOL, bioportal:ATOL, fairsharing:FAIRsharing.wsfk5z, @@ -949,8 +949,8 @@ bioregistry:atol a bioregistry.schema:0000001 ; bioregistry:autdb a bioregistry.schema:0000001 ; rdfs:label "AutDB" ; dc:description "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:AUTDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:AUTDB, n2t:autdb, miriam:autdb ; foaf:homepage "http://autism.mindspec.org/autdb/"^^xsd:string ; @@ -962,8 +962,8 @@ bioregistry:autdb a bioregistry.schema:0000001 ; bioregistry:bacdive a bioregistry.schema:0000001 ; rdfs:label "Bacterial Diversity Metadatabase" ; dc:description "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:bacdive, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:bacdive, fairsharing:FAIRsharing.aSszvY, miriam:bacdive ; foaf:homepage "https://bacdive.dsmz.de/"^^xsd:string ; @@ -975,8 +975,8 @@ bioregistry:bacdive a bioregistry.schema:0000001 ; bioregistry:bacmap.biog a bioregistry.schema:0000001 ; rdfs:label "BacMap Biography" ; dc:description "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BACMAP.BIOG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BACMAP.BIOG, n2t:bacmap.biog, miriam:bacmap.biog ; foaf:homepage "http://bacmap.wishartlab.com/"^^xsd:string ; @@ -988,8 +988,8 @@ bioregistry:bacmap.biog a bioregistry.schema:0000001 ; bioregistry:bacmap.map a bioregistry.schema:0000001 ; rdfs:label "BacMap Map" ; dc:description "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BACMAP.MAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BACMAP.MAP, n2t:bacmap.map, miriam:bacmap.map ; foaf:homepage "http://bacmap.wishartlab.com/"^^xsd:string ; @@ -1001,8 +1001,8 @@ bioregistry:bacmap.map a bioregistry.schema:0000001 ; bioregistry:bao a bioregistry.schema:0000001 ; rdfs:label "BioAssay Ontology" ; dc:description "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BAO, ontobee:BAO, bioportal:BAO, biocontext:BAO, @@ -1019,8 +1019,8 @@ bioregistry:bao a bioregistry.schema:0000001 ; bioregistry:bbkg a bioregistry.schema:0000001 ; rdfs:label "Blue Brain Project Knowledge Graph" ; dc:description "Blue Brain Project's published data as knowledge graphs and Web Studios."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:bbkg ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:bbkg ; foaf:homepage "https://portal.bluebrain.epfl.ch"^^xsd:string ; bioregistry.schema:0000005 "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^xsd:string ; bioregistry.schema:0000006 "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^xsd:string ; @@ -1030,8 +1030,8 @@ bioregistry:bbkg a bioregistry.schema:0000001 ; bioregistry:bbtp a bioregistry.schema:0000001 ; rdfs:label "Blue Brain Project Topological sampling Knowledge Graph" ; dc:description "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:bbtp ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:bbtp ; foaf:homepage "https://portal.bluebrain.epfl.ch"^^xsd:string ; bioregistry.schema:0000005 "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^xsd:string ; bioregistry.schema:0000006 "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^xsd:string ; @@ -1041,9 +1041,9 @@ bioregistry:bbtp a bioregistry.schema:0000001 ; bioregistry:bcgo a bioregistry.schema:0000001 ; rdfs:label "Beta Cell Genomics Ontology" ; dc:description "An application ontology built for beta cell genomics studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BCGO, - obofoundry:BCGO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BCGO, + obofoundry:bcgo, ontobee:BCGO, bioportal:BCGO, biocontext:BCGO, @@ -1058,8 +1058,8 @@ bioregistry:bcgo a bioregistry.schema:0000001 ; bioregistry:bcio a bioregistry.schema:0000001 ; rdfs:label "The Behaviour Change Intervention Ontology" ; dc:description "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BCI-O, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BCI-O, bioportal:BCI-O, ols:bcio ; foaf:homepage "https://www.humanbehaviourchange.org/"^^xsd:string ; @@ -1070,8 +1070,8 @@ bioregistry:bcio a bioregistry.schema:0000001 ; bioregistry:bcrj a bioregistry.schema:0000001 ; rdfs:label "Banco de Celulas do Rio de Janeiro" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:BCRJ ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:BCRJ ; foaf:homepage "http://bcrj.org.br/celula/bcrj"^^xsd:string ; bioregistry.schema:0000005 "0278"^^xsd:string ; bioregistry.schema:0000006 "http://bcrj.org.br/celula/$1"^^xsd:string ; @@ -1081,8 +1081,8 @@ bioregistry:bcrj a bioregistry.schema:0000001 ; bioregistry:bdgp.est a bioregistry.schema:0000001 ; rdfs:label "Berkeley Drosophila Genome Project EST database" ; dc:description "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BDGP.EST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BDGP.EST, n2t:bdgp.est, ncbi.resource:BDGP_EST, miriam:bdgp.est ; @@ -1096,8 +1096,8 @@ bioregistry:bdgp.est a bioregistry.schema:0000001 ; bioregistry:bdgp.insertion a bioregistry.schema:0000001 ; rdfs:label "BDGP insertion DB" ; dc:description "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BDGP.INSERTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BDGP.INSERTION, n2t:bdgp.insertion, miriam:bdgp.insertion ; foaf:homepage "http://flypush.imgen.bcm.tmc.edu/pscreen/"^^xsd:string ; @@ -1109,8 +1109,8 @@ bioregistry:bdgp.insertion a bioregistry.schema:0000001 ; bioregistry:bdsc a bioregistry.schema:0000001 ; rdfs:label "Bloomington Drosophila Stock Center" ; dc:description "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:bdsc, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:bdsc, miriam:bdsc ; foaf:homepage "https://bdsc.indiana.edu/about/mission.html"^^xsd:string ; bioregistry.schema:0000005 "33607"^^xsd:string ; @@ -1121,8 +1121,8 @@ bioregistry:bdsc a bioregistry.schema:0000001 ; bioregistry:beetlebase a bioregistry.schema:0000001 ; rdfs:label "Tribolium Genome Database -- Insertion" ; dc:description "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BEETLEBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BEETLEBASE, n2t:beetlebase, ncbi.resource:BEETLEBASE, fairsharing:FAIRsharing.h5f091, @@ -1137,8 +1137,8 @@ bioregistry:beetlebase a bioregistry.schema:0000001 ; bioregistry:begdb a bioregistry.schema:0000001 ; rdfs:label "Benchmark Energy & Geometry Database" ; dc:description "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BEGDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BEGDB, n2t:begdb, fairsharing:FAIRsharing.nbe4fq, miriam:begdb ; @@ -1151,8 +1151,8 @@ bioregistry:begdb a bioregistry.schema:0000001 ; bioregistry:bgee.family a bioregistry.schema:0000001 ; rdfs:label "Bgee family" ; dc:description "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BGEE.FAMILY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BGEE.FAMILY, n2t:bgee.family, miriam:bgee.family ; foaf:homepage "http://bgee.unil.ch/bgee/bgee"^^xsd:string ; @@ -1164,8 +1164,8 @@ bioregistry:bgee.family a bioregistry.schema:0000001 ; bioregistry:bgee.gene a bioregistry.schema:0000001 ; rdfs:label "Bgee gene" ; dc:description "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BGEE.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BGEE.GENE, n2t:bgee.gene, miriam:bgee.gene ; foaf:homepage "https://bgee.org/"^^xsd:string ; @@ -1177,8 +1177,8 @@ bioregistry:bgee.gene a bioregistry.schema:0000001 ; bioregistry:bgee.organ a bioregistry.schema:0000001 ; rdfs:label "Bgee organ" ; dc:description "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BGEE.ORGAN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BGEE.ORGAN, n2t:bgee.organ, miriam:bgee.organ ; foaf:homepage "http://bgee.unil.ch/bgee/bgee"^^xsd:string ; @@ -1190,8 +1190,8 @@ bioregistry:bgee.organ a bioregistry.schema:0000001 ; bioregistry:bgee.stage a bioregistry.schema:0000001 ; rdfs:label "Bgee stage" ; dc:description "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BGEE.STAGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BGEE.STAGE, n2t:bgee.stage, miriam:bgee.stage ; foaf:homepage "http://bgee.unil.ch/bgee/bgee"^^xsd:string ; @@ -1203,8 +1203,8 @@ bioregistry:bgee.stage a bioregistry.schema:0000001 ; bioregistry:bigg.compartment a bioregistry.schema:0000001 ; rdfs:label "BiGG Compartment" ; dc:description "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIGG.COMPARTMENT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIGG.COMPARTMENT, n2t:bigg.compartment, miriam:bigg.compartment ; foaf:homepage "http://bigg.ucsd.edu/compartments/"^^xsd:string ; @@ -1216,8 +1216,8 @@ bioregistry:bigg.compartment a bioregistry.schema:0000001 ; bioregistry:bigg.metabolite a bioregistry.schema:0000001 ; rdfs:label "BiGG Metabolite" ; dc:description "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIGG.METABOLITE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIGG.METABOLITE, n2t:bigg.metabolite, miriam:bigg.metabolite ; foaf:homepage "http://bigg.ucsd.edu/universal/metabolites"^^xsd:string ; @@ -1229,8 +1229,8 @@ bioregistry:bigg.metabolite a bioregistry.schema:0000001 ; bioregistry:bigg.model a bioregistry.schema:0000001 ; rdfs:label "BiGG Model" ; dc:description "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIGG.MODEL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIGG.MODEL, n2t:bigg.model, miriam:bigg.model ; foaf:homepage "http://bigg.ucsd.edu/models"^^xsd:string ; @@ -1242,8 +1242,8 @@ bioregistry:bigg.model a bioregistry.schema:0000001 ; bioregistry:bigg.reaction a bioregistry.schema:0000001 ; rdfs:label "BiGG Reaction" ; dc:description "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIGG.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIGG.REACTION, n2t:bigg.reaction, miriam:bigg.reaction ; foaf:homepage "http://bigg.ucsd.edu/universal/reactions"^^xsd:string ; @@ -1255,18 +1255,21 @@ bioregistry:bigg.reaction a bioregistry.schema:0000001 ; bioregistry:bila a bioregistry.schema:0000001 ; rdfs:label "Bilateria anatomy" ; dc:description "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:BILA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:bila, biocontext:BILA, fairsharing:FAIRsharing.eqgjeq ; + foaf:homepage "http://4dx.embl.de/4DXpress"^^xsd:string ; + bioregistry.schema:0000005 "0000000"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/BILA_$1"^^xsd:string ; - bioregistry.schema:0000012 true . + bioregistry.schema:0000012 true ; + bioregistry.schema:0000019 [ rdfs:label "Thorsten Heinrich" ] . bioregistry:bindingdb a bioregistry.schema:0000001 ; rdfs:label "BindingDB" ; dc:description "BindingDB is the first public database of protein-small molecule affinity data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BINDINGDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BINDINGDB, n2t:bindingdb, fairsharing:FAIRsharing.3b36hk, prefixcommons:bindingdb, @@ -1281,8 +1284,8 @@ bioregistry:bindingdb a bioregistry.schema:0000001 ; bioregistry:biocarta.pathway a bioregistry.schema:0000001 ; rdfs:label "BioCarta Pathway" ; dc:description "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOCARTA.PATHWAY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOCARTA.PATHWAY, n2t:biocarta.pathway, miriam:biocarta.pathway ; foaf:homepage "https://www.biocarta.com/"^^xsd:string ; @@ -1294,8 +1297,8 @@ bioregistry:biocarta.pathway a bioregistry.schema:0000001 ; bioregistry:biocatalogue.service a bioregistry.schema:0000001 ; rdfs:label "BioCatalogue Service" ; dc:description "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOCATALOGUE.SERVICE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOCATALOGUE.SERVICE, n2t:biocatalogue.service, miriam:biocatalogue.service ; foaf:homepage "https://www.biocatalogue.org/"^^xsd:string ; @@ -1307,8 +1310,8 @@ bioregistry:biocatalogue.service a bioregistry.schema:0000001 ; bioregistry:biocyc a bioregistry.schema:0000001 ; rdfs:label "BioCyc collection of metabolic pathway databases" ; dc:description "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2104, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2104, biocontext:BIOCYC, go.resource:BioCyc, n2t:biocyc, @@ -1324,8 +1327,8 @@ bioregistry:biocyc a bioregistry.schema:0000001 ; bioregistry:biolink a bioregistry.schema:0000001 ; rdfs:label "Biolink Model" ; dc:description "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BIOLINK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BIOLINK, bioportal:BIOLINK, biolink:biolink, fairsharing:FAIRsharing.ad9d85, @@ -1339,8 +1342,8 @@ bioregistry:biolink a bioregistry.schema:0000001 ; bioregistry:biominder a bioregistry.schema:0000001 ; rdfs:label "Bio-MINDER Tissue Database" ; dc:description "Database of the dielectric properties of biological tissues."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOMINDER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOMINDER, n2t:biominder, miriam:biominder ; foaf:homepage "https://datalab.rwth-aachen.de/MINDER"^^xsd:string ; @@ -1352,8 +1355,8 @@ bioregistry:biominder a bioregistry.schema:0000001 ; bioregistry:biomodels.db a bioregistry.schema:0000001 ; rdfs:label "BioModels Database" ; dc:description "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOMODELS.DB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOMODELS.DB, go.resource:BIOMD, n2t:biomodels.db, miriam:biomodels.db ; @@ -1366,9 +1369,9 @@ bioregistry:biomodels.db a bioregistry.schema:0000001 ; bioregistry:biomodels.kisao a bioregistry.schema:0000001 ; rdfs:label "Kinetic Simulation Algorithm Ontology" ; dc:description "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:KISAO, - obofoundry:KISAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:KISAO, + obofoundry:kisao, ontobee:KISAO, bioportal:KISAO, biocontext:KISAO, @@ -1387,8 +1390,8 @@ bioregistry:biomodels.kisao a bioregistry.schema:0000001 ; bioregistry:biomodels.teddy a bioregistry.schema:0000001 ; rdfs:label "Terminology for Description of Dynamics" ; dc:description "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TEDDY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TEDDY, bioportal:TEDDY, biocontext:BIOMODELS.TEDDY, n2t:biomodels.teddy, @@ -1405,8 +1408,8 @@ bioregistry:biomodels.teddy a bioregistry.schema:0000001 ; bioregistry:biomodels.vocabulary a bioregistry.schema:0000001 ; rdfs:label "SBML RDF Vocabulary" ; dc:description "Vocabulary used in the RDF representation of SBML models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOMODELS.VOCABULARY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOMODELS.VOCABULARY, n2t:biomodels.vocabulary, miriam:biomodels.vocabulary ; foaf:homepage "http://biomodels.net/rdf/vocabulary.rdf"^^xsd:string ; @@ -1418,8 +1421,8 @@ bioregistry:biomodels.vocabulary a bioregistry.schema:0000001 ; bioregistry:bionumbers a bioregistry.schema:0000001 ; rdfs:label "BioNumbers" ; dc:description "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2660, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2660, biocontext:BIONUMBERS, n2t:bionumbers, prefixcommons:bionumbers, @@ -1433,8 +1436,8 @@ bioregistry:bionumbers a bioregistry.schema:0000001 ; bioregistry:bioportal a bioregistry.schema:0000001 ; rdfs:label "BioPortal" ; dc:description "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOPORTAL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOPORTAL, n2t:bioportal, fairsharing:FAIRsharing.4m97ah, prefixcommons:bioportal, @@ -1448,8 +1451,8 @@ bioregistry:bioportal a bioregistry.schema:0000001 ; bioregistry:bioproject a bioregistry.schema:0000001 ; rdfs:label "BioProject" ; dc:description "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOPROJECT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOPROJECT, n2t:bioproject, fairsharing:FAIRsharing.aqhv1y, miriam:bioproject ; @@ -1462,8 +1465,8 @@ bioregistry:bioproject a bioregistry.schema:0000001 ; bioregistry:biorxiv a bioregistry.schema:0000001 ; rdfs:label "bioRxiv" ; dc:description "The bioRxiv is a preprint server for biology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:bioRxiv ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:bioRxiv ; foaf:homepage "https://biorxiv.org"^^xsd:string ; bioregistry.schema:0000005 "2022.07.08.499378"^^xsd:string ; bioregistry.schema:0000006 "https://www.biorxiv.org/content/10.1101/$1"^^xsd:string ; @@ -1473,8 +1476,8 @@ bioregistry:biorxiv a bioregistry.schema:0000001 ; bioregistry:biosample a bioregistry.schema:0000001 ; rdfs:label "BioSample" ; dc:description "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOSAMPLE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOSAMPLE, cellosaurus.resource:BioSamples, n2t:biosample, fairsharing:FAIRsharing.qr6pqk, @@ -1488,8 +1491,8 @@ bioregistry:biosample a bioregistry.schema:0000001 ; bioregistry:biosimulations a bioregistry.schema:0000001 ; rdfs:label "biosimulations" ; dc:description "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:biosimulations ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:biosimulations ; foaf:homepage "https://icahn.mssm.edu/"^^xsd:string ; bioregistry.schema:0000005 "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^xsd:string ; bioregistry.schema:0000006 "https://biosimulations.org/projects/$1"^^xsd:string ; @@ -1499,8 +1502,8 @@ bioregistry:biosimulations a bioregistry.schema:0000001 ; bioregistry:biosimulators a bioregistry.schema:0000001 ; rdfs:label "BioSimulators" ; dc:description "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.pwEima, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.pwEima, miriam:biosimulators ; foaf:homepage "https://biosimulators.org/"^^xsd:string ; bioregistry.schema:0000005 "vcell"^^xsd:string ; @@ -1511,8 +1514,8 @@ bioregistry:biosimulators a bioregistry.schema:0000001 ; bioregistry:biosystems a bioregistry.schema:0000001 ; rdfs:label "BioSystems" ; dc:description "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOSYSTEMS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOSYSTEMS, n2t:biosystems, fairsharing:FAIRsharing.w2eeqr, prefixcommons:biosystems, @@ -1526,8 +1529,8 @@ bioregistry:biosystems a bioregistry.schema:0000001 ; bioregistry:biotools a bioregistry.schema:0000001 ; rdfs:label "BioTools" ; dc:description "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOTOOLS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOTOOLS, n2t:biotools, fairsharing:FAIRsharing.63520c, miriam:biotools ; @@ -1540,8 +1543,8 @@ bioregistry:biotools a bioregistry.schema:0000001 ; bioregistry:birnlex a bioregistry.schema:0000001 ; rdfs:label "Biomedical Informatics Research Network Lexicon" ; dc:description "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BIRNLEX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BIRNLEX, bioportal:BIRNLEX, fairsharing:FAIRsharing.jedbbt ; foaf:homepage "https://bioportal.bioontology.org/ontologies/BIRNLEX"^^xsd:string ; @@ -1553,8 +1556,8 @@ bioregistry:birnlex a bioregistry.schema:0000001 ; bioregistry:bitbucket a bioregistry.schema:0000001 ; rdfs:label "Bitbucket" ; dc:description "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.fc3431, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.fc3431, miriam:bitbucket ; foaf:homepage "https://www.atlassian.com/"^^xsd:string ; bioregistry.schema:0000005 "andreadega/systems-biology-compiler"^^xsd:string ; @@ -1565,8 +1568,8 @@ bioregistry:bitbucket a bioregistry.schema:0000001 ; bioregistry:bitterdb.cpd a bioregistry.schema:0000001 ; rdfs:label "BitterDB Compound" ; dc:description "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BITTERDB.CPD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BITTERDB.CPD, n2t:bitterdb.cpd, miriam:bitterdb.cpd ; foaf:homepage "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^xsd:string ; @@ -1578,8 +1581,8 @@ bioregistry:bitterdb.cpd a bioregistry.schema:0000001 ; bioregistry:bitterdb.rec a bioregistry.schema:0000001 ; rdfs:label "BitterDB Receptor" ; dc:description "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BITTERDB.REC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BITTERDB.REC, n2t:bitterdb.rec, miriam:bitterdb.rec ; foaf:homepage "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^xsd:string ; @@ -1591,8 +1594,8 @@ bioregistry:bitterdb.rec a bioregistry.schema:0000001 ; bioregistry:bold.taxonomy a bioregistry.schema:0000001 ; rdfs:label "Barcode of Life database" ; dc:description "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BOLD.TAXONOMY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BOLD.TAXONOMY, n2t:bold.taxonomy, ncbi.resource:BOLD, miriam:bold.taxonomy ; @@ -1604,8 +1607,8 @@ bioregistry:bold.taxonomy a bioregistry.schema:0000001 ; bioregistry:bootstrep a bioregistry.schema:0000001 ; rdfs:label "Gene Regulation Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:BOOTSTREP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:bootstrep, biocontext:BOOTSTREP ; foaf:homepage "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^xsd:string ; @@ -1615,8 +1618,8 @@ bioregistry:bootstrep a bioregistry.schema:0000001 ; bioregistry:brenda a bioregistry.schema:0000001 ; rdfs:label "BRENDA, The Comprehensive Enzyme Information System" ; dc:description "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BRENDA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BRENDA, go.resource:BRENDA, n2t:brenda, fairsharing:FAIRsharing.etp533, @@ -1632,8 +1635,8 @@ bioregistry:brenda a bioregistry.schema:0000001 ; bioregistry:broad a bioregistry.schema:0000001 ; rdfs:label "Broad Fungal Genome Initiative" ; dc:description "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BROAD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BROAD, n2t:broad, miriam:broad ; foaf:homepage "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^xsd:string ; @@ -1645,9 +1648,9 @@ bioregistry:broad a bioregistry.schema:0000001 ; bioregistry:bto a bioregistry.schema:0000001 ; rdfs:label "BRENDA tissue / enzyme source" ; dc:description "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BTO, - obofoundry:BTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BTO, + obofoundry:bto, ontobee:BTO, bioportal:BTO, biocontext:BTO, @@ -1669,8 +1672,8 @@ bioregistry:bto a bioregistry.schema:0000001 ; bioregistry:bugbase.expt a bioregistry.schema:0000001 ; rdfs:label "BugBase Expt" ; dc:description "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BUGBASE.EXPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BUGBASE.EXPT, n2t:bugbase.expt, miriam:bugbase.expt ; foaf:homepage "http://bugs.sgul.ac.uk/E-BUGS"^^xsd:string ; @@ -1682,8 +1685,8 @@ bioregistry:bugbase.expt a bioregistry.schema:0000001 ; bioregistry:bugbase.protocol a bioregistry.schema:0000001 ; rdfs:label "BugBase Protocol" ; dc:description "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BUGBASE.PROTOCOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BUGBASE.PROTOCOL, n2t:bugbase.protocol, miriam:bugbase.protocol ; foaf:homepage "http://bugs.sgul.ac.uk/E-BUGS"^^xsd:string ; @@ -1695,8 +1698,8 @@ bioregistry:bugbase.protocol a bioregistry.schema:0000001 ; bioregistry:bykdb a bioregistry.schema:0000001 ; rdfs:label "Bacterial Tyrosine Kinase Database" ; dc:description "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BYKDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BYKDB, n2t:bykdb, fairsharing:FAIRsharing.jr30xc, prefixcommons:bykdb, @@ -1711,8 +1714,8 @@ bioregistry:bykdb a bioregistry.schema:0000001 ; bioregistry:cabri a bioregistry.schema:0000001 ; rdfs:label "Common Access to Biological Resources and Information Project" ; dc:description "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2380, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2380, biocontext:CABRI, n2t:cabri, ncbi.resource:CABRI, @@ -1727,8 +1730,8 @@ bioregistry:cabri a bioregistry.schema:0000001 ; bioregistry:cadsr a bioregistry.schema:0000001 ; rdfs:label "Cancer Data Standards Registry and Repository" ; dc:description "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:cadsr, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:cadsr, miriam:cadsr ; foaf:homepage "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^xsd:string ; bioregistry.schema:0000005 "3771992"^^xsd:string ; @@ -1739,8 +1742,8 @@ bioregistry:cadsr a bioregistry.schema:0000001 ; bioregistry:cameo a bioregistry.schema:0000001 ; rdfs:label "Continuous Automated Model Evaluation" ; dc:description "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CAMEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CAMEO, n2t:cameo, fairsharing:FAIRsharing.dq34p2, miriam:cameo ; @@ -1753,8 +1756,8 @@ bioregistry:cameo a bioregistry.schema:0000001 ; bioregistry:caps a bioregistry.schema:0000001 ; rdfs:label "CAPS-DB" ; dc:description "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CAPS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CAPS, n2t:caps, miriam:caps ; foaf:homepage "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home"^^xsd:string ; @@ -1766,8 +1769,8 @@ bioregistry:caps a bioregistry.schema:0000001 ; bioregistry:cas a bioregistry.schema:0000001 ; rdfs:label "CAS Chemical Registry" ; dc:description "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1002, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1002, biocontext:CAS, go.resource:CAS, n2t:cas, @@ -1785,8 +1788,8 @@ bioregistry:cas a bioregistry.schema:0000001 ; bioregistry:cath.domain a bioregistry.schema:0000001 ; rdfs:label "CATH domain" ; dc:description "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1040, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1040, biocontext:CATH.DOMAIN, n2t:cath.domain, miriam:cath.domain ; @@ -1799,8 +1802,8 @@ bioregistry:cath.domain a bioregistry.schema:0000001 ; bioregistry:cazy a bioregistry.schema:0000001 ; rdfs:label "Carbohydrate Active EnZYmes" ; dc:description "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CAZY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CAZY, go.resource:CAZY, n2t:cazy, fairsharing:FAIRsharing.ntyq70, @@ -1816,8 +1819,8 @@ bioregistry:cazy a bioregistry.schema:0000001 ; bioregistry:cbioportal a bioregistry.schema:0000001 ; rdfs:label "The cBioPortal for Cancer Genomics" ; dc:description "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:cbioportal, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:cbioportal, fairsharing:FAIRsharing.6L6MjA, miriam:cbioportal ; foaf:homepage "http://www.cbioportal.org"^^xsd:string ; @@ -1829,8 +1832,8 @@ bioregistry:cbioportal a bioregistry.schema:0000001 ; bioregistry:ccdc a bioregistry.schema:0000001 ; rdfs:label "CCDC Number" ; dc:description "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:ccdc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:ccdc ; foaf:homepage "https://www.ccdc.cam.ac.uk/"^^xsd:string ; bioregistry.schema:0000005 "1829126"^^xsd:string ; bioregistry.schema:0000006 "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^xsd:string ; @@ -1840,8 +1843,8 @@ bioregistry:ccdc a bioregistry.schema:0000001 ; bioregistry:ccds a bioregistry.schema:0000001 ; rdfs:label "Consensus CDS" ; dc:description "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CCDS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CCDS, n2t:ccds, fairsharing:FAIRsharing.46s4nt, prefixcommons:ccds, @@ -1856,8 +1859,8 @@ bioregistry:ccds a bioregistry.schema:0000001 ; bioregistry:ccle a bioregistry.schema:0000001 ; rdfs:label "Cancer Cell Line Encyclopedia Cells" ; dc:description "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CCLE ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CCLE ; foaf:homepage "https://www.cbioportal.org/study/summary?id=ccle_broad_2019"^^xsd:string ; bioregistry.schema:0000005 "BT20_BREAST"^^xsd:string ; bioregistry.schema:0000006 "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^xsd:string ; @@ -1866,8 +1869,8 @@ bioregistry:ccle a bioregistry.schema:0000001 ; bioregistry:cco a bioregistry.schema:0000001 ; rdfs:label "Cell Cycle Ontology" ; dc:description "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CCO, bioportal:CCO, biocontext:CCO, n2t:cco, @@ -1884,10 +1887,10 @@ bioregistry:cco a bioregistry.schema:0000001 ; bioregistry:cdao a bioregistry.schema:0000001 ; rdfs:label "Comparative Data Analysis Ontology" ; dc:description "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CDAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CDAO, agroportal:CDAO, - obofoundry:CDAO, + obofoundry:cdao, ontobee:CDAO, bioportal:CDAO, biocontext:CDAO, @@ -1903,8 +1906,8 @@ bioregistry:cdao a bioregistry.schema:0000001 ; bioregistry:cdd a bioregistry.schema:0000001 ; rdfs:label "Conserved Domain Database at NCBI" ; dc:description "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2666, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2666, biocontext:CDD, go.resource:CDD, n2t:cdd, @@ -1922,8 +1925,8 @@ bioregistry:cdd a bioregistry.schema:0000001 ; bioregistry:cdpd a bioregistry.schema:0000001 ; rdfs:label "Canadian Drug Product Database" ; dc:description "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CDPD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CDPD, n2t:cdpd, miriam:cdpd ; foaf:homepage "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp"^^xsd:string ; @@ -1935,8 +1938,8 @@ bioregistry:cdpd a bioregistry.schema:0000001 ; bioregistry:cell_biolabs a bioregistry.schema:0000001 ; rdfs:label "Cell Biolabs cell line products" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Cell_Biolabs ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Cell_Biolabs ; foaf:homepage "https://www.cellbiolabs.com"^^xsd:string ; bioregistry.schema:0000005 "AKR-270"^^xsd:string ; bioregistry.schema:0000006 "https://www.cellbiolabs.com/search?keywords=$1"^^xsd:string ; @@ -1945,8 +1948,8 @@ bioregistry:cell_biolabs a bioregistry.schema:0000001 ; bioregistry:cell_model_passport a bioregistry.schema:0000001 ; rdfs:label "Sanger Cell Model Passports" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Cell_Model_Passport ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Cell_Model_Passport ; foaf:homepage "https://cellmodelpassports.sanger.ac.uk/"^^xsd:string ; bioregistry.schema:0000005 "SIDM01262"^^xsd:string ; bioregistry.schema:0000006 "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^xsd:string ; @@ -1955,8 +1958,8 @@ bioregistry:cell_model_passport a bioregistry.schema:0000001 ; bioregistry:cellbank.australia a bioregistry.schema:0000001 ; rdfs:label "CellBank Australia" ; dc:description "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CBA ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CBA ; foaf:homepage "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/"^^xsd:string ; bioregistry.schema:0000005 "ab-1-ha"^^xsd:string ; bioregistry.schema:0000006 "https://www.cellbankaustralia.com/$1.html"^^xsd:string ; @@ -1965,8 +1968,8 @@ bioregistry:cellbank.australia a bioregistry.schema:0000001 ; bioregistry:cellrepo a bioregistry.schema:0000001 ; rdfs:label "Cell Version Control Repository" ; dc:description "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:cellrepo ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:cellrepo ; foaf:homepage "https://cellrepo.ico2s.org/"^^xsd:string ; bioregistry.schema:0000005 "82"^^xsd:string ; bioregistry.schema:0000006 "https://cellrepo.ico2s.org/repositories/$1"^^xsd:string ; @@ -1976,9 +1979,9 @@ bioregistry:cellrepo a bioregistry.schema:0000001 ; bioregistry:ceph a bioregistry.schema:0000001 ; rdfs:label "Cephalopod Ontology" ; dc:description "An anatomical and developmental ontology for cephalopods"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CEPH, - obofoundry:CEPH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CEPH, + obofoundry:ceph, ontobee:CEPH, bioportal:CEPH, biocontext:CEPH, @@ -1994,8 +1997,8 @@ bioregistry:ceph a bioregistry.schema:0000001 ; bioregistry:cgd a bioregistry.schema:0000001 ; rdfs:label "Candida Genome Database" ; dc:description "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CGD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CGD, go.resource:CGD, n2t:cgd, ncbi.resource:CGD, @@ -2012,8 +2015,8 @@ bioregistry:cgd a bioregistry.schema:0000001 ; bioregistry:cghdb a bioregistry.schema:0000001 ; rdfs:label "CGH Data Base" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CGH-DB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CGH-DB ; foaf:homepage "http://www.cghtmd.jp/CGHDatabase/index_e.jsp"^^xsd:string ; bioregistry.schema:0000005 "300165/p13898_2106T"^^xsd:string ; bioregistry.schema:0000006 "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^xsd:string ; @@ -2022,8 +2025,8 @@ bioregistry:cghdb a bioregistry.schema:0000001 ; bioregistry:cgsc a bioregistry.schema:0000001 ; rdfs:label "Coli Genetic Stock Center" ; dc:description "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CGSC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CGSC, go.resource:CGSC, n2t:cgsc, fairsharing:FAIRsharing.1tbrdz, @@ -2038,8 +2041,8 @@ bioregistry:cgsc a bioregistry.schema:0000001 ; bioregistry:charprot a bioregistry.schema:0000001 ; rdfs:label "CharProt" ; dc:description "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CHARPROT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CHARPROT, n2t:charprot, miriam:charprot ; foaf:homepage "http://www.jcvi.org/charprotdb"^^xsd:string ; @@ -2051,8 +2054,8 @@ bioregistry:charprot a bioregistry.schema:0000001 ; bioregistry:chemdb a bioregistry.schema:0000001 ; rdfs:label "ChemDB" ; dc:description "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CHEMDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CHEMDB, n2t:chemdb, fairsharing:FAIRsharing.dstf7h, prefixcommons:chemdb, @@ -2066,8 +2069,8 @@ bioregistry:chemdb a bioregistry.schema:0000001 ; bioregistry:chemspider a bioregistry.schema:0000001 ; rdfs:label "ChemSpider" ; dc:description "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1173, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1173, biocontext:CHEMSPIDER, n2t:chemspider, fairsharing:FAIRsharing.96f3gm, @@ -2084,9 +2087,9 @@ bioregistry:chemspider a bioregistry.schema:0000001 ; bioregistry:cido a bioregistry.schema:0000001 ; rdfs:label "Coronavirus Infectious Disease Ontology" ; dc:description "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CIDO, - obofoundry:CIDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CIDO, + obofoundry:cido, ontobee:CIDO, bioportal:CIDO, fairsharing:FAIRsharing.aVmpKl, @@ -2101,9 +2104,9 @@ bioregistry:cido a bioregistry.schema:0000001 ; bioregistry:cio a bioregistry.schema:0000001 ; rdfs:label "Confidence Information Ontology" ; dc:description "An ontology to capture confidence information about annotations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CIO, - obofoundry:CIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CIO, + obofoundry:cio, ontobee:CIO, bioportal:CIO, biocontext:CIO, @@ -2119,8 +2122,8 @@ bioregistry:cio a bioregistry.schema:0000001 ; bioregistry:civic.aid a bioregistry.schema:0000001 ; rdfs:label "CIViC Assertion" ; dc:description "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:civic.aid ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:civic.aid ; foaf:homepage "https://civicdb.org/"^^xsd:string ; bioregistry.schema:0000005 "3"^^xsd:string ; bioregistry.schema:0000006 "https://civicdb.org/links/assertions/$1"^^xsd:string ; @@ -2130,8 +2133,8 @@ bioregistry:civic.aid a bioregistry.schema:0000001 ; bioregistry:civic.eid a bioregistry.schema:0000001 ; rdfs:label "CIViC Evidence" ; dc:description "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:civic.eid ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:civic.eid ; foaf:homepage "https://civicdb.org/"^^xsd:string ; bioregistry.schema:0000005 "1199"^^xsd:string ; bioregistry.schema:0000006 "https://civicdb.org/links/evidence/$1"^^xsd:string ; @@ -2141,8 +2144,8 @@ bioregistry:civic.eid a bioregistry.schema:0000001 ; bioregistry:classyfire a bioregistry.schema:0000001 ; rdfs:label "ClassyFire" ; dc:description "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:classyfire ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:classyfire ; foaf:homepage "http://classyfire.wishartlab.com/"^^xsd:string ; bioregistry.schema:0000005 "0004828"^^xsd:string ; bioregistry.schema:0000006 "http://classyfire.wishartlab.com/tax_nodes/C$1"^^xsd:string ; @@ -2152,8 +2155,8 @@ bioregistry:classyfire a bioregistry.schema:0000001 ; bioregistry:cldb a bioregistry.schema:0000001 ; rdfs:label "Cell Line Database" ; dc:description "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CLDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CLDB, cellosaurus.resource:CLDB, n2t:cldb, miriam:cldb ; @@ -2166,8 +2169,8 @@ bioregistry:cldb a bioregistry.schema:0000001 ; bioregistry:clingene a bioregistry.schema:0000001 ; rdfs:label "ClinGen Allele Registry" ; dc:description "The allele registry provides and maintains identifiers for genetic variants"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:CAID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:CAID ; foaf:homepage "https://reg.clinicalgenome.org"^^xsd:string ; bioregistry.schema:0000005 "CA981206459"^^xsd:string ; bioregistry.schema:0000006 "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^xsd:string ; @@ -2176,8 +2179,8 @@ bioregistry:clingene a bioregistry.schema:0000001 ; bioregistry:clinicaltrials a bioregistry.schema:0000001 ; rdfs:label "ClinicalTrials.gov" ; dc:description "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CLINICALTRIALS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CLINICALTRIALS, n2t:clinicaltrials, prefixcommons:clinicaltrials, miriam:clinicaltrials ; @@ -2190,8 +2193,8 @@ bioregistry:clinicaltrials a bioregistry.schema:0000001 ; bioregistry:clinvar a bioregistry.schema:0000001 ; rdfs:label "ClinVar Variation" ; dc:description "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ClinVar, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ClinVar, biolink:CLINVAR, cellosaurus.resource:ClinVar, n2t:clinvar, @@ -2207,8 +2210,8 @@ bioregistry:clinvar a bioregistry.schema:0000001 ; bioregistry:clinvar.record a bioregistry.schema:0000001 ; rdfs:label "ClinVar Record" ; dc:description "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CLINVAR.RECORD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CLINVAR.RECORD, n2t:clinvar.record, miriam:clinvar.record ; foaf:homepage "http://www.ncbi.nlm.nih.gov/clinvar/"^^xsd:string ; @@ -2220,8 +2223,8 @@ bioregistry:clinvar.record a bioregistry.schema:0000001 ; bioregistry:clinvar.submission a bioregistry.schema:0000001 ; rdfs:label "ClinVar Submission" ; dc:description "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CLINVAR.SUBMISSION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CLINVAR.SUBMISSION, n2t:clinvar.submission, miriam:clinvar.submission ; foaf:homepage "http://www.ncbi.nlm.nih.gov/clinvar/"^^xsd:string ; @@ -2233,8 +2236,8 @@ bioregistry:clinvar.submission a bioregistry.schema:0000001 ; bioregistry:clinvar.submitter a bioregistry.schema:0000001 ; rdfs:label "ClinVar Submitter" ; dc:description "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:clinvar.submitter ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:clinvar.submitter ; foaf:homepage "https://www.ncbi.nlm.nih.gov/clinvar/"^^xsd:string ; bioregistry.schema:0000005 "26957"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^xsd:string ; @@ -2244,8 +2247,8 @@ bioregistry:clinvar.submitter a bioregistry.schema:0000001 ; bioregistry:cls a bioregistry.schema:0000001 ; rdfs:label "Cell Lines Service" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CLS ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CLS ; foaf:homepage "https://cls.shop/"^^xsd:string ; bioregistry.schema:0000005 "300108/p3934_A-172"^^xsd:string ; bioregistry.schema:0000006 "https://cls.shop/$1"^^xsd:string ; @@ -2254,9 +2257,9 @@ bioregistry:cls a bioregistry.schema:0000001 ; bioregistry:cmf a bioregistry.schema:0000001 ; rdfs:label "CranioMaxilloFacial ontology" ; dc:description "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CMF, - obofoundry:CMF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CMF, + obofoundry:cmf, ontobee:CMF, biocontext:CMF ; foaf:homepage "https://code.google.com/p/craniomaxillofacial-ontology/"^^xsd:string ; @@ -2267,8 +2270,8 @@ bioregistry:cmf a bioregistry.schema:0000001 ; bioregistry:cmpo a bioregistry.schema:0000001 ; rdfs:label "Cellular Microscopy Phenotype Ontology" ; dc:description "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CMPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CMPO, bioportal:CMPO, fairsharing:FAIRsharing.knp11s, ols:cmpo ; @@ -2280,8 +2283,8 @@ bioregistry:cmpo a bioregistry.schema:0000001 ; bioregistry:co_320 a bioregistry.schema:0000001 ; rdfs:label "Rice ontology" ; dc:description "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_320, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_320, fairsharing:FAIRsharing.2jkxp5, cropoct:CO_320, ols:co_320 ; @@ -2294,8 +2297,8 @@ bioregistry:co_320 a bioregistry.schema:0000001 ; bioregistry:co_321 a bioregistry.schema:0000001 ; rdfs:label "Wheat ontology" ; dc:description "July 2018"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_321, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_321, fairsharing:FAIRsharing.czzmpg, cropoct:CO_321, ols:co_321 ; @@ -2308,8 +2311,8 @@ bioregistry:co_321 a bioregistry.schema:0000001 ; bioregistry:co_322 a bioregistry.schema:0000001 ; rdfs:label "Maize ontology" ; dc:description "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_322, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_322, fairsharing:FAIRsharing.eeyne8, cropoct:CO_322, ols:co_322 ; @@ -2322,8 +2325,8 @@ bioregistry:co_322 a bioregistry.schema:0000001 ; bioregistry:co_323 a bioregistry.schema:0000001 ; rdfs:label "Barley ontology" ; dc:description "ICARDA - TDv5 - Sept 2018"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_323, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_323, fairsharing:FAIRsharing.f69084, cropoct:CO_323, ols:co_323 ; @@ -2336,8 +2339,8 @@ bioregistry:co_323 a bioregistry.schema:0000001 ; bioregistry:co_324 a bioregistry.schema:0000001 ; rdfs:label "Sorghum ontology" ; dc:description "Sorghum TDv5 - Oct 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_324, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_324, fairsharing:FAIRsharing.dxx0c, cropoct:CO_324, ols:co_324 ; @@ -2350,8 +2353,8 @@ bioregistry:co_324 a bioregistry.schema:0000001 ; bioregistry:co_325 a bioregistry.schema:0000001 ; rdfs:label "Banana ontology" ; dc:description "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_325, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_325, fairsharing:FAIRsharing.gdszhh, cropoct:CO_325, ols:co_325 ; @@ -2364,8 +2367,8 @@ bioregistry:co_325 a bioregistry.schema:0000001 ; bioregistry:co_326 a bioregistry.schema:0000001 ; rdfs:label "Coconut ontology" ; dc:description "Draft version"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cropoct:CO_326, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cropoct:CO_326, ols:co_326 ; foaf:homepage "https://cropontology.org/ontology/CO_326/Coconut"^^xsd:string ; bioregistry.schema:0000005 "0000254"^^xsd:string ; @@ -2375,8 +2378,8 @@ bioregistry:co_326 a bioregistry.schema:0000001 ; bioregistry:co_327 a bioregistry.schema:0000001 ; rdfs:label "Pearl millet ontology" ; dc:description "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_327, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_327, fairsharing:FAIRsharing.4e3qh9, cropoct:CO_327, ols:co_327 ; @@ -2389,8 +2392,8 @@ bioregistry:co_327 a bioregistry.schema:0000001 ; bioregistry:co_330 a bioregistry.schema:0000001 ; rdfs:label "Potato ontology" ; dc:description "CIP - potato ontology - december 2018"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_330, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_330, fairsharing:FAIRsharing.4fa657, cropoct:CO_330, ols:co_330 ; @@ -2403,8 +2406,8 @@ bioregistry:co_330 a bioregistry.schema:0000001 ; bioregistry:co_331 a bioregistry.schema:0000001 ; rdfs:label "Sweet Potato ontology" ; dc:description "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_331, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_331, fairsharing:FAIRsharing.4g5qcw, cropoct:CO_331, ols:co_331 ; @@ -2417,8 +2420,8 @@ bioregistry:co_331 a bioregistry.schema:0000001 ; bioregistry:co_333 a bioregistry.schema:0000001 ; rdfs:label "Beet Ontology ontology" ; dc:description "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_333, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_333, fairsharing:FAIRsharing.af5655, cropoct:CO_333, ols:co_333 ; @@ -2431,8 +2434,8 @@ bioregistry:co_333 a bioregistry.schema:0000001 ; bioregistry:co_334 a bioregistry.schema:0000001 ; rdfs:label "Cassava ontology" ; dc:description "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_334, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_334, fairsharing:FAIRsharing.v06c4q, cropoct:CO_334, ols:co_334 ; @@ -2445,8 +2448,8 @@ bioregistry:co_334 a bioregistry.schema:0000001 ; bioregistry:co_335 a bioregistry.schema:0000001 ; rdfs:label "Common Bean ontology" ; dc:description "CIAT Common bean trait dictionary - version August 2014"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_335, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_335, fairsharing:FAIRsharing.a14123, cropoct:CO_335, ols:co_335 ; @@ -2459,8 +2462,8 @@ bioregistry:co_335 a bioregistry.schema:0000001 ; bioregistry:co_336 a bioregistry.schema:0000001 ; rdfs:label "Soybean ontology" ; dc:description "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_336, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_336, fairsharing:FAIRsharing.j75srj, cropoct:CO_336, ols:co_336 ; @@ -2473,8 +2476,8 @@ bioregistry:co_336 a bioregistry.schema:0000001 ; bioregistry:co_337 a bioregistry.schema:0000001 ; rdfs:label "Groundnut ontology" ; dc:description "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_337, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_337, fairsharing:FAIRsharing.ge8y23, cropoct:CO_337, ols:co_337 ; @@ -2487,8 +2490,8 @@ bioregistry:co_337 a bioregistry.schema:0000001 ; bioregistry:co_338 a bioregistry.schema:0000001 ; rdfs:label "Chickpea ontology" ; dc:description "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_338, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_338, fairsharing:FAIRsharing.js20q3, cropoct:CO_338, ols:co_338 ; @@ -2501,8 +2504,8 @@ bioregistry:co_338 a bioregistry.schema:0000001 ; bioregistry:co_339 a bioregistry.schema:0000001 ; rdfs:label "Lentil ontology" ; dc:description "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_339, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_339, fairsharing:FAIRsharing.ry1ezg, cropoct:CO_339, ols:co_339 ; @@ -2515,8 +2518,8 @@ bioregistry:co_339 a bioregistry.schema:0000001 ; bioregistry:co_340 a bioregistry.schema:0000001 ; rdfs:label "Cowpea ontology" ; dc:description "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_340, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_340, fairsharing:FAIRsharing.31apg2, cropoct:CO_340, ols:co_340 ; @@ -2529,8 +2532,8 @@ bioregistry:co_340 a bioregistry.schema:0000001 ; bioregistry:co_341 a bioregistry.schema:0000001 ; rdfs:label "Pigeonpea ontology" ; dc:description "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_341, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_341, fairsharing:FAIRsharing.ehe3yp, cropoct:CO_341, ols:co_341 ; @@ -2543,8 +2546,8 @@ bioregistry:co_341 a bioregistry.schema:0000001 ; bioregistry:co_343 a bioregistry.schema:0000001 ; rdfs:label "Yam ontology" ; dc:description "version 2019 - pvs"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_343, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_343, fairsharing:FAIRsharing.7e9cff, cropoct:CO_343, ols:co_343 ; @@ -2557,8 +2560,8 @@ bioregistry:co_343 a bioregistry.schema:0000001 ; bioregistry:co_345 a bioregistry.schema:0000001 ; rdfs:label "Brachiaria ontology" ; dc:description "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_345, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_345, fairsharing:FAIRsharing.9e9683, cropoct:CO_345, ols:co_345 ; @@ -2571,8 +2574,8 @@ bioregistry:co_345 a bioregistry.schema:0000001 ; bioregistry:co_346 a bioregistry.schema:0000001 ; rdfs:label "Mungbean ontology" ; dc:description "oct 2016"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_346, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_346, fairsharing:FAIRsharing.fgd5gq, cropoct:CO_346, ols:co_346 ; @@ -2585,8 +2588,8 @@ bioregistry:co_346 a bioregistry.schema:0000001 ; bioregistry:co_347 a bioregistry.schema:0000001 ; rdfs:label "Castor bean ontology" ; dc:description "March 2017 version "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_347, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_347, fairsharing:FAIRsharing.qrrvyk, cropoct:CO_347, ols:co_347 ; @@ -2599,8 +2602,8 @@ bioregistry:co_347 a bioregistry.schema:0000001 ; bioregistry:co_348 a bioregistry.schema:0000001 ; rdfs:label "Brassica ontology" ; dc:description "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_348, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_348, fairsharing:FAIRsharing.af7a2d, cropoct:CO_348, ols:co_348 ; @@ -2613,8 +2616,8 @@ bioregistry:co_348 a bioregistry.schema:0000001 ; bioregistry:co_350 a bioregistry.schema:0000001 ; rdfs:label "Oat ontology" ; dc:description "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_350, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_350, fairsharing:FAIRsharing.35e1c3, cropoct:CO_350, ols:co_350 ; @@ -2627,8 +2630,8 @@ bioregistry:co_350 a bioregistry.schema:0000001 ; bioregistry:co_356 a bioregistry.schema:0000001 ; rdfs:label "Vitis ontology" ; dc:description "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_356, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_356, fairsharing:FAIRsharing.c7f4d7, cropoct:CO_356, ols:co_356 ; @@ -2641,8 +2644,8 @@ bioregistry:co_356 a bioregistry.schema:0000001 ; bioregistry:co_357 a bioregistry.schema:0000001 ; rdfs:label "Woody Plant Ontology ontology" ; dc:description "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_357, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_357, fairsharing:FAIRsharing.2b04ae, cropoct:CO_357, ols:co_357 ; @@ -2655,8 +2658,8 @@ bioregistry:co_357 a bioregistry.schema:0000001 ; bioregistry:co_358 a bioregistry.schema:0000001 ; rdfs:label "Cotton ontology" ; dc:description "Cotton ontology from CottonGen database - June 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_358, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_358, cropoct:CO_358, ols:co_358 ; foaf:homepage "https://cropontology.org/ontology/CO_358/Cotton"^^xsd:string ; @@ -2668,8 +2671,8 @@ bioregistry:co_358 a bioregistry.schema:0000001 ; bioregistry:co_359 a bioregistry.schema:0000001 ; rdfs:label "Sunflower ontology" ; dc:description "December 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_359, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_359, cropoct:CO_359, ols:co_359 ; foaf:homepage "https://cropontology.org/ontology/CO_359/Sunflower"^^xsd:string ; @@ -2681,8 +2684,8 @@ bioregistry:co_359 a bioregistry.schema:0000001 ; bioregistry:co_360 a bioregistry.schema:0000001 ; rdfs:label "Sugar Kelp trait ontology" ; dc:description "Sugar Kelp trait ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_360, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_360, fairsharing:FAIRsharing.1c1738, cropoct:CO_360, ols:co_360 ; @@ -2695,8 +2698,8 @@ bioregistry:co_360 a bioregistry.schema:0000001 ; bioregistry:co_365 a bioregistry.schema:0000001 ; rdfs:label "Fababean ontology" ; dc:description "developed by ICARDA - Dec 2018"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_365, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_365, cropoct:CO_365, ols:co_365 ; foaf:homepage "https://cropontology.org/ontology/CO_365/Fababean"^^xsd:string ; @@ -2708,8 +2711,8 @@ bioregistry:co_365 a bioregistry.schema:0000001 ; bioregistry:co_366 a bioregistry.schema:0000001 ; rdfs:label "Bambara groundnut ontology" ; dc:description "version Dec 2019"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:CO_366, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:CO_366, cropoct:CO_366, ols:co_366 ; foaf:homepage "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut"^^xsd:string ; @@ -2721,9 +2724,9 @@ bioregistry:co_366 a bioregistry.schema:0000001 ; bioregistry:cob a bioregistry.schema:0000001 ; rdfs:label "Core Ontology for Biology and Biomedicine" ; dc:description "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:COB, - obofoundry:COB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:COB, + obofoundry:cob, ontobee:COB, bioportal:COB, ols:cob ; @@ -2737,8 +2740,8 @@ bioregistry:cob a bioregistry.schema:0000001 ; bioregistry:colonatlas a bioregistry.schema:0000001 ; rdfs:label "Colorectal Cancer Atlas" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ColonAtlas ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ColonAtlas ; foaf:homepage "http://www.coloncanceratlas.org"^^xsd:string ; bioregistry.schema:0000005 "ALA"^^xsd:string ; bioregistry.schema:0000006 "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^xsd:string ; @@ -2747,8 +2750,8 @@ bioregistry:colonatlas a bioregistry.schema:0000001 ; bioregistry:combine.specifications a bioregistry.schema:0000001 ; rdfs:label "COMBINE specifications" ; dc:description "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:COMBINE.SPECIFICATIONS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:COMBINE.SPECIFICATIONS, n2t:combine.specifications, miriam:combine.specifications ; foaf:homepage "https://co.mbine.org/standards/"^^xsd:string ; @@ -2760,8 +2763,8 @@ bioregistry:combine.specifications a bioregistry.schema:0000001 ; bioregistry:comptox a bioregistry.schema:0000001 ; rdfs:label "CompTox Chemistry Dashboard" ; dc:description "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:COMPTOX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:COMPTOX, n2t:comptox, miriam:comptox, wikidata:P3117 ; @@ -2774,8 +2777,8 @@ bioregistry:comptox a bioregistry.schema:0000001 ; bioregistry:compulyeast a bioregistry.schema:0000001 ; rdfs:label "Compluyeast-2D-DB" ; dc:description "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:COMPULYEAST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:COMPULYEAST, n2t:compulyeast, fairsharing:FAIRsharing.rbjs3e, miriam:compulyeast ; @@ -2789,8 +2792,8 @@ bioregistry:compulyeast a bioregistry.schema:0000001 ; bioregistry:conoserver a bioregistry.schema:0000001 ; rdfs:label "ConoServer" ; dc:description "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CONOSERVER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CONOSERVER, n2t:conoserver, fairsharing:FAIRsharing.y00hz4, miriam:conoserver, @@ -2804,8 +2807,8 @@ bioregistry:conoserver a bioregistry.schema:0000001 ; bioregistry:coriell a bioregistry.schema:0000001 ; rdfs:label "Coriell Institute for Medical Research" ; dc:description "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:Coriell, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:Coriell, cellosaurus.resource:Coriell, go.resource:CORIELL, n2t:coriell, @@ -2819,8 +2822,8 @@ bioregistry:coriell a bioregistry.schema:0000001 ; bioregistry:corrdb a bioregistry.schema:0000001 ; rdfs:label "CorrDB" ; dc:description "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.IziuCK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.IziuCK, miriam:corrdb ; foaf:homepage "https://www.animalgenome.org"^^xsd:string ; bioregistry.schema:0000005 "37232"^^xsd:string ; @@ -2831,8 +2834,8 @@ bioregistry:corrdb a bioregistry.schema:0000001 ; bioregistry:corum a bioregistry.schema:0000001 ; rdfs:label "Comprehensive Resource of Mammalian protein complexes" ; dc:description "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CORUM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CORUM, go.resource:CORUM, n2t:corum, fairsharing:FAIRsharing.ohbpNw, @@ -2848,8 +2851,8 @@ bioregistry:corum a bioregistry.schema:0000001 ; bioregistry:cosmic a bioregistry.schema:0000001 ; rdfs:label "COSMIC Gene" ; dc:description "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:3264, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:3264, biocontext:COSMIC, cellosaurus.resource:Cosmic, n2t:cosmic, @@ -2864,8 +2867,8 @@ bioregistry:cosmic a bioregistry.schema:0000001 ; bioregistry:covid19 a bioregistry.schema:0000001 ; rdfs:label "COVID-19 Surveillance Ontology" ; dc:description "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:COVID19, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:COVID19, bioportal:COVID19, miriam:covid19 ; foaf:homepage "https://covid19.sfb.uit.no"^^xsd:string ; @@ -2877,8 +2880,8 @@ bioregistry:covid19 a bioregistry.schema:0000001 ; bioregistry:covoc a bioregistry.schema:0000001 ; rdfs:label "CoVoc Coronavirus Vocabulary" ; dc:description "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ols:covoc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ols:covoc ; foaf:homepage "https://github.com/EBISPOT/covoc"^^xsd:string ; bioregistry.schema:0000005 "0010034"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -2888,8 +2891,8 @@ bioregistry:covoc a bioregistry.schema:0000001 ; bioregistry:cpc a bioregistry.schema:0000001 ; rdfs:label "Cooperative Patent Classification" ; dc:description "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CPC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CPC, n2t:cpc, fairsharing:FAIRsharing.e08886, miriam:cpc ; @@ -2901,20 +2904,20 @@ bioregistry:cpc a bioregistry.schema:0000001 ; bioregistry:cpga a bioregistry.schema:0000001 ; rdfs:label "Cereal Plant Gross Anatomy" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:GRO, + dc:description "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:gro, bioportal:GRO-CPGA, biocontext:gro.cpga ; foaf:homepage "http://www.gramene.org/plant_ontology/"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/GRO_$1"^^xsd:string ; bioregistry.schema:0000012 true ; bioregistry.schema:0000019 [ rdfs:label "Plant Ontology Administrators" ] . bioregistry:crisprdb a bioregistry.schema:0000001 ; rdfs:label "CRISPRdb" ; dc:description "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CRISPRDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CRISPRDB, n2t:crisprdb, fairsharing:FAIRsharing.7sfedh, miriam:crisprdb ; @@ -2927,9 +2930,9 @@ bioregistry:crisprdb a bioregistry.schema:0000001 ; bioregistry:cro a bioregistry.schema:0000001 ; rdfs:label "Contributor Role Ontology" ; dc:description "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CRO, - obofoundry:CRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CRO, + obofoundry:cro, ontobee:CRO, bioportal:CRO, biocontext:CRO, @@ -2944,8 +2947,8 @@ bioregistry:cro a bioregistry.schema:0000001 ; bioregistry:cryoem a bioregistry.schema:0000001 ; rdfs:label "Cryo Electron Microscopy ontology" ; dc:description "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CRYOEM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CRYOEM, bioportal:CRYOEM, ols:cryoem ; foaf:homepage "http://scipion.i2pc.es/ontology/cryoem"^^xsd:string ; @@ -2956,8 +2959,8 @@ bioregistry:cryoem a bioregistry.schema:0000001 ; bioregistry:cryptodb a bioregistry.schema:0000001 ; rdfs:label "CryptoDB" ; dc:description "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CRYPTODB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CRYPTODB, n2t:cryptodb, fairsharing:FAIRsharing.t3nprm, prefixcommons:cryptodb, @@ -2971,8 +2974,8 @@ bioregistry:cryptodb a bioregistry.schema:0000001 ; bioregistry:csa a bioregistry.schema:0000001 ; rdfs:label "Catalytic Site Atlas" ; dc:description "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CSA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CSA, n2t:csa, fairsharing:FAIRsharing.2ajtcf, prefixcommons:csa, @@ -2986,8 +2989,8 @@ bioregistry:csa a bioregistry.schema:0000001 ; bioregistry:csd a bioregistry.schema:0000001 ; rdfs:label "Cambridge Structural Database" ; dc:description "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.vs7865, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.vs7865, miriam:csd ; foaf:homepage "https://www.ccdc.cam.ac.uk/"^^xsd:string ; bioregistry.schema:0000005 "PELNAW"^^xsd:string ; @@ -2997,8 +3000,8 @@ bioregistry:csd a bioregistry.schema:0000001 ; bioregistry:csp a bioregistry.schema:0000001 ; rdfs:label "Computer Retrieval of Information on Science Projects Thesaurus" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CRISP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CRISP, bioportal:CRISP ; foaf:homepage "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm"^^xsd:string ; bioregistry.schema:0000005 "2004-2820"^^xsd:string ; @@ -3007,8 +3010,8 @@ bioregistry:csp a bioregistry.schema:0000001 ; bioregistry:cst a bioregistry.schema:0000001 ; rdfs:label "Cancer Staging Terms" ; dc:description "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CST, bioportal:CST, biocontext:CST, n2t:cst, @@ -3024,8 +3027,8 @@ bioregistry:cst a bioregistry.schema:0000001 ; bioregistry:cst.ab a bioregistry.schema:0000001 ; rdfs:label "Cell Signaling Technology Antibody" ; dc:description "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CST.AB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CST.AB, n2t:cst.ab, miriam:cst.ab ; foaf:homepage "http://www.cellsignal.com/catalog/index.html"^^xsd:string ; @@ -3037,9 +3040,9 @@ bioregistry:cst.ab a bioregistry.schema:0000001 ; bioregistry:cto a bioregistry.schema:0000001 ; rdfs:label "Clinical Trials Ontology" ; dc:description "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CTO, - obofoundry:CTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CTO, + obofoundry:cto, ontobee:CTO, bioportal:CTO, fairsharing:FAIRsharing.qp211a, @@ -3054,8 +3057,8 @@ bioregistry:cto a bioregistry.schema:0000001 ; bioregistry:cubedb a bioregistry.schema:0000001 ; rdfs:label "Cube db" ; dc:description "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CUBEDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CUBEDB, n2t:cubedb, miriam:cubedb ; foaf:homepage "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html"^^xsd:string ; @@ -3067,9 +3070,9 @@ bioregistry:cubedb a bioregistry.schema:0000001 ; bioregistry:cvdo a bioregistry.schema:0000001 ; rdfs:label "Cardiovascular Disease Ontology" ; dc:description "An ontology to describe entities related to cardiovascular diseases"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CVDO, - obofoundry:CVDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CVDO, + obofoundry:cvdo, ontobee:CVDO, bioportal:CVDO, biocontext:CVDO, @@ -3085,8 +3088,8 @@ bioregistry:cvdo a bioregistry.schema:0000001 ; bioregistry:d1id a bioregistry.schema:0000001 ; rdfs:label "DataONE" ; dc:description "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:D1ID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:D1ID, n2t:d1id, miriam:d1id ; foaf:homepage "https://www.dataone.org"^^xsd:string ; @@ -3098,8 +3101,8 @@ bioregistry:d1id a bioregistry.schema:0000001 ; bioregistry:dailymed a bioregistry.schema:0000001 ; rdfs:label "DailyMed" ; dc:description "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DAILYMED, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DAILYMED, n2t:dailymed, prefixcommons:dailymed, miriam:dailymed ; @@ -3114,8 +3117,8 @@ bioregistry:dandi a bioregistry.schema:0000001 ; dc:description """DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). DANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. These data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dandi ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dandi ; foaf:homepage "https://dandiarchive.org/"^^xsd:string ; bioregistry.schema:0000005 "000017"^^xsd:string ; bioregistry.schema:0000006 "https://dandiarchive.org/dandiset/$1"^^xsd:string ; @@ -3125,8 +3128,8 @@ These data will help scientists uncover and understand cellular level mechanisms bioregistry:darc a bioregistry.schema:0000001 ; rdfs:label "Database of Aligned Ribosomal Complexes" ; dc:description "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DARC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DARC, n2t:darc, fairsharing:FAIRsharing.evfe2s, miriam:darc ; @@ -3139,8 +3142,8 @@ bioregistry:darc a bioregistry.schema:0000001 ; bioregistry:dashr a bioregistry.schema:0000001 ; rdfs:label "Database of small human noncoding RNAs" ; dc:description "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DASHR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DASHR, n2t:dashr, fairsharing:FAIRsharing.ztvs34, miriam:dashr ; @@ -3153,8 +3156,8 @@ bioregistry:dashr a bioregistry.schema:0000001 ; bioregistry:dashr.expression a bioregistry.schema:0000001 ; rdfs:label "DASHR expression" ; dc:description "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DASHR.EXPRESSION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DASHR.EXPRESSION, n2t:dashr.expression, miriam:dashr.expression ; foaf:homepage "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0"^^xsd:string ; @@ -3166,8 +3169,8 @@ bioregistry:dashr.expression a bioregistry.schema:0000001 ; bioregistry:datanator.reaction a bioregistry.schema:0000001 ; rdfs:label "Datanator Reaction" ; dc:description " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:datanator.reaction ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:datanator.reaction ; foaf:homepage "https://icahn.mssm.edu/"^^xsd:string ; bioregistry.schema:0000005 "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^xsd:string ; bioregistry.schema:0000006 "https://datanator.info/reaction/$1"^^xsd:string ; @@ -3177,8 +3180,8 @@ bioregistry:datanator.reaction a bioregistry.schema:0000001 ; bioregistry:datf a bioregistry.schema:0000001 ; rdfs:label "Database of Arabidopsis Transcription Factors" ; dc:description "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DATF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DATF, n2t:datf, prefixcommons:datf, miriam:datf ; @@ -3191,8 +3194,8 @@ bioregistry:datf a bioregistry.schema:0000001 ; bioregistry:dbd a bioregistry.schema:0000001 ; rdfs:label "Transcription Factor Database" ; dc:description "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2716, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2716, biocontext:DBD, n2t:dbd, prefixcommons:dbd, @@ -3206,8 +3209,8 @@ bioregistry:dbd a bioregistry.schema:0000001 ; bioregistry:dbg2introns a bioregistry.schema:0000001 ; rdfs:label "DBG2 Introns" ; dc:description "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DBG2INTRONS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DBG2INTRONS, n2t:dbg2introns, miriam:dbg2introns ; foaf:homepage "http://webapps2.ucalgary.ca/~groupii/"^^xsd:string ; @@ -3219,8 +3222,8 @@ bioregistry:dbg2introns a bioregistry.schema:0000001 ; bioregistry:dbgap a bioregistry.schema:0000001 ; rdfs:label "Database of Genotypes and Phenotypes" ; dc:description "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DBGAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DBGAP, n2t:dbgap, fairsharing:FAIRsharing.88v2k0, miriam:dbgap ; @@ -3233,8 +3236,8 @@ bioregistry:dbgap a bioregistry.schema:0000001 ; bioregistry:dbmhc a bioregistry.schema:0000001 ; rdfs:label "Database of human Major Histocompatibility Complex" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:dbMHC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:dbMHC ; foaf:homepage "https://www.ncbi.nlm.nih.gov/gv/mhc/"^^xsd:string ; bioregistry.schema:0000005 "48439"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -3244,8 +3247,8 @@ bioregistry:dbmhc a bioregistry.schema:0000001 ; bioregistry:dbprobe a bioregistry.schema:0000001 ; rdfs:label "NCBI Probe database Public registry of nucleic acid reagents" ; dc:description "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2719, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2719, biocontext:DBPROBE, n2t:dbprobe, ncbi.resource:dbProbe, @@ -3259,8 +3262,8 @@ bioregistry:dbprobe a bioregistry.schema:0000001 ; bioregistry:dc_cl a bioregistry.schema:0000001 ; rdfs:label "Dendritic cell" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:DC_CL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:dc_cl, biocontext:DC_CL ; foaf:homepage "http://www.dukeontologygroup.org/Projects.html"^^xsd:string ; bioregistry.schema:0000005 "0000003"^^xsd:string ; @@ -3272,9 +3275,9 @@ bioregistry:dc_cl a bioregistry.schema:0000001 ; bioregistry:ddanat a bioregistry.schema:0000001 ; rdfs:label "Dictyostelium discoideum anatomy" ; dc:description "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DDANAT, - obofoundry:DDANAT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DDANAT, + obofoundry:ddanat, ontobee:DDANAT, bioportal:DDANAT, biocontext:DDANAT, @@ -3292,9 +3295,9 @@ bioregistry:ddanat a bioregistry.schema:0000001 ; bioregistry:ddpheno a bioregistry.schema:0000001 ; rdfs:label "Dictyostelium discoideum phenotype ontology" ; dc:description "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DDPHENO, - obofoundry:DDPHENO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DDPHENO, + obofoundry:ddpheno, ontobee:DDPHENO, bioportal:DDPHENO, biocontext:DDPHENO, @@ -3310,8 +3313,8 @@ bioregistry:ddpheno a bioregistry.schema:0000001 ; bioregistry:degradome a bioregistry.schema:0000001 ; rdfs:label "Degradome Database" ; dc:description "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DEGRADOME, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DEGRADOME, n2t:degradome, miriam:degradome ; foaf:homepage "http://degradome.uniovi.es/"^^xsd:string ; @@ -3323,8 +3326,8 @@ bioregistry:degradome a bioregistry.schema:0000001 ; bioregistry:depmap a bioregistry.schema:0000001 ; rdfs:label "DepMap Cell Lines" ; dc:description "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:DepMap ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:DepMap ; foaf:homepage "https://depmap.org/portal"^^xsd:string ; bioregistry.schema:0000005 "ACH-000001"^^xsd:string ; bioregistry.schema:0000006 "https://depmap.org/portal/cell_line/$1"^^xsd:string ; @@ -3334,8 +3337,8 @@ bioregistry:depmap a bioregistry.schema:0000001 ; bioregistry:depod a bioregistry.schema:0000001 ; rdfs:label "Human Dephosphorylation Database" ; dc:description "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DEPOD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DEPOD, n2t:depod, fairsharing:FAIRsharing.q9j2e3, miriam:depod, @@ -3350,8 +3353,8 @@ bioregistry:depod a bioregistry.schema:0000001 ; bioregistry:dermo a bioregistry.schema:0000001 ; rdfs:label "Human Dermatological Disease Ontology" ; dc:description "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DERMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DERMO, bioportal:DERMO, fairsharing:FAIRsharing.k008w7 ; foaf:homepage "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x"^^xsd:string ; @@ -3362,8 +3365,8 @@ bioregistry:dermo a bioregistry.schema:0000001 ; bioregistry:dev.ga4ghdos a bioregistry.schema:0000001 ; rdfs:label "Development Data Object Service" ; dc:description "Assists in resolving data across cloud resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DEV.GA4GHDOS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DEV.GA4GHDOS, n2t:dev.ga4ghdos, miriam:dev.ga4ghdos ; foaf:homepage "http://github.com/ga4gh/data-object-service-schemas"^^xsd:string ; @@ -3375,8 +3378,8 @@ bioregistry:dev.ga4ghdos a bioregistry.schema:0000001 ; bioregistry:dg.4503 a bioregistry.schema:0000001 ; rdfs:label "BioData Catalyst" ; dc:description "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.4503 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.4503 ; foaf:homepage "https://gen3.biodatacatalyst.nhlbi.nih.gov"^^xsd:string ; bioregistry.schema:0000005 "0000ffeb-36e0-4a29-b21d-84423bda979d"^^xsd:string ; bioregistry.schema:0000006 "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3386,8 +3389,8 @@ bioregistry:dg.4503 a bioregistry.schema:0000001 ; bioregistry:dg.4dfc a bioregistry.schema:0000001 ; rdfs:label "NCI Data Commons Framework Services" ; dc:description "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.4dfc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.4dfc ; foaf:homepage "https://nci-crdc.datacommons.io/"^^xsd:string ; bioregistry.schema:0000005 "81944ba1-81d0-436e-8552-33d77a27834b"^^xsd:string ; bioregistry.schema:0000006 "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3397,8 +3400,8 @@ bioregistry:dg.4dfc a bioregistry.schema:0000001 ; bioregistry:dg.6vts a bioregistry.schema:0000001 ; rdfs:label "JCOIN" ; dc:description "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.6vts ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.6vts ; foaf:homepage "https://jcoin.datacommons.io"^^xsd:string ; bioregistry.schema:0000005 "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^xsd:string ; bioregistry.schema:0000006 "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3408,8 +3411,8 @@ bioregistry:dg.6vts a bioregistry.schema:0000001 ; bioregistry:dg.anv0 a bioregistry.schema:0000001 ; rdfs:label "Anvil" ; dc:description "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.anv0 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.anv0 ; foaf:homepage "https://gen3.theanvil.io"^^xsd:string ; bioregistry.schema:0000005 "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^xsd:string ; bioregistry.schema:0000006 "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3419,8 +3422,8 @@ bioregistry:dg.anv0 a bioregistry.schema:0000001 ; bioregistry:dg.f82a1a a bioregistry.schema:0000001 ; rdfs:label "Kids First" ; dc:description "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.f82a1a ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.f82a1a ; foaf:homepage "https://kidsfirstdrc.org"^^xsd:string ; bioregistry.schema:0000005 "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^xsd:string ; bioregistry.schema:0000006 "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3430,8 +3433,8 @@ bioregistry:dg.f82a1a a bioregistry.schema:0000001 ; bioregistry:dg5b0d a bioregistry.schema:0000001 ; rdfs:label "BloodPAC" ; dc:description "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:dg.5b0d ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:dg.5b0d ; foaf:homepage "https://data.bloodpac.org/."^^xsd:string ; bioregistry.schema:0000005 "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^xsd:string ; bioregistry.schema:0000006 "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^xsd:string ; @@ -3441,8 +3444,8 @@ bioregistry:dg5b0d a bioregistry.schema:0000001 ; bioregistry:dgrc a bioregistry.schema:0000001 ; rdfs:label "Drosophila Genomics Resource Center" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:DGRC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:DGRC ; foaf:homepage "https://dgrc.bio.indiana.edu/cells/Catalog"^^xsd:string ; bioregistry.schema:0000005 "215"^^xsd:string ; bioregistry.schema:0000006 "https://dgrc.bio.indiana.edu/product/View?product=$1"^^xsd:string ; @@ -3452,8 +3455,8 @@ bioregistry:dgrc a bioregistry.schema:0000001 ; bioregistry:dicom a bioregistry.schema:0000001 ; rdfs:label "DICOM Controlled Terminology" ; dc:description "DICOM Controlled Terminology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:DCM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:DCM, fairsharing:FAIRsharing.b7z8by, ols:dicom ; foaf:homepage "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html"^^xsd:string ; @@ -3464,8 +3467,8 @@ bioregistry:dicom a bioregistry.schema:0000001 ; bioregistry:did a bioregistry.schema:0000001 ; rdfs:label "Decentralized Identifier" ; dc:description "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:did, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:did, miriam:did ; foaf:homepage "https://w3c-ccg.github.io/did-spec/"^^xsd:string ; bioregistry.schema:0000005 "sov:WRfXPg8dantKVubE3HX8pw"^^xsd:string ; @@ -3476,9 +3479,9 @@ bioregistry:did a bioregistry.schema:0000001 ; bioregistry:dideo a bioregistry.schema:0000001 ; rdfs:label "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" ; dc:description "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DIDEO, - obofoundry:DIDEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DIDEO, + obofoundry:dideo, ontobee:DIDEO, bioportal:DIDEO, biocontext:DIDEO, @@ -3494,9 +3497,9 @@ bioregistry:dideo a bioregistry.schema:0000001 ; bioregistry:dinto a bioregistry.schema:0000001 ; rdfs:label "The Drug-Drug Interactions Ontology" ; dc:description "A formal represention for drug-drug interactions knowledge."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DINTO, - obofoundry:DINTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DINTO, + obofoundry:dinto, ontobee:DINTO, bioportal:DINTO, biocontext:DINTO ; @@ -3508,8 +3511,8 @@ bioregistry:dinto a bioregistry.schema:0000001 ; bioregistry:dip a bioregistry.schema:0000001 ; rdfs:label "Database of Interacting Proteins" ; dc:description "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2616, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2616, biocontext:DIP, n2t:dip, fairsharing:FAIRsharing.qje0v8, @@ -3525,8 +3528,8 @@ bioregistry:dip a bioregistry.schema:0000001 ; bioregistry:discoverx a bioregistry.schema:0000001 ; rdfs:label "DiscoverX cell line products" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:DiscoverX ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:DiscoverX ; foaf:homepage "https://www.discoverx.com/products-applications/cell-lines"^^xsd:string ; bioregistry.schema:0000005 "95-0166C6"^^xsd:string ; bioregistry.schema:0000006 "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^xsd:string ; @@ -3535,9 +3538,9 @@ bioregistry:discoverx a bioregistry.schema:0000001 ; bioregistry:disdriv a bioregistry.schema:0000001 ; rdfs:label "Disease Drivers Ontology" ; dc:description "Drivers of human diseases including environmental, maternal and social exposures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DISDRIV, - obofoundry:DISDRIV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DISDRIV, + obofoundry:disdriv, bioportal:DISDRIV, ols:disdriv ; foaf:homepage "http://www.disease-ontology.org"^^xsd:string ; @@ -3550,8 +3553,8 @@ bioregistry:disdriv a bioregistry.schema:0000001 ; bioregistry:diseasesdb a bioregistry.schema:0000001 ; rdfs:label "Diseases Database" ; dc:description "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P557 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P557 ; foaf:homepage "http://www.diseasesdatabase.com/"^^xsd:string ; bioregistry.schema:0000005 "1784"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -3560,8 +3563,8 @@ bioregistry:diseasesdb a bioregistry.schema:0000001 ; bioregistry:disprot a bioregistry.schema:0000001 ; rdfs:label "DisProt" ; dc:description "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2723, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2723, biocontext:DISPROT, n2t:disprot, fairsharing:FAIRsharing.dt9z89, @@ -3577,8 +3580,8 @@ bioregistry:disprot a bioregistry.schema:0000001 ; bioregistry:disprot.region a bioregistry.schema:0000001 ; rdfs:label "DisProt region" ; dc:description "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:disprot.region ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:disprot.region ; foaf:homepage "https://www.disprot.org"^^xsd:string ; bioregistry.schema:0000005 "DP00086r013"^^xsd:string ; bioregistry.schema:0000006 "https://www.disprot.org/$1"^^xsd:string ; @@ -3588,8 +3591,8 @@ bioregistry:disprot.region a bioregistry.schema:0000001 ; bioregistry:doi a bioregistry.schema:0000001 ; rdfs:label "Digital Object Identifier" ; dc:description "The Digital Object Identifier System is for identifying content objects in the digital environment."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1188, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1188, biocontext:DOI, biolink:doi, cellosaurus.resource:DOI, @@ -3607,8 +3610,8 @@ bioregistry:doi a bioregistry.schema:0000001 ; bioregistry:dommino a bioregistry.schema:0000001 ; rdfs:label "Database of Macromolecular Interactions" ; dc:description "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DOMMINO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DOMMINO, n2t:dommino, miriam:dommino ; foaf:homepage "http://korkinlab.org/dommino"^^xsd:string ; @@ -3620,8 +3623,8 @@ bioregistry:dommino a bioregistry.schema:0000001 ; bioregistry:door a bioregistry.schema:0000001 ; rdfs:label "Database for Prokaryotic Operons" ; dc:description "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DOOR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DOOR, n2t:door, prefixcommons:door, miriam:door ; @@ -3634,8 +3637,8 @@ bioregistry:door a bioregistry.schema:0000001 ; bioregistry:dpv a bioregistry.schema:0000001 ; rdfs:label "Description of Plant Viruses" ; dc:description "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DPV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DPV, n2t:dpv, miriam:dpv ; foaf:homepage "http://www.dpvweb.net/"^^xsd:string ; @@ -3647,8 +3650,8 @@ bioregistry:dpv a bioregistry.schema:0000001 ; bioregistry:drsc a bioregistry.schema:0000001 ; rdfs:label "Drosophila RNAi Screening Center" ; dc:description "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DRSC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DRSC, n2t:drsc, miriam:drsc ; foaf:homepage "http://flyrnai.org/"^^xsd:string ; @@ -3660,8 +3663,8 @@ bioregistry:drsc a bioregistry.schema:0000001 ; bioregistry:drugcentral a bioregistry.schema:0000001 ; rdfs:label "Drug Central" ; dc:description "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:DrugCentral, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:DrugCentral, fairsharing:FAIRsharing.3me82d, uniprot.resource:DrugCentral ; foaf:homepage "http://drugcentral.org"^^xsd:string ; @@ -3673,8 +3676,8 @@ bioregistry:drugcentral a bioregistry.schema:0000001 ; bioregistry:dto a bioregistry.schema:0000001 ; rdfs:label "Drug Target Ontology" ; dc:description "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DTO, bioportal:DTO, fairsharing:FAIRsharing.tke3y2 ; foaf:homepage "https://github.com/DrugTargetOntology/DTO"^^xsd:string ; @@ -3686,8 +3689,8 @@ bioregistry:dto a bioregistry.schema:0000001 ; bioregistry:ebisc a bioregistry.schema:0000001 ; rdfs:label "European Bank for induced pluripotent Stem Cells" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:EBiSC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:EBiSC ; foaf:homepage "https://www.ebisc.org"^^xsd:string ; bioregistry.schema:0000005 "ESi007-A"^^xsd:string ; bioregistry.schema:0000006 "https://cells.ebisc.org/$1"^^xsd:string ; @@ -3696,8 +3699,8 @@ bioregistry:ebisc a bioregistry.schema:0000001 ; bioregistry:ecacc a bioregistry.schema:0000001 ; rdfs:label "European Collection of Authenticated Cell Culture" ; dc:description "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ECACC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ECACC ; foaf:homepage "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx"^^xsd:string ; bioregistry.schema:0000005 "90062901"^^xsd:string ; bioregistry.schema:0000006 "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^xsd:string ; @@ -3707,8 +3710,8 @@ bioregistry:ecacc a bioregistry.schema:0000001 ; bioregistry:ecg a bioregistry.schema:0000001 ; rdfs:label "Electrocardiogram Ontology" ; dc:description "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ECG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ECG, bioportal:ECG, fairsharing:FAIRsharing.azr389 ; foaf:homepage "https://bioportal.bioontology.org/ontologies/ECG"^^xsd:string ; @@ -3719,8 +3722,8 @@ bioregistry:ecg a bioregistry.schema:0000001 ; bioregistry:echobase a bioregistry.schema:0000001 ; rdfs:label "EchoBASE post-genomic database for Escherichia coli" ; dc:description "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ECHOBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ECHOBASE, go.resource:EchoBASE, n2t:echobase, prefixcommons:echobase, @@ -3735,9 +3738,9 @@ bioregistry:echobase a bioregistry.schema:0000001 ; bioregistry:eco a bioregistry.schema:0000001 ; rdfs:label "Evidence ontology" ; dc:description "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ECO, - obofoundry:ECO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ECO, + obofoundry:eco, ontobee:ECO, bioportal:ECO, biocontext:ECO, @@ -3757,8 +3760,8 @@ bioregistry:eco a bioregistry.schema:0000001 ; bioregistry:ecocyc a bioregistry.schema:0000001 ; rdfs:label "EcoCyc" ; dc:description "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:EcoCyc, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:EcoCyc, ncbi.resource:ECOCYC, fairsharing:FAIRsharing.65dmtr ; foaf:homepage "http://ecocyc.org/"^^xsd:string ; @@ -3769,8 +3772,8 @@ bioregistry:ecocyc a bioregistry.schema:0000001 ; bioregistry:ecogene a bioregistry.schema:0000001 ; rdfs:label "Database of Escherichia coli Sequence and Function" ; dc:description "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EcoGene, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EcoGene, n2t:ecogene, ncbi.resource:EcoGene, fairsharing:FAIRsharing.3q3kvn, @@ -3785,8 +3788,8 @@ bioregistry:ecogene a bioregistry.schema:0000001 ; bioregistry:ecoliwiki a bioregistry.schema:0000001 ; rdfs:label "EcoliWiki from EcoliHub" ; dc:description "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ECOLIWIKI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ECOLIWIKI, go.resource:EcoliWiki, n2t:ecoliwiki, fairsharing:FAIRsharing.tx95wa, @@ -3800,8 +3803,8 @@ bioregistry:ecoliwiki a bioregistry.schema:0000001 ; bioregistry:ecyano.model a bioregistry.schema:0000001 ; rdfs:label "E-cyanobacterium model" ; dc:description "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ECYANO.MODEL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ECYANO.MODEL, n2t:ecyano.model, miriam:ecyano.model ; foaf:homepage "http://e-cyanobacterium.org/models/"^^xsd:string ; @@ -3813,8 +3816,8 @@ bioregistry:ecyano.model a bioregistry.schema:0000001 ; bioregistry:edda a bioregistry.schema:0000001 ; rdfs:label "EDDA Study Designs Taxonomy" ; dc:description "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EDDA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EDDA, bioportal:EDDA, fairsharing:FAIRsharing.2ffmsb ; foaf:homepage "https://bioportal.bioontology.org/ontologies/EDDA"^^xsd:string ; @@ -3824,8 +3827,8 @@ bioregistry:edda a bioregistry.schema:0000001 ; bioregistry:eggnog a bioregistry.schema:0000001 ; rdfs:label "eggNOG" ; dc:description "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EGGNOG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EGGNOG, n2t:eggnog, fairsharing:FAIRsharing.j1wj7d, prefixcommons:eggnog, @@ -3839,9 +3842,9 @@ bioregistry:eggnog a bioregistry.schema:0000001 ; bioregistry:ehda a bioregistry.schema:0000001 ; rdfs:label "Human developmental anatomy, timed version" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EHDA, - obofoundry:EHDA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EHDA, + obofoundry:ehda, bioportal:EHDA, biocontext:EHDA, prefixcommons:ehda ; @@ -3854,9 +3857,9 @@ bioregistry:ehda a bioregistry.schema:0000001 ; bioregistry:ehdaa a bioregistry.schema:0000001 ; rdfs:label "Human developmental anatomy, abstract version" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EHDAA, - obofoundry:EHDAA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EHDAA, + obofoundry:ehdaa, bioportal:EHDAA, biocontext:EHDAA, prefixcommons:ehdaa ; @@ -3866,11 +3869,32 @@ bioregistry:ehdaa a bioregistry.schema:0000001 ; bioregistry.schema:0000012 true ; bioregistry.schema:0000019 [ rdfs:label "Jonathan Bard" ] . +bioregistry:ehdaa2 a bioregistry.schema:0000001 ; + rdfs:label "Human developmental anatomy, abstract" ; + dc:description "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EHDAA2, + obofoundry:ehdaa2, + ontobee:EHDAA2, + bioportal:EHDAA2, + biocontext:EHDAA2, + fairsharing:FAIRsharing.7zxrs6, + ols:ehdaa2 ; + foaf:homepage "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^xsd:string ; + bioregistry.schema:0000005 "0000000"^^xsd:string ; + bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/EHDAA2_$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000017 bioregistry:aeo, + bioregistry:caro, + bioregistry:cl ; + bioregistry.schema:0000019 [ rdfs:label "Jonathan Bard" ] . + bioregistry:elm a bioregistry.schema:0000001 ; rdfs:label "Eukaryotic Linear Motif Resource" ; dc:description "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ELM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ELM, n2t:elm, fairsharing:FAIRsharing.rj3kj5, miriam:elm, @@ -3884,8 +3908,8 @@ bioregistry:elm a bioregistry.schema:0000001 ; bioregistry:emap a bioregistry.schema:0000001 ; rdfs:label "Mouse gross anatomy and development, timed" ; dc:description "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:EMAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:emap, bioportal:EMAP, biocontext:EMAP ; foaf:homepage "http://emouseatlas.org"^^xsd:string ; @@ -3898,9 +3922,9 @@ bioregistry:emap a bioregistry.schema:0000001 ; bioregistry:emapa a bioregistry.schema:0000001 ; rdfs:label "Mouse Developmental Anatomy Ontology" ; dc:description "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EMAPA, - obofoundry:EMAPA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EMAPA, + obofoundry:emapa, ontobee:EMAPA, bioportal:EMAPA, biocontext:EMAPA, @@ -3917,8 +3941,8 @@ bioregistry:emapa a bioregistry.schema:0000001 ; bioregistry:encode a bioregistry.schema:0000001 ; rdfs:label "Encyclopedia of DNA Elements" ; dc:description "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENCODE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENCODE, cellosaurus.resource:ENCODE, n2t:encode, fairsharing:FAIRsharing.v0hbjs, @@ -3932,8 +3956,8 @@ bioregistry:encode a bioregistry.schema:0000001 ; bioregistry:enm a bioregistry.schema:0000001 ; rdfs:label "eNanoMapper Ontology" ; dc:description "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ENM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ENM, bioportal:ENM, fairsharing:FAIRsharing.2gpf81, ols:enm ; @@ -3945,8 +3969,8 @@ bioregistry:enm a bioregistry.schema:0000001 ; bioregistry:ensembl a bioregistry.schema:0000001 ; rdfs:label "Ensembl Gene" ; dc:description "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2610, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2610, biocontext:ENSEMBL, go.resource:ENSEMBL, n2t:ensembl, @@ -3965,8 +3989,8 @@ bioregistry:ensembl a bioregistry.schema:0000001 ; bioregistry:ensembl.bacteria a bioregistry.schema:0000001 ; rdfs:label "Ensembl Bacteria" ; dc:description "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENSEMBL.BACTERIA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENSEMBL.BACTERIA, n2t:ensembl.bacteria, fairsharing:FAIRsharing.zsgmvd, prefixcommons:ensembl.bacteria, @@ -3981,8 +4005,8 @@ bioregistry:ensembl.bacteria a bioregistry.schema:0000001 ; bioregistry:ensembl.fungi a bioregistry.schema:0000001 ; rdfs:label "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." ; dc:description "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENSEMBL.FUNGI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENSEMBL.FUNGI, go.resource:EnsemblFungi, n2t:ensembl.fungi, fairsharing:FAIRsharing.bg5xqs, @@ -3998,8 +4022,8 @@ bioregistry:ensembl.fungi a bioregistry.schema:0000001 ; bioregistry:ensembl.metazoa a bioregistry.schema:0000001 ; rdfs:label "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." ; dc:description "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENSEMBL.METAZOA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENSEMBL.METAZOA, go.resource:EnsemblMetazoa, n2t:ensembl.metazoa, fairsharing:FAIRsharing.c23cqq, @@ -4015,8 +4039,8 @@ bioregistry:ensembl.metazoa a bioregistry.schema:0000001 ; bioregistry:ensembl.plant a bioregistry.schema:0000001 ; rdfs:label "Ensembl Plants" ; dc:description "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENSEMBL.PLANT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENSEMBL.PLANT, n2t:ensembl.plant, prefixcommons:ensembl.plant, miriam:ensembl.plant ; @@ -4029,8 +4053,8 @@ bioregistry:ensembl.plant a bioregistry.schema:0000001 ; bioregistry:ensembl.protist a bioregistry.schema:0000001 ; rdfs:label "Ensembl Protists" ; dc:description "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENSEMBL.PROTIST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENSEMBL.PROTIST, n2t:ensembl.protist, prefixcommons:ensembl.protist, miriam:ensembl.protist ; @@ -4043,8 +4067,8 @@ bioregistry:ensembl.protist a bioregistry.schema:0000001 ; bioregistry:ensemblglossary a bioregistry.schema:0000001 ; rdfs:label "Ensembl Glossary" ; dc:description "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ols:ensemblglossary ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ols:ensemblglossary ; foaf:homepage "http://ensembl.org/glossary"^^xsd:string ; bioregistry.schema:0000005 "0000198"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -4053,8 +4077,8 @@ bioregistry:ensemblglossary a bioregistry.schema:0000001 ; bioregistry:envipath a bioregistry.schema:0000001 ; rdfs:label "enviPath" ; dc:description "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.g0c5qn, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.g0c5qn, miriam:envipath ; foaf:homepage "https://envipath.org/"^^xsd:string ; bioregistry.schema:0000005 "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^xsd:string ; @@ -4062,11 +4086,30 @@ bioregistry:envipath a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:eo a bioregistry.schema:0000001 ; + rdfs:label "Plant Environment Ontology" ; + dc:description "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EO, + agroportal:EO, + obofoundry:eo, + biocontext:EO, + n2t:eo, + prefixcommons:eo, + miriam:eo ; + foaf:homepage "http://planteome.org/"^^xsd:string ; + bioregistry.schema:0000005 "0007404"^^xsd:string ; + bioregistry.schema:0000006 "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000018 bioregistry:foodon ; + bioregistry.schema:0000019 orcid:0000-0002-1005-8383 . + bioregistry:epd a bioregistry.schema:0000001 ; rdfs:label "Eukaryotic Promoter Database" ; dc:description "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2386, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2386, biocontext:EPD, n2t:epd, ncbi.resource:EPD, @@ -4082,9 +4125,9 @@ bioregistry:epd a bioregistry.schema:0000001 ; bioregistry:epo a bioregistry.schema:0000001 ; rdfs:label "Epidemiology Ontology" ; dc:description "An ontology designed to support the semantic annotation of epidemiology resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EPO, - obofoundry:EPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EPO, + obofoundry:epo, ontobee:EPO, bioportal:EPO, biocontext:EPO ; @@ -4095,8 +4138,8 @@ bioregistry:epo a bioregistry.schema:0000001 ; bioregistry:epso a bioregistry.schema:0000001 ; rdfs:label "Epilepsy and Seizure Ontology" ; dc:description "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EPSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EPSO, ontobee:EPSO, bioportal:EPSO, fairsharing:FAIRsharing.ttprgy ; @@ -4108,8 +4151,8 @@ bioregistry:epso a bioregistry.schema:0000001 ; bioregistry:erm a bioregistry.schema:0000001 ; rdfs:label "European Registry of Materials" ; dc:description "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:erm, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:erm, miriam:erm ; foaf:homepage "https://nanocommons.github.io/identifiers/"^^xsd:string ; bioregistry.schema:0000005 "ERM00000044"^^xsd:string ; @@ -4120,9 +4163,9 @@ bioregistry:erm a bioregistry.schema:0000001 ; bioregistry:ero a bioregistry.schema:0000001 ; rdfs:label "eagle-i resource ontology" ; dc:description "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ERO, - obofoundry:ERO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ERO, + obofoundry:ero, ontobee:ERO, bioportal:ERO, biocontext:ERO, @@ -4138,8 +4181,8 @@ bioregistry:ero a bioregistry.schema:0000001 ; bioregistry:erv a bioregistry.schema:0000001 ; rdfs:label "Human Endogenous Retrovirus Database" ; dc:description "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ERV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ERV, n2t:erv, miriam:erv ; foaf:homepage "https://herv.img.cas.cz/"^^xsd:string ; @@ -4151,8 +4194,8 @@ bioregistry:erv a bioregistry.schema:0000001 ; bioregistry:estdab a bioregistry.schema:0000001 ; rdfs:label "European Searchable Tumour Line Database" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ESTDAB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ESTDAB ; foaf:homepage "https://www.ebi.ac.uk/ipd/estdab/"^^xsd:string ; bioregistry.schema:0000005 "046"^^xsd:string ; bioregistry.schema:0000006 "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^xsd:string ; @@ -4162,8 +4205,8 @@ bioregistry:estdab a bioregistry.schema:0000001 ; bioregistry:eu89h a bioregistry.schema:0000001 ; rdfs:label "JRC Data Catalogue" ; dc:description "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EU89H, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EU89H, n2t:eu89h, miriam:eu89h ; foaf:homepage "http://data.jrc.ec.europa.eu/"^^xsd:string ; @@ -4176,8 +4219,8 @@ bioregistry:euclinicaltrials a bioregistry.schema:0000001 ; rdfs:label "EU Clinical Trials" ; dc:description """The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EUCLINICALTRIALS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EUCLINICALTRIALS, n2t:euclinicaltrials, miriam:euclinicaltrials ; foaf:homepage "https://www.clinicaltrialsregister.eu/"^^xsd:string ; @@ -4188,8 +4231,8 @@ It also includes trials conducted outside these areas if they form part of a pae bioregistry:ev a bioregistry.schema:0000001 ; rdfs:label "eVOC (Expressed Sequence Annotation for Humans)" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:EV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:ev, biocontext:EV ; foaf:homepage "http://www.evocontology.org/"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/EV_$1"^^xsd:string ; @@ -4200,8 +4243,8 @@ bioregistry:ev a bioregistry.schema:0000001 ; bioregistry:exac.gene a bioregistry.schema:0000001 ; rdfs:label "ExAC Gene" ; dc:description "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EXAC.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EXAC.GENE, n2t:exac.gene, miriam:exac.gene ; foaf:homepage "http://exac.broadinstitute.org/"^^xsd:string ; @@ -4213,8 +4256,8 @@ bioregistry:exac.gene a bioregistry.schema:0000001 ; bioregistry:exac.transcript a bioregistry.schema:0000001 ; rdfs:label "ExAC Transcript" ; dc:description "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EXAC.TRANSCRIPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EXAC.TRANSCRIPT, n2t:exac.transcript, miriam:exac.transcript ; foaf:homepage "http://exac.broadinstitute.org/"^^xsd:string ; @@ -4226,8 +4269,8 @@ bioregistry:exac.transcript a bioregistry.schema:0000001 ; bioregistry:exac.variant a bioregistry.schema:0000001 ; rdfs:label "ExAC Variant" ; dc:description "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EXAC.VARIANT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EXAC.VARIANT, n2t:exac.variant, miriam:exac.variant ; foaf:homepage "http://exac.broadinstitute.org/"^^xsd:string ; @@ -4239,8 +4282,8 @@ bioregistry:exac.variant a bioregistry.schema:0000001 ; bioregistry:facebase a bioregistry.schema:0000001 ; rdfs:label "FaceBase Data Repository" ; dc:description "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FACEBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FACEBASE, n2t:facebase, fairsharing:FAIRsharing.mqvqde, miriam:facebase ; @@ -4253,8 +4296,8 @@ bioregistry:facebase a bioregistry.schema:0000001 ; bioregistry:fairsharing a bioregistry.schema:0000001 ; rdfs:label "FAIRsharing" ; dc:description "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FAIRSHARING, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FAIRSHARING, n2t:fairsharing, fairsharing:FAIRsharing.2abjs5, miriam:fairsharing ; @@ -4267,9 +4310,9 @@ bioregistry:fairsharing a bioregistry.schema:0000001 ; bioregistry:fao a bioregistry.schema:0000001 ; rdfs:label "Fungal gross anatomy" ; dc:description "A structured controlled vocabulary for the anatomy of fungi."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FAO, - obofoundry:FAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FAO, + obofoundry:fao, ontobee:FAO, bioportal:FAO, biocontext:FAO, @@ -4286,9 +4329,9 @@ bioregistry:fao a bioregistry.schema:0000001 ; bioregistry:fbbi a bioregistry.schema:0000001 ; rdfs:label "Biological Imaging Methods Ontology" ; dc:description "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FBbi, - obofoundry:FBbi, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FBbi, + obofoundry:fbbi, ontobee:FBBI, bioportal:FBbi, biocontext:FBbi, @@ -4305,9 +4348,9 @@ bioregistry:fbbi a bioregistry.schema:0000001 ; bioregistry:fbdv a bioregistry.schema:0000001 ; rdfs:label "Drosophila development" ; dc:description "An ontology of Drosophila melanogaster developmental stages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FBDV, - obofoundry:FBdv, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FBDV, + obofoundry:fbdv, ontobee:FBdv, bioportal:FB-DV, biocontext:FBdv, @@ -4324,8 +4367,8 @@ bioregistry:fbdv a bioregistry.schema:0000001 ; bioregistry:fbol a bioregistry.schema:0000001 ; rdfs:label "International Fungal Working Group Fungal Barcoding." ; dc:description "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FBOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FBOL, n2t:fbol, ncbi.resource:FBOL, miriam:fbol ; @@ -4340,8 +4383,8 @@ bioregistry:fcb a bioregistry.schema:0000001 ; dc:description """Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). """^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:fcb ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:fcb ; foaf:homepage "https://w3id.org"^^xsd:string ; bioregistry.schema:0000005 "FCB005"^^xsd:string ; bioregistry.schema:0000006 "https://w3id.org/faircookbook/$1"^^xsd:string ; @@ -4351,9 +4394,9 @@ bioregistry:fcb a bioregistry.schema:0000001 ; bioregistry:fideo a bioregistry.schema:0000001 ; rdfs:label "Food Interactions with Drugs Evidence Ontology" ; dc:description "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FIDEO, - obofoundry:FIDEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FIDEO, + obofoundry:fideo, ontobee:FIDEO, bioportal:FIDEO, ols:fideo ; @@ -4367,8 +4410,8 @@ bioregistry:fideo a bioregistry.schema:0000001 ; bioregistry:fishbase.species a bioregistry.schema:0000001 ; rdfs:label "FishBase" ; dc:description "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P938 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P938 ; foaf:homepage "http://fishbase.org"^^xsd:string ; bioregistry.schema:0000005 "6472"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -4377,10 +4420,10 @@ bioregistry:fishbase.species a bioregistry.schema:0000001 ; bioregistry:flopo a bioregistry.schema:0000001 ; rdfs:label "Flora Phenotype Ontology" ; dc:description "Traits and phenotypes of flowering plants occurring in digitized Floras"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FLOPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FLOPO, agroportal:FLOPO, - obofoundry:FLOPO, + obofoundry:flopo, ontobee:FLOPO, bioportal:FLOPO, biocontext:FLOPO, @@ -4396,8 +4439,8 @@ bioregistry:flopo a bioregistry.schema:0000001 ; bioregistry:flowrepository a bioregistry.schema:0000001 ; rdfs:label "FlowRepository" ; dc:description "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:flowrepository, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:flowrepository, fairsharing:FAIRsharing.veg2d6, miriam:flowrepository ; foaf:homepage "https://flowrepository.org/"^^xsd:string ; @@ -4408,9 +4451,9 @@ bioregistry:flowrepository a bioregistry.schema:0000001 ; bioregistry:flu a bioregistry.schema:0000001 ; rdfs:label "Influenza Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FLU, - obofoundry:FLU, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FLU, + obofoundry:flu, bioportal:FLU, biocontext:FLU ; foaf:homepage "http://purl.obolibrary.org/obo/flu/"^^xsd:string ; @@ -4423,10 +4466,10 @@ bioregistry:flu a bioregistry.schema:0000001 ; bioregistry:fma a bioregistry.schema:0000001 ; rdfs:label "Foundational Model of Anatomy" ; dc:description "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FMA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FMA, edam.data:1182, - obofoundry:FMA, + obofoundry:fma, ontobee:FMA, bioportal:FMA, biocontext:FMA, @@ -4446,8 +4489,8 @@ bioregistry:fma a bioregistry.schema:0000001 ; bioregistry:foodb.compound a bioregistry.schema:0000001 ; rdfs:label "FooDB Compound" ; dc:description "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FOODB.COMPOUND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FOODB.COMPOUND, biolink:foodb.compound, n2t:foodb.compound, miriam:foodb.compound ; @@ -4460,8 +4503,8 @@ bioregistry:foodb.compound a bioregistry.schema:0000001 ; bioregistry:fplx a bioregistry.schema:0000001 ; rdfs:label "FamPlex" ; dc:description "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FPLX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FPLX, bioportal:FPLX, biocontext:FPLX, n2t:fplx, @@ -4475,8 +4518,8 @@ bioregistry:fplx a bioregistry.schema:0000001 ; bioregistry:fsnp a bioregistry.schema:0000001 ; rdfs:label "F-SNP" ; dc:description "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FSNP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FSNP, n2t:fsnp, prefixcommons:fsnp, miriam:fsnp ; @@ -4489,8 +4532,8 @@ bioregistry:fsnp a bioregistry.schema:0000001 ; bioregistry:funcbase.fly a bioregistry.schema:0000001 ; rdfs:label "FuncBase Fly" ; dc:description "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FUNCBASE.FLY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FUNCBASE.FLY, n2t:funcbase.fly, miriam:funcbase.fly ; foaf:homepage "http://func.mshri.on.ca/fly"^^xsd:string ; @@ -4502,8 +4545,8 @@ bioregistry:funcbase.fly a bioregistry.schema:0000001 ; bioregistry:funcbase.human a bioregistry.schema:0000001 ; rdfs:label "FuncBase Human" ; dc:description "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FUNCBASE.HUMAN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FUNCBASE.HUMAN, n2t:funcbase.human, miriam:funcbase.human ; foaf:homepage "http://func.mshri.on.ca/human/"^^xsd:string ; @@ -4515,8 +4558,8 @@ bioregistry:funcbase.human a bioregistry.schema:0000001 ; bioregistry:funcbase.mouse a bioregistry.schema:0000001 ; rdfs:label "FuncBase Mouse" ; dc:description "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FUNCBASE.MOUSE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FUNCBASE.MOUSE, n2t:funcbase.mouse, miriam:funcbase.mouse ; foaf:homepage "http://func.mshri.on.ca/mouse/"^^xsd:string ; @@ -4528,8 +4571,8 @@ bioregistry:funcbase.mouse a bioregistry.schema:0000001 ; bioregistry:funcbase.yeast a bioregistry.schema:0000001 ; rdfs:label "FuncBase Yeast" ; dc:description "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FUNCBASE.YEAST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FUNCBASE.YEAST, n2t:funcbase.yeast, miriam:funcbase.yeast ; foaf:homepage "http://func.mshri.on.ca/yeast"^^xsd:string ; @@ -4541,8 +4584,8 @@ bioregistry:funcbase.yeast a bioregistry.schema:0000001 ; bioregistry:funderregistry a bioregistry.schema:0000001 ; rdfs:label "FunderRegistry" ; dc:description "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:funderregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:funderregistry ; foaf:homepage "https://www.crossref.org/"^^xsd:string ; bioregistry.schema:0000005 "100000001"^^xsd:string ; bioregistry.schema:0000006 "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^xsd:string ; @@ -4552,8 +4595,8 @@ bioregistry:funderregistry a bioregistry.schema:0000001 ; bioregistry:fungidb a bioregistry.schema:0000001 ; rdfs:label "FungiDB" ; dc:description "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:FUNGIDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:FUNGIDB, n2t:fungidb, fairsharing:FAIRsharing.xf30yc, miriam:fungidb ; @@ -4566,9 +4609,9 @@ bioregistry:fungidb a bioregistry.schema:0000001 ; bioregistry:fypo a bioregistry.schema:0000001 ; rdfs:label "Fission Yeast Phenotype Ontology" ; dc:description "A formal ontology of phenotypes observed in fission yeast."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FYPO, - obofoundry:FYPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FYPO, + obofoundry:fypo, ontobee:FYPO, bioportal:FYPO, biocontext:FYPO, @@ -4586,8 +4629,8 @@ bioregistry:fypo a bioregistry.schema:0000001 ; bioregistry:ga4ghdos a bioregistry.schema:0000001 ; rdfs:label "Data Object Service" ; dc:description "Assists in resolving data across cloud resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GA4GHDOS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GA4GHDOS, n2t:ga4ghdos, miriam:ga4ghdos ; foaf:homepage "http://github.com/ga4gh/data-object-service-schemas"^^xsd:string ; @@ -4599,8 +4642,8 @@ bioregistry:ga4ghdos a bioregistry.schema:0000001 ; bioregistry:gabi a bioregistry.schema:0000001 ; rdfs:label "Network of Different Plant Genomic Research Projects" ; dc:description "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GABI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GABI, n2t:gabi, ncbi.resource:GABI, prefixcommons:gabi, @@ -4613,8 +4656,8 @@ bioregistry:gabi a bioregistry.schema:0000001 ; bioregistry:galen a bioregistry.schema:0000001 ; rdfs:label "GALEN" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GALEN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GALEN, bioportal:GALEN ; foaf:homepage "https://www.opengalen.org"^^xsd:string ; bioregistry.schema:0000005 "MagnitudeValueType"^^xsd:string ; @@ -4623,8 +4666,8 @@ bioregistry:galen a bioregistry.schema:0000001 ; bioregistry:gard a bioregistry.schema:0000001 ; rdfs:label "Genetic and Rare Diseases Information Center" ; dc:description "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P4317 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P4317 ; foaf:homepage "https://rarediseases.info.nih.gov/diseases"^^xsd:string ; bioregistry.schema:0000005 "6038"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -4633,20 +4676,40 @@ bioregistry:gard a bioregistry.schema:0000001 ; bioregistry:gateway a bioregistry.schema:0000001 ; rdfs:label "Health Data Research Innovation Gateway" ; dc:description "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:gateway ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:gateway ; foaf:homepage "https://www.hdruk.ac.uk"^^xsd:string ; bioregistry.schema:0000005 "fd8d0743-344a-4758-bb97-f8ad84a37357"^^xsd:string ; bioregistry.schema:0000006 "https://web.www.healthdatagateway.org/dataset/$1"^^xsd:string ; bioregistry.schema:0000008 "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:gaz a bioregistry.schema:0000001 ; + rdfs:label "Gazetteer" ; + dc:description "A gazetteer constructed on ontological principles"^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GAZ, + obofoundry:gaz, + ontobee:GAZ, + bioportal:GAZ, + biocontext:GAZ, + fairsharing:FAIRsharing.wkdjpb, + ols:gaz, + wikidata:P6778 ; + foaf:homepage "http://environmentontology.github.io/gaz/"^^xsd:string ; + bioregistry.schema:0000005 "00620027"^^xsd:string ; + bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/GAZ_$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d{8}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000018 bioregistry:scdo ; + bioregistry.schema:0000019 orcid:0000-0001-8910-9851 . + bioregistry:gbif a bioregistry.schema:0000001 ; rdfs:label "Global Biodiversity Information Facility" ; dc:description """Database of living organisms, taxonomic. The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.zv11j3, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.zv11j3, wikidata:P846 ; foaf:homepage "https://www.gbif.org/species"^^xsd:string ; bioregistry.schema:0000005 "4238"^^xsd:string ; @@ -4657,8 +4720,8 @@ bioregistry:gbif a bioregistry.schema:0000001 ; bioregistry:gcst a bioregistry.schema:0000001 ; rdfs:label "GWAS Catalog" ; dc:description "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:gcst, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:gcst, miriam:gcst ; foaf:homepage "https://www.ebi.ac.uk"^^xsd:string ; bioregistry.schema:0000005 "GCST000035"^^xsd:string ; @@ -4669,8 +4732,8 @@ bioregistry:gcst a bioregistry.schema:0000001 ; bioregistry:gdc a bioregistry.schema:0000001 ; rdfs:label "Genomic Data Commons Data Portal" ; dc:description "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GDC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GDC, n2t:gdc, miriam:gdc ; foaf:homepage "https://gdc.cancer.gov"^^xsd:string ; @@ -4682,8 +4745,8 @@ bioregistry:gdc a bioregistry.schema:0000001 ; bioregistry:gdsc a bioregistry.schema:0000001 ; rdfs:label "Genomics of Drug Sensitivity in Cancer" ; dc:description "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:GDSC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:GDSC, n2t:gdsc, miriam:gdsc ; foaf:homepage "https://www.cancerrxgene.org"^^xsd:string ; @@ -4695,9 +4758,9 @@ bioregistry:gdsc a bioregistry.schema:0000001 ; bioregistry:gecko a bioregistry.schema:0000001 ; rdfs:label "Genomics Cohorts Knowledge Ontology" ; dc:description "An ontology to represent genomics cohort attributes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GECKO, - obofoundry:GECKO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GECKO, + obofoundry:gecko, ontobee:GECKO, bioportal:GECKO, fairsharing:FAIRsharing.3da56b, @@ -4712,8 +4775,8 @@ bioregistry:gecko a bioregistry.schema:0000001 ; bioregistry:genatlas a bioregistry.schema:0000001 ; rdfs:label "Genatlas" ; dc:description "GenAtlas is a database containing information on human genes, markers and phenotypes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENATLAS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENATLAS, n2t:genatlas, fairsharing:FAIRsharing.pmg2vd, prefixcommons:genatlas, @@ -4728,8 +4791,8 @@ bioregistry:genatlas a bioregistry.schema:0000001 ; bioregistry:genecards a bioregistry.schema:0000001 ; rdfs:label "GeneCards" ; dc:description "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENECARDS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENECARDS, n2t:genecards, fairsharing:FAIRsharing.g7jbvn, prefixcommons:genecards, @@ -4744,8 +4807,8 @@ bioregistry:genecards a bioregistry.schema:0000001 ; bioregistry:genedb a bioregistry.schema:0000001 ; rdfs:label "GeneDB" ; dc:description "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1035, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1035, biocontext:GENEDB, go.resource:GeneDB, n2t:genedb, @@ -4764,8 +4827,8 @@ bioregistry:genedb a bioregistry.schema:0000001 ; bioregistry:genefarm a bioregistry.schema:0000001 ; rdfs:label "GeneFarm" ; dc:description "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENEFARM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENEFARM, n2t:genefarm, fairsharing:FAIRsharing.2mayq0, prefixcommons:genefarm, @@ -4779,8 +4842,8 @@ bioregistry:genefarm a bioregistry.schema:0000001 ; bioregistry:genetree a bioregistry.schema:0000001 ; rdfs:label "GeneTree" ; dc:description "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENETREE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENETREE, n2t:genetree, prefixcommons:genetree, miriam:genetree, @@ -4794,8 +4857,8 @@ bioregistry:genetree a bioregistry.schema:0000001 ; bioregistry:genewiki a bioregistry.schema:0000001 ; rdfs:label "Gene Wiki" ; dc:description "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENEWIKI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENEWIKI, n2t:genewiki, fairsharing:FAIRsharing.t3snf, miriam:genewiki, @@ -4811,9 +4874,9 @@ bioregistry:geno a bioregistry.schema:0000001 ; dc:description """GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GENO, - obofoundry:GENO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GENO, + obofoundry:geno, ontobee:GENO, bioportal:GENO, biocontext:GENO, @@ -4829,8 +4892,8 @@ Documentation is under development as well, and for now a slidedeck is available bioregistry:genpept a bioregistry.schema:0000001 ; rdfs:label "GenPept" ; dc:description "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENPEPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENPEPT, n2t:genpept, miriam:genpept ; foaf:homepage "https://www.ncbi.nlm.nih.gov/protein"^^xsd:string ; @@ -4842,8 +4905,8 @@ bioregistry:genpept a bioregistry.schema:0000001 ; bioregistry:genprop a bioregistry.schema:0000001 ; rdfs:label "Genome Properties" ; dc:description "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GENPROP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GENPROP, n2t:genprop, miriam:genprop ; foaf:homepage "https://www.ebi.ac.uk/interpro/genomeproperties/"^^xsd:string ; @@ -4855,8 +4918,8 @@ bioregistry:genprop a bioregistry.schema:0000001 ; bioregistry:geogeo a bioregistry.schema:0000001 ; rdfs:label "Geographical Entity Ontology" ; dc:description "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:GEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:geo, ontobee:GEO, bioportal:GEO, biocontext:GEO, @@ -4867,13 +4930,13 @@ bioregistry:geogeo a bioregistry.schema:0000001 ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/GEO_$1"^^xsd:string ; bioregistry.schema:0000008 "^\\d{9}$"^^xsd:string ; bioregistry.schema:0000012 false ; - bioregistry.schema:0000019 [ rdfs:label "Bill Hogan" ] . + bioregistry.schema:0000019 orcid:0000-0002-9881-1017 . bioregistry:gexo a bioregistry.schema:0000001 ; rdfs:label "Gene Expression Ontology" ; dc:description "Gene Expression Ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GEXO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GEXO, bioportal:GEXO, fairsharing:FAIRsharing.3e0sn4, ols:gexo ; @@ -4883,8 +4946,8 @@ bioregistry:gexo a bioregistry.schema:0000001 ; bioregistry:giardiadb a bioregistry.schema:0000001 ; rdfs:label "GiardiaDB" ; dc:description "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GIARDIADB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GIARDIADB, n2t:giardiadb, fairsharing:FAIRsharing.e7skwg, prefixcommons:giardiadb, @@ -4898,8 +4961,8 @@ bioregistry:giardiadb a bioregistry.schema:0000001 ; bioregistry:github a bioregistry.schema:0000001 ; rdfs:label "github" ; dc:description "GitHub is an online host of Git source code repositories."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.c55d5e, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.c55d5e, miriam:github ; foaf:homepage "https://github.com/"^^xsd:string ; bioregistry.schema:0000005 "biopragmatics/bioregistry"^^xsd:string ; @@ -4910,8 +4973,8 @@ bioregistry:github a bioregistry.schema:0000001 ; bioregistry:gitlab a bioregistry.schema:0000001 ; rdfs:label "GitLab" ; dc:description "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.530e61, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.530e61, miriam:gitlab ; foaf:homepage "https://gitlab.com/"^^xsd:string ; bioregistry.schema:0000005 "morpheus.lab/morpheus"^^xsd:string ; @@ -4922,8 +4985,8 @@ bioregistry:gitlab a bioregistry.schema:0000001 ; bioregistry:glida.gpcr a bioregistry.schema:0000001 ; rdfs:label "GLIDA GPCR" ; dc:description "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GLIDA.GPCR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GLIDA.GPCR, n2t:glida.gpcr, miriam:glida.gpcr ; foaf:homepage "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^xsd:string ; @@ -4935,8 +4998,8 @@ bioregistry:glida.gpcr a bioregistry.schema:0000001 ; bioregistry:glida.ligand a bioregistry.schema:0000001 ; rdfs:label "GLIDA Ligand" ; dc:description "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GLIDA.LIGAND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GLIDA.LIGAND, n2t:glida.ligand, miriam:glida.ligand ; foaf:homepage "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^xsd:string ; @@ -4948,8 +5011,8 @@ bioregistry:glida.ligand a bioregistry.schema:0000001 ; bioregistry:glycoepitope a bioregistry.schema:0000001 ; rdfs:label "GlycoEpitope" ; dc:description "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GLYCOEPITOPE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GLYCOEPITOPE, n2t:glycoepitope, miriam:glycoepitope ; foaf:homepage "https://www.glycoepitope.jp/epitopes/"^^xsd:string ; @@ -4961,8 +5024,8 @@ bioregistry:glycoepitope a bioregistry.schema:0000001 ; bioregistry:glycomedb a bioregistry.schema:0000001 ; rdfs:label "GlycomeDB" ; dc:description "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2664, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2664, biocontext:GLYCOMEDB, n2t:glycomedb, fairsharing:FAIRsharing.k5k0yh, @@ -4978,8 +5041,8 @@ bioregistry:glycomedb a bioregistry.schema:0000001 ; bioregistry:glyconavi a bioregistry.schema:0000001 ; rdfs:label "GlycoNAVI" ; dc:description "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.wvp1t7, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.wvp1t7, miriam:glyconavi ; foaf:homepage "https://www.noguchi.or.jp/"^^xsd:string ; bioregistry.schema:0000005 "GN_G03681DA"^^xsd:string ; @@ -4990,8 +5053,8 @@ bioregistry:glyconavi a bioregistry.schema:0000001 ; bioregistry:glycopost a bioregistry.schema:0000001 ; rdfs:label "GlycoPOST" ; dc:description "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.2y1KMt, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.2y1KMt, miriam:glycopost ; foaf:homepage "https://glycopost.glycosmos.org"^^xsd:string ; bioregistry.schema:0000005 "GPST000024"^^xsd:string ; @@ -5002,8 +5065,8 @@ bioregistry:glycopost a bioregistry.schema:0000001 ; bioregistry:glygen a bioregistry.schema:0000001 ; rdfs:label "Computational and Informatics Resources for Glycoscience" ; dc:description "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.aI1J5W, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.aI1J5W, uniprot.resource:GlyGen ; foaf:homepage "https://glygen.org/glycan/"^^xsd:string ; bioregistry.schema:0000005 "G24361QY"^^xsd:string ; @@ -5013,8 +5076,8 @@ bioregistry:glygen a bioregistry.schema:0000001 ; bioregistry:gmd a bioregistry.schema:0000001 ; rdfs:label "Golm Metabolome Database" ; dc:description "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GMD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GMD, n2t:gmd, fairsharing:FAIRsharing.jykmkw, miriam:gmd ; @@ -5027,8 +5090,8 @@ bioregistry:gmd a bioregistry.schema:0000001 ; bioregistry:gmd.analyte a bioregistry.schema:0000001 ; rdfs:label "Golm Metabolome Database Analyte" ; dc:description "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GMD.ANALYTE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GMD.ANALYTE, n2t:gmd.analyte, miriam:gmd.analyte ; foaf:homepage "http://gmd.mpimp-golm.mpg.de/"^^xsd:string ; @@ -5040,8 +5103,8 @@ bioregistry:gmd.analyte a bioregistry.schema:0000001 ; bioregistry:gmd.gcms a bioregistry.schema:0000001 ; rdfs:label "Golm Metabolome Database GC-MS spectra" ; dc:description "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GMD.GCMS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GMD.GCMS, n2t:gmd.gcms, miriam:gmd.gcms ; foaf:homepage "http://gmd.mpimp-golm.mpg.de/"^^xsd:string ; @@ -5053,8 +5116,8 @@ bioregistry:gmd.gcms a bioregistry.schema:0000001 ; bioregistry:gmd.profile a bioregistry.schema:0000001 ; rdfs:label "Golm Metabolome Database Profile" ; dc:description "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GMD.PROFILE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GMD.PROFILE, n2t:gmd.profile, miriam:gmd.profile ; foaf:homepage "http://gmd.mpimp-golm.mpg.de/"^^xsd:string ; @@ -5066,8 +5129,8 @@ bioregistry:gmd.profile a bioregistry.schema:0000001 ; bioregistry:gmd.ref a bioregistry.schema:0000001 ; rdfs:label "Golm Metabolome Database Reference Substance" ; dc:description "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GMD.REF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GMD.REF, n2t:gmd.ref, miriam:gmd.ref ; foaf:homepage "http://gmd.mpimp-golm.mpg.de/"^^xsd:string ; @@ -5079,8 +5142,8 @@ bioregistry:gmd.ref a bioregistry.schema:0000001 ; bioregistry:gmelin a bioregistry.schema:0000001 ; rdfs:label "Gmelins Handbuch der anorganischen Chemie" ; dc:description "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1004, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1004, wikidata:P1578 ; foaf:homepage "https://link.springer.com/bookseries/562"^^xsd:string ; bioregistry.schema:0000005 "1466"^^xsd:string ; @@ -5090,9 +5153,9 @@ bioregistry:gmelin a bioregistry.schema:0000001 ; bioregistry:gno a bioregistry.schema:0000001 ; rdfs:label "Glycan Naming and Subsumption Ontology" ; dc:description "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GNO, - obofoundry:GNO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GNO, + obofoundry:gno, ontobee:GNO, bioportal:GNO, ols:gno ; @@ -5106,8 +5169,8 @@ bioregistry:gno a bioregistry.schema:0000001 ; bioregistry:gnpis a bioregistry.schema:0000001 ; rdfs:label "GnpIS" ; dc:description "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GNPIS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GNPIS, n2t:gnpis, fairsharing:FAIRsharing.dw22y3, miriam:gnpis ; @@ -5120,8 +5183,8 @@ bioregistry:gnpis a bioregistry.schema:0000001 ; bioregistry:go.model a bioregistry.schema:0000001 ; rdfs:label "Gene Ontology Causal Assembly Model" ; dc:description "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:gomodel ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:gomodel ; foaf:homepage "http://www.geneontology.org/gocam"^^xsd:string ; bioregistry.schema:0000005 "5fce9b7300001250"^^xsd:string ; bioregistry.schema:0000006 "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^xsd:string ; @@ -5130,8 +5193,8 @@ bioregistry:go.model a bioregistry.schema:0000001 ; bioregistry:go.ref a bioregistry.schema:0000001 ; rdfs:label "Gene Ontology Database references" ; dc:description "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GO_REF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GO_REF, go.resource:GO_REF, n2t:go.ref, miriam:go_ref ; @@ -5144,8 +5207,8 @@ bioregistry:go.ref a bioregistry.schema:0000001 ; bioregistry:goa a bioregistry.schema:0000001 ; rdfs:label "Gene Ontology Annotation Database" ; dc:description "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GOA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GOA, n2t:goa, ncbi.resource:GOA, fairsharing:FAIRsharing.7zffgc, @@ -5161,8 +5224,8 @@ bioregistry:goa a bioregistry.schema:0000001 ; bioregistry:gold a bioregistry.schema:0000001 ; rdfs:label "Genomes Online Database" ; dc:description "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.5q1p14, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.5q1p14, prefixcommons:gold, miriam:gold ; foaf:homepage "https://gold.jgi.doe.gov/"^^xsd:string ; @@ -5177,8 +5240,8 @@ bioregistry:gold.genome a bioregistry.schema:0000001 ; Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GOLD.GENOME, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GOLD.GENOME, n2t:gold.genome, miriam:gold.genome ; foaf:homepage "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^xsd:string ; @@ -5193,8 +5256,8 @@ bioregistry:gold.meta a bioregistry.schema:0000001 ; Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GOLD.META, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GOLD.META, n2t:gold.meta, miriam:gold.meta ; foaf:homepage "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^xsd:string ; @@ -5206,8 +5269,8 @@ The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of ge bioregistry:google.scholar a bioregistry.schema:0000001 ; rdfs:label "Google Scholar Researcher" ; dc:description "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:GSID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:GSID ; foaf:homepage "https://scholar.google.com/"^^xsd:string ; bioregistry.schema:0000005 "PjrpzUIAAAAJ"^^xsd:string ; bioregistry.schema:0000012 false . @@ -5215,8 +5278,8 @@ bioregistry:google.scholar a bioregistry.schema:0000001 ; bioregistry:gorel a bioregistry.schema:0000001 ; rdfs:label "GO Relations" ; dc:description "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:GOREL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:GOREL, go.resource:GOREL ; foaf:homepage "http://geneontology.org/docs/ontology-relations/"^^xsd:string ; bioregistry.schema:0000005 "0002005"^^xsd:string ; @@ -5226,8 +5289,8 @@ bioregistry:gorel a bioregistry.schema:0000001 ; bioregistry:gpcrdb a bioregistry.schema:0000001 ; rdfs:label "G protein-coupled receptor database" ; dc:description "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GPCRDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GPCRDB, n2t:gpcrdb, fairsharing:FAIRsharing.e4n3an, prefixcommons:gpcrdb, @@ -5242,8 +5305,8 @@ bioregistry:gpcrdb a bioregistry.schema:0000001 ; bioregistry:gpmdb a bioregistry.schema:0000001 ; rdfs:label "Global Proteome Machine Database" ; dc:description "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GPMDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GPMDB, n2t:gpmdb, fairsharing:FAIRsharing.fhcmwq, miriam:gpmdb ; @@ -5256,8 +5319,8 @@ bioregistry:gpmdb a bioregistry.schema:0000001 ; bioregistry:gramene.gene a bioregistry.schema:0000001 ; rdfs:label "Gramene Gene" ; dc:description "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRAMENE.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRAMENE.GENE, go.resource:GR_GENE, n2t:gramene.gene, miriam:gramene.gene ; @@ -5270,8 +5333,8 @@ bioregistry:gramene.gene a bioregistry.schema:0000001 ; bioregistry:gramene.growthstage a bioregistry.schema:0000001 ; rdfs:label "Gramene Growth Stage Ontology" ; dc:description "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRAMENE.GROWTHSTAGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRAMENE.GROWTHSTAGE, n2t:gramene.growthstage, miriam:gramene.growthstage ; foaf:homepage "http://www.gramene.org/"^^xsd:string ; @@ -5283,8 +5346,8 @@ bioregistry:gramene.growthstage a bioregistry.schema:0000001 ; bioregistry:gramene.protein a bioregistry.schema:0000001 ; rdfs:label "Gramene protein" ; dc:description "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRAMENE.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRAMENE.PROTEIN, go.resource:GR_PROTEIN, n2t:gramene.protein, miriam:gramene.protein ; @@ -5297,8 +5360,8 @@ bioregistry:gramene.protein a bioregistry.schema:0000001 ; bioregistry:gramene.qtl a bioregistry.schema:0000001 ; rdfs:label "Gramene QTL" ; dc:description "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRAMENE.QTL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRAMENE.QTL, go.resource:GR_QTL, n2t:gramene.qtl, miriam:gramene.qtl ; @@ -5311,8 +5374,8 @@ bioregistry:gramene.qtl a bioregistry.schema:0000001 ; bioregistry:gramene.taxonomy a bioregistry.schema:0000001 ; rdfs:label "Gramene Taxonomy" ; dc:description "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRAMENE.TAXONOMY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRAMENE.TAXONOMY, n2t:gramene.taxonomy, miriam:gramene.taxonomy ; foaf:homepage "http://www.gramene.org/"^^xsd:string ; @@ -5324,8 +5387,8 @@ bioregistry:gramene.taxonomy a bioregistry.schema:0000001 ; bioregistry:greengenes a bioregistry.schema:0000001 ; rdfs:label "16S rRNA gene database" ; dc:description "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GREENGENES, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GREENGENES, n2t:greengenes, ncbi.resource:Greengenes, fairsharing:FAIRsharing.bpxgb6, @@ -5340,8 +5403,8 @@ bioregistry:greengenes a bioregistry.schema:0000001 ; bioregistry:grid a bioregistry.schema:0000001 ; rdfs:label "Global Research Identifier Database" ; dc:description "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRID, n2t:grid, fairsharing:FAIRsharing.0pUMYW, miriam:grid ; @@ -5354,8 +5417,8 @@ bioregistry:grid a bioregistry.schema:0000001 ; bioregistry:grin.taxonomy a bioregistry.schema:0000001 ; rdfs:label "Germplasm Resources Information Network" ; dc:description "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRIN.TAXONOMY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRIN.TAXONOMY, go.resource:GRIN, n2t:grin.taxonomy, ncbi.resource:GRIN, @@ -5368,16 +5431,16 @@ bioregistry:grin.taxonomy a bioregistry.schema:0000001 ; bioregistry:gro a bioregistry.schema:0000001 ; rdfs:label "Gene Regulation Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GRO, bioportal:GRO ; bioregistry.schema:0000012 true . bioregistry:grsdb a bioregistry.schema:0000001 ; rdfs:label "G-Rich Sequences Database" ; dc:description "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GRSDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GRSDB, n2t:grsdb, prefixcommons:grsdb, miriam:grsdb ; @@ -5390,8 +5453,8 @@ bioregistry:grsdb a bioregistry.schema:0000001 ; bioregistry:gtex a bioregistry.schema:0000001 ; rdfs:label "Genotype-Tissue Expression" ; dc:description "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GTEX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GTEX, biolink:GTEx, n2t:gtex, miriam:gtex ; @@ -5404,8 +5467,8 @@ bioregistry:gtex a bioregistry.schema:0000001 ; bioregistry:gudmap a bioregistry.schema:0000001 ; rdfs:label "Genitourinary Development Molecular Anatomy Project" ; dc:description "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GUDMAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GUDMAP, n2t:gudmap, fairsharing:FAIRsharing.910c39, miriam:gudmap ; @@ -5418,8 +5481,8 @@ bioregistry:gudmap a bioregistry.schema:0000001 ; bioregistry:gwascentral.marker a bioregistry.schema:0000001 ; rdfs:label "GWAS Central Marker" ; dc:description "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GWASCENTRAL.MARKER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GWASCENTRAL.MARKER, n2t:gwascentral.marker, miriam:gwascentral.marker ; foaf:homepage "https://www.gwascentral.org/markers"^^xsd:string ; @@ -5431,8 +5494,8 @@ bioregistry:gwascentral.marker a bioregistry.schema:0000001 ; bioregistry:gwascentral.phenotype a bioregistry.schema:0000001 ; rdfs:label "GWAS Central Phenotype" ; dc:description "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GWASCENTRAL.PHENOTYPE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GWASCENTRAL.PHENOTYPE, n2t:gwascentral.phenotype, miriam:gwascentral.phenotype ; foaf:homepage "https://www.gwascentral.org/phenotypes"^^xsd:string ; @@ -5444,8 +5507,8 @@ bioregistry:gwascentral.phenotype a bioregistry.schema:0000001 ; bioregistry:gwascentral.study a bioregistry.schema:0000001 ; rdfs:label "GWAS Central Study" ; dc:description "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GWASCENTRAL.STUDY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GWASCENTRAL.STUDY, n2t:gwascentral.study, miriam:gwascentral.study ; foaf:homepage "https://www.gwascentral.org/studies"^^xsd:string ; @@ -5457,8 +5520,8 @@ bioregistry:gwascentral.study a bioregistry.schema:0000001 ; bioregistry:gxa.expt a bioregistry.schema:0000001 ; rdfs:label "GXA Expt" ; dc:description "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GXA.EXPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GXA.EXPT, n2t:gxa.expt, miriam:gxa.expt ; foaf:homepage "https://www.ebi.ac.uk/gxa/"^^xsd:string ; @@ -5470,8 +5533,8 @@ bioregistry:gxa.expt a bioregistry.schema:0000001 ; bioregistry:gxa.gene a bioregistry.schema:0000001 ; rdfs:label "GXA Gene" ; dc:description "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GXA.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GXA.GENE, n2t:gxa.gene, miriam:gxa.gene ; foaf:homepage "https://www.ebi.ac.uk/gxa/"^^xsd:string ; @@ -5482,8 +5545,8 @@ bioregistry:gxa.gene a bioregistry.schema:0000001 ; bioregistry:habronattus a bioregistry.schema:0000001 ; rdfs:label "Habronattus courtship" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:HABRONATTUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:habronattus, biocontext:HABRONATTUS ; foaf:homepage "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^xsd:string ; @@ -5493,8 +5556,8 @@ bioregistry:habronattus a bioregistry.schema:0000001 ; bioregistry:hamap a bioregistry.schema:0000001 ; rdfs:label "High-quality Automated and Manual Annotation of microbial Proteomes" ; dc:description "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2766, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2766, biocontext:HAMAP, go.resource:HAMAP, n2t:hamap, @@ -5511,9 +5574,9 @@ bioregistry:hamap a bioregistry.schema:0000001 ; bioregistry:hancestro a bioregistry.schema:0000001 ; rdfs:label "Human Ancestry Ontology" ; dc:description "Human ancestry ontology for the NHGRI GWAS Catalog"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HANCESTRO, - obofoundry:HANCESTRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HANCESTRO, + obofoundry:hancestro, ontobee:HANCESTRO, bioportal:HANCESTRO, biolink:HANCESTRO, @@ -5529,9 +5592,9 @@ bioregistry:hancestro a bioregistry.schema:0000001 ; bioregistry:hao a bioregistry.schema:0000001 ; rdfs:label "Hymenoptera Anatomy Ontology" ; dc:description "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HAO, - obofoundry:HAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HAO, + obofoundry:hao, ontobee:HAO, bioportal:HAO, biocontext:HAO, @@ -5547,16 +5610,16 @@ bioregistry:hao a bioregistry.schema:0000001 ; bioregistry:hcao a bioregistry.schema:0000001 ; rdfs:label "Human Cell Atlas Ontology" ; dc:description "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ols:hcao ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ols:hcao ; foaf:homepage "https://www.humancellatlas.org"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:hcpcs a bioregistry.schema:0000001 ; rdfs:label "Healthcare Common Procedure Coding System" ; dc:description "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HCPCS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HCPCS, bioportal:HCPCS, biolink:HCPCS, fairsharing:FAIRsharing.x81wz8 ; @@ -5567,8 +5630,8 @@ bioregistry:hcpcs a bioregistry.schema:0000001 ; bioregistry:hcvdb a bioregistry.schema:0000001 ; rdfs:label "Hepatitis C Virus Database" ; dc:description "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HCVDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HCVDB, n2t:hcvdb, miriam:hcvdb ; foaf:homepage "http://euhcvdb.ibcp.fr"^^xsd:string ; @@ -5580,8 +5643,8 @@ bioregistry:hcvdb a bioregistry.schema:0000001 ; bioregistry:hdr a bioregistry.schema:0000001 ; rdfs:label "Homeodomain Research" ; dc:description "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HDR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HDR, n2t:hdr, prefixcommons:hdr, miriam:hdr ; @@ -5594,8 +5657,8 @@ bioregistry:hdr a bioregistry.schema:0000001 ; bioregistry:hgmd a bioregistry.schema:0000001 ; rdfs:label "Human Gene Mutation Database" ; dc:description "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:3265, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:3265, biocontext:HGMD, n2t:hgmd, miriam:hgmd ; @@ -5608,8 +5671,8 @@ bioregistry:hgmd a bioregistry.schema:0000001 ; bioregistry:hgnc a bioregistry.schema:0000001 ; rdfs:label "HUGO Gene Nomenclature Committee" ; dc:description "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HGNC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HGNC, edam.data:2298, bioportal:HGNC, biocontext:HGNC, @@ -5631,8 +5694,8 @@ bioregistry:hgnc a bioregistry.schema:0000001 ; bioregistry:hgnc.genefamily a bioregistry.schema:0000001 ; rdfs:label "HGNC gene family" ; dc:description "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HGNC.GENEFAMILY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HGNC.GENEFAMILY, n2t:hgnc.genefamily, miriam:hgnc.genefamily ; foaf:homepage "http://www.genenames.org"^^xsd:string ; @@ -5645,8 +5708,8 @@ bioregistry:hgnc.genefamily a bioregistry.schema:0000001 ; bioregistry:hinv.locus a bioregistry.schema:0000001 ; rdfs:label "H-InvDb Locus" ; dc:description "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HINV.LOCUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HINV.LOCUS, n2t:hinv.locus, miriam:hinv.locus ; foaf:homepage "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^xsd:string ; @@ -5658,8 +5721,8 @@ bioregistry:hinv.locus a bioregistry.schema:0000001 ; bioregistry:hinv.protein a bioregistry.schema:0000001 ; rdfs:label "H-InvDb Protein" ; dc:description "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HINV.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HINV.PROTEIN, n2t:hinv.protein, miriam:hinv.protein ; foaf:homepage "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^xsd:string ; @@ -5671,8 +5734,8 @@ bioregistry:hinv.protein a bioregistry.schema:0000001 ; bioregistry:hinv.transcript a bioregistry.schema:0000001 ; rdfs:label "H-InvDb Transcript" ; dc:description "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HINV.TRANSCRIPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HINV.TRANSCRIPT, n2t:hinv.transcript, miriam:hinv.transcript ; foaf:homepage "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^xsd:string ; @@ -5684,8 +5747,8 @@ bioregistry:hinv.transcript a bioregistry.schema:0000001 ; bioregistry:hipsci a bioregistry.schema:0000001 ; rdfs:label "Human Induced Pluripotent Stem Cells Initiative" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:HipSci ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:HipSci ; foaf:homepage "http://www.hipsci.org"^^xsd:string ; bioregistry.schema:0000005 "HPSI0114i-bezi_1"^^xsd:string ; bioregistry.schema:0000006 "http://www.hipsci.org/lines/#/lines/$1"^^xsd:string ; @@ -5694,8 +5757,8 @@ bioregistry:hipsci a bioregistry.schema:0000001 ; bioregistry:hivreagentprogram a bioregistry.schema:0000001 ; rdfs:label "NIH HIV Reagent Program" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:HIVReagentProgram ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:HIVReagentProgram ; foaf:homepage "https://www.hivreagentprogram.org/Home.aspx"^^xsd:string ; bioregistry.schema:0000005 "ARP-1513"^^xsd:string ; bioregistry.schema:0000006 "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^xsd:string ; @@ -5704,8 +5767,8 @@ bioregistry:hivreagentprogram a bioregistry.schema:0000001 ; bioregistry:hogenom a bioregistry.schema:0000001 ; rdfs:label "Database of Complete Genome Homologous Genes Families" ; dc:description "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HOGENOM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HOGENOM, n2t:hogenom, fairsharing:FAIRsharing.qe8tz8, prefixcommons:hogenom, @@ -5720,9 +5783,9 @@ bioregistry:hogenom a bioregistry.schema:0000001 ; bioregistry:hom a bioregistry.schema:0000001 ; rdfs:label "Homology Ontology" ; dc:description "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HOM, - obofoundry:HOM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HOM, + obofoundry:hom, ontobee:HOM, bioportal:HOM, biocontext:HOM, @@ -5738,8 +5801,8 @@ bioregistry:hom a bioregistry.schema:0000001 ; bioregistry:homd.seq a bioregistry.schema:0000001 ; rdfs:label "HOMD Sequence Metainformation" ; dc:description "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HOMD.SEQ, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HOMD.SEQ, n2t:homd.seq, prefixcommons:homd.seq, miriam:homd.seq ; @@ -5752,8 +5815,8 @@ bioregistry:homd.seq a bioregistry.schema:0000001 ; bioregistry:homd.taxon a bioregistry.schema:0000001 ; rdfs:label "HOMD Taxonomy" ; dc:description "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HOMD.TAXON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HOMD.TAXON, n2t:homd.taxon, prefixcommons:homd.taxon, miriam:homd.taxon ; @@ -5766,8 +5829,8 @@ bioregistry:homd.taxon a bioregistry.schema:0000001 ; bioregistry:homologene a bioregistry.schema:0000001 ; rdfs:label "HomoloGene" ; dc:description "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HOMOLOGENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HOMOLOGENE, n2t:homologene, fairsharing:FAIRsharing.mzc066, prefixcommons:homologene, @@ -5782,8 +5845,8 @@ bioregistry:homologene a bioregistry.schema:0000001 ; bioregistry:horizon_discovery a bioregistry.schema:0000001 ; rdfs:label "Horizon Discovery cell line collection" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Horizon_Discovery ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Horizon_Discovery ; foaf:homepage "https://horizondiscovery.com/"^^xsd:string ; bioregistry.schema:0000005 "HD+118-001"^^xsd:string ; bioregistry.schema:0000006 "https://horizondiscovery.com/en/search?searchterm=$1"^^xsd:string ; @@ -5792,8 +5855,8 @@ bioregistry:horizon_discovery a bioregistry.schema:0000001 ; bioregistry:hovergen a bioregistry.schema:0000001 ; rdfs:label "Homologous Vertebrate Genes Database" ; dc:description "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HOVERGEN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HOVERGEN, n2t:hovergen, fairsharing:FAIRsharing.dg1f0e, prefixcommons:hovergen, @@ -5807,8 +5870,8 @@ bioregistry:hovergen a bioregistry.schema:0000001 ; bioregistry:hpa a bioregistry.schema:0000001 ; rdfs:label "Human Protein Atlas tissue profile information" ; dc:description "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HPA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HPA, go.resource:HPA, n2t:hpa, fairsharing:FAIRsharing.j0t0pe, @@ -5824,8 +5887,8 @@ bioregistry:hpa a bioregistry.schema:0000001 ; bioregistry:hpath a bioregistry.schema:0000001 ; rdfs:label "Histopathology Ontology" ; dc:description "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ols:hpath ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ols:hpath ; foaf:homepage "https://github.com/Novartis/hpath"^^xsd:string ; bioregistry.schema:0000005 "2000191"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -5834,8 +5897,8 @@ bioregistry:hpath a bioregistry.schema:0000001 ; bioregistry:hpm.peptide a bioregistry.schema:0000001 ; rdfs:label "Human Proteome Map Peptide" ; dc:description "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HPM.PEPTIDE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HPM.PEPTIDE, n2t:hpm.peptide, miriam:hpm.peptide ; foaf:homepage "http://www.humanproteomemap.org/index.php"^^xsd:string ; @@ -5847,8 +5910,8 @@ bioregistry:hpm.peptide a bioregistry.schema:0000001 ; bioregistry:hpm.protein a bioregistry.schema:0000001 ; rdfs:label "Human Proteome Map Protein" ; dc:description "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HPM.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HPM.PROTEIN, n2t:hpm.protein, miriam:hpm.protein ; foaf:homepage "http://www.humanproteomemap.org/index.php"^^xsd:string ; @@ -5860,8 +5923,8 @@ bioregistry:hpm.protein a bioregistry.schema:0000001 ; bioregistry:hprd a bioregistry.schema:0000001 ; rdfs:label "Human Protein Reference Database" ; dc:description "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HPRD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HPRD, n2t:hprd, fairsharing:FAIRsharing.y2qws7, prefixcommons:hprd, @@ -5875,8 +5938,8 @@ bioregistry:hprd a bioregistry.schema:0000001 ; bioregistry:hpscreg a bioregistry.schema:0000001 ; rdfs:label "Human Pluripotent Stem Cell Registry" ; dc:description "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:hPSCreg, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:hPSCreg, n2t:hpscreg, fairsharing:FAIRsharing.7C0aVE, miriam:hpscreg ; @@ -5889,8 +5952,8 @@ bioregistry:hpscreg a bioregistry.schema:0000001 ; bioregistry:hsdb a bioregistry.schema:0000001 ; rdfs:label "Hazardous Substances Data Bank" ; dc:description "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P2062 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P2062 ; foaf:homepage "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^xsd:string ; bioregistry.schema:0000005 "5621"^^xsd:string ; bioregistry.schema:0000006 "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^xsd:string ; @@ -5900,8 +5963,8 @@ bioregistry:hsdb a bioregistry.schema:0000001 ; bioregistry:hssp a bioregistry.schema:0000001 ; rdfs:label "Database of homology-derived secondary structure of proteins" ; dc:description "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HSSP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HSSP, n2t:hssp, ncbi.resource:HSSP, prefixcommons:hssp, @@ -5915,9 +5978,9 @@ bioregistry:hssp a bioregistry.schema:0000001 ; bioregistry:htn a bioregistry.schema:0000001 ; rdfs:label "Hypertension Ontology" ; dc:description "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HTN, - obofoundry:HTN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HTN, + obofoundry:htn, ontobee:HTN, bioportal:HTN, ols:htn ; @@ -5931,8 +5994,8 @@ bioregistry:htn a bioregistry.schema:0000001 ; bioregistry:huge a bioregistry.schema:0000001 ; rdfs:label "Human Unidentified Gene-Encoded" ; dc:description "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HUGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HUGE, n2t:huge, fairsharing:FAIRsharing.zx2ztd, prefixcommons:huge, @@ -5947,8 +6010,8 @@ bioregistry:huge a bioregistry.schema:0000001 ; bioregistry:icdc a bioregistry.schema:0000001 ; rdfs:label "Integrated Canine Data Commons" ; dc:description "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.d95034, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.d95034, miriam:icdc ; foaf:homepage "https://caninecommons.cancer.gov/#/"^^xsd:string ; bioregistry.schema:0000005 "000009"^^xsd:string ; @@ -5959,8 +6022,8 @@ bioregistry:icdc a bioregistry.schema:0000001 ; bioregistry:iceberg.element a bioregistry.schema:0000001 ; rdfs:label "ICEberg element" ; dc:description "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ICEBERG.ELEMENT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ICEBERG.ELEMENT, n2t:iceberg.element, miriam:iceberg.element ; foaf:homepage "http://db-mml.sjtu.edu.cn/ICEberg/"^^xsd:string ; @@ -5972,8 +6035,8 @@ bioregistry:iceberg.element a bioregistry.schema:0000001 ; bioregistry:iceberg.family a bioregistry.schema:0000001 ; rdfs:label "ICEberg family" ; dc:description "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ICEBERG.FAMILY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ICEBERG.FAMILY, n2t:iceberg.family, miriam:iceberg.family ; foaf:homepage "http://db-mml.sjtu.edu.cn/ICEberg/"^^xsd:string ; @@ -5985,9 +6048,9 @@ bioregistry:iceberg.family a bioregistry.schema:0000001 ; bioregistry:iceo a bioregistry.schema:0000001 ; rdfs:label "Integrative and Conjugative Element Ontology" ; dc:description "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICEO, - obofoundry:ICEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICEO, + obofoundry:iceo, ontobee:ICEO, bioportal:ICEO, ols:iceo ; @@ -6001,8 +6064,8 @@ bioregistry:iceo a bioregistry.schema:0000001 ; bioregistry:iclc a bioregistry.schema:0000001 ; rdfs:label "Interlab Cell Line Collection" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:ICLC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:ICLC ; foaf:homepage "http://www.iclc.it"^^xsd:string ; bioregistry.schema:0000005 "ATL98012"^^xsd:string ; bioregistry.schema:0000006 "http://www.iclc.it/details/det_list.php?line_id=$1"^^xsd:string ; @@ -6011,8 +6074,8 @@ bioregistry:iclc a bioregistry.schema:0000001 ; bioregistry:ideal a bioregistry.schema:0000001 ; rdfs:label "Intrinsically Disordered proteins with Extensive Annotations and Literature" ; dc:description "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IDEAL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IDEAL, n2t:ideal, fairsharing:FAIRsharing.h3y42f, miriam:ideal, @@ -6026,8 +6089,8 @@ bioregistry:ideal a bioregistry.schema:0000001 ; bioregistry:idocovid19 a bioregistry.schema:0000001 ; rdfs:label "The COVID-19 Infectious Disease Ontology" ; dc:description "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:IDO-COVID-19, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:IDO-COVID-19, bioportal:IDO-COVID-19, ols:idocovid19 ; foaf:homepage "https://github.com/infectious-disease-ontology-extensions/ido-covid-19"^^xsd:string ; @@ -6039,8 +6102,8 @@ bioregistry:idocovid19 a bioregistry.schema:0000001 ; bioregistry:idoden a bioregistry.schema:0000001 ; rdfs:label "Dengue Fever Ontology" ; dc:description "An ontology for dengue fever."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:IDODEN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:IDODEN, bioportal:IDODEN, fairsharing:FAIRsharing.askzq4 ; foaf:homepage "https://bioportal.bioontology.org/ontologies/IDODEN"^^xsd:string ; @@ -6048,11 +6111,30 @@ bioregistry:idoden a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:idomal a bioregistry.schema:0000001 ; + rdfs:label "Malaria Ontology" ; + dc:description "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:IDOMAL, + obofoundry:idomal, + ontobee:IDOMAL, + bioportal:IDOMAL, + biocontext:IDOMAL, + fairsharing:FAIRsharing.2q8c28, + ols:idomal ; + foaf:homepage "https://www.vectorbase.org/ontology-browser"^^xsd:string ; + bioregistry.schema:0000005 "0002350"^^xsd:string ; + bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/IDOMAL_$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000018 bioregistry:scdo ; + bioregistry.schema:0000019 [ rdfs:label "Pantelis Topalis" ] . + bioregistry:idoo a bioregistry.schema:0000001 ; rdfs:label "Identifiers.org Ontology" ; dc:description "Identifiers.org Ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:idoo, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:idoo, miriam:idoo ; foaf:homepage "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology"^^xsd:string ; bioregistry.schema:0000005 "DataCollection"^^xsd:string ; @@ -6063,8 +6145,8 @@ bioregistry:idoo a bioregistry.schema:0000001 ; bioregistry:iedb a bioregistry.schema:0000001 ; rdfs:label "Immune Epitope Database" ; dc:description "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.c886cd, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.c886cd, miriam:iedb ; foaf:homepage "https://www.lji.org/"^^xsd:string ; bioregistry.schema:0000005 "1038233"^^xsd:string ; @@ -6074,8 +6156,8 @@ bioregistry:iedb a bioregistry.schema:0000001 ; bioregistry:iev a bioregistry.schema:0000001 ; rdfs:label "Event (INOH pathway ontology)" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:IEV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:iev, biocontext:IEV, prefixcommons:iev ; foaf:homepage "http://www.inoh.org"^^xsd:string ; @@ -6087,8 +6169,8 @@ bioregistry:iev a bioregistry.schema:0000001 ; bioregistry:igrhcellid a bioregistry.schema:0000001 ; rdfs:label "Integrated Genomic Resources of human Cell Lines for Identification" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:IGRhCellID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:IGRhCellID ; foaf:homepage "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi"^^xsd:string ; bioregistry.schema:0000005 "ACHN"^^xsd:string ; bioregistry.schema:0000006 "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^xsd:string ; @@ -6097,8 +6179,8 @@ bioregistry:igrhcellid a bioregistry.schema:0000001 ; bioregistry:igsn a bioregistry.schema:0000001 ; rdfs:label "International Geo Sample Number" ; dc:description "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:igsn, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:igsn, fairsharing:FAIRsharing.Yvc76F, miriam:igsn ; foaf:homepage "http://www.geosamples.org/"^^xsd:string ; @@ -6110,8 +6192,8 @@ bioregistry:igsn a bioregistry.schema:0000001 ; bioregistry:igsr a bioregistry.schema:0000001 ; rdfs:label "International Genome Sample Resource" ; dc:description "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:IGSR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:IGSR, fairsharing:FAIRsharing.4Vs9VM ; foaf:homepage "https://www.internationalgenome.org/"^^xsd:string ; bioregistry.schema:0000005 "NA06985"^^xsd:string ; @@ -6121,8 +6203,8 @@ bioregistry:igsr a bioregistry.schema:0000001 ; bioregistry:ihw a bioregistry.schema:0000001 ; rdfs:label "International Histocompatibility Workshop cell lines" ; dc:description "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:IHW ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:IHW ; foaf:homepage "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html"^^xsd:string ; bioregistry.schema:0000005 "IHW09326"^^xsd:string ; bioregistry.schema:0000008 "^IHW\\d+$"^^xsd:string ; @@ -6131,8 +6213,8 @@ bioregistry:ihw a bioregistry.schema:0000001 ; bioregistry:imanis a bioregistry.schema:0000001 ; rdfs:label "Imanis Life Sciences cell line products" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Imanis ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Imanis ; foaf:homepage "https://www.imanislife.com/collections/cell-lines/"^^xsd:string ; bioregistry.schema:0000005 "CL070"^^xsd:string ; bioregistry.schema:0000006 "https://www.imanislife.com/?s=$1"^^xsd:string ; @@ -6141,8 +6223,8 @@ bioregistry:imanis a bioregistry.schema:0000001 ; bioregistry:imex a bioregistry.schema:0000001 ; rdfs:label "International Molecular Exchange" ; dc:description "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IMEX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IMEX, n2t:imex, prefixcommons:imex, miriam:imex ; @@ -6155,8 +6237,8 @@ bioregistry:imex a bioregistry.schema:0000001 ; bioregistry:img.gene a bioregistry.schema:0000001 ; rdfs:label "Integrated Microbial Genomes Gene" ; dc:description "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IMG.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IMG.GENE, n2t:img.gene, prefixcommons:img.gene, miriam:img.gene ; @@ -6169,8 +6251,8 @@ bioregistry:img.gene a bioregistry.schema:0000001 ; bioregistry:img.taxon a bioregistry.schema:0000001 ; rdfs:label "Integrated Microbial Genomes Taxon" ; dc:description "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IMG.TAXON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IMG.TAXON, n2t:img.taxon, prefixcommons:img.taxon, miriam:img.taxon ; @@ -6183,8 +6265,8 @@ bioregistry:img.taxon a bioregistry.schema:0000001 ; bioregistry:imgt.hla a bioregistry.schema:0000001 ; rdfs:label "IMGT/HLA human major histocompatibility complex sequence database" ; dc:description "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2773, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2773, biocontext:IMGT.HLA, , go.resource:IMGT_HLA, @@ -6202,8 +6284,8 @@ bioregistry:imgt.hla a bioregistry.schema:0000001 ; bioregistry:imgt.ligm a bioregistry.schema:0000001 ; rdfs:label "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" ; dc:description "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IMGT.LIGM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IMGT.LIGM, go.resource:IMGT_LIGM, n2t:imgt.ligm, , @@ -6217,8 +6299,8 @@ bioregistry:imgt.ligm a bioregistry.schema:0000001 ; bioregistry:imr a bioregistry.schema:0000001 ; rdfs:label "Molecule role (INOH Protein name/family name ontology)" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:IMR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:imr, biocontext:IMR, prefixcommons:imr ; foaf:homepage "http://www.inoh.org"^^xsd:string ; @@ -6231,8 +6313,8 @@ bioregistry:imr a bioregistry.schema:0000001 ; bioregistry:inchi a bioregistry.schema:0000001 ; rdfs:label "InChI" ; dc:description "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INCHI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INCHI, n2t:inchi, fairsharing:FAIRsharing.ddk9t9, miriam:inchi, @@ -6246,8 +6328,8 @@ bioregistry:inchi a bioregistry.schema:0000001 ; bioregistry:inchikey a bioregistry.schema:0000001 ; rdfs:label "InChIKey" ; dc:description "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INCHIKEY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INCHIKEY, n2t:inchikey, miriam:inchikey, wikidata:P235 ; @@ -6260,8 +6342,8 @@ bioregistry:inchikey a bioregistry.schema:0000001 ; bioregistry:inn a bioregistry.schema:0000001 ; rdfs:label "International Nonproprietary Names" ; dc:description "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P2275 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P2275 ; foaf:homepage "https://www.who.int/teams/health-product-and-policy-standards/inn"^^xsd:string ; bioregistry.schema:0000005 "fluticasone"^^xsd:string ; bioregistry.schema:0000006 "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^xsd:string ; @@ -6270,9 +6352,9 @@ bioregistry:inn a bioregistry.schema:0000001 ; bioregistry:ino a bioregistry.schema:0000001 ; rdfs:label "Interaction Network Ontology" ; dc:description "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:INO, - obofoundry:INO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:INO, + obofoundry:ino, ontobee:INO, bioportal:INO, biolink:INO, @@ -6288,8 +6370,8 @@ bioregistry:ino a bioregistry.schema:0000001 ; bioregistry:insdc.cds a bioregistry.schema:0000001 ; rdfs:label "INSDC CDS" ; dc:description "The coding sequence or protein identifiers as maintained in INSDC."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INSDC.CDS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INSDC.CDS, n2t:insdc.cds, miriam:insdc.cds ; foaf:homepage "http://getentry.ddbj.nig.ac.jp"^^xsd:string ; @@ -6302,8 +6384,8 @@ bioregistry:insdc.cds a bioregistry.schema:0000001 ; bioregistry:insdc.gca a bioregistry.schema:0000001 ; rdfs:label "Genome assembly database" ; dc:description "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INSDC.GCA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INSDC.GCA, n2t:insdc.gca, miriam:insdc.gca ; foaf:homepage "https://www.ebi.ac.uk/ena/browse/genome-assembly-database"^^xsd:string ; @@ -6315,8 +6397,8 @@ bioregistry:insdc.gca a bioregistry.schema:0000001 ; bioregistry:intact a bioregistry.schema:0000001 ; rdfs:label "IntAct protein interaction database" ; dc:description "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INTACT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INTACT, go.resource:IntAct, n2t:intact, fairsharing:FAIRsharing.d05nwx, @@ -6332,8 +6414,8 @@ bioregistry:intact a bioregistry.schema:0000001 ; bioregistry:intact.molecule a bioregistry.schema:0000001 ; rdfs:label "IntAct Molecule" ; dc:description "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INTACT.MOLECULE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INTACT.MOLECULE, n2t:intact.molecule, miriam:intact.molecule ; foaf:homepage "https://www.ebi.ac.uk/intact/"^^xsd:string ; @@ -6345,8 +6427,8 @@ bioregistry:intact.molecule a bioregistry.schema:0000001 ; bioregistry:interlex a bioregistry.schema:0000001 ; rdfs:label "InterLex" ; dc:description "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.67sssf, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.67sssf, miriam:ilx ; foaf:homepage "https://www.fdilab.org"^^xsd:string ; bioregistry.schema:0000005 "0101963"^^xsd:string ; @@ -6357,9 +6439,9 @@ bioregistry:interlex a bioregistry.schema:0000001 ; bioregistry:interpro a bioregistry.schema:0000001 ; rdfs:label "InterPro" ; dc:description "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1133, - obofoundry:IPR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1133, + obofoundry:ipr, biocontext:IPR, biolink:interpro, go.resource:InterPro, @@ -6380,8 +6462,8 @@ bioregistry:interpro a bioregistry.schema:0000001 ; bioregistry:ird.segment a bioregistry.schema:0000001 ; rdfs:label "IRD Segment Sequence" ; dc:description "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IRD.SEGMENT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IRD.SEGMENT, n2t:ird.segment, prefixcommons:ird.segment, miriam:ird.segment ; @@ -6394,8 +6476,8 @@ bioregistry:ird.segment a bioregistry.schema:0000001 ; bioregistry:irefweb a bioregistry.schema:0000001 ; rdfs:label "iRefWeb" ; dc:description "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IREFWEB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IREFWEB, n2t:irefweb, fairsharing:FAIRsharing.t31wcb, prefixcommons:irefweb, @@ -6409,8 +6491,8 @@ bioregistry:irefweb a bioregistry.schema:0000001 ; bioregistry:isbn a bioregistry.schema:0000001 ; rdfs:label "International Standard Book Number" ; dc:description "The International Standard Book Number (ISBN) is for identifying printed books."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2634, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2634, biocontext:ISBN-13, biolink:isbn, go.resource:ISBN, @@ -6426,8 +6508,8 @@ bioregistry:isbn a bioregistry.schema:0000001 ; bioregistry:isfinder a bioregistry.schema:0000001 ; rdfs:label "Insertion sequence elements database" ; dc:description "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ISFINDER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ISFINDER, n2t:isfinder, ncbi.resource:ISFinder, fairsharing:FAIRsharing.xhpc3h, @@ -6444,8 +6526,8 @@ bioregistry:isni a bioregistry.schema:0000001 ; dc:description """ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r \r The mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:isni, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:isni, n2t:isni, miriam:isni ; foaf:homepage "http://www.isni.org"^^xsd:string ; @@ -6457,8 +6539,8 @@ The mission of the ISNI International Authority (ISNI-IA) is to assign to the pu bioregistry:issn a bioregistry.schema:0000001 ; rdfs:label "International Standard Serial Number" ; dc:description "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ISSN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ISSN, biolink:issn, go.resource:ISSN, n2t:issn, @@ -6472,8 +6554,8 @@ bioregistry:issn a bioregistry.schema:0000001 ; bioregistry:itis a bioregistry.schema:0000001 ; rdfs:label "Integrated Taxonomic Information System" ; dc:description "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.t19hpa, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.t19hpa, wikidata:P815 ; foaf:homepage "https://www.itis.gov/"^^xsd:string ; bioregistry.schema:0000005 "589462"^^xsd:string ; @@ -6484,8 +6566,8 @@ bioregistry:itis a bioregistry.schema:0000001 ; bioregistry:ito a bioregistry.schema:0000001 ; rdfs:label "Intelligence Task Ontology" ; dc:description "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ITO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ITO, bioportal:ITO, miriam:ito ; foaf:homepage "https://bioportal.bioontology.org/"^^xsd:string ; @@ -6497,8 +6579,8 @@ bioregistry:ito a bioregistry.schema:0000001 ; bioregistry:iuphar.family a bioregistry.schema:0000001 ; rdfs:label "IUPHAR family" ; dc:description "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IUPHAR.FAMILY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IUPHAR.FAMILY, n2t:iuphar.family, prefixcommons:iuphar.family, miriam:iuphar.family ; @@ -6511,8 +6593,8 @@ bioregistry:iuphar.family a bioregistry.schema:0000001 ; bioregistry:iuphar.ligand a bioregistry.schema:0000001 ; rdfs:label "Guide to Pharmacology Ligand" ; dc:description "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IUPHAR.LIGAND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IUPHAR.LIGAND, biolink:GTOPDB, n2t:iuphar.ligand, miriam:iuphar.ligand, @@ -6526,8 +6608,8 @@ bioregistry:iuphar.ligand a bioregistry.schema:0000001 ; bioregistry:iuphar.receptor a bioregistry.schema:0000001 ; rdfs:label "Guide to Pharmacology Target" ; dc:description "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:IUPHAR.RECEPTOR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:IUPHAR.RECEPTOR, go.resource:IUPHAR_RECEPTOR, n2t:iuphar.receptor, miriam:iuphar.receptor, @@ -6541,8 +6623,8 @@ bioregistry:iuphar.receptor a bioregistry.schema:0000001 ; bioregistry:jax a bioregistry.schema:0000001 ; rdfs:label "Jackson Laboratories Strain" ; dc:description "Information about the C57BL/6J. Includes genetic background and disease data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JAX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JAX, fairsharing:FAIRsharing.5701h1 ; foaf:homepage "https://www.jax.org/strain"^^xsd:string ; bioregistry.schema:0000005 "004435"^^xsd:string ; @@ -6553,8 +6635,8 @@ bioregistry:jax a bioregistry.schema:0000001 ; bioregistry:jaxmice a bioregistry.schema:0000001 ; rdfs:label "JAX Mice" ; dc:description "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JAXMICE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JAXMICE, n2t:jaxmice, miriam:jaxmice ; foaf:homepage "http://jaxmice.jax.org/"^^xsd:string ; @@ -6566,8 +6648,8 @@ bioregistry:jaxmice a bioregistry.schema:0000001 ; bioregistry:jcggdb a bioregistry.schema:0000001 ; rdfs:label "Japan Consortium for Glycobiology and Glycotechnology Database" ; dc:description "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JCGGDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JCGGDB, n2t:jcggdb, miriam:jcggdb ; foaf:homepage "http://jcggdb.jp/index_en.html"^^xsd:string ; @@ -6579,8 +6661,8 @@ bioregistry:jcggdb a bioregistry.schema:0000001 ; bioregistry:jcm a bioregistry.schema:0000001 ; rdfs:label "Japan Collection of Microorganisms" ; dc:description "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JCM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JCM, n2t:jcm, ncbi.resource:JCM, fairsharing:FAIRsharing.h2wrt2, @@ -6595,8 +6677,8 @@ bioregistry:jcm a bioregistry.schema:0000001 ; bioregistry:jcsd a bioregistry.schema:0000001 ; rdfs:label "Japan Chemical Substance Dictionary" ; dc:description "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JCSD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JCSD, n2t:jcsd, prefixcommons:jcsd, miriam:jcsd ; @@ -6609,8 +6691,8 @@ bioregistry:jcsd a bioregistry.schema:0000001 ; bioregistry:jstor a bioregistry.schema:0000001 ; rdfs:label "Digital archive of scholarly articles" ; dc:description "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JSTOR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JSTOR, go.resource:JSTOR, n2t:jstor, miriam:jstor ; @@ -6623,8 +6705,8 @@ bioregistry:jstor a bioregistry.schema:0000001 ; bioregistry:jws a bioregistry.schema:0000001 ; rdfs:label "JWS Online" ; dc:description "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:JWS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:JWS, n2t:jws, prefixcommons:jws, miriam:jws ; @@ -6637,8 +6719,8 @@ bioregistry:jws a bioregistry.schema:0000001 ; bioregistry:kaggle a bioregistry.schema:0000001 ; rdfs:label "Kaggle" ; dc:description "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:kaggle, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:kaggle, miriam:kaggle ; foaf:homepage "https://kaggle.com"^^xsd:string ; bioregistry.schema:0000005 "nasa/kepler-exoplanet-search-results"^^xsd:string ; @@ -6649,8 +6731,8 @@ bioregistry:kaggle a bioregistry.schema:0000001 ; bioregistry:kerafast a bioregistry.schema:0000001 ; rdfs:label "Kerafast cell lines" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Kerafast ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Kerafast ; foaf:homepage "https://www.kerafast.com/"^^xsd:string ; bioregistry.schema:0000005 "EJH014"^^xsd:string ; bioregistry.schema:0000006 "https://www.kerafast.com/Search?SearchTerm="$1""^^xsd:string ; @@ -6659,8 +6741,8 @@ bioregistry:kerafast a bioregistry.schema:0000001 ; bioregistry:kyinno a bioregistry.schema:0000001 ; rdfs:label "KYinno cell lines" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:KYinno ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:KYinno ; foaf:homepage "https://www.kyinno.com/"^^xsd:string ; bioregistry.schema:0000005 "KC-0979"^^xsd:string ; bioregistry.schema:0000006 "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^xsd:string ; @@ -6669,8 +6751,8 @@ bioregistry:kyinno a bioregistry.schema:0000001 ; bioregistry:lbo a bioregistry.schema:0000001 ; rdfs:label "Livestock Breed Ontology" ; dc:description "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LBO, agroportal:LBO, bioportal:LBO, fairsharing:FAIRsharing.309v57, @@ -6684,8 +6766,8 @@ bioregistry:lbo a bioregistry.schema:0000001 ; bioregistry:lei a bioregistry.schema:0000001 ; rdfs:label "Global LEI Index" ; dc:description "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:lei, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:lei, miriam:lei ; foaf:homepage "https://www.gleif.org/"^^xsd:string ; bioregistry.schema:0000005 "HWUPKR0MPOU8FGXBT394"^^xsd:string ; @@ -6696,8 +6778,8 @@ bioregistry:lei a bioregistry.schema:0000001 ; bioregistry:lgai.cede a bioregistry.schema:0000001 ; rdfs:label "LG Chemical Entity Detection Dataset (LGCEDe)" ; dc:description "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:lgai.cede ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:lgai.cede ; foaf:homepage "https://www.lgresearch.ai"^^xsd:string ; bioregistry.schema:0000005 "LGCEDe-S-000002244"^^xsd:string ; bioregistry.schema:0000006 "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^xsd:string ; @@ -6707,8 +6789,8 @@ bioregistry:lgai.cede a bioregistry.schema:0000001 ; bioregistry:lgic a bioregistry.schema:0000001 ; rdfs:label "Ligand-Gated Ion Channel database" ; dc:description "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LGIC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LGIC, n2t:lgic, miriam:lgic ; foaf:homepage "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^xsd:string ; @@ -6720,8 +6802,8 @@ bioregistry:lgic a bioregistry.schema:0000001 ; bioregistry:licebase a bioregistry.schema:0000001 ; rdfs:label "LiceBase" ; dc:description "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LICEBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LICEBASE, n2t:licebase, fairsharing:FAIRsharing.c7w81a, miriam:licebase ; @@ -6734,8 +6816,8 @@ bioregistry:licebase a bioregistry.schema:0000001 ; bioregistry:ligandbook a bioregistry.schema:0000001 ; rdfs:label "LigandBook" ; dc:description "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:ligandbook, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:ligandbook, miriam:ligandbook ; foaf:homepage "https://ligandbook.org/"^^xsd:string ; bioregistry.schema:0000005 "785"^^xsd:string ; @@ -6746,8 +6828,8 @@ bioregistry:ligandbook a bioregistry.schema:0000001 ; bioregistry:ligandbox a bioregistry.schema:0000001 ; rdfs:label "LigandBox" ; dc:description "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LIGANDBOX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LIGANDBOX, n2t:ligandbox, miriam:ligandbox ; foaf:homepage "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en"^^xsd:string ; @@ -6759,8 +6841,8 @@ bioregistry:ligandbox a bioregistry.schema:0000001 ; bioregistry:ligandexpo a bioregistry.schema:0000001 ; rdfs:label "Ligand Expo" ; dc:description "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LIGANDEXPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LIGANDEXPO, n2t:ligandexpo, fairsharing:FAIRsharing.2ma4gq, prefixcommons:ligandexpo, @@ -6774,8 +6856,8 @@ bioregistry:ligandexpo a bioregistry.schema:0000001 ; bioregistry:ligea a bioregistry.schema:0000001 ; rdfs:label "Cancer cell LInes GEne fusions portAl" ; dc:description "Polymorphism and mutation databases"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:LiGeA ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:LiGeA ; foaf:homepage "http://hpc-bioinformatics.cineca.it/fusion/main"^^xsd:string ; bioregistry.schema:0000005 "CCLE_867"^^xsd:string ; bioregistry.schema:0000006 "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^xsd:string ; @@ -6784,8 +6866,8 @@ bioregistry:ligea a bioregistry.schema:0000001 ; bioregistry:limore a bioregistry.schema:0000001 ; rdfs:label "Liver Cancer Model Repository" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:LIMORE ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:LIMORE ; foaf:homepage "https://www.picb.ac.cn/limore/home"^^xsd:string ; bioregistry.schema:0000005 "Li7"^^xsd:string ; bioregistry.schema:0000006 "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^xsd:string ; @@ -6794,8 +6876,8 @@ bioregistry:limore a bioregistry.schema:0000001 ; bioregistry:lincs.cell a bioregistry.schema:0000001 ; rdfs:label "LINCS Cell" ; dc:description "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LINCS.CELL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LINCS.CELL, cellosaurus.resource:LINCS_LDP, n2t:lincs.cell, miriam:lincs.cell ; @@ -6808,8 +6890,8 @@ bioregistry:lincs.cell a bioregistry.schema:0000001 ; bioregistry:lincs.data a bioregistry.schema:0000001 ; rdfs:label "LINCS Data" ; dc:description "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LINCS.DATA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LINCS.DATA, n2t:lincs.data, miriam:lincs.data ; foaf:homepage "http://lincsportal.ccs.miami.edu/datasets/"^^xsd:string ; @@ -6821,8 +6903,8 @@ bioregistry:lincs.data a bioregistry.schema:0000001 ; bioregistry:lincs.protein a bioregistry.schema:0000001 ; rdfs:label "LINCS Protein" ; dc:description "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LINCS.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LINCS.PROTEIN, n2t:lincs.protein, miriam:lincs.protein ; foaf:homepage "http://lincs.hms.harvard.edu/db/proteins/"^^xsd:string ; @@ -6834,8 +6916,8 @@ bioregistry:lincs.protein a bioregistry.schema:0000001 ; bioregistry:linguist a bioregistry.schema:0000001 ; rdfs:label "Linguist" ; dc:description "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:linguist ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:linguist ; foaf:homepage "https://github.com/github/linguist"^^xsd:string ; bioregistry.schema:0000005 "Python"^^xsd:string ; bioregistry.schema:0000006 "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^xsd:string ; @@ -6845,8 +6927,8 @@ bioregistry:linguist a bioregistry.schema:0000001 ; bioregistry:lipidbank a bioregistry.schema:0000001 ; rdfs:label "LipidBank" ; dc:description "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2665, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2665, biocontext:LIPIDBANK, n2t:lipidbank, fairsharing:FAIRsharing.bdn9br, @@ -6861,9 +6943,9 @@ bioregistry:lipidbank a bioregistry.schema:0000001 ; bioregistry:lipro a bioregistry.schema:0000001 ; rdfs:label "Lipid Ontology" ; dc:description "An ontology representation of the LIPIDMAPS nomenclature classification."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LIPRO, - obofoundry:LIPRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LIPRO, + obofoundry:lipro, bioportal:LIPRO, biocontext:LIPRO ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/LIPRO_$1"^^xsd:string ; @@ -6872,8 +6954,8 @@ bioregistry:lipro a bioregistry.schema:0000001 ; bioregistry:loggerhead a bioregistry.schema:0000001 ; rdfs:label "Loggerhead nesting" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:LOGGERHEAD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:loggerhead, biocontext:LOGGERHEAD ; foaf:homepage "http://www.mesquiteproject.org/ontology/Loggerhead/index.html"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^xsd:string ; @@ -6883,8 +6965,8 @@ bioregistry:loggerhead a bioregistry.schema:0000001 ; bioregistry:loinc a bioregistry.schema:0000001 ; rdfs:label "Logical Observation Identifiers Names and Codes" ; dc:description "The international standard for identifying health measurements, observations, and documents."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LOINC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LOINC, bioportal:LOINC, biolink:LOINC, fairsharing:FAIRsharing.2mk2zb ; @@ -6896,8 +6978,8 @@ bioregistry:loinc a bioregistry.schema:0000001 ; bioregistry:lrg a bioregistry.schema:0000001 ; rdfs:label "Locus Reference Genomic" ; dc:description "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LRG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LRG, n2t:lrg, miriam:lrg ; foaf:homepage "http://www.lrg-sequence.org/"^^xsd:string ; @@ -6909,9 +6991,9 @@ bioregistry:lrg a bioregistry.schema:0000001 ; bioregistry:ma a bioregistry.schema:0000001 ; rdfs:label "Mouse adult gross anatomy" ; dc:description "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MA, - obofoundry:MA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MA, + obofoundry:ma, ontobee:MA, bioportal:MA, biocontext:MA, @@ -6931,8 +7013,8 @@ bioregistry:ma a bioregistry.schema:0000001 ; bioregistry:macie a bioregistry.schema:0000001 ; rdfs:label "Mechanism, Annotation and Classification in Enzymes" ; dc:description "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2641, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2641, biocontext:MACIE, n2t:macie, fairsharing:FAIRsharing.7xkx69, @@ -6947,8 +7029,8 @@ bioregistry:macie a bioregistry.schema:0000001 ; bioregistry:maizegdb.locus a bioregistry.schema:0000001 ; rdfs:label "MaizeGDB Locus" ; dc:description "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MAIZEGDB.LOCUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MAIZEGDB.LOCUS, go.resource:MaizeGDB_Locus, n2t:maizegdb.locus, ncbi.resource:MaizeGDB, @@ -6965,9 +7047,9 @@ bioregistry:maizegdb.locus a bioregistry.schema:0000001 ; bioregistry:mamo a bioregistry.schema:0000001 ; rdfs:label "Mathematical modeling ontology" ; dc:description "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MAMO, - obofoundry:MAMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MAMO, + obofoundry:mamo, ontobee:MAMO, bioportal:MAMO, biocontext:MAMO, @@ -6983,8 +7065,8 @@ bioregistry:mamo a bioregistry.schema:0000001 ; bioregistry:mao a bioregistry.schema:0000001 ; rdfs:label "Multiple alignment" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:MAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:mao, biocontext:MAO, prefixcommons:mao ; foaf:homepage "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html"^^xsd:string ; @@ -6995,8 +7077,8 @@ bioregistry:mao a bioregistry.schema:0000001 ; bioregistry:massbank a bioregistry.schema:0000001 ; rdfs:label "MassBank" ; dc:description "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MASSBANK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MASSBANK, n2t:massbank, fairsharing:FAIRsharing.dk451a, miriam:massbank, @@ -7009,9 +7091,9 @@ bioregistry:massbank a bioregistry.schema:0000001 ; bioregistry:mat a bioregistry.schema:0000001 ; rdfs:label "Minimal Anatomical Terminology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MAT, - obofoundry:MAT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MAT, + obofoundry:mat, bioportal:MAT, biocontext:MAT ; bioregistry.schema:0000005 "0000000"^^xsd:string ; @@ -7023,8 +7105,8 @@ bioregistry:mat a bioregistry.schema:0000001 ; bioregistry:matrixdb.association a bioregistry.schema:0000001 ; rdfs:label "MatrixDB Association" ; dc:description "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MATRIXDB.ASSOCIATION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MATRIXDB.ASSOCIATION, n2t:matrixdb.association, miriam:matrixdb.association ; foaf:homepage "http://matrixdb.univ-lyon1.fr/"^^xsd:string ; @@ -7035,15 +7117,15 @@ bioregistry:matrixdb.association a bioregistry.schema:0000001 ; bioregistry:mcc a bioregistry.schema:0000001 ; rdfs:label "Cell Line Ontology [derivative]" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:MCCL ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:MCCL ; bioregistry.schema:0000012 true . bioregistry:mdm a bioregistry.schema:0000001 ; rdfs:label "Medical Data Models" ; dc:description "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MDM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MDM, bioportal:MDM, biocontext:MDM, n2t:mdm, @@ -7058,8 +7140,8 @@ bioregistry:mdm a bioregistry.schema:0000001 ; bioregistry:meddra a bioregistry.schema:0000001 ; rdfs:label "Medical Dictionary for Regulatory Activities Terminology" ; dc:description "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MEDDRA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MEDDRA, bioportal:MEDDRA, biocontext:MEDDRA, n2t:meddra, @@ -7075,8 +7157,8 @@ bioregistry:meddra a bioregistry.schema:0000001 ; bioregistry:medgen a bioregistry.schema:0000001 ; rdfs:label "Human Medical Genetics" ; dc:description "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MedGen, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MedGen, biolink:medgen, n2t:medgen, ncbi.resource:MedGen, @@ -7090,8 +7172,8 @@ bioregistry:medgen a bioregistry.schema:0000001 ; bioregistry:medlineplus a bioregistry.schema:0000001 ; rdfs:label "MedlinePlus Health Topics" ; dc:description "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MEDLINEPLUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MEDLINEPLUS, bioportal:MEDLINEPLUS, biocontext:MEDLINEPLUS, n2t:medlineplus, @@ -7106,8 +7188,8 @@ bioregistry:medlineplus a bioregistry.schema:0000001 ; bioregistry:merops.entry a bioregistry.schema:0000001 ; rdfs:label "MEROPS Entry" ; dc:description "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2629, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2629, biocontext:MEROPS.INHIBITOR, go.resource:MEROPS, n2t:merops.inhibitor, @@ -7124,8 +7206,8 @@ bioregistry:merops.entry a bioregistry.schema:0000001 ; bioregistry:mesh.2012 a bioregistry.schema:0000001 ; rdfs:label "MeSH 2012" ; dc:description "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MESH.2012, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MESH.2012, n2t:mesh.2012, miriam:mesh.2012 ; foaf:homepage "http://www.nlm.nih.gov/mesh/"^^xsd:string ; @@ -7137,8 +7219,8 @@ bioregistry:mesh.2012 a bioregistry.schema:0000001 ; bioregistry:mesh.2013 a bioregistry.schema:0000001 ; rdfs:label "MeSH 2013" ; dc:description "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MESH.2013, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MESH.2013, n2t:mesh.2013, miriam:mesh.2013 ; foaf:homepage "http://www.nlm.nih.gov/mesh/"^^xsd:string ; @@ -7150,8 +7232,8 @@ bioregistry:mesh.2013 a bioregistry.schema:0000001 ; bioregistry:metabolights a bioregistry.schema:0000001 ; rdfs:label "MetaboLights Compound" ; dc:description "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METABOLIGHTS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METABOLIGHTS, cellosaurus.resource:MetaboLights, n2t:metabolights, miriam:metabolights, @@ -7165,8 +7247,8 @@ bioregistry:metabolights a bioregistry.schema:0000001 ; bioregistry:metacyc.reaction a bioregistry.schema:0000001 ; rdfs:label "MetaCyc Reaction" ; dc:description "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METACYC.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METACYC.REACTION, biolink:metacyc.reaction, n2t:metacyc.reaction, miriam:metacyc.reaction ; @@ -7179,8 +7261,8 @@ bioregistry:metacyc.reaction a bioregistry.schema:0000001 ; bioregistry:metanetx.chemical a bioregistry.schema:0000001 ; rdfs:label "MetaNetX chemical" ; dc:description "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METANETX.CHEMICAL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METANETX.CHEMICAL, n2t:metanetx.chemical, miriam:metanetx.chemical ; foaf:homepage "https://www.metanetx.org/"^^xsd:string ; @@ -7192,8 +7274,8 @@ bioregistry:metanetx.chemical a bioregistry.schema:0000001 ; bioregistry:metanetx.compartment a bioregistry.schema:0000001 ; rdfs:label "MetaNetX compartment" ; dc:description "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METANETX.COMPARTMENT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METANETX.COMPARTMENT, n2t:metanetx.compartment, miriam:metanetx.compartment ; foaf:homepage "https://www.metanetx.org/"^^xsd:string ; @@ -7205,8 +7287,8 @@ bioregistry:metanetx.compartment a bioregistry.schema:0000001 ; bioregistry:metanetx.reaction a bioregistry.schema:0000001 ; rdfs:label "MetaNetX reaction" ; dc:description "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METANETX.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METANETX.REACTION, biolink:METANETX.REACTION, n2t:metanetx.reaction, miriam:metanetx.reaction ; @@ -7219,8 +7301,8 @@ bioregistry:metanetx.reaction a bioregistry.schema:0000001 ; bioregistry:metlin a bioregistry.schema:0000001 ; rdfs:label "Metabolite and Tandem Mass Spectrometry Database" ; dc:description "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METLIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METLIN, n2t:metlin, miriam:metlin ; foaf:homepage "http://masspec.scripps.edu/"^^xsd:string ; @@ -7232,8 +7314,8 @@ bioregistry:metlin a bioregistry.schema:0000001 ; bioregistry:mex a bioregistry.schema:0000001 ; rdfs:label "Metabolome Express" ; dc:description "A public place to process, interpret and share GC/MS metabolomics datasets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MEX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MEX, n2t:mex, miriam:mex ; foaf:homepage "https://www.metabolome-express.org/"^^xsd:string ; @@ -7245,9 +7327,9 @@ bioregistry:mex a bioregistry.schema:0000001 ; bioregistry:mf a bioregistry.schema:0000001 ; rdfs:label "Mental Functioning Ontology" ; dc:description "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MF, - obofoundry:MF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MF, + obofoundry:mf, ontobee:MF, bioportal:MF, biocontext:MF, @@ -7263,9 +7345,9 @@ bioregistry:mf a bioregistry.schema:0000001 ; bioregistry:mfo a bioregistry.schema:0000001 ; rdfs:label "Medaka fish anatomy and development" ; dc:description "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MFO, - obofoundry:MFO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MFO, + obofoundry:mfo, bioportal:MFO, biocontext:MFO, prefixcommons:mfo ; @@ -7276,9 +7358,9 @@ bioregistry:mfo a bioregistry.schema:0000001 ; bioregistry:mfoem a bioregistry.schema:0000001 ; rdfs:label "Emotion Ontology" ; dc:description "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MFOEM, - obofoundry:MFOEM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MFOEM, + obofoundry:mfoem, ontobee:MFOEM, bioportal:MFOEM, biocontext:MFOEM, @@ -7294,9 +7376,9 @@ bioregistry:mfoem a bioregistry.schema:0000001 ; bioregistry:mfomd a bioregistry.schema:0000001 ; rdfs:label "Mental Disease Ontology" ; dc:description "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MFOMD, - obofoundry:MFOMD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MFOMD, + obofoundry:mfomd, ontobee:MFOMD, bioportal:MFOMD, biocontext:MFOMD, @@ -7312,8 +7394,8 @@ bioregistry:mfomd a bioregistry.schema:0000001 ; bioregistry:mge a bioregistry.schema:0000001 ; rdfs:label "Aclame" ; dc:description "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:mge, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:mge, miriam:mge ; foaf:homepage "http://aclame.ulb.ac.be/"^^xsd:string ; bioregistry.schema:0000005 "2"^^xsd:string ; @@ -7324,8 +7406,8 @@ bioregistry:mge a bioregistry.schema:0000001 ; bioregistry:mgi a bioregistry.schema:0000001 ; rdfs:label "Mouse Genome Informatics" ; dc:description "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:3274, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:3274, biocontext:MGI, cellosaurus.resource:MGI, go.resource:MGI, @@ -7345,8 +7427,8 @@ bioregistry:mgi a bioregistry.schema:0000001 ; bioregistry:mgnify.proj a bioregistry.schema:0000001 ; rdfs:label "MGnify Project" ; dc:description "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:mgnify.proj, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:mgnify.proj, miriam:mgnify.proj ; foaf:homepage "https://www.ebi.ac.uk/metagenomics"^^xsd:string ; bioregistry.schema:0000005 "ERP004492"^^xsd:string ; @@ -7357,8 +7439,8 @@ bioregistry:mgnify.proj a bioregistry.schema:0000001 ; bioregistry:mgnify.samp a bioregistry.schema:0000001 ; rdfs:label "MGnify Sample" ; dc:description "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:mgnify.samp, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:mgnify.samp, miriam:mgnify.samp ; foaf:homepage "https://www.ebi.ac.uk/metagenomics"^^xsd:string ; bioregistry.schema:0000005 "SRS086444"^^xsd:string ; @@ -7369,9 +7451,9 @@ bioregistry:mgnify.samp a bioregistry.schema:0000001 ; bioregistry:mi a bioregistry.schema:0000001 ; rdfs:label "Molecular Interactions Controlled Vocabulary" ; dc:description "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MI, - obofoundry:MI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MI, + obofoundry:mi, ontobee:MI, bioportal:MI, biocontext:PSIMI, @@ -7393,9 +7475,9 @@ bioregistry:miapa a bioregistry.schema:0000001 ; dc:description """The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MIAPA, - obofoundry:MIAPA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MIAPA, + obofoundry:miapa, ontobee:MIAPA, bioportal:MIAPA, biocontext:MIAPA, @@ -7411,8 +7493,8 @@ This ontology is maintained at http://github.com/miapa/miapa, and requests for c bioregistry:microscope a bioregistry.schema:0000001 ; rdfs:label "MicroScope" ; dc:description "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MICROSCOPE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MICROSCOPE, n2t:microscope, fairsharing:FAIRsharing.3t5qc3, miriam:microscope ; @@ -7425,8 +7507,8 @@ bioregistry:microscope a bioregistry.schema:0000001 ; bioregistry:microsporidia a bioregistry.schema:0000001 ; rdfs:label "MicrosporidiaDB" ; dc:description "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MICROSPORIDIA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MICROSPORIDIA, n2t:microsporidia, prefixcommons:microsporidia, miriam:microsporidia ; @@ -7439,8 +7521,8 @@ bioregistry:microsporidia a bioregistry.schema:0000001 ; bioregistry:millipore a bioregistry.schema:0000001 ; rdfs:label "Merck Millipore (EMD Millipore)" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Millipore ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Millipore ; foaf:homepage "https://www.merckmillipore.com/"^^xsd:string ; bioregistry.schema:0000005 "SCC111"^^xsd:string ; bioregistry.schema:0000006 "https://www.merckmillipore.com/catalogue/item/$1"^^xsd:string ; @@ -7449,8 +7531,8 @@ bioregistry:millipore a bioregistry.schema:0000001 ; bioregistry:mimodb a bioregistry.schema:0000001 ; rdfs:label "MimoDB" ; dc:description "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIMODB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIMODB, n2t:mimodb, fairsharing:FAIRsharing.bv0zjz, prefixcommons:mimodb, @@ -7464,8 +7546,8 @@ bioregistry:mimodb a bioregistry.schema:0000001 ; bioregistry:minid a bioregistry.schema:0000001 ; rdfs:label "Minimal Viable Identifier" ; dc:description "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MINID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MINID, n2t:minid, miriam:minid ; foaf:homepage "https://fair-research.org"^^xsd:string ; @@ -7477,8 +7559,8 @@ bioregistry:minid a bioregistry.schema:0000001 ; bioregistry:minid.test a bioregistry.schema:0000001 ; rdfs:label "MINID Test" ; dc:description "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:minid.test ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:minid.test ; foaf:homepage "https://fair-research.org"^^xsd:string ; bioregistry.schema:0000005 "3SBPLMKKVEVR"^^xsd:string ; bioregistry.schema:0000006 "https://hdl.handle.net/hdl:20.500.12633/$1"^^xsd:string ; @@ -7488,8 +7570,8 @@ bioregistry:minid.test a bioregistry.schema:0000001 ; bioregistry:mint a bioregistry.schema:0000001 ; rdfs:label "Molecular Interaction Database" ; dc:description "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2615, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2615, biocontext:MINT, n2t:mint, fairsharing:FAIRsharing.2bdvmk, @@ -7505,8 +7587,8 @@ bioregistry:mint a bioregistry.schema:0000001 ; bioregistry:mipmod a bioregistry.schema:0000001 ; rdfs:label "MIPModDB" ; dc:description "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIPMOD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIPMOD, n2t:mipmod, prefixcommons:mipmod, miriam:mipmod ; @@ -7519,8 +7601,8 @@ bioregistry:mipmod a bioregistry.schema:0000001 ; bioregistry:mir a bioregistry.schema:0000001 ; rdfs:label "Identifiers.org Registry" ; dc:description "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIR, n2t:mir, miriam:mir ; foaf:homepage "https://registry.identifiers.org/registry"^^xsd:string ; @@ -7532,8 +7614,8 @@ bioregistry:mir a bioregistry.schema:0000001 ; bioregistry:mirbase a bioregistry.schema:0000001 ; rdfs:label "miRBase pre-miRNA" ; dc:description "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2642, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2642, biocontext:MIRBASE, biolink:mirbase, n2t:mirbase, @@ -7551,8 +7633,8 @@ bioregistry:mirbase a bioregistry.schema:0000001 ; bioregistry:mirbase.mature a bioregistry.schema:0000001 ; rdfs:label "miRBase mature miRNA" ; dc:description "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIRBASE.MATURE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIRBASE.MATURE, n2t:mirbase.mature, prefixcommons:mirbase.mature, miriam:mirbase.mature, @@ -7566,8 +7648,8 @@ bioregistry:mirbase.mature a bioregistry.schema:0000001 ; bioregistry:mirex a bioregistry.schema:0000001 ; rdfs:label "mirEX" ; dc:description "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIREX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIREX, n2t:mirex, fairsharing:FAIRsharing.q3b39v, miriam:mirex ; @@ -7580,8 +7662,8 @@ bioregistry:mirex a bioregistry.schema:0000001 ; bioregistry:miriam a bioregistry.schema:0000001 ; rdfs:label "Identifiers.org namespace" ; dc:description "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1162, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1162, fairsharing:FAIRsharing.ap169a, miriam:identifiers.namespace ; foaf:homepage "https://www.ebi.ac.uk"^^xsd:string ; @@ -7593,8 +7675,8 @@ bioregistry:miriam a bioregistry.schema:0000001 ; bioregistry:miriam.collection a bioregistry.schema:0000001 ; rdfs:label "MIRIAM Registry collection" ; dc:description "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIRIAM.COLLECTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIRIAM.COLLECTION, n2t:miriam.collection, miriam:miriam.collection ; foaf:homepage "https://www.ebi.ac.uk/miriam/"^^xsd:string ; @@ -7606,8 +7688,8 @@ bioregistry:miriam.collection a bioregistry.schema:0000001 ; bioregistry:miriam.resource a bioregistry.schema:0000001 ; rdfs:label "MIRIAM Registry resource" ; dc:description "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIRIAM.RESOURCE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIRIAM.RESOURCE, n2t:miriam.resource, prefixcommons:miriam.resource, miriam:miriam.resource ; @@ -7620,9 +7702,9 @@ bioregistry:miriam.resource a bioregistry.schema:0000001 ; bioregistry:mirnao a bioregistry.schema:0000001 ; rdfs:label "microRNA Ontology" ; dc:description "An application ontology for use with miRNA databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MIRNAO, - obofoundry:MIRNAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MIRNAO, + obofoundry:mirnao, ontobee:miRNAO, bioportal:MIRNAO, biocontext:MIRNAO ; @@ -7634,8 +7716,8 @@ bioregistry:mirnao a bioregistry.schema:0000001 ; bioregistry:mirnest a bioregistry.schema:0000001 ; rdfs:label "miRNEST" ; dc:description "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIRNEST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIRNEST, n2t:mirnest, fairsharing:FAIRsharing.5pfx4r, prefixcommons:mirnest, @@ -7649,9 +7731,9 @@ bioregistry:mirnest a bioregistry.schema:0000001 ; bioregistry:miro a bioregistry.schema:0000001 ; rdfs:label "Mosquito insecticide resistance" ; dc:description "Application ontology for entities related to insecticide resistance in mosquitos"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MIRO, - obofoundry:MIRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MIRO, + obofoundry:miro, ontobee:MIRO, bioportal:MIRO, biocontext:MIRO, @@ -7667,8 +7749,8 @@ bioregistry:miro a bioregistry.schema:0000001 ; bioregistry:mirtarbase a bioregistry.schema:0000001 ; rdfs:label "miRTarBase" ; dc:description "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MIRTARBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MIRTARBASE, n2t:mirtarbase, fairsharing:FAIRsharing.f0bxfg, miriam:mirtarbase ; @@ -7681,8 +7763,8 @@ bioregistry:mirtarbase a bioregistry.schema:0000001 ; bioregistry:mlc a bioregistry.schema:0000001 ; rdfs:label "MLCommons Association" ; dc:description "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:mlc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:mlc ; foaf:homepage "https://mlcommons.org/en/"^^xsd:string ; bioregistry.schema:0000005 "0.7-123"^^xsd:string ; bioregistry.schema:0000006 "https://www.mlcommons.org/mlc-id/$1"^^xsd:string ; @@ -7692,8 +7774,8 @@ bioregistry:mlc a bioregistry.schema:0000001 ; bioregistry:mmdb a bioregistry.schema:0000001 ; rdfs:label "Molecular Modeling Database" ; dc:description "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2667, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2667, biocontext:MMDB, n2t:mmdb, prefixcommons:mmdb, @@ -7707,8 +7789,8 @@ bioregistry:mmdb a bioregistry.schema:0000001 ; bioregistry:mmmp.biomaps a bioregistry.schema:0000001 ; rdfs:label "Melanoma Molecular Map Project Biomaps" ; dc:description "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch , + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch , biolink:mmmp.biomaps, n2t:biomaps, ; @@ -7721,9 +7803,9 @@ bioregistry:mmmp.biomaps a bioregistry.schema:0000001 ; bioregistry:mmo a bioregistry.schema:0000001 ; rdfs:label "Measurement method ontology" ; dc:description "A representation of the variety of methods used to make clinical and phenotype measurements. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MMO, - obofoundry:MMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MMO, + obofoundry:mmo, ontobee:MMO, bioportal:MMO, biocontext:MMO, @@ -7739,8 +7821,8 @@ bioregistry:mmo a bioregistry.schema:0000001 ; bioregistry:mmp.cat a bioregistry.schema:0000001 ; rdfs:label "MarCat" ; dc:description "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MMP.CAT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MMP.CAT, n2t:mmp.cat, miriam:mmp.cat ; foaf:homepage "https://mmp.sfb.uit.no/databases/marcat/"^^xsd:string ; @@ -7752,8 +7834,8 @@ bioregistry:mmp.cat a bioregistry.schema:0000001 ; bioregistry:mmp.db a bioregistry.schema:0000001 ; rdfs:label "MarDB" ; dc:description "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MMP.DB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MMP.DB, n2t:mmp.db, miriam:mmp.db ; foaf:homepage "https://mmp.sfb.uit.no/databases/mardb/"^^xsd:string ; @@ -7765,8 +7847,8 @@ bioregistry:mmp.db a bioregistry.schema:0000001 ; bioregistry:mmp.fun a bioregistry.schema:0000001 ; rdfs:label "MarFun" ; dc:description "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:mmp.fun ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:mmp.fun ; foaf:homepage "https://mmp.sfb.uit.no/databases/marfun"^^xsd:string ; bioregistry.schema:0000005 "MMP3888430"^^xsd:string ; bioregistry.schema:0000006 "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^xsd:string ; @@ -7776,8 +7858,8 @@ bioregistry:mmp.fun a bioregistry.schema:0000001 ; bioregistry:mmp.ref a bioregistry.schema:0000001 ; rdfs:label "MarRef" ; dc:description "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MMP.REF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MMP.REF, n2t:mmp.ref, miriam:mmp.ref ; foaf:homepage "https://mmp.sfb.uit.no/databases/marref/"^^xsd:string ; @@ -7789,8 +7871,8 @@ bioregistry:mmp.ref a bioregistry.schema:0000001 ; bioregistry:mmrrc a bioregistry.schema:0000001 ; rdfs:label "Mutant Mouse Resource and Research Centers" ; dc:description "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MMRRC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MMRRC, cellosaurus.resource:MMRRC, n2t:mmrrc, fairsharing:FAIRsharing.9dpd18, @@ -7804,9 +7886,9 @@ bioregistry:mmrrc a bioregistry.schema:0000001 ; bioregistry:mmusdv a bioregistry.schema:0000001 ; rdfs:label "Mouse Developmental Stages" ; dc:description "Life cycle stages for Mus Musculus"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MMUSDV, - obofoundry:MmusDv, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MMUSDV, + obofoundry:mmusdv, ontobee:MMUSDV, bioportal:MMUSDV, biocontext:MMUSDV, @@ -7823,9 +7905,9 @@ bioregistry:mmusdv a bioregistry.schema:0000001 ; bioregistry:mo a bioregistry.schema:0000001 ; rdfs:label "Microarray experimental conditions" ; dc:description "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MO, - obofoundry:MO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MO, + obofoundry:mo, bioportal:MO, biocontext:MO, n2t:mo, @@ -7840,8 +7922,8 @@ bioregistry:mo a bioregistry.schema:0000001 ; bioregistry:mobidb a bioregistry.schema:0000001 ; rdfs:label "MobiDB" ; dc:description "MobiDB is a database of protein disorder and mobility annotations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MOBIDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MOBIDB, n2t:mobidb, fairsharing:FAIRsharing.jwra3e, miriam:mobidb, @@ -7856,9 +7938,9 @@ bioregistry:mobidb a bioregistry.schema:0000001 ; bioregistry:mod a bioregistry.schema:0000001 ; rdfs:label "Protein modification" ; dc:description "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PSIMOD, - obofoundry:MOD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PSIMOD, + obofoundry:mod, ontobee:MOD, bioportal:PSIMOD, biocontext:MOD, @@ -7878,8 +7960,8 @@ bioregistry:mod a bioregistry.schema:0000001 ; bioregistry:modeldb a bioregistry.schema:0000001 ; rdfs:label "ModelDB" ; dc:description "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2669, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2669, biocontext:MODELDB, n2t:modeldb, fairsharing:FAIRsharing.5rb3fk, @@ -7894,8 +7976,8 @@ bioregistry:modeldb a bioregistry.schema:0000001 ; bioregistry:molbase a bioregistry.schema:0000001 ; rdfs:label "Molbase" ; dc:description "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MOLBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MOLBASE, n2t:molbase, miriam:molbase ; foaf:homepage "http://www.molbase.com/"^^xsd:string ; @@ -7907,8 +7989,8 @@ bioregistry:molbase a bioregistry.schema:0000001 ; bioregistry:molmedb a bioregistry.schema:0000001 ; rdfs:label "MolMeDB" ; dc:description "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.CWzk3C, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.CWzk3C, miriam:molmedb ; foaf:homepage "http://www.upol.cz/en/"^^xsd:string ; bioregistry.schema:0000005 "MM00040"^^xsd:string ; @@ -7919,9 +8001,9 @@ bioregistry:molmedb a bioregistry.schema:0000001 ; bioregistry:mop a bioregistry.schema:0000001 ; rdfs:label "Molecular Process Ontology" ; dc:description "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MOP, - obofoundry:MOP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MOP, + obofoundry:mop, ontobee:MOP, bioportal:MOP, biocontext:MOP, @@ -7938,8 +8020,8 @@ bioregistry:morpheus a bioregistry.schema:0000001 ; rdfs:label "Morpheus model repository" ; dc:description """The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. """^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:morpheus ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:morpheus ; foaf:homepage "https://morpheus.gitlab.io/"^^xsd:string ; bioregistry.schema:0000005 "M0001"^^xsd:string ; bioregistry.schema:0000006 "https://morpheus.gitlab.io/models/$1"^^xsd:string ; @@ -7949,9 +8031,9 @@ bioregistry:morpheus a bioregistry.schema:0000001 ; bioregistry:mpath a bioregistry.schema:0000001 ; rdfs:label "Mouse pathology ontology" ; dc:description "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MPATH, - obofoundry:MPATH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MPATH, + obofoundry:mpath, ontobee:MPATH, bioportal:MPATH, biocontext:MPATH, @@ -7968,8 +8050,8 @@ bioregistry:mpath a bioregistry.schema:0000001 ; bioregistry:mpid a bioregistry.schema:0000001 ; rdfs:label "Microbial Protein Interaction Database" ; dc:description "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MPID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MPID, n2t:mpid, fairsharing:FAIRsharing.eyjkws, miriam:mpid ; @@ -7982,9 +8064,9 @@ bioregistry:mpid a bioregistry.schema:0000001 ; bioregistry:mpio a bioregistry.schema:0000001 ; rdfs:label "Minimum PDDI Information Ontology" ; dc:description "An ontology of minimum information regarding potential drug-drug interaction information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MPIO, - obofoundry:MPIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MPIO, + obofoundry:mpio, ontobee:MPIO, bioportal:MPIO, biocontext:MPIO, @@ -7999,9 +8081,9 @@ bioregistry:mpio a bioregistry.schema:0000001 ; bioregistry:mro a bioregistry.schema:0000001 ; rdfs:label "MHC Restriction Ontology" ; dc:description "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MRO, - obofoundry:MRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MRO, + obofoundry:mro, ontobee:MRO, bioportal:MRO, biocontext:MRO, @@ -8017,8 +8099,8 @@ bioregistry:mro a bioregistry.schema:0000001 ; bioregistry:msigdb a bioregistry.schema:0000001 ; rdfs:label "Molecular Signatures Database" ; dc:description "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:MSigDB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:MSigDB ; foaf:homepage "https://www.gsea-msigdb.org"^^xsd:string ; bioregistry.schema:0000005 "M1"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/providers/msigdb/$1"^^xsd:string ; @@ -8028,8 +8110,8 @@ bioregistry:msigdb a bioregistry.schema:0000001 ; bioregistry:msio a bioregistry.schema:0000001 ; rdfs:label "Metabolomics Standards Initiative Ontology" ; dc:description "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ols:msio ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ols:msio ; foaf:homepage "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO"^^xsd:string ; bioregistry.schema:0000005 "0000111"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -8038,8 +8120,8 @@ bioregistry:msio a bioregistry.schema:0000001 ; bioregistry:mw.project a bioregistry.schema:0000001 ; rdfs:label "Metabolomics Workbench Project" ; dc:description "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MW.PROJECT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MW.PROJECT, n2t:mw.project, miriam:mw.project ; foaf:homepage "http://www.metabolomicsworkbench.org/"^^xsd:string ; @@ -8051,8 +8133,8 @@ bioregistry:mw.project a bioregistry.schema:0000001 ; bioregistry:mw.study a bioregistry.schema:0000001 ; rdfs:label "Metabolomics Workbench Study" ; dc:description "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MW.STUDY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MW.STUDY, n2t:mw.study, miriam:mw.study ; foaf:homepage "http://www.metabolomicsworkbench.org/"^^xsd:string ; @@ -8064,8 +8146,8 @@ bioregistry:mw.study a bioregistry.schema:0000001 ; bioregistry:myco.lepra a bioregistry.schema:0000001 ; rdfs:label "MycoBrowser leprae" ; dc:description "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MYCO.LEPRA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MYCO.LEPRA, n2t:myco.lepra, prefixcommons:myco.lepra, miriam:myco.lepra ; @@ -8078,8 +8160,8 @@ bioregistry:myco.lepra a bioregistry.schema:0000001 ; bioregistry:myco.marinum a bioregistry.schema:0000001 ; rdfs:label "MycoBrowser marinum" ; dc:description "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MYCO.MARINUM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MYCO.MARINUM, n2t:myco.marinum, prefixcommons:myco.marinum, miriam:myco.marinum ; @@ -8092,8 +8174,8 @@ bioregistry:myco.marinum a bioregistry.schema:0000001 ; bioregistry:myco.smeg a bioregistry.schema:0000001 ; rdfs:label "MycoBrowser smegmatis" ; dc:description "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MYCO.SMEG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MYCO.SMEG, n2t:myco.smeg, prefixcommons:myco.smeg, miriam:myco.smeg ; @@ -8106,8 +8188,8 @@ bioregistry:myco.smeg a bioregistry.schema:0000001 ; bioregistry:myco.tuber a bioregistry.schema:0000001 ; rdfs:label "TubercuList knowledge base" ; dc:description "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MYCO.TUBER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MYCO.TUBER, n2t:myco.tuber, ncbi.resource:TubercuList, prefixcommons:tuberculist, @@ -8122,8 +8204,8 @@ bioregistry:myco.tuber a bioregistry.schema:0000001 ; bioregistry:mycobank a bioregistry.schema:0000001 ; rdfs:label "Fungal Nomenclature and Species Bank" ; dc:description "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MYCOBANK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MYCOBANK, n2t:mycobank, ncbi.resource:MycoBank, fairsharing:FAIRsharing.v8se8r, @@ -8138,8 +8220,8 @@ bioregistry:mycobank a bioregistry.schema:0000001 ; bioregistry:mzspec a bioregistry.schema:0000001 ; rdfs:label "Universal Spectrum Identifier" ; dc:description "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MZSPEC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MZSPEC, n2t:mzspec, miriam:mzspec ; foaf:homepage "http://proteomecentral.proteomexchange.org/"^^xsd:string ; @@ -8151,8 +8233,8 @@ bioregistry:mzspec a bioregistry.schema:0000001 ; bioregistry:napdi a bioregistry.schema:0000001 ; rdfs:label "Natural Product-Drug Interaction Research Data Repository" ; dc:description "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NAPDI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NAPDI, n2t:napdi, fairsharing:FAIRsharing.y9x8wk, miriam:napdi ; @@ -8165,8 +8247,8 @@ bioregistry:napdi a bioregistry.schema:0000001 ; bioregistry:napp a bioregistry.schema:0000001 ; rdfs:label "Nucleic Acids Phylogenetic Profiling" ; dc:description "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NAPP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NAPP, n2t:napp, fairsharing:FAIRsharing.vr52p3, prefixcommons:napp, @@ -8180,8 +8262,8 @@ bioregistry:napp a bioregistry.schema:0000001 ; bioregistry:narcis a bioregistry.schema:0000001 ; rdfs:label "National Academic Research and Collaborations Information System" ; dc:description "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NARCIS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NARCIS, n2t:narcis, fairsharing:FAIRsharing.f63h4k, miriam:narcis ; @@ -8194,8 +8276,8 @@ bioregistry:narcis a bioregistry.schema:0000001 ; bioregistry:nasc a bioregistry.schema:0000001 ; rdfs:label "NASC code" ; dc:description "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NASC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NASC, n2t:nasc, fairsharing:FAIRsharing.2sqcxs, prefixcommons:nasc, @@ -8209,8 +8291,8 @@ bioregistry:nasc a bioregistry.schema:0000001 ; bioregistry:nbn a bioregistry.schema:0000001 ; rdfs:label "National Bibliography Number" ; dc:description "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NBN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NBN, n2t:nbn, miriam:nbn ; foaf:homepage "http://nbn-resolving.org/resolve_urn.htm"^^xsd:string ; @@ -8222,8 +8304,8 @@ bioregistry:nbn a bioregistry.schema:0000001 ; bioregistry:nbrc a bioregistry.schema:0000001 ; rdfs:label "NITE Biological Resource Center" ; dc:description "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NBRC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NBRC, n2t:nbrc, ncbi.resource:NBRC, fairsharing:FAIRsharing.ftamrc, @@ -8238,8 +8320,8 @@ bioregistry:nbrc a bioregistry.schema:0000001 ; bioregistry:ncbi.assembly a bioregistry.schema:0000001 ; rdfs:label "Assembly" ; dc:description "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NCBIAssembly, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NCBIAssembly, miriam:assembly ; foaf:homepage "https://www.ncbi.nlm.nih.gov/"^^xsd:string ; bioregistry.schema:0000005 "GCF_000005845.2"^^xsd:string ; @@ -8250,8 +8332,8 @@ bioregistry:ncbi.assembly a bioregistry.schema:0000001 ; bioregistry:ncim a bioregistry.schema:0000001 ; rdfs:label "NCI Metathesaurus" ; dc:description "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NCIM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NCIM, n2t:ncim, miriam:ncim ; foaf:homepage "http://ncim.nci.nih.gov/"^^xsd:string ; @@ -8263,9 +8345,9 @@ bioregistry:ncim a bioregistry.schema:0000001 ; bioregistry:ncro a bioregistry.schema:0000001 ; rdfs:label "Non-Coding RNA Ontology" ; dc:description "An ontology for non-coding RNA, both of biological origin, and engineered."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NCRO, - obofoundry:NCRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NCRO, + obofoundry:ncro, ontobee:NCRO, bioportal:NCRO, biocontext:NCRO, @@ -8281,8 +8363,8 @@ bioregistry:ncro a bioregistry.schema:0000001 ; bioregistry:ndc a bioregistry.schema:0000001 ; rdfs:label "National Drug Code" ; dc:description "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NDC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NDC, n2t:ndc, miriam:ndc ; foaf:homepage "http://www.accessdata.fda.gov/scripts/cder/ndc/"^^xsd:string ; @@ -8294,8 +8376,8 @@ bioregistry:ndc a bioregistry.schema:0000001 ; bioregistry:nddf a bioregistry.schema:0000001 ; rdfs:label "National Drug Data File" ; dc:description "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NDDF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NDDF, bioportal:NDDF, biolink:NDDF, fairsharing:FAIRsharing.8qcbs0 ; @@ -8307,8 +8389,8 @@ bioregistry:nddf a bioregistry.schema:0000001 ; bioregistry:ndfrt a bioregistry.schema:0000001 ; rdfs:label "National Drug File - Reference Terminology" ; dc:description "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NDFRT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NDFRT, ontobee:NDF-RT, bioportal:NDFRT, fairsharing:FAIRsharing.901nkj, @@ -8321,8 +8403,8 @@ bioregistry:ndfrt a bioregistry.schema:0000001 ; bioregistry:nemo a bioregistry.schema:0000001 ; rdfs:label "Neural ElectroMagnetic Ontology" ; dc:description "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NEMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NEMO, bioportal:NEMO, fairsharing:FAIRsharing.n66krd, miriam:nemo ; @@ -8335,8 +8417,8 @@ bioregistry:nemo a bioregistry.schema:0000001 ; bioregistry:neuromorpho a bioregistry.schema:0000001 ; rdfs:label "NeuroMorpho" ; dc:description "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2657, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2657, biocontext:NEUROMORPHO, n2t:neuromorpho, prefixcommons:neuromorpho, @@ -8350,8 +8432,8 @@ bioregistry:neuromorpho a bioregistry.schema:0000001 ; bioregistry:neuronames a bioregistry.schema:0000001 ; rdfs:label "NeuroNames" ; dc:description "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P4394 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P4394 ; foaf:homepage "http://braininfo.rprc.washington.edu/"^^xsd:string ; bioregistry.schema:0000005 "268"^^xsd:string ; bioregistry.schema:0000006 "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^xsd:string ; @@ -8361,8 +8443,8 @@ bioregistry:neuronames a bioregistry.schema:0000001 ; bioregistry:neurondb a bioregistry.schema:0000001 ; rdfs:label "NeuronDB" ; dc:description "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2656, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2656, biocontext:NEURONDB, n2t:neurondb, fairsharing:FAIRsharing.45a10e, @@ -8377,8 +8459,8 @@ bioregistry:neurondb a bioregistry.schema:0000001 ; bioregistry:neurovault.collection a bioregistry.schema:0000001 ; rdfs:label "NeuroVault Collection" ; dc:description "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NEUROVAULT.COLLECTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NEUROVAULT.COLLECTION, n2t:neurovault.collection, miriam:neurovault.collection ; foaf:homepage "http://neurovault.org"^^xsd:string ; @@ -8390,8 +8472,8 @@ bioregistry:neurovault.collection a bioregistry.schema:0000001 ; bioregistry:neurovault.image a bioregistry.schema:0000001 ; rdfs:label "NeuroVault Image" ; dc:description "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NEUROVAULT.IMAGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NEUROVAULT.IMAGE, n2t:neurovault.image, miriam:neurovault.image ; foaf:homepage "http://neurovault.org"^^xsd:string ; @@ -8403,8 +8485,8 @@ bioregistry:neurovault.image a bioregistry.schema:0000001 ; bioregistry:nextdb a bioregistry.schema:0000001 ; rdfs:label "Nematode Expression Pattern DataBase" ; dc:description "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NEXTDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NEXTDB, n2t:nextdb, ncbi.resource:NextDB, fairsharing:FAIRsharing.xz5m1a, @@ -8419,8 +8501,8 @@ bioregistry:nextdb a bioregistry.schema:0000001 ; bioregistry:nextprot a bioregistry.schema:0000001 ; rdfs:label "nextProt" ; dc:description "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NEXTPROT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NEXTPROT, n2t:nextprot, fairsharing:FAIRsharing.62evqh, miriam:nextprot, @@ -8434,8 +8516,8 @@ bioregistry:nextprot a bioregistry.schema:0000001 ; bioregistry:ngl a bioregistry.schema:0000001 ; rdfs:label "NASA GeneLab" ; dc:description "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NGL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NGL, n2t:ngl, miriam:ngl ; foaf:homepage "https://genelab-data.ndc.nasa.gov/genelab/"^^xsd:string ; @@ -8447,8 +8529,8 @@ bioregistry:ngl a bioregistry.schema:0000001 ; bioregistry:nhcdr a bioregistry.schema:0000001 ; rdfs:label "NINDS Human Cell and Data Repository" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:NHCDR ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:NHCDR ; foaf:homepage "https://stemcells.nindsgenetics.org"^^xsd:string ; bioregistry.schema:0000005 "ND50028"^^xsd:string ; bioregistry.schema:0000006 "https://stemcells.nindsgenetics.org?line=$1"^^xsd:string ; @@ -8457,8 +8539,8 @@ bioregistry:nhcdr a bioregistry.schema:0000001 ; bioregistry:niaest a bioregistry.schema:0000001 ; rdfs:label "NIA Mouse cDNA Project" ; dc:description "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NIAEST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NIAEST, n2t:niaest, ncbi.resource:niaEST, fairsharing:FAIRsharing.xwqg9h, @@ -8473,8 +8555,8 @@ bioregistry:niaest a bioregistry.schema:0000001 ; bioregistry:nlm a bioregistry.schema:0000001 ; rdfs:label "National Library of Medicine Catalog" ; dc:description "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:NLMID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:NLMID ; foaf:homepage "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^xsd:string ; bioregistry.schema:0000005 "101775319"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^xsd:string ; @@ -8484,9 +8566,9 @@ bioregistry:nlm a bioregistry.schema:0000001 ; bioregistry:nmr a bioregistry.schema:0000001 ; rdfs:label "NMR-instrument specific component of metabolomics investigations" ; dc:description "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NMR, - obofoundry:NMR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NMR, + obofoundry:nmr, bioportal:NMR, biocontext:NMR, n2t:nmr, @@ -8503,8 +8585,8 @@ bioregistry:nmr a bioregistry.schema:0000001 ; bioregistry:nmrshiftdb2 a bioregistry.schema:0000001 ; rdfs:label "NMR Shift Database" ; dc:description "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.nYaZ1N, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.nYaZ1N, miriam:nmrshiftdb2 ; foaf:homepage "https://nmrshiftdb.nmr.uni-koeln.de"^^xsd:string ; bioregistry.schema:0000005 "234"^^xsd:string ; @@ -8515,9 +8597,9 @@ bioregistry:nmrshiftdb2 a bioregistry.schema:0000001 ; bioregistry:nomen a bioregistry.schema:0000001 ; rdfs:label "A nomenclatural ontology for biological names" ; dc:description "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NOMEN, - obofoundry:NOMEN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NOMEN, + obofoundry:nomen, ontobee:NOMEN, bioportal:NOMEN, ols:nomen ; @@ -8531,8 +8613,8 @@ bioregistry:nomen a bioregistry.schema:0000001 ; bioregistry:noncodev3 a bioregistry.schema:0000001 ; rdfs:label "NONCODE v3" ; dc:description "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NONCODEV3, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NONCODEV3, n2t:noncodev3, miriam:noncodev3 ; foaf:homepage "http://www.noncode.org/"^^xsd:string ; @@ -8544,8 +8626,8 @@ bioregistry:noncodev3 a bioregistry.schema:0000001 ; bioregistry:noncodev4.gene a bioregistry.schema:0000001 ; rdfs:label "NONCODE v4 Gene" ; dc:description "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NONCODEV4.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NONCODEV4.GENE, n2t:noncodev4.gene, miriam:noncodev4.gene ; foaf:homepage "http://www.bioinfo.org/NONCODEv4/"^^xsd:string ; @@ -8557,8 +8639,8 @@ bioregistry:noncodev4.gene a bioregistry.schema:0000001 ; bioregistry:noncodev4.rna a bioregistry.schema:0000001 ; rdfs:label "NONCODE v4 Transcript" ; dc:description "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NONCODEV4.RNA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NONCODEV4.RNA, n2t:noncodev4.rna, miriam:noncodev4.rna ; foaf:homepage "http://www.bioinfo.org/NONCODEv4/"^^xsd:string ; @@ -8570,8 +8652,8 @@ bioregistry:noncodev4.rna a bioregistry.schema:0000001 ; bioregistry:norine a bioregistry.schema:0000001 ; rdfs:label "Nonribosomal Peptides Database" ; dc:description "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NORINE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NORINE, n2t:norine, fairsharing:FAIRsharing.gf8yhy, prefixcommons:norine, @@ -8585,8 +8667,8 @@ bioregistry:norine a bioregistry.schema:0000001 ; bioregistry:npo a bioregistry.schema:0000001 ; rdfs:label "NanoParticle Ontology" ; dc:description "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NPO, bioportal:NPO, fairsharing:FAIRsharing.vy0p71 ; foaf:homepage "https://bioportal.bioontology.org/ontologies/NPO"^^xsd:string ; @@ -8598,8 +8680,8 @@ bioregistry:npo a bioregistry.schema:0000001 ; bioregistry:nuclearbd a bioregistry.schema:0000001 ; rdfs:label "NucleaRDB" ; dc:description "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NUCLEARBD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NUCLEARBD, n2t:nuclearbd, miriam:nuclearbd ; foaf:homepage "http://www.receptors.org/nucleardb/"^^xsd:string ; @@ -8611,8 +8693,8 @@ bioregistry:nuclearbd a bioregistry.schema:0000001 ; bioregistry:nucleotide a bioregistry.schema:0000001 ; rdfs:label "Nucleotide" ; dc:description "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:nucleotide ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:nucleotide ; foaf:homepage "https://www.ncbi.nlm.nih.gov/"^^xsd:string ; bioregistry.schema:0000005 "880798137"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^xsd:string ; @@ -8623,9 +8705,9 @@ bioregistry:nucleotide a bioregistry.schema:0000001 ; bioregistry:oae a bioregistry.schema:0000001 ; rdfs:label "Ontology of Adverse Events" ; dc:description "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OAE, - obofoundry:OAE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OAE, + obofoundry:oae, ontobee:OAE, bioportal:OAE, biocontext:OAE, @@ -8641,9 +8723,9 @@ bioregistry:oae a bioregistry.schema:0000001 ; bioregistry:oarcs a bioregistry.schema:0000001 ; rdfs:label "Ontology of Arthropod Circulatory Systems" ; dc:description "OArCS is an ontology describing the Arthropod ciruclatory system."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OARCS, - obofoundry:OARCS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OARCS, + obofoundry:oarcs, ontobee:OARCS, bioportal:OARCS, biocontext:OARCS, @@ -8659,9 +8741,9 @@ bioregistry:oarcs a bioregistry.schema:0000001 ; bioregistry:obcs a bioregistry.schema:0000001 ; rdfs:label "Ontology of Biological and Clinical Statistics" ; dc:description "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OBCS, - obofoundry:OBCS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OBCS, + obofoundry:obcs, ontobee:OBCS, bioportal:OBCS, biocontext:OBCS, @@ -8677,9 +8759,9 @@ bioregistry:obcs a bioregistry.schema:0000001 ; bioregistry:obib a bioregistry.schema:0000001 ; rdfs:label "Ontology for Biobanking" ; dc:description "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OBIB, - obofoundry:OBIB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OBIB, + obofoundry:obib, ontobee:OBIB, bioportal:OBIB, biocontext:OBIB, @@ -8695,8 +8777,8 @@ bioregistry:obib a bioregistry.schema:0000001 ; bioregistry:obo a bioregistry.schema:0000001 ; rdfs:label "Internal OBO and PyOBO Relations" ; dc:description "Community development of interoperable ontologies for the biological sciences"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OBO, fairsharing:FAIRsharing.847069 ; foaf:homepage "http://www.obofoundry.org/"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/$1"^^xsd:string ; @@ -8705,8 +8787,8 @@ bioregistry:obo a bioregistry.schema:0000001 ; bioregistry:occ a bioregistry.schema:0000001 ; rdfs:label "OpenCitations Corpus" ; dc:description "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:occ, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:occ, miriam:occ ; foaf:homepage "https://w3id.org/oc/corpus"^^xsd:string ; bioregistry.schema:0000005 "br/1"^^xsd:string ; @@ -8723,8 +8805,8 @@ OCIs for citations stored within the OpenCitations Corpus are constructed by com OCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r \r OCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OCI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OCI, n2t:oci, miriam:oci ; foaf:homepage "http://opencitations.net"^^xsd:string ; @@ -8736,8 +8818,8 @@ OCIs can also be created for bibliographic resources described in external bibli bioregistry:ocid a bioregistry.schema:0000001 ; rdfs:label "Ontology Concept Identifiers" ; dc:description "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:ocid ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:ocid ; foaf:homepage "https://ontochem.com/"^^xsd:string ; bioregistry.schema:0000005 "190000021540"^^xsd:string ; bioregistry.schema:0000006 "https://ocid.ontochem.com/prefname?ocid=$1"^^xsd:string ; @@ -8747,8 +8829,8 @@ bioregistry:ocid a bioregistry.schema:0000001 ; bioregistry:oclc a bioregistry.schema:0000001 ; rdfs:label "Online Computer Library Center WorldCat" ; dc:description "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OCLC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OCLC, n2t:oclc, miriam:oclc ; foaf:homepage "https://www.oclc.org/en/about.html"^^xsd:string ; @@ -8760,8 +8842,8 @@ bioregistry:oclc a bioregistry.schema:0000001 ; bioregistry:odam a bioregistry.schema:0000001 ; rdfs:label "Open Data for Access and Mining" ; dc:description "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:odam ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:odam ; foaf:homepage "https://metabolome.cgfb.u-bordeaux.fr/"^^xsd:string ; bioregistry.schema:0000005 "frim1"^^xsd:string ; bioregistry.schema:0000006 "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^xsd:string ; @@ -8771,8 +8853,8 @@ bioregistry:odam a bioregistry.schema:0000001 ; bioregistry:odc.sci a bioregistry.schema:0000001 ; rdfs:label "Open Data Commons for Spinal Cord Injury" ; dc:description "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.M6Ruz3, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.M6Ruz3, miriam:odc.sci ; foaf:homepage "https://odc-sci.org"^^xsd:string ; bioregistry.schema:0000005 "602"^^xsd:string ; @@ -8783,8 +8865,8 @@ bioregistry:odc.sci a bioregistry.schema:0000001 ; bioregistry:odc.tbi a bioregistry.schema:0000001 ; rdfs:label "Open Data Commons for Traumatic Brain Injury" ; dc:description "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:odc.tbi ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:odc.tbi ; foaf:homepage "https://odc-tbi.org"^^xsd:string ; bioregistry.schema:0000005 "408"^^xsd:string ; bioregistry.schema:0000006 "https://odc-tbi.org/data/$1"^^xsd:string ; @@ -8794,8 +8876,8 @@ bioregistry:odc.tbi a bioregistry.schema:0000001 ; bioregistry:odor a bioregistry.schema:0000001 ; rdfs:label "Odor Molecules DataBase" ; dc:description "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ODOR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ODOR, n2t:odor, miriam:odor ; foaf:homepage "http://senselab.med.yale.edu/OdorDB"^^xsd:string ; @@ -8807,9 +8889,9 @@ bioregistry:odor a bioregistry.schema:0000001 ; bioregistry:ogg a bioregistry.schema:0000001 ; rdfs:label "The Ontology of Genes and Genomes" ; dc:description "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OGG, - obofoundry:OGG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OGG, + obofoundry:ogg, ontobee:OGG, bioportal:OGG, biocontext:OGG, @@ -8836,9 +8918,9 @@ Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” """^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OGI, - obofoundry:OGI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OGI, + obofoundry:ogi, ontobee:OGI, bioportal:OGI, biocontext:OGI, @@ -8853,9 +8935,9 @@ Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” bioregistry:ogsf a bioregistry.schema:0000001 ; rdfs:label "Ontology of Genetic Susceptibility Factor" ; dc:description "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OGSF, - obofoundry:OGSF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OGSF, + obofoundry:ogsf, ontobee:OGSF, bioportal:OGSF, biocontext:OGSF, @@ -8871,9 +8953,9 @@ bioregistry:ogsf a bioregistry.schema:0000001 ; bioregistry:ohmi a bioregistry.schema:0000001 ; rdfs:label "Ontology of Host-Microbiome Interactions" ; dc:description "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OHMI, - obofoundry:OHMI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OHMI, + obofoundry:ohmi, ontobee:OHMI, bioportal:OHMI, biocontext:OHMI, @@ -8889,9 +8971,9 @@ bioregistry:ohmi a bioregistry.schema:0000001 ; bioregistry:ohpi a bioregistry.schema:0000001 ; rdfs:label "Ontology of Host Pathogen Interactions" ; dc:description "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OHPI, - obofoundry:OHPI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OHPI, + obofoundry:ohpi, ontobee:OHPI, bioportal:OHPI, fairsharing:FAIRsharing.vxpUJ6, @@ -8906,8 +8988,8 @@ bioregistry:ohpi a bioregistry.schema:0000001 ; bioregistry:oid a bioregistry.schema:0000001 ; rdfs:label "OID Repository" ; dc:description "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:oid, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:oid, miriam:oid ; foaf:homepage "http://www.oid-info.com/introduction.htm"^^xsd:string ; bioregistry.schema:0000005 "2.16.840"^^xsd:string ; @@ -8918,9 +9000,9 @@ bioregistry:oid a bioregistry.schema:0000001 ; bioregistry:olatdv a bioregistry.schema:0000001 ; rdfs:label "Medaka Developmental Stages" ; dc:description "Life cycle stages for Medaka"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OLATDV, - obofoundry:OlatDv, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OLATDV, + obofoundry:olatdv, ontobee:OLATDV, bioportal:OLATDV, biocontext:OLATDV, @@ -8936,8 +9018,8 @@ bioregistry:olatdv a bioregistry.schema:0000001 ; bioregistry:om a bioregistry.schema:0000001 ; rdfs:label "Ontology of units of Measure" ; dc:description "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OM, agroportal:OM, bioportal:OM, ols:om ; @@ -8949,8 +9031,8 @@ bioregistry:om a bioregistry.schema:0000001 ; bioregistry:oma.grp a bioregistry.schema:0000001 ; rdfs:label "OMA Group" ; dc:description "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OMA.GRP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OMA.GRP, n2t:oma.grp, miriam:oma.grp ; foaf:homepage "https://omabrowser.org/cgi-bin/gateway.pl"^^xsd:string ; @@ -8962,8 +9044,8 @@ bioregistry:oma.grp a bioregistry.schema:0000001 ; bioregistry:oma.hog a bioregistry.schema:0000001 ; rdfs:label "OMA HOGs" ; dc:description "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:oma.hog ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:oma.hog ; foaf:homepage "https://omabrowser.org"^^xsd:string ; bioregistry.schema:0000005 "0459895"^^xsd:string ; bioregistry.schema:0000006 "https://omabrowser.org/oma/hog/HOG:$1"^^xsd:string ; @@ -8973,8 +9055,8 @@ bioregistry:oma.hog a bioregistry.schema:0000001 ; bioregistry:oma.protein a bioregistry.schema:0000001 ; rdfs:label "OMA Protein" ; dc:description "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OMA.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OMA.PROTEIN, n2t:oma.protein, miriam:oma.protein ; foaf:homepage "https://omabrowser.org/cgi-bin/gateway.pl"^^xsd:string ; @@ -8986,8 +9068,8 @@ bioregistry:oma.protein a bioregistry.schema:0000001 ; bioregistry:omia a bioregistry.schema:0000001 ; rdfs:label "Online Mendelian Inheritance in Animals" ; dc:description "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OMIA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OMIA, n2t:omia, prefixcommons:omia, miriam:omia ; @@ -8997,12 +9079,30 @@ bioregistry:omia a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 true . +bioregistry:omiabis a bioregistry.schema:0000001 ; + rdfs:label "Ontologized MIABIS" ; + dc:description "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMIABIS, + obofoundry:omiabis, + ontobee:OMIABIS, + bioportal:OMIABIS, + biocontext:OMIABIS, + ols:omiabis ; + foaf:homepage "https://github.com/OMIABIS/omiabis-dev"^^xsd:string ; + bioregistry.schema:0000005 "0001079"^^xsd:string ; + bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/OMIABIS_$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000018 bioregistry:labo ; + bioregistry.schema:0000019 orcid:0000-0003-1834-3856 . + bioregistry:ontoneo a bioregistry.schema:0000001 ; rdfs:label "Obstetric and Neonatal Ontology" ; dc:description "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ONTONEO, - obofoundry:ONTONEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ONTONEO, + obofoundry:ontoneo, ontobee:ONTONEO, bioportal:ONTONEO, biocontext:ONTONEO, @@ -9018,9 +9118,9 @@ bioregistry:ontoneo a bioregistry.schema:0000001 ; bioregistry:oostt a bioregistry.schema:0000001 ; rdfs:label "Ontology of Organizational Structures of Trauma centers and Trauma systems" ; dc:description "An ontology built for representating the organizational components of trauma centers and trauma systems."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OOSTT, - obofoundry:OOSTT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OOSTT, + obofoundry:oostt, ontobee:OOSTT, bioportal:OOSTT, biocontext:OOSTT, @@ -9036,8 +9136,8 @@ bioregistry:oostt a bioregistry.schema:0000001 ; bioregistry:opb a bioregistry.schema:0000001 ; rdfs:label "Ontology of Physics for Biology" ; dc:description "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OPB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OPB, bioportal:OPB, biocontext:OPB, n2t:opb, @@ -9053,9 +9153,9 @@ bioregistry:opb a bioregistry.schema:0000001 ; bioregistry:opl a bioregistry.schema:0000001 ; rdfs:label "Ontology for Parasite LifeCycle" ; dc:description "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OPL, - obofoundry:OPL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OPL, + obofoundry:opl, ontobee:OPL, bioportal:OPL, biocontext:OPL, @@ -9071,8 +9171,8 @@ bioregistry:opl a bioregistry.schema:0000001 ; bioregistry:opm a bioregistry.schema:0000001 ; rdfs:label "Orientations of Proteins in Membranes Database" ; dc:description "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OPM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OPM, n2t:opm, fairsharing:FAIRsharing.7c683b, miriam:opm ; @@ -9085,8 +9185,8 @@ bioregistry:opm a bioregistry.schema:0000001 ; bioregistry:orcid a bioregistry.schema:0000001 ; rdfs:label "Open Researcher and Contributor" ; dc:description "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORCID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORCID, biolink:ORCID, n2t:orcid, miriam:orcid, @@ -9100,8 +9200,8 @@ bioregistry:orcid a bioregistry.schema:0000001 ; bioregistry:ordb a bioregistry.schema:0000001 ; rdfs:label "Olfactory Receptor Database" ; dc:description "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORDB, n2t:ordb, fairsharing:FAIRsharing.6375zh, prefixcommons:ordb, @@ -9115,8 +9215,8 @@ bioregistry:ordb a bioregistry.schema:0000001 ; bioregistry:oridb.sacch a bioregistry.schema:0000001 ; rdfs:label "OriDB Saccharomyces" ; dc:description "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORIDB.SACCH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORIDB.SACCH, n2t:oridb.sacch, miriam:oridb.sacch ; foaf:homepage "http://cerevisiae.oridb.org/index.php"^^xsd:string ; @@ -9128,8 +9228,8 @@ bioregistry:oridb.sacch a bioregistry.schema:0000001 ; bioregistry:oridb.schizo a bioregistry.schema:0000001 ; rdfs:label "OriDB Schizosaccharomyces" ; dc:description "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORIDB.SCHIZO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORIDB.SCHIZO, n2t:oridb.schizo, miriam:oridb.schizo ; foaf:homepage "http://pombe.oridb.org/index.php"^^xsd:string ; @@ -9141,9 +9241,9 @@ bioregistry:oridb.schizo a bioregistry.schema:0000001 ; bioregistry:ornaseq a bioregistry.schema:0000001 ; rdfs:label "Ontology of RNA Sequencing" ; dc:description "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ORNASEQ, - obofoundry:ORNASEQ, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ORNASEQ, + obofoundry:ornaseq, ontobee:ORNASEQ, bioportal:ORNASEQ, ols:ornaseq ; @@ -9157,8 +9257,8 @@ bioregistry:ornaseq a bioregistry.schema:0000001 ; bioregistry:orphanet a bioregistry.schema:0000001 ; rdfs:label "Orphanet" ; dc:description "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:Orphanet, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:Orphanet, n2t:orphanet, fairsharing:FAIRsharing.6bd5k6, prefixcommons:orphanet, @@ -9175,8 +9275,8 @@ bioregistry:orphanet.ordo a bioregistry.schema:0000001 ; rdfs:label "Orphanet Rare Disease Ontology" ; dc:description """The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ordo, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ordo, bioportal:ORDO, biocontext:ORPHANET.ORDO, biolink:ORPHA, @@ -9194,8 +9294,8 @@ It integrates a nosology (classification of rare diseases), relationships (gene- bioregistry:orth a bioregistry.schema:0000001 ; rdfs:label "Orthology Ontology" ; dc:description "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ORTH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ORTH, bioportal:ORTH, fairsharing:FAIRsharing.4877h0, ols:orth ; @@ -9207,8 +9307,8 @@ bioregistry:orth a bioregistry.schema:0000001 ; bioregistry:orthodb a bioregistry.schema:0000001 ; rdfs:label "OrthoDB" ; dc:description "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORTHODB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORTHODB, n2t:orthodb, fairsharing:FAIRsharing.x989d5, prefixcommons:orthodb, @@ -9224,8 +9324,8 @@ bioregistry:orthodb a bioregistry.schema:0000001 ; bioregistry:oryzabase.gene a bioregistry.schema:0000001 ; rdfs:label "Oryzabase Gene" ; dc:description "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORYZABASE.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORYZABASE.GENE, n2t:oryzabase.gene, miriam:oryzabase.gene ; foaf:homepage "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^xsd:string ; @@ -9237,8 +9337,8 @@ bioregistry:oryzabase.gene a bioregistry.schema:0000001 ; bioregistry:oryzabase.mutant a bioregistry.schema:0000001 ; rdfs:label "Oryzabase Mutant" ; dc:description "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORYZABASE.MUTANT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORYZABASE.MUTANT, n2t:oryzabase.mutant, miriam:oryzabase.mutant ; foaf:homepage "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^xsd:string ; @@ -9250,8 +9350,8 @@ bioregistry:oryzabase.mutant a bioregistry.schema:0000001 ; bioregistry:oryzabase.reference a bioregistry.schema:0000001 ; rdfs:label "Oryzabase Reference" ; dc:description "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:oryzabase.reference, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:oryzabase.reference, miriam:oryzabase.reference ; foaf:homepage "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^xsd:string ; bioregistry.schema:0000005 "42840"^^xsd:string ; @@ -9262,8 +9362,8 @@ bioregistry:oryzabase.reference a bioregistry.schema:0000001 ; bioregistry:oryzabase.stage a bioregistry.schema:0000001 ; rdfs:label "Oryzabase Stage" ; dc:description "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORYZABASE.STAGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORYZABASE.STAGE, n2t:oryzabase.stage, miriam:oryzabase.stage ; foaf:homepage "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^xsd:string ; @@ -9275,8 +9375,8 @@ bioregistry:oryzabase.stage a bioregistry.schema:0000001 ; bioregistry:oryzabase.strain a bioregistry.schema:0000001 ; rdfs:label "Oryzabase Strain" ; dc:description "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ORYZABASE.STRAIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ORYZABASE.STRAIN, n2t:oryzabase.strain, miriam:oryzabase.strain ; foaf:homepage "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^xsd:string ; @@ -9288,8 +9388,8 @@ bioregistry:oryzabase.strain a bioregistry.schema:0000001 ; bioregistry:otl a bioregistry.schema:0000001 ; rdfs:label "Oryza Tag Line" ; dc:description "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:OTL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:OTL, n2t:otl, fairsharing:FAIRsharing.61c2x6, prefixcommons:otl, @@ -9303,9 +9403,9 @@ bioregistry:otl a bioregistry.schema:0000001 ; bioregistry:ovae a bioregistry.schema:0000001 ; rdfs:label "Ontology of Vaccine Adverse Events" ; dc:description "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OVAE, - obofoundry:OVAE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OVAE, + obofoundry:ovae, ontobee:OVAE, bioportal:OVAE, biocontext:OVAE, @@ -9321,8 +9421,8 @@ bioregistry:ovae a bioregistry.schema:0000001 ; bioregistry:p3db.protein a bioregistry.schema:0000001 ; rdfs:label "P3DB Protein" ; dc:description "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:P3DB.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:P3DB.PROTEIN, n2t:p3db.protein, miriam:p3db.protein ; foaf:homepage "http://www.p3db.org/"^^xsd:string ; @@ -9334,8 +9434,8 @@ bioregistry:p3db.protein a bioregistry.schema:0000001 ; bioregistry:p3db.site a bioregistry.schema:0000001 ; rdfs:label "P3DB Site" ; dc:description "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:P3DB.SITE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:P3DB.SITE, n2t:p3db.site, miriam:p3db.site ; foaf:homepage "http://www.p3db.org/"^^xsd:string ; @@ -9347,8 +9447,8 @@ bioregistry:p3db.site a bioregistry.schema:0000001 ; bioregistry:paleodb a bioregistry.schema:0000001 ; rdfs:label "Paleobiology Database" ; dc:description "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PALEODB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PALEODB, n2t:paleodb, prefixcommons:paleodb, miriam:paleodb ; @@ -9360,8 +9460,8 @@ bioregistry:paleodb a bioregistry.schema:0000001 ; bioregistry:pao a bioregistry.schema:0000001 ; rdfs:label "Plant Anatomy Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:PAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:pao, biocontext:PAO ; foaf:homepage "http://www.plantontology.org"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/PAO_$1"^^xsd:string ; @@ -9371,8 +9471,8 @@ bioregistry:pao a bioregistry.schema:0000001 ; bioregistry:pass2 a bioregistry.schema:0000001 ; rdfs:label "Protein Alignment organised as Structural Superfamily" ; dc:description "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PASS2, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PASS2, n2t:pass2, prefixcommons:pass2, miriam:pass2 ; @@ -9385,8 +9485,8 @@ bioregistry:pass2 a bioregistry.schema:0000001 ; bioregistry:pathwaycommons a bioregistry.schema:0000001 ; rdfs:label "Pathway Commons" ; dc:description "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PATHWAYCOMMONS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PATHWAYCOMMONS, n2t:pathwaycommons, prefixcommons:pathwaycommons, miriam:pathwaycommons, @@ -9400,8 +9500,8 @@ bioregistry:pathwaycommons a bioregistry.schema:0000001 ; bioregistry:paxdb.organism a bioregistry.schema:0000001 ; rdfs:label "PaxDb Organism" ; dc:description "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PAXDB.ORGANISM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PAXDB.ORGANISM, n2t:paxdb.organism, miriam:paxdb.organism ; foaf:homepage "http://pax-db.org/"^^xsd:string ; @@ -9413,8 +9513,8 @@ bioregistry:paxdb.organism a bioregistry.schema:0000001 ; bioregistry:paxdb.protein a bioregistry.schema:0000001 ; rdfs:label "PaxDb Protein" ; dc:description "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PAXDB.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PAXDB.PROTEIN, n2t:paxdb.protein, miriam:paxdb.protein ; foaf:homepage "http://pax-db.org/"^^xsd:string ; @@ -9426,8 +9526,8 @@ bioregistry:paxdb.protein a bioregistry.schema:0000001 ; bioregistry:pazar a bioregistry.schema:0000001 ; rdfs:label "Pazar Transcription Factor" ; dc:description "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PAZAR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PAZAR, n2t:pazar, fairsharing:FAIRsharing.33yggg, prefixcommons:pazar, @@ -9440,8 +9540,8 @@ bioregistry:pazar a bioregistry.schema:0000001 ; bioregistry:pd_st a bioregistry.schema:0000001 ; rdfs:label "Platynereis stage ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:PD_ST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:pd_st, biocontext:PD_ST ; foaf:homepage "http://4dx.embl.de/platy"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/PD_ST_$1"^^xsd:string ; @@ -9451,9 +9551,9 @@ bioregistry:pd_st a bioregistry.schema:0000001 ; bioregistry:pdro a bioregistry.schema:0000001 ; rdfs:label "The Prescription of Drugs Ontology" ; dc:description "An ontology to describe entities related to prescription of drugs"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PDRO, - obofoundry:PDRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PDRO, + obofoundry:pdro, ontobee:PDRO, bioportal:PDRO, biocontext:PDRO, @@ -9469,9 +9569,9 @@ bioregistry:pdro a bioregistry.schema:0000001 ; bioregistry:pdumdv a bioregistry.schema:0000001 ; rdfs:label "Platynereis Developmental Stages" ; dc:description "Life cycle stages for Platynereis dumerilii"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PDUMDV, - obofoundry:PdumDv, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PDUMDV, + obofoundry:pdumdv, ontobee:PDUMDV, bioportal:PDUMDV, biocontext:PDUMDV, @@ -9487,8 +9587,8 @@ bioregistry:pdumdv a bioregistry.schema:0000001 ; bioregistry:peptideatlas a bioregistry.schema:0000001 ; rdfs:label "PeptideAtlas" ; dc:description "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2626, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2626, biocontext:PEPTIDEATLAS, n2t:peptideatlas, fairsharing:FAIRsharing.dvyrsz, @@ -9504,8 +9604,8 @@ bioregistry:peptideatlas a bioregistry.schema:0000001 ; bioregistry:perkinelmer a bioregistry.schema:0000001 ; rdfs:label "PerkinElmer cell line collection" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:PerkinElmer ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:PerkinElmer ; foaf:homepage "https://www.perkinelmer.com/"^^xsd:string ; bioregistry.schema:0000005 "SCC111"^^xsd:string ; bioregistry.schema:0000006 "https://www.perkinelmer.com/searchresult?searchName=$1"^^xsd:string ; @@ -9514,8 +9614,8 @@ bioregistry:perkinelmer a bioregistry.schema:0000001 ; bioregistry:peroxibase a bioregistry.schema:0000001 ; rdfs:label "Peroxibase" ; dc:description "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PEROXIBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PEROXIBASE, n2t:peroxibase, fairsharing:FAIRsharing.z1czxj, prefixcommons:peroxibase, @@ -9530,8 +9630,8 @@ bioregistry:peroxibase a bioregistry.schema:0000001 ; bioregistry:pfam a bioregistry.schema:0000001 ; rdfs:label "Pfam" ; dc:description "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1138, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1138, biocontext:PFAM, go.resource:Pfam, n2t:pfam, @@ -9549,8 +9649,8 @@ bioregistry:pfam a bioregistry.schema:0000001 ; bioregistry:pgdso a bioregistry.schema:0000001 ; rdfs:label "Plant Growth and Development Stage" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:PGDSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:pgdso, biocontext:PGDSO ; foaf:homepage "http://www.plantontology.org"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/PGDSO_$1"^^xsd:string ; @@ -9560,8 +9660,8 @@ bioregistry:pgdso a bioregistry.schema:0000001 ; bioregistry:pgs a bioregistry.schema:0000001 ; rdfs:label "Polygenic Score Catalog" ; dc:description "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:pgs ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:pgs ; foaf:homepage "http://pgscatalog.org"^^xsd:string ; bioregistry.schema:0000005 "PGS000018"^^xsd:string ; bioregistry.schema:0000006 "https://www.pgscatalog.org/pgs/$1"^^xsd:string ; @@ -9571,8 +9671,8 @@ bioregistry:pgs a bioregistry.schema:0000001 ; bioregistry:pgx a bioregistry.schema:0000001 ; rdfs:label "Progenetix" ; dc:description "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PGX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PGX, cellosaurus.resource:Progenetix, n2t:pgx, fairsharing:FAIRsharing.65tdnz, @@ -9586,8 +9686,8 @@ bioregistry:pgx a bioregistry.schema:0000001 ; bioregistry:pharmacodb.cell a bioregistry.schema:0000001 ; rdfs:label "PharmacoDB Cells" ; dc:description "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:PharmacoDB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:PharmacoDB ; foaf:homepage "https://pharmacodb.ca/cell_lines"^^xsd:string ; bioregistry.schema:0000005 "22RV1_12_2019"^^xsd:string ; bioregistry.schema:0000006 "https://pharmacodb.ca/cell_lines/$1"^^xsd:string ; @@ -9596,8 +9696,8 @@ bioregistry:pharmacodb.cell a bioregistry.schema:0000001 ; bioregistry:pharmgkb.disease a bioregistry.schema:0000001 ; rdfs:label "PharmGKB Disease" ; dc:description "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2651, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2651, biocontext:PHARMGKB.DISEASE, n2t:pharmgkb.disease, prefixcommons:pharmgkb.disease, @@ -9612,8 +9712,8 @@ bioregistry:pharmgkb.disease a bioregistry.schema:0000001 ; bioregistry:pharmgkb.drug a bioregistry.schema:0000001 ; rdfs:label "PharmGKB Drug" ; dc:description "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2652, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2652, biocontext:PHARMGKB.DRUG, n2t:pharmgkb.drug, prefixcommons:pharmgkb.drug, @@ -9628,8 +9728,8 @@ bioregistry:pharmgkb.drug a bioregistry.schema:0000001 ; bioregistry:pharmgkb.gene a bioregistry.schema:0000001 ; rdfs:label "Pharmacogenetics and Pharmacogenomics Knowledge Base" ; dc:description "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:PHARMGKB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:PHARMGKB, biocontext:PHARMGKB.GENE, go.resource:PharmGKB, n2t:pharmgkb.gene, @@ -9646,8 +9746,8 @@ bioregistry:pharmgkb.pathways a bioregistry.schema:0000001 ; rdfs:label "PharmGKB Pathways" ; dc:description """The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2650, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2650, biocontext:PHARMGKB.PATHWAYS, n2t:pharmgkb.pathways, prefixcommons:pharmgkb.pathways, @@ -9662,8 +9762,8 @@ PharmGKB Pathways are drug centric, gene based, interactive pathways which focus bioregistry:phenolexplorer a bioregistry.schema:0000001 ; rdfs:label "Phenol-Explorer" ; dc:description "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHENOLEXPLORER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHENOLEXPLORER, n2t:phenolexplorer, miriam:phenolexplorer ; foaf:homepage "http://www.phenol-explorer.eu/foods/"^^xsd:string ; @@ -9675,8 +9775,8 @@ bioregistry:phenolexplorer a bioregistry.schema:0000001 ; bioregistry:phenx a bioregistry.schema:0000001 ; rdfs:label "PhenX Toolkit" ; dc:description "A Web-based catalog of recommended measurement protocols"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PHENX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PHENX, bioportal:PHENX, fairsharing:FAIRsharing.y5jcwa ; foaf:homepage "https://www.phenxtoolkit.org/"^^xsd:string ; @@ -9688,8 +9788,8 @@ bioregistry:phenx a bioregistry.schema:0000001 ; bioregistry:phosphopoint.kinase a bioregistry.schema:0000001 ; rdfs:label "PhosphoPoint Kinase" ; dc:description "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHOSPHOPOINT.KINASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHOSPHOPOINT.KINASE, n2t:phosphopoint.kinase, miriam:phosphopoint.kinase ; foaf:homepage "http://kinase.bioinformatics.tw/"^^xsd:string ; @@ -9701,8 +9801,8 @@ bioregistry:phosphopoint.kinase a bioregistry.schema:0000001 ; bioregistry:phosphopoint.protein a bioregistry.schema:0000001 ; rdfs:label "PhosphoPoint Phosphoprotein" ; dc:description "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHOSPHOPOINT.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHOSPHOPOINT.PROTEIN, n2t:phosphopoint.protein, miriam:phosphopoint.protein ; foaf:homepage "http://kinase.bioinformatics.tw/"^^xsd:string ; @@ -9714,8 +9814,8 @@ bioregistry:phosphopoint.protein a bioregistry.schema:0000001 ; bioregistry:phosphosite.protein a bioregistry.schema:0000001 ; rdfs:label "PhosphoSite Protein" ; dc:description "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHOSPHOSITE.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHOSPHOSITE.PROTEIN, n2t:phosphosite.protein, miriam:phosphosite.protein ; foaf:homepage "http://www.phosphosite.org/homeAction.do"^^xsd:string ; @@ -9727,8 +9827,8 @@ bioregistry:phosphosite.protein a bioregistry.schema:0000001 ; bioregistry:phosphosite.residue a bioregistry.schema:0000001 ; rdfs:label "PhosphoSite Residue" ; dc:description "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHOSPHOSITE.RESIDUE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHOSPHOSITE.RESIDUE, n2t:phosphosite.residue, miriam:phosphosite.residue ; foaf:homepage "http://www.phosphosite.org/homeAction.do"^^xsd:string ; @@ -9740,8 +9840,8 @@ bioregistry:phosphosite.residue a bioregistry.schema:0000001 ; bioregistry:phylomedb a bioregistry.schema:0000001 ; rdfs:label "PhylomeDB" ; dc:description "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHYLOMEDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHYLOMEDB, n2t:phylomedb, fairsharing:FAIRsharing.7hxxc4, prefixcommons:phylomedb, @@ -9756,8 +9856,8 @@ bioregistry:phylomedb a bioregistry.schema:0000001 ; bioregistry:phytozome.locus a bioregistry.schema:0000001 ; rdfs:label "Plant Genome Network" ; dc:description "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PHYTOZOME.LOCUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PHYTOZOME.LOCUS, n2t:phytozome.locus, ncbi.resource:Phytozome, miriam:phytozome.locus ; @@ -9770,8 +9870,8 @@ bioregistry:phytozome.locus a bioregistry.schema:0000001 ; bioregistry:pid.pathway a bioregistry.schema:0000001 ; rdfs:label "NCI Pathway Interaction Database: Pathway" ; dc:description "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2344, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2344, biocontext:PID.PATHWAY, n2t:pid.pathway, fairsharing:FAIRsharing.ncgh1j, @@ -9786,8 +9886,8 @@ bioregistry:pid.pathway a bioregistry.schema:0000001 ; bioregistry:pina a bioregistry.schema:0000001 ; rdfs:label "Protein Interaction Network Analysis" ; dc:description "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PINA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PINA, n2t:pina, fairsharing:FAIRsharing.7q4gsz, miriam:pina ; @@ -9801,8 +9901,8 @@ bioregistry:pina a bioregistry.schema:0000001 ; bioregistry:piroplasma a bioregistry.schema:0000001 ; rdfs:label "PiroplasmaDB" ; dc:description "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PIROPLASMA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PIROPLASMA, n2t:piroplasma, miriam:piroplasma ; foaf:homepage "http://piroplasmadb.org/"^^xsd:string ; @@ -9814,8 +9914,8 @@ bioregistry:piroplasma a bioregistry.schema:0000001 ; bioregistry:pirsf a bioregistry.schema:0000001 ; rdfs:label "PIR Superfamily Classification System" ; dc:description "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1136, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1136, biocontext:PIRSF, go.resource:PIRSF, n2t:pirsf, @@ -9832,8 +9932,8 @@ bioregistry:pirsf a bioregistry.schema:0000001 ; bioregistry:pkdb a bioregistry.schema:0000001 ; rdfs:label "PK-DB" ; dc:description "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.AYegqK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.AYegqK, miriam:pkdb ; foaf:homepage "https://www.hu-berlin.de/?set_language=en&cl=en"^^xsd:string ; bioregistry.schema:0000005 "PKDB00198"^^xsd:string ; @@ -9844,8 +9944,8 @@ bioregistry:pkdb a bioregistry.schema:0000001 ; bioregistry:planttfdb a bioregistry.schema:0000001 ; rdfs:label "Plant Transcription Factor Database" ; dc:description "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PLANTTFDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PLANTTFDB, n2t:planttfdb, fairsharing:FAIRsharing.ex3fqk, prefixcommons:planttfdb, @@ -9859,8 +9959,8 @@ bioregistry:planttfdb a bioregistry.schema:0000001 ; bioregistry:plasmodb a bioregistry.schema:0000001 ; rdfs:label "PlasmoDB" ; dc:description "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PLASMODB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PLASMODB, go.resource:PlasmoDB, n2t:plasmodb, ncbi.resource:ApiDB_PlasmoDB, @@ -9875,8 +9975,8 @@ bioregistry:plasmodb a bioregistry.schema:0000001 ; bioregistry:plo a bioregistry.schema:0000001 ; rdfs:label "Plasmodium Life Cycle" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:PLO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:plo, biocontext:PLO ; foaf:homepage "http://www.sanger.ac.uk/Users/mb4/PLO/"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/PLO_$1"^^xsd:string ; @@ -9886,8 +9986,8 @@ bioregistry:plo a bioregistry.schema:0000001 ; bioregistry:pmap.cutdb a bioregistry.schema:0000001 ; rdfs:label "CutDB" ; dc:description "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PMAP.CUTDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PMAP.CUTDB, n2t:pmap.cutdb, prefixcommons:pmap.cutdb, miriam:pmap.cutdb ; @@ -9900,8 +10000,8 @@ bioregistry:pmap.cutdb a bioregistry.schema:0000001 ; bioregistry:pmap.substratedb a bioregistry.schema:0000001 ; rdfs:label "SubstrateDB" ; dc:description "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PMAP.SUBSTRATEDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PMAP.SUBSTRATEDB, n2t:pmap.substratedb, prefixcommons:pmap.substratedb, miriam:pmap.substratedb ; @@ -9914,8 +10014,8 @@ bioregistry:pmap.substratedb a bioregistry.schema:0000001 ; bioregistry:pmc a bioregistry.schema:0000001 ; rdfs:label "Pubmed Central" ; dc:description "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PMCID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PMCID, go.resource:PMCID, n2t:pmc, fairsharing:FAIRsharing.wpt5mp, @@ -9931,8 +10031,8 @@ bioregistry:pmc a bioregistry.schema:0000001 ; bioregistry:pmdb a bioregistry.schema:0000001 ; rdfs:label "Protein Model Database" ; dc:description "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PMDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PMDB, n2t:pmdb, fairsharing:FAIRsharing.wkaakq, prefixcommons:pmdb, @@ -9946,8 +10046,8 @@ bioregistry:pmdb a bioregistry.schema:0000001 ; bioregistry:pmp a bioregistry.schema:0000001 ; rdfs:label "Protein Model Portal" ; dc:description "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PMP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PMP, n2t:pmp, prefixcommons:pmp, miriam:pmp ; @@ -9961,8 +10061,8 @@ bioregistry:pmp a bioregistry.schema:0000001 ; bioregistry:pmr a bioregistry.schema:0000001 ; rdfs:label "Physical Medicine and Rehabilitation" ; dc:description "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PMR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PMR, bioportal:PMR, fairsharing:FAIRsharing.bcjrnq, miriam:pmr ; @@ -9975,8 +10075,8 @@ bioregistry:pmr a bioregistry.schema:0000001 ; bioregistry:pocketome a bioregistry.schema:0000001 ; rdfs:label "Pocketome" ; dc:description "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:POCKETOME, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:POCKETOME, n2t:pocketome, fairsharing:FAIRsharing.tc6df8, miriam:pocketome ; @@ -9989,8 +10089,8 @@ bioregistry:pocketome a bioregistry.schema:0000001 ; bioregistry:polbase a bioregistry.schema:0000001 ; rdfs:label "PolBase" ; dc:description "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:POLBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:POLBASE, n2t:polbase, fairsharing:FAIRsharing.s9ztmd, miriam:polbase ; @@ -10003,8 +10103,8 @@ bioregistry:polbase a bioregistry.schema:0000001 ; bioregistry:pombase a bioregistry.schema:0000001 ; rdfs:label "PomBase" ; dc:description "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PomBase, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PomBase, biolink:PomBase, go.resource:PomBase, n2t:pombase, @@ -10023,10 +10123,10 @@ bioregistry:pombase a bioregistry.schema:0000001 ; bioregistry:ppo a bioregistry.schema:0000001 ; rdfs:label "Plant Phenology Ontology" ; dc:description "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PPO, agroportal:PPO, - obofoundry:PPO, + obofoundry:ppo, ontobee:PPO, bioportal:PPO, biocontext:PPO, @@ -10042,8 +10142,8 @@ bioregistry:ppo a bioregistry.schema:0000001 ; bioregistry:pride.project a bioregistry.schema:0000001 ; rdfs:label "PRIDE Project" ; dc:description "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PRIDE.PROJECT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PRIDE.PROJECT, n2t:pride.project, miriam:pride.project ; foaf:homepage "https://www.ebi.ac.uk/pride/"^^xsd:string ; @@ -10055,8 +10155,8 @@ bioregistry:pride.project a bioregistry.schema:0000001 ; bioregistry:prints a bioregistry.schema:0000001 ; rdfs:label "PRINTS compendium of protein fingerprints" ; dc:description "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PRINTS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PRINTS, go.resource:PRINTS, n2t:prints, fairsharing:FAIRsharing.h8r843, @@ -10071,8 +10171,8 @@ bioregistry:prints a bioregistry.schema:0000001 ; bioregistry:probonto a bioregistry.schema:0000001 ; rdfs:label "Probability Distribution Ontology" ; dc:description "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROBONTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROBONTO, n2t:probonto, fairsharing:FAIRsharing.8zqzm9, miriam:probonto, @@ -10086,8 +10186,8 @@ bioregistry:probonto a bioregistry.schema:0000001 ; bioregistry:prodom a bioregistry.schema:0000001 ; rdfs:label "ProDom" ; dc:description "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PRODOM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PRODOM, n2t:prodom, fairsharing:FAIRsharing.a8z6gz, prefixcommons:prodom, @@ -10101,8 +10201,8 @@ bioregistry:prodom a bioregistry.schema:0000001 ; bioregistry:proglyc a bioregistry.schema:0000001 ; rdfs:label "ProGlycProt" ; dc:description "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROGLYC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROGLYC, n2t:proglyc, miriam:proglyc ; foaf:homepage "http://www.proglycprot.org/"^^xsd:string ; @@ -10113,9 +10213,9 @@ bioregistry:proglyc a bioregistry.schema:0000001 ; bioregistry:propreo a bioregistry.schema:0000001 ; rdfs:label "Proteomics data and process provenance" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PROPREO, - obofoundry:PROPREO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PROPREO, + obofoundry:propreo, bioportal:PROPREO, biocontext:PROPREO, prefixcommons:propreo ; @@ -10127,8 +10227,8 @@ bioregistry:propreo a bioregistry.schema:0000001 ; bioregistry:prosite a bioregistry.schema:0000001 ; rdfs:label "PROSITE" ; dc:description "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROSITE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROSITE, go.resource:Prosite, n2t:prosite, fairsharing:FAIRsharing.vwc6bd, @@ -10145,8 +10245,8 @@ bioregistry:prosite a bioregistry.schema:0000001 ; bioregistry:protclustdb a bioregistry.schema:0000001 ; rdfs:label "ProtClustDB" ; dc:description "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROTCLUSTDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROTCLUSTDB, n2t:protclustdb, fairsharing:FAIRsharing.da493y, prefixcommons:protclustdb, @@ -10160,8 +10260,8 @@ bioregistry:protclustdb a bioregistry.schema:0000001 ; bioregistry:proteomicsdb.peptide a bioregistry.schema:0000001 ; rdfs:label "ProteomicsDB Peptide" ; dc:description "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROTEOMICSDB.PEPTIDE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROTEOMICSDB.PEPTIDE, n2t:proteomicsdb.peptide, miriam:proteomicsdb.peptide ; foaf:homepage "https://www.proteomicsdb.org/#peptideSearch"^^xsd:string ; @@ -10173,8 +10273,8 @@ bioregistry:proteomicsdb.peptide a bioregistry.schema:0000001 ; bioregistry:proteomicsdb.protein a bioregistry.schema:0000001 ; rdfs:label "ProteomicsDB Protein" ; dc:description "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROTEOMICSDB.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROTEOMICSDB.PROTEIN, n2t:proteomicsdb.protein, miriam:proteomicsdb.protein ; foaf:homepage "https://www.proteomicsdb.org/#human"^^xsd:string ; @@ -10186,8 +10286,8 @@ bioregistry:proteomicsdb.protein a bioregistry.schema:0000001 ; bioregistry:protonet.cluster a bioregistry.schema:0000001 ; rdfs:label "ProtoNet Cluster" ; dc:description "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROTONET.CLUSTER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROTONET.CLUSTER, n2t:protonet.cluster, prefixcommons:protonet.cluster, miriam:protonet.cluster ; @@ -10200,8 +10300,8 @@ bioregistry:protonet.cluster a bioregistry.schema:0000001 ; bioregistry:protonet.proteincard a bioregistry.schema:0000001 ; rdfs:label "ProtoNet ProteinCard" ; dc:description "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PROTONET.PROTEINCARD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PROTONET.PROTEINCARD, n2t:protonet.proteincard, prefixcommons:protonet.proteincard, miriam:protonet.proteincard ; @@ -10214,8 +10314,8 @@ bioregistry:protonet.proteincard a bioregistry.schema:0000001 ; bioregistry:pscdb a bioregistry.schema:0000001 ; rdfs:label "Protein Structural Change Database" ; dc:description "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PSCDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PSCDB, n2t:pscdb, fairsharing:FAIRsharing.3d4jx0, miriam:pscdb ; @@ -10228,8 +10328,8 @@ bioregistry:pscdb a bioregistry.schema:0000001 ; bioregistry:pseudogene a bioregistry.schema:0000001 ; rdfs:label "PseudoGene" ; dc:description "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:pseudo, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:pseudo, prefixcommons:pseudogene ; foaf:homepage "http://www.pseudogene.org"^^xsd:string ; bioregistry.schema:0000005 "PGOHUM00000289843"^^xsd:string ; @@ -10239,8 +10339,8 @@ bioregistry:pseudogene a bioregistry.schema:0000001 ; bioregistry:pseudomonas a bioregistry.schema:0000001 ; rdfs:label "Pseudomonas Genome Database" ; dc:description "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PSEUDOMONAS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PSEUDOMONAS, n2t:pseudomonas, miriam:pseudomonas ; foaf:homepage "http://www.pseudomonas.com/"^^xsd:string ; @@ -10252,8 +10352,8 @@ bioregistry:pseudomonas a bioregistry.schema:0000001 ; bioregistry:psipar a bioregistry.schema:0000001 ; rdfs:label "Protein Affinity Reagents" ; dc:description "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PSIPAR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PSIPAR, n2t:psipar, miriam:psipar ; foaf:homepage "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR"^^xsd:string ; @@ -10265,8 +10365,8 @@ bioregistry:psipar a bioregistry.schema:0000001 ; bioregistry:publons.researcher a bioregistry.schema:0000001 ; rdfs:label "Publons Researcher" ; dc:description "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:ResearchID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:ResearchID ; foaf:homepage "https://publons.com/researcher"^^xsd:string ; bioregistry.schema:0000005 "1981638"^^xsd:string ; bioregistry.schema:0000006 "https://publons.com/researcher/$1"^^xsd:string ; @@ -10276,8 +10376,8 @@ bioregistry:publons.researcher a bioregistry.schema:0000001 ; bioregistry:pubmed a bioregistry.schema:0000001 ; rdfs:label "PubMed" ; dc:description "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1187, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1187, biocontext:PUBMED, cellosaurus.resource:PubMed, go.resource:PMID, @@ -10296,9 +10396,9 @@ bioregistry:pubmed a bioregistry.schema:0000001 ; bioregistry:pw a bioregistry.schema:0000001 ; rdfs:label "Pathway ontology" ; dc:description "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PW, - obofoundry:PW, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PW, + obofoundry:pw, ontobee:PW, bioportal:PW, biocontext:PW, @@ -10318,8 +10418,8 @@ bioregistry:pw a bioregistry.schema:0000001 ; bioregistry:px a bioregistry.schema:0000001 ; rdfs:label "ProteomeXchange" ; dc:description "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PX, n2t:px, miriam:px ; foaf:homepage "http://www.proteomexchange.org/"^^xsd:string ; @@ -10331,8 +10431,8 @@ bioregistry:px a bioregistry.schema:0000001 ; bioregistry:pypi a bioregistry.schema:0000001 ; rdfs:label "PyPI" ; dc:description "The Python Package Index (PyPI) is a repository for Python packages."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:pypi ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:pypi ; foaf:homepage "https://www.python.org/psf/"^^xsd:string ; bioregistry.schema:0000005 "numpy"^^xsd:string ; bioregistry.schema:0000006 "https://pypi.org/project/$1"^^xsd:string ; @@ -10342,8 +10442,8 @@ bioregistry:pypi a bioregistry.schema:0000001 ; bioregistry:qudt a bioregistry.schema:0000001 ; rdfs:label "Quantities, Units, Dimensions, and Types Ontology" ; dc:description "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:QUDT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:QUDT, bioportal:QUDT, biolink:qud, fairsharing:FAIRsharing.d3pqw7 ; @@ -10355,8 +10455,8 @@ bioregistry:qudt a bioregistry.schema:0000001 ; bioregistry:radiomics a bioregistry.schema:0000001 ; rdfs:label "Radiomics Ontology" ; dc:description "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:RO ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:RO ; foaf:homepage "http://www.radiomics.org/RO"^^xsd:string ; bioregistry.schema:0000005 "LK99"^^xsd:string ; bioregistry.schema:0000012 false . @@ -10364,8 +10464,8 @@ bioregistry:radiomics a bioregistry.schema:0000001 ; bioregistry:rapdb.locus a bioregistry.schema:0000001 ; rdfs:label "RAP-DB Locus" ; dc:description "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:rapdb.locus ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:rapdb.locus ; foaf:homepage "https://rapdb.dna.affrc.go.jp/"^^xsd:string ; bioregistry.schema:0000005 "Os01g0883800"^^xsd:string ; bioregistry.schema:0000006 "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^xsd:string ; @@ -10375,8 +10475,8 @@ bioregistry:rapdb.locus a bioregistry.schema:0000001 ; bioregistry:rapdb.transcript a bioregistry.schema:0000001 ; rdfs:label "RAP-DB Transcript" ; dc:description "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:rapdb.transcript ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:rapdb.transcript ; foaf:homepage "https://rapdb.dna.affrc.go.jp/"^^xsd:string ; bioregistry.schema:0000005 "Os01t0883800-02"^^xsd:string ; bioregistry.schema:0000006 "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^xsd:string ; @@ -10386,8 +10486,8 @@ bioregistry:rapdb.transcript a bioregistry.schema:0000001 ; bioregistry:rbk a bioregistry.schema:0000001 ; rdfs:label "Rebuilding a Kidney" ; dc:description "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RBK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RBK, n2t:rbk, fairsharing:FAIRsharing.78d3ad, miriam:rbk ; @@ -10400,8 +10500,8 @@ bioregistry:rbk a bioregistry.schema:0000001 ; bioregistry:rdo a bioregistry.schema:0000001 ; rdfs:label "RGD Disease_Ontology" ; dc:description "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RDO, bioportal:RDO ; foaf:homepage "https://ratmine.mcw.edu/ontology/disease/"^^xsd:string ; bioregistry.schema:0000005 "9002859"^^xsd:string ; @@ -10411,8 +10511,8 @@ bioregistry:rdo a bioregistry.schema:0000001 ; bioregistry:re3data a bioregistry.schema:0000001 ; rdfs:label "re3data" ; dc:description "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:re3data ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:re3data ; foaf:homepage "https://datacite.org"^^xsd:string ; bioregistry.schema:0000005 "r3d100010772"^^xsd:string ; bioregistry.schema:0000006 "https://www.re3data.org/repository/$1"^^xsd:string ; @@ -10422,8 +10522,8 @@ bioregistry:re3data a bioregistry.schema:0000001 ; bioregistry:reactome a bioregistry.schema:0000001 ; rdfs:label "Reactome" ; dc:description "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1155, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1155, biocontext:REACTOME, go.resource:Reactome, n2t:reactome, @@ -10441,8 +10541,8 @@ bioregistry:reactome a bioregistry.schema:0000001 ; bioregistry:reaxys a bioregistry.schema:0000001 ; rdfs:label "Reaxys" ; dc:description "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1003, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1003, wikidata:P1579 ; foaf:homepage "https://www.reaxys.com"^^xsd:string ; bioregistry.schema:0000005 "1257009"^^xsd:string ; @@ -10452,8 +10552,8 @@ bioregistry:reaxys a bioregistry.schema:0000001 ; bioregistry:rebase a bioregistry.schema:0000001 ; rdfs:label "REBASE restriction enzyme database" ; dc:description "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2325, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2325, biocontext:REBASE, go.resource:REBASE, n2t:rebase, @@ -10470,8 +10570,8 @@ bioregistry:rebase a bioregistry.schema:0000001 ; bioregistry:refseq a bioregistry.schema:0000001 ; rdfs:label "Reference Sequence Collection" ; dc:description "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1098, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1098, biocontext:RefSeq, go.resource:RefSeq, n2t:refseq, @@ -10489,8 +10589,8 @@ bioregistry:refseq a bioregistry.schema:0000001 ; bioregistry:repeatsdb.protein a bioregistry.schema:0000001 ; rdfs:label "RepeatsDB Protein" ; dc:description "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:repeatsdb.protein ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:repeatsdb.protein ; foaf:homepage "https://repeatsdb.org/"^^xsd:string ; bioregistry.schema:0000005 "P29894"^^xsd:string ; bioregistry.schema:0000006 "https://repeatsdb.org/protein/$1"^^xsd:string ; @@ -10501,8 +10601,8 @@ bioregistry:repeatsdb.protein a bioregistry.schema:0000001 ; bioregistry:repeatsdb.structure a bioregistry.schema:0000001 ; rdfs:label "RepeatsDB Structure" ; dc:description "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:repeatsdb.structure ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:repeatsdb.structure ; foaf:homepage "https://repeatsdb.org/"^^xsd:string ; bioregistry.schema:0000005 "2gc4E"^^xsd:string ; bioregistry.schema:0000006 "https://repeatsdb.org/structure/$1"^^xsd:string ; @@ -10512,8 +10612,8 @@ bioregistry:repeatsdb.structure a bioregistry.schema:0000001 ; bioregistry:reproduceme a bioregistry.schema:0000001 ; rdfs:label "REPRODUCE-ME Ontology" ; dc:description "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:REPRODUCE-ME, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:REPRODUCE-ME, bioportal:REPRODUCE-ME, ols:reproduceme ; foaf:homepage "https://w3id.org/reproduceme/research"^^xsd:string ; @@ -10523,8 +10623,8 @@ bioregistry:reproduceme a bioregistry.schema:0000001 ; bioregistry:reto a bioregistry.schema:0000001 ; rdfs:label "Regulation of Transcription Ontology" ; dc:description "Regulation of Transcription"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RETO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RETO, bioportal:RETO, fairsharing:FAIRsharing.4qyf0f, ols:reto ; @@ -10534,8 +10634,8 @@ bioregistry:reto a bioregistry.schema:0000001 ; bioregistry:rexo a bioregistry.schema:0000001 ; rdfs:label "Regulation of Gene Expression Ontology" ; dc:description "Regulation of Gene Expression"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:REXO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:REXO, bioportal:REXO, fairsharing:FAIRsharing.recas1, ols:rexo ; @@ -10545,8 +10645,8 @@ bioregistry:rexo a bioregistry.schema:0000001 ; bioregistry:rfam a bioregistry.schema:0000001 ; rdfs:label "Rfam database of RNA families" ; dc:description "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2356, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2356, biocontext:RFAM, go.resource:Rfam, n2t:rfam, @@ -10562,8 +10662,8 @@ bioregistry:rfam a bioregistry.schema:0000001 ; bioregistry:rgd a bioregistry.schema:0000001 ; rdfs:label "Rat Genome Database" ; dc:description "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RGD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RGD, edam.data:2620, bioportal:RGD, biocontext:RGD, @@ -10585,8 +10685,8 @@ bioregistry:rgd a bioregistry.schema:0000001 ; bioregistry:rgd.qtl a bioregistry.schema:0000001 ; rdfs:label "Rat Genome Database qTL" ; dc:description "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RGD.QTL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RGD.QTL, n2t:rgd.qtl, miriam:rgd.qtl ; foaf:homepage "http://rgd.mcw.edu/"^^xsd:string ; @@ -10598,8 +10698,8 @@ bioregistry:rgd.qtl a bioregistry.schema:0000001 ; bioregistry:rgd.strain a bioregistry.schema:0000001 ; rdfs:label "Rat Genome Database strain" ; dc:description "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RGD.STRAIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RGD.STRAIN, n2t:rgd.strain, miriam:rgd.strain ; foaf:homepage "http://rgd.mcw.edu/"^^xsd:string ; @@ -10613,8 +10713,8 @@ bioregistry:rhea a bioregistry.schema:0000001 ; dc:description """ Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants. Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2644, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2644, biocontext:RHEA, go.resource:RHEA, n2t:rhea, @@ -10630,8 +10730,8 @@ Rhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as bioregistry:ricegap a bioregistry.schema:0000001 ; rdfs:label "Rice Genome Annotation Project" ; dc:description "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICEGAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICEGAP, n2t:ricegap, miriam:ricegap ; foaf:homepage "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml"^^xsd:string ; @@ -10643,8 +10743,8 @@ bioregistry:ricegap a bioregistry.schema:0000001 ; bioregistry:ricenetdb.compound a bioregistry.schema:0000001 ; rdfs:label "RiceNetDB Compound" ; dc:description "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICENETDB.COMPOUND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICENETDB.COMPOUND, n2t:ricenetdb.compound, miriam:ricenetdb.compound ; foaf:homepage "http://bis.zju.edu.cn/ricenetdb"^^xsd:string ; @@ -10656,8 +10756,8 @@ bioregistry:ricenetdb.compound a bioregistry.schema:0000001 ; bioregistry:ricenetdb.gene a bioregistry.schema:0000001 ; rdfs:label "RiceNetDB Gene" ; dc:description "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICENETDB.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICENETDB.GENE, n2t:ricenetdb.gene, miriam:ricenetdb.gene ; foaf:homepage "http://bis.zju.edu.cn/ricenetdb/"^^xsd:string ; @@ -10669,8 +10769,8 @@ bioregistry:ricenetdb.gene a bioregistry.schema:0000001 ; bioregistry:ricenetdb.mirna a bioregistry.schema:0000001 ; rdfs:label "RiceNetDB miRNA" ; dc:description "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICENETDB.MIRNA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICENETDB.MIRNA, n2t:ricenetdb.mirna, miriam:ricenetdb.mirna ; foaf:homepage "http://bis.zju.edu.cn/ricenetdb"^^xsd:string ; @@ -10682,8 +10782,8 @@ bioregistry:ricenetdb.mirna a bioregistry.schema:0000001 ; bioregistry:ricenetdb.protein a bioregistry.schema:0000001 ; rdfs:label "RiceNetDB Protein" ; dc:description "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICENETDB.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICENETDB.PROTEIN, n2t:ricenetdb.protein, miriam:ricenetdb.protein ; foaf:homepage "http://bis.zju.edu.cn/ricenetdb/"^^xsd:string ; @@ -10695,8 +10795,8 @@ bioregistry:ricenetdb.protein a bioregistry.schema:0000001 ; bioregistry:ricenetdb.reaction a bioregistry.schema:0000001 ; rdfs:label "RiceNetDB Reaction" ; dc:description "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RICENETDB.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RICENETDB.REACTION, n2t:ricenetdb.reaction, miriam:ricenetdb.reaction ; foaf:homepage "http://bis.zju.edu.cn/ricenetdb"^^xsd:string ; @@ -10708,8 +10808,8 @@ bioregistry:ricenetdb.reaction a bioregistry.schema:0000001 ; bioregistry:rnacentral a bioregistry.schema:0000001 ; rdfs:label "RNAcentral" ; dc:description "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:3856, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:3856, biocontext:RNACENTRAL, go.resource:RNAcentral, n2t:rnacentral, @@ -10725,8 +10825,8 @@ bioregistry:rnacentral a bioregistry.schema:0000001 ; bioregistry:rnamods a bioregistry.schema:0000001 ; rdfs:label "RNA Modification Database" ; dc:description "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RNAMODS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RNAMODS, go.resource:RNAmods, n2t:rnamods, prefixcommons:rnamods, @@ -10740,9 +10840,9 @@ bioregistry:rnamods a bioregistry.schema:0000001 ; bioregistry:rnao a bioregistry.schema:0000001 ; rdfs:label "RNA ontology" ; dc:description "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RNAO, - obofoundry:RNAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RNAO, + obofoundry:rnao, ontobee:RNAO, bioportal:RNAO, biocontext:RNAO, @@ -10759,8 +10859,8 @@ bioregistry:rnao a bioregistry.schema:0000001 ; bioregistry:rouge a bioregistry.schema:0000001 ; rdfs:label "Rodent Unidentified Gene-Encoded Large Proteins" ; dc:description "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ROUGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ROUGE, n2t:rouge, fairsharing:FAIRsharing.vdbagq, prefixcommons:rouge, @@ -10776,8 +10876,8 @@ bioregistry:rrid a bioregistry.schema:0000001 ; rdfs:label "Research Resource Identification" ; dc:description """The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:RRID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:RRID, n2t:rrid, fairsharing:FAIRsharing.ATwSZG, miriam:rrid ; @@ -10790,9 +10890,9 @@ The initiative works with participating journals to intercept manuscripts in the bioregistry:rs a bioregistry.schema:0000001 ; rdfs:label "Rat Strain Ontology" ; dc:description "Ontology of rat strains"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RS, - obofoundry:RS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RS, + obofoundry:rs, ontobee:RS, bioportal:RS, biocontext:RS, @@ -10809,8 +10909,8 @@ bioregistry:rs a bioregistry.schema:0000001 ; bioregistry:runbiosimulations a bioregistry.schema:0000001 ; rdfs:label "runBioSimulations" ; dc:description "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:runbiosimulations ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:runbiosimulations ; foaf:homepage "https://icahn.mssm.edu/"^^xsd:string ; bioregistry.schema:0000005 "5fde96bdc5f1aa9ff0cce18a"^^xsd:string ; bioregistry.schema:0000006 "https://run.biosimulations.org/simulations/$1"^^xsd:string ; @@ -10820,9 +10920,9 @@ bioregistry:runbiosimulations a bioregistry.schema:0000001 ; bioregistry:rxno a bioregistry.schema:0000001 ; rdfs:label "Name Reaction Ontology" ; dc:description "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RXNO, - obofoundry:RXNO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RXNO, + obofoundry:rxno, ontobee:RXNO, bioportal:RXNO, biocontext:RXNO, @@ -10839,8 +10939,8 @@ bioregistry:rxno a bioregistry.schema:0000001 ; bioregistry:rxnorm a bioregistry.schema:0000001 ; rdfs:label "RxNorm" ; dc:description "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RXNORM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RXNORM, bioportal:RXNORM, biocontext:RXCUI, biolink:RXNORM, @@ -10855,8 +10955,8 @@ bioregistry:rxnorm a bioregistry.schema:0000001 ; bioregistry:sabiork.compound a bioregistry.schema:0000001 ; rdfs:label "SABIO-RK Compound" ; dc:description "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:sabiork.compound, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:sabiork.compound, miriam:sabiork.compound ; foaf:homepage "http://sabiork.h-its.org/"^^xsd:string ; bioregistry.schema:0000005 "75"^^xsd:string ; @@ -10867,8 +10967,8 @@ bioregistry:sabiork.compound a bioregistry.schema:0000001 ; bioregistry:sabiork.ec a bioregistry.schema:0000001 ; rdfs:label "SABIO-RK EC Record" ; dc:description "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SABIORK.EC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SABIORK.EC, n2t:sabiork.ec, prefixcommons:sabiork.ec, miriam:sabiork.ec ; @@ -10882,8 +10982,8 @@ bioregistry:sabiork.ec a bioregistry.schema:0000001 ; bioregistry:sabiork.kineticrecord a bioregistry.schema:0000001 ; rdfs:label "SABIO Reaction Kinetics" ; dc:description "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SABIORK.KINETICRECORD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SABIORK.KINETICRECORD, go.resource:SABIO-RK, n2t:sabiork.kineticrecord, miriam:sabiork.kineticrecord ; @@ -10896,8 +10996,8 @@ bioregistry:sabiork.kineticrecord a bioregistry.schema:0000001 ; bioregistry:sabiork.reaction a bioregistry.schema:0000001 ; rdfs:label "SABIO-RK Reaction" ; dc:description "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2309, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2309, biocontext:SABIORK.REACTION, n2t:sabiork.reaction, fairsharing:FAIRsharing.cwx04e, @@ -10912,9 +11012,9 @@ bioregistry:sabiork.reaction a bioregistry.schema:0000001 ; bioregistry:sao a bioregistry.schema:0000001 ; rdfs:label "Subcellular Anatomy Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SAO, - obofoundry:SAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SAO, + obofoundry:sao, bioportal:SAO, biocontext:SAO, prefixcommons:sao ; @@ -10928,8 +11028,8 @@ bioregistry:sao a bioregistry.schema:0000001 ; bioregistry:sasbdb a bioregistry.schema:0000001 ; rdfs:label "Small Angle Scattering Biological Data Bank" ; dc:description "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SASBDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SASBDB, n2t:sasbdb, fairsharing:FAIRsharing.i1F3Hb, miriam:sasbdb, @@ -10943,8 +11043,8 @@ bioregistry:sasbdb a bioregistry.schema:0000001 ; bioregistry:scop a bioregistry.schema:0000001 ; rdfs:label "Structural Classification of Protein" ; dc:description "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SCOP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SCOP, n2t:scop, fairsharing:FAIRsharing.wjzty, prefixcommons:scop, @@ -10960,8 +11060,8 @@ bioregistry:scopus a bioregistry.schema:0000001 ; dc:description """Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. Delivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts and humanities, Scopus features smart tools to track, analyze and visualize research."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:ScopusID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:ScopusID, fairsharing:FAIRsharing.0a674c ; foaf:homepage "https://www.scopus.com"^^xsd:string ; bioregistry.schema:0000005 "56305849200"^^xsd:string ; @@ -10971,8 +11071,8 @@ and humanities, Scopus features smart tools to track, analyze and visualize res bioregistry:scretf a bioregistry.schema:0000001 ; rdfs:label "ScerTF" ; dc:description "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SCRETF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SCRETF, n2t:scretf, miriam:scretf ; foaf:homepage "http://stormo.wustl.edu/ScerTF/"^^xsd:string ; @@ -10984,8 +11084,8 @@ bioregistry:scretf a bioregistry.schema:0000001 ; bioregistry:sdbs a bioregistry.schema:0000001 ; rdfs:label "Spectral Database for Organic Compounds" ; dc:description "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SDBS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SDBS, n2t:sdbs, miriam:sdbs ; foaf:homepage "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"^^xsd:string ; @@ -10997,8 +11097,8 @@ bioregistry:sdbs a bioregistry.schema:0000001 ; bioregistry:sdgio a bioregistry.schema:0000001 ; rdfs:label "Sustainable Development Goals Interface Ontology" ; dc:description "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:SDGIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:SDGIO, ontobee:SDGIO, fairsharing:FAIRsharing.d5ff6e, ols:sdgio ; @@ -11010,8 +11110,8 @@ bioregistry:sdgio a bioregistry.schema:0000001 ; bioregistry:sedml.format a bioregistry.schema:0000001 ; rdfs:label "SED-ML data format" ; dc:description "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:sedml.format ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:sedml.format ; foaf:homepage "http://sed-ml.org/"^^xsd:string ; bioregistry.schema:0000005 "csv"^^xsd:string ; bioregistry.schema:0000006 "https://sed-ml.org/urns.html#format:$1"^^xsd:string ; @@ -11021,8 +11121,8 @@ bioregistry:sedml.format a bioregistry.schema:0000001 ; bioregistry:sedml.language a bioregistry.schema:0000001 ; rdfs:label "SED-ML model format" ; dc:description "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:sedml.language ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:sedml.language ; foaf:homepage "http://sed-ml.org/"^^xsd:string ; bioregistry.schema:0000005 "sbml.level-3.version-2"^^xsd:string ; bioregistry.schema:0000006 "https://sed-ml.org/urns.html#language:$1"^^xsd:string ; @@ -11032,8 +11132,8 @@ bioregistry:sedml.language a bioregistry.schema:0000001 ; bioregistry:seed a bioregistry.schema:0000001 ; rdfs:label "The SEED;" ; dc:description "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SEED, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SEED, go.resource:SEED, n2t:seed, ncbi.resource:SEED, @@ -11047,8 +11147,8 @@ bioregistry:seed a bioregistry.schema:0000001 ; bioregistry:seed.compound a bioregistry.schema:0000001 ; rdfs:label "SEED Compound" ; dc:description "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SEED.COMPOUND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SEED.COMPOUND, n2t:seed.compound, miriam:seed.compound ; foaf:homepage "http://modelseed.org/"^^xsd:string ; @@ -11060,8 +11160,8 @@ bioregistry:seed.compound a bioregistry.schema:0000001 ; bioregistry:seed.reaction a bioregistry.schema:0000001 ; rdfs:label "SEED Reactions" ; dc:description "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:SEED.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:SEED.REACTION, n2t:seed.reaction, miriam:seed.reaction ; foaf:homepage "http://modelseed.org/biochem/reactions/"^^xsd:string ; @@ -11073,9 +11173,9 @@ bioregistry:seed.reaction a bioregistry.schema:0000001 ; bioregistry:sep a bioregistry.schema:0000001 ; rdfs:label "Sample processing and separation techniques" ; dc:description "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SEP, - obofoundry:SEP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SEP, + obofoundry:sep, ontobee:SEP, bioportal:SEP, biocontext:SEP, @@ -11090,9 +11190,9 @@ bioregistry:sep a bioregistry.schema:0000001 ; bioregistry:sepio a bioregistry.schema:0000001 ; rdfs:label "Scientific Evidence and Provenance Information Ontology" ; dc:description "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SEPIO, - obofoundry:SEPIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SEPIO, + obofoundry:sepio, ontobee:SEPIO, bioportal:SEPIO, biocontext:SEPIO, @@ -11107,8 +11207,8 @@ bioregistry:sepio a bioregistry.schema:0000001 ; bioregistry:sgd a bioregistry.schema:0000001 ; rdfs:label "Saccharomyces Genome Database" ; dc:description "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2632, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2632, biocontext:SGD, go.resource:SGD, n2t:sgd, @@ -11127,8 +11227,8 @@ bioregistry:sgd a bioregistry.schema:0000001 ; bioregistry:sgd.pathways a bioregistry.schema:0000001 ; rdfs:label "Saccharomyces genome database pathways" ; dc:description "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SGD.PATHWAYS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SGD.PATHWAYS, n2t:sgd.pathways, prefixcommons:sgd.pathways, miriam:sgd.pathways ; @@ -11141,8 +11241,8 @@ bioregistry:sgd.pathways a bioregistry.schema:0000001 ; bioregistry:sgn a bioregistry.schema:0000001 ; rdfs:label "Sol Genomics Network" ; dc:description "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SGN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SGN, go.resource:SGN, n2t:sgn, ncbi.resource:SGN, @@ -11158,9 +11258,9 @@ bioregistry:sgn a bioregistry.schema:0000001 ; bioregistry:sibo a bioregistry.schema:0000001 ; rdfs:label "Social Insect Behavior Ontology" ; dc:description "Social Behavior in insects"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SIBO, - obofoundry:SIBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SIBO, + obofoundry:sibo, ontobee:SIBO, bioportal:SIBO, biocontext:SIBO, @@ -11176,8 +11276,8 @@ bioregistry:sibo a bioregistry.schema:0000001 ; bioregistry:sider.drug a bioregistry.schema:0000001 ; rdfs:label "SIDER Drug" ; dc:description "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SIDER.DRUG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SIDER.DRUG, n2t:sider.drug, miriam:sider.drug ; foaf:homepage "http://sideeffects.embl.de/"^^xsd:string ; @@ -11189,8 +11289,8 @@ bioregistry:sider.drug a bioregistry.schema:0000001 ; bioregistry:sider.effect a bioregistry.schema:0000001 ; rdfs:label "SIDER Side Effect" ; dc:description "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SIDER.EFFECT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SIDER.EFFECT, n2t:sider.effect, miriam:sider.effect ; foaf:homepage "http://sideeffects.embl.de/"^^xsd:string ; @@ -11203,8 +11303,8 @@ bioregistry:sider.effect a bioregistry.schema:0000001 ; bioregistry:signaling-gateway a bioregistry.schema:0000001 ; rdfs:label "Signaling Gateway" ; dc:description "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SIGNALING-GATEWAY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SIGNALING-GATEWAY, n2t:signaling-gateway, prefixcommons:signaling-gateway, miriam:signaling-gateway ; @@ -11217,8 +11317,8 @@ bioregistry:signaling-gateway a bioregistry.schema:0000001 ; bioregistry:sio a bioregistry.schema:0000001 ; rdfs:label "Semanticscience Integrated Ontology" ; dc:description "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SIO, agroportal:SIO, ontobee:SIO, bioportal:SIO, @@ -11236,8 +11336,8 @@ bioregistry:sio a bioregistry.schema:0000001 ; bioregistry:sisu a bioregistry.schema:0000001 ; rdfs:label "Sequencing Initiative Suomi" ; dc:description "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SISU, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SISU, n2t:sisu, fairsharing:FAIRsharing.t1a232, miriam:sisu ; @@ -11250,8 +11350,8 @@ bioregistry:sisu a bioregistry.schema:0000001 ; bioregistry:sitex a bioregistry.schema:0000001 ; rdfs:label "SitEx" ; dc:description "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SITEX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SITEX, n2t:sitex, fairsharing:FAIRsharing.5mr9c5, prefixcommons:sitex, @@ -11265,8 +11365,8 @@ bioregistry:sitex a bioregistry.schema:0000001 ; bioregistry:skip a bioregistry.schema:0000001 ; rdfs:label "Stemcell Knowledge and Information Portal" ; dc:description "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:SKIP ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:SKIP ; foaf:homepage "https://skip.stemcellinformatics.org/en/"^^xsd:string ; bioregistry.schema:0000005 "SKIP001214"^^xsd:string ; bioregistry.schema:0000006 "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^xsd:string ; @@ -11275,8 +11375,8 @@ bioregistry:skip a bioregistry.schema:0000001 ; bioregistry:slkbase a bioregistry.schema:0000001 ; rdfs:label "SUM Breast Cancer Cell Line Knowledge Base" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:SLKBase ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:SLKBase ; foaf:homepage "https://sumlineknowledgebase.com/"^^xsd:string ; bioregistry.schema:0000005 "3618"^^xsd:string ; bioregistry.schema:0000006 "https://sumlineknowledgebase.com/?page_id=$1"^^xsd:string ; @@ -11286,8 +11386,8 @@ bioregistry:slkbase a bioregistry.schema:0000001 ; bioregistry:smart a bioregistry.schema:0000001 ; rdfs:label "Simple Modular Architecture Research Tool" ; dc:description "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SMART, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SMART, go.resource:SMART, n2t:smart, fairsharing:FAIRsharing.hsbpq3, @@ -11303,8 +11403,8 @@ bioregistry:smart a bioregistry.schema:0000001 ; bioregistry:smiles a bioregistry.schema:0000001 ; rdfs:label "Simplified molecular-input line-entry system" ; dc:description "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.qv4b3c, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.qv4b3c, wikidata:P233 ; foaf:homepage "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"^^xsd:string ; bioregistry.schema:0000005 "COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1"^^xsd:string ; @@ -11313,8 +11413,8 @@ bioregistry:smiles a bioregistry.schema:0000001 ; bioregistry:smpdb a bioregistry.schema:0000001 ; rdfs:label "Small Molecule Pathway Database" ; dc:description "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2659, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2659, biocontext:SMPDB, biolink:PathWhiz, n2t:smpdb, @@ -11330,8 +11430,8 @@ bioregistry:smpdb a bioregistry.schema:0000001 ; bioregistry:snomedct a bioregistry.schema:0000001 ; rdfs:label "SNOMED CT (International Edition)" ; dc:description "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SNOMEDCT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SNOMEDCT, bioportal:SNOMEDCT, biocontext:SNOMEDCT, biolink:SNOMEDCT, @@ -11350,8 +11450,8 @@ bioregistry:snomedct a bioregistry.schema:0000001 ; bioregistry:snp2tfbs a bioregistry.schema:0000001 ; rdfs:label "SNP to Transcription Factor Binding Sites" ; dc:description "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:snp2tfbs ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:snp2tfbs ; foaf:homepage "https://ccg.epfl.ch/snp2tfbs/"^^xsd:string ; bioregistry.schema:0000005 "rs11603840"^^xsd:string ; bioregistry.schema:0000006 "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^xsd:string ; @@ -11361,9 +11461,9 @@ bioregistry:snp2tfbs a bioregistry.schema:0000001 ; bioregistry:sopharm a bioregistry.schema:0000001 ; rdfs:label "Suggested Ontology for Pharmacogenomics" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SOPHARM, - obofoundry:SOPHARM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SOPHARM, + obofoundry:sopharm, bioportal:SOPHARM, biocontext:SOPHARM ; foaf:homepage "http://www.loria.fr/~coulet/sopharm2.0_description.php"^^xsd:string ; @@ -11374,8 +11474,8 @@ bioregistry:sopharm a bioregistry.schema:0000001 ; bioregistry:soybase a bioregistry.schema:0000001 ; rdfs:label "Glycine max Genome Database" ; dc:description "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SOYBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SOYBASE, n2t:soybase, ncbi.resource:SoyBase, fairsharing:FAIRsharing.z4agsr, @@ -11389,9 +11489,9 @@ bioregistry:soybase a bioregistry.schema:0000001 ; bioregistry:spd a bioregistry.schema:0000001 ; rdfs:label "Spider Ontology" ; dc:description "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SPD, - obofoundry:SPD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SPD, + obofoundry:spd, ontobee:SPD, bioportal:SPD, biocontext:SPD, @@ -11409,8 +11509,8 @@ bioregistry:spd a bioregistry.schema:0000001 ; bioregistry:spdx a bioregistry.schema:0000001 ; rdfs:label "Software Package Data Exchange License" ; dc:description "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:spdx, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:spdx, miriam:spdx ; foaf:homepage "https://spdx.org/licenses"^^xsd:string ; bioregistry.schema:0000005 "CC-BY-1.0"^^xsd:string ; @@ -11421,8 +11521,8 @@ bioregistry:spdx a bioregistry.schema:0000001 ; bioregistry:spike.map a bioregistry.schema:0000001 ; rdfs:label "SPIKE Map" ; dc:description "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SPIKE.MAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SPIKE.MAP, n2t:spike.map, miriam:spike.map ; foaf:homepage "http://www.cs.tau.ac.il/~spike/"^^xsd:string ; @@ -11434,8 +11534,8 @@ bioregistry:spike.map a bioregistry.schema:0000001 ; bioregistry:splash a bioregistry.schema:0000001 ; rdfs:label "Spectra Hash Code" ; dc:description "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SPLASH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SPLASH, n2t:splash, miriam:splash ; foaf:homepage "http://mona.fiehnlab.ucdavis.edu/"^^xsd:string ; @@ -11447,8 +11547,8 @@ bioregistry:splash a bioregistry.schema:0000001 ; bioregistry:spp a bioregistry.schema:0000001 ; rdfs:label "Signaling Pathways Project" ; dc:description "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.WxI96O, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.WxI96O, miriam:spp ; foaf:homepage "https://www.signalingpathways.org/index.jsf"^^xsd:string ; bioregistry.schema:0000005 "10.1621/vwN2g2HaX3"^^xsd:string ; @@ -11459,8 +11559,8 @@ bioregistry:spp a bioregistry.schema:0000001 ; bioregistry:srao a bioregistry.schema:0000001 ; rdfs:label "FAIRsharing Subject Ontology" ; dc:description "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.b1xD9f, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.b1xD9f, ols:srao ; foaf:homepage "https://github.com/FAIRsharing/subject-ontology"^^xsd:string ; bioregistry.schema:0000005 "0000400"^^xsd:string ; @@ -11470,8 +11570,8 @@ bioregistry:srao a bioregistry.schema:0000001 ; bioregistry:stap a bioregistry.schema:0000001 ; rdfs:label "Statistical Torsional Angles Potentials" ; dc:description "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:STAP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:STAP, n2t:stap, fairsharing:FAIRsharing.ja9cdq, miriam:stap ; @@ -11484,8 +11584,8 @@ bioregistry:stap a bioregistry.schema:0000001 ; bioregistry:stitch a bioregistry.schema:0000001 ; rdfs:label "Search Tool for Interactions of Chemicals" ; dc:description "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:STITCH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:STITCH, n2t:stitch, fairsharing:FAIRsharing.zhwa8x, prefixcommons:stitch, @@ -11500,8 +11600,8 @@ bioregistry:string a bioregistry.schema:0000001 ; rdfs:label "Search Tool for Retrieval of Interacting Genes/Proteins" ; dc:description """STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2302, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2302, biocontext:STRING, n2t:string, fairsharing:FAIRsharing.9b7wvk, @@ -11518,8 +11618,8 @@ The interactions include direct (physical) and indirect (functional) association bioregistry:sty a bioregistry.schema:0000001 ; rdfs:label "Semantic Types Ontology" ; dc:description "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:STY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:STY, agroportal:STY, ecoportal:STY, bioportal:STY, @@ -11534,8 +11634,8 @@ bioregistry:subtilist a bioregistry.schema:0000001 ; rdfs:label "Bacillus subtilis genome sequencing project" ; dc:description """SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r SubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SUBTILIST, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SUBTILIST, n2t:subtilist, ncbi.resource:SubtiList, fairsharing:FAIRsharing.40j2vd, @@ -11551,8 +11651,8 @@ bioregistry:subtiwiki a bioregistry.schema:0000001 ; rdfs:label "SubtiWiki" ; dc:description """SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r Note: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SUBTIWIKI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SUBTIWIKI, n2t:subtiwiki, fairsharing:FAIRsharing.2ck3st, prefixcommons:subtiwiki, @@ -11566,8 +11666,8 @@ Note: Currently, direct access to RNA products is restricted. This is expected t bioregistry:sugarbind a bioregistry.schema:0000001 ; rdfs:label "SugarBind" ; dc:description "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SUGARBIND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SUGARBIND, n2t:sugarbind, fairsharing:FAIRsharing.d064y6, miriam:sugarbind ; @@ -11580,8 +11680,8 @@ bioregistry:sugarbind a bioregistry.schema:0000001 ; bioregistry:supfam a bioregistry.schema:0000001 ; rdfs:label "SUPERFAMILY" ; dc:description "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SUPFAM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SUPFAM, n2t:supfam, miriam:supfam, uniprot.resource:SUPFAM ; @@ -11594,8 +11694,8 @@ bioregistry:supfam a bioregistry.schema:0000001 ; bioregistry:sweetrealm a bioregistry.schema:0000001 ; rdfs:label "Semantic Web for Earth and Environment Technology Ontology" ; dc:description "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch bioportal:SWEET ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch bioportal:SWEET ; foaf:homepage "https://bioportal.bioontology.org/ontologies/SWEET"^^xsd:string ; bioregistry.schema:0000005 "ANOVA"^^xsd:string ; bioregistry.schema:0000012 false . @@ -11603,8 +11703,8 @@ bioregistry:sweetrealm a bioregistry.schema:0000001 ; bioregistry:swh a bioregistry.schema:0000001 ; rdfs:label "Software Heritage" ; dc:description "Software Heritage is the universal archive of software source code."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SWH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SWH, n2t:swh, miriam:swh ; foaf:homepage "https://archive.softwareheritage.org"^^xsd:string ; @@ -11616,8 +11716,8 @@ bioregistry:swh a bioregistry.schema:0000001 ; bioregistry:swiss-model a bioregistry.schema:0000001 ; rdfs:label "SWISS-MODEL Repository" ; dc:description "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SWISS-MODEL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SWISS-MODEL, n2t:swiss-model, fairsharing:FAIRsharing.vxz9pn, prefixcommons:swissmodel, @@ -11632,8 +11732,8 @@ bioregistry:swiss-model a bioregistry.schema:0000001 ; bioregistry:swisslipid a bioregistry.schema:0000001 ; rdfs:label "SwissLipid" ; dc:description "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SWISSLIPID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SWISSLIPID, n2t:swisslipid, fairsharing:FAIRsharing.pxr7x2, miriam:slm, @@ -11648,8 +11748,8 @@ bioregistry:swisslipid a bioregistry.schema:0000001 ; bioregistry:swissregulon a bioregistry.schema:0000001 ; rdfs:label "SwissRegulon" ; dc:description "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:SWISSREGULON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:SWISSREGULON, n2t:swissregulon, fairsharing:FAIRsharing.7fnx38, miriam:swissregulon ; @@ -11662,9 +11762,9 @@ bioregistry:swissregulon a bioregistry.schema:0000001 ; bioregistry:swo a bioregistry.schema:0000001 ; rdfs:label "Software ontology" ; dc:description "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SWO, - obofoundry:SWO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SWO, + obofoundry:swo, ontobee:SWO, bioportal:SWO, biocontext:SWO, @@ -11681,8 +11781,8 @@ bioregistry:swo a bioregistry.schema:0000001 ; bioregistry:t3db a bioregistry.schema:0000001 ; rdfs:label "Toxin and Toxin Target Database" ; dc:description "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2662, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2662, biocontext:T3DB, n2t:t3db, fairsharing:FAIRsharing.psn0h2, @@ -11697,9 +11797,9 @@ bioregistry:t3db a bioregistry.schema:0000001 ; bioregistry:tads a bioregistry.schema:0000001 ; rdfs:label "Tick Anatomy Ontology" ; dc:description "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TADS, - obofoundry:TADS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TADS, + obofoundry:tads, ontobee:TADS, bioportal:TADS, biocontext:TADS, @@ -11714,8 +11814,8 @@ bioregistry:tads a bioregistry.schema:0000001 ; bioregistry:tahe a bioregistry.schema:0000001 ; rdfs:label "Terminology of Anatomy of Human Embryology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:TAHE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:tahe, biocontext:TAHE ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/TAHE_$1"^^xsd:string ; bioregistry.schema:0000012 true ; @@ -11723,8 +11823,8 @@ bioregistry:tahe a bioregistry.schema:0000001 ; bioregistry:tahh a bioregistry.schema:0000001 ; rdfs:label "Terminology of Anatomy of Human Histology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:TAHH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:tahh, biocontext:TAHH ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/TAHH_$1"^^xsd:string ; bioregistry.schema:0000012 true ; @@ -11733,8 +11833,8 @@ bioregistry:tahh a bioregistry.schema:0000001 ; bioregistry:tair.gene a bioregistry.schema:0000001 ; rdfs:label "TAIR Gene" ; dc:description "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TAIR.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TAIR.GENE, n2t:tair.gene, prefixcommons:tair.gene, miriam:tair.gene ; @@ -11747,8 +11847,8 @@ bioregistry:tair.gene a bioregistry.schema:0000001 ; bioregistry:tair.locus a bioregistry.schema:0000001 ; rdfs:label "The Arabidopsis Information Resource" ; dc:description "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TAIR.LOCUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TAIR.LOCUS, go.resource:TAIR, n2t:tair.locus, ncbi.resource:TAIR, @@ -11763,8 +11863,8 @@ bioregistry:tair.locus a bioregistry.schema:0000001 ; bioregistry:tair.protein a bioregistry.schema:0000001 ; rdfs:label "TAIR Protein" ; dc:description "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TAIR.PROTEIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TAIR.PROTEIN, n2t:tair.protein, prefixcommons:tair.protein, miriam:tair.protein ; @@ -11777,9 +11877,9 @@ bioregistry:tair.protein a bioregistry.schema:0000001 ; bioregistry:tao a bioregistry.schema:0000001 ; rdfs:label "Teleost Anatomy Ontology" ; dc:description "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TAO, - obofoundry:TAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TAO, + obofoundry:tao, bioportal:TAO, biocontext:TAO, prefixcommons:tao ; @@ -11793,8 +11893,8 @@ bioregistry:tao a bioregistry.schema:0000001 ; bioregistry:tarbase a bioregistry.schema:0000001 ; rdfs:label "TarBase" ; dc:description "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TARBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TARBASE, n2t:tarbase, fairsharing:FAIRsharing.a0k4cd, miriam:tarbase ; @@ -11807,9 +11907,9 @@ bioregistry:tarbase a bioregistry.schema:0000001 ; bioregistry:taxrank a bioregistry.schema:0000001 ; rdfs:label "Taxonomic rank vocabulary" ; dc:description "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TAXRANK, - obofoundry:TAXRANK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TAXRANK, + obofoundry:taxrank, ontobee:TAXRANK, bioportal:TAXRANK, biocontext:TAXRANK, @@ -11826,8 +11926,8 @@ bioregistry:taxrank a bioregistry.schema:0000001 ; bioregistry:tcb a bioregistry.schema:0000001 ; rdfs:label "Tick Cell Biobank" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:TCB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:TCB ; foaf:homepage "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^xsd:string ; bioregistry.schema:0000005 "2966"^^xsd:string ; bioregistry.schema:0000006 "https://www.pirbright.ac.uk/node/$1"^^xsd:string ; @@ -11837,8 +11937,8 @@ bioregistry:tcb a bioregistry.schema:0000001 ; bioregistry:tcdb a bioregistry.schema:0000001 ; rdfs:label "Transporter Classification Database" ; dc:description "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2756, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2756, biocontext:TCDB, go.resource:TC, n2t:tcdb, @@ -11856,8 +11956,8 @@ bioregistry:tcdb a bioregistry.schema:0000001 ; bioregistry:te a bioregistry.schema:0000001 ; rdfs:label "Terminologia Embryologica" ; dc:description "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P1693 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P1693 ; foaf:homepage "https://ifaa.unifr.ch/"^^xsd:string ; bioregistry.schema:0000005 "E5.11.2.0.0.0.4"^^xsd:string ; bioregistry.schema:0000012 false . @@ -11865,8 +11965,8 @@ bioregistry:te a bioregistry.schema:0000001 ; bioregistry:tfclass a bioregistry.schema:0000001 ; rdfs:label "Classification of Transcription Factors in Mammalia" ; dc:description "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:TFClass, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:TFClass, fairsharing:FAIRsharing.XykycZ ; foaf:homepage "http://tfclass.bioinf.med.uni-goettingen.de"^^xsd:string ; bioregistry.schema:0000005 "2.1.1"^^xsd:string ; @@ -11876,8 +11976,8 @@ bioregistry:tfclass a bioregistry.schema:0000001 ; bioregistry:tgd a bioregistry.schema:0000001 ; rdfs:label "Tetrahymena Genome Database" ; dc:description "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TGD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TGD, go.resource:TGD, n2t:tgd, prefixcommons:tgd, @@ -11891,9 +11991,9 @@ bioregistry:tgd a bioregistry.schema:0000001 ; bioregistry:tgma a bioregistry.schema:0000001 ; rdfs:label "Mosquito gross anatomy ontology" ; dc:description "A structured controlled vocabulary of the anatomy of mosquitoes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TGMA, - obofoundry:TGMA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TGMA, + obofoundry:tgma, ontobee:TGMA, bioportal:TGMA, biocontext:TGMA, @@ -11910,8 +12010,8 @@ bioregistry:tgma a bioregistry.schema:0000001 ; bioregistry:tigrfam a bioregistry.schema:0000001 ; rdfs:label "TIGR protein families" ; dc:description "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1141, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1141, biocontext:TIGRFAM, n2t:tigrfam, ncbi.resource:TIGRFAM, @@ -11925,8 +12025,8 @@ bioregistry:tigrfam a bioregistry.schema:0000001 ; bioregistry:tngb a bioregistry.schema:0000001 ; rdfs:label "Telethon Network of Genetic Biobanks" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:TNGB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:TNGB ; foaf:homepage "http://biobanknetwork.telethon.it/"^^xsd:string ; bioregistry.schema:0000005 "67035"^^xsd:string ; bioregistry.schema:0000006 "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^xsd:string ; @@ -11936,8 +12036,8 @@ bioregistry:tngb a bioregistry.schema:0000001 ; bioregistry:tokue a bioregistry.schema:0000001 ; rdfs:label "TOKU-E Cell-culture Database" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:TOKU-E ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:TOKU-E ; foaf:homepage "http://cell-lines.toku-e.com"^^xsd:string ; bioregistry.schema:0000006 "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^xsd:string ; bioregistry.schema:0000012 true . @@ -11947,8 +12047,8 @@ bioregistry:tol a bioregistry.schema:0000001 ; dc:description """The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r \r Each page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TOL, n2t:tol, miriam:tol, wikidata:P5221 ; @@ -11961,8 +12061,8 @@ Each page contains information about a particular group, with pages linked one t bioregistry:topdb a bioregistry.schema:0000001 ; rdfs:label "Topology Data Bank of Transmembrane Proteins" ; dc:description "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2789, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2789, biocontext:TOPDB, n2t:topdb, prefixcommons:topdb, @@ -11976,8 +12076,8 @@ bioregistry:topdb a bioregistry.schema:0000001 ; bioregistry:topfind a bioregistry.schema:0000001 ; rdfs:label "TopFind" ; dc:description "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TOPFIND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TOPFIND, n2t:topfind, fairsharing:FAIRsharing.rkpmhn, miriam:topfind ; @@ -11991,8 +12091,8 @@ bioregistry:topfind a bioregistry.schema:0000001 ; bioregistry:toxoplasma a bioregistry.schema:0000001 ; rdfs:label "ToxoDB" ; dc:description "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TOXOPLASMA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TOXOPLASMA, n2t:toxoplasma, miriam:toxoplasma ; foaf:homepage "http://toxodb.org/toxo/"^^xsd:string ; @@ -12004,9 +12104,9 @@ bioregistry:toxoplasma a bioregistry.schema:0000001 ; bioregistry:trans a bioregistry.schema:0000001 ; rdfs:label "Pathogen Transmission Ontology" ; dc:description "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TRANS, - obofoundry:TRANS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TRANS, + obofoundry:trans, ontobee:TRANS, bioportal:TRANS, biocontext:TRANS, @@ -12022,8 +12122,8 @@ bioregistry:trans a bioregistry.schema:0000001 ; bioregistry:transyt a bioregistry.schema:0000001 ; rdfs:label "Transport Systems Tracker" ; dc:description "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:transyt ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:transyt ; foaf:homepage "https://www.bio.di.uminho.pt/"^^xsd:string ; bioregistry.schema:0000005 "TR0000001"^^xsd:string ; bioregistry.schema:0000006 "https://transyt.bio.di.uminho.pt/reactions/$1"^^xsd:string ; @@ -12033,8 +12133,8 @@ bioregistry:transyt a bioregistry.schema:0000001 ; bioregistry:treebase a bioregistry.schema:0000001 ; rdfs:label "TreeBASE" ; dc:description "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TREEBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TREEBASE, n2t:treebase, fairsharing:FAIRsharing.zcn4w4, prefixcommons:treebase, @@ -12048,8 +12148,8 @@ bioregistry:treebase a bioregistry.schema:0000001 ; bioregistry:treefam a bioregistry.schema:0000001 ; rdfs:label "TreeFam" ; dc:description "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TREEFAM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TREEFAM, n2t:treefam, prefixcommons:treefam, miriam:treefam, @@ -12063,8 +12163,8 @@ bioregistry:treefam a bioregistry.schema:0000001 ; bioregistry:trichdb a bioregistry.schema:0000001 ; rdfs:label "TrichDB" ; dc:description "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TRICHDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TRICHDB, n2t:trichdb, fairsharing:FAIRsharing.pv0ezt, miriam:trichdb ; @@ -12077,8 +12177,8 @@ bioregistry:trichdb a bioregistry.schema:0000001 ; bioregistry:tritrypdb a bioregistry.schema:0000001 ; rdfs:label "TriTrypDB" ; dc:description "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:TRITRYPDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:TRITRYPDB, go.resource:TriTrypDB, n2t:tritrypdb, fairsharing:FAIRsharing.fs1z27, @@ -12092,8 +12192,8 @@ bioregistry:tritrypdb a bioregistry.schema:0000001 ; bioregistry:ttd.drug a bioregistry.schema:0000001 ; rdfs:label "TTD Drug" ; dc:description "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2653, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2653, biocontext:TTD.DRUG, n2t:ttd.drug, miriam:ttd.drug ; @@ -12106,8 +12206,8 @@ bioregistry:ttd.drug a bioregistry.schema:0000001 ; bioregistry:ttd.target a bioregistry.schema:0000001 ; rdfs:label "TTD Target" ; dc:description "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2654, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2654, biocontext:TTD.TARGET, n2t:ttd.target, miriam:ttd.target ; @@ -12120,9 +12220,9 @@ bioregistry:ttd.target a bioregistry.schema:0000001 ; bioregistry:tto a bioregistry.schema:0000001 ; rdfs:label "Teleost taxonomy ontology" ; dc:description "An ontology covering the taxonomy of teleosts (bony fish)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TTO, - obofoundry:TTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TTO, + obofoundry:tto, ontobee:TTO, bioportal:TTO, biocontext:TTO, @@ -12143,9 +12243,9 @@ bioregistry:txpo a bioregistry.schema:0000001 ; The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TXPO, - obofoundry:TXPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TXPO, + obofoundry:txpo, ontobee:TXPO, bioportal:TXPO, ols:txpo ; @@ -12159,8 +12259,8 @@ In applied work, we have developed a prototype of TOXPILOT, a TOXic Process Inte bioregistry:ubio.namebank a bioregistry.schema:0000001 ; rdfs:label "uBio NameBank" ; dc:description "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UBIO.NAMEBANK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UBIO.NAMEBANK, n2t:ubio.namebank, miriam:ubio.namebank ; foaf:homepage "http://www.ubio.org"^^xsd:string ; @@ -12172,8 +12272,8 @@ bioregistry:ubio.namebank a bioregistry.schema:0000001 ; bioregistry:ucsc a bioregistry.schema:0000001 ; rdfs:label "UCSC Genome Browser" ; dc:description "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UCSC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UCSC, uniprot.resource:UCSC, wikidata:P2576 ; foaf:homepage "https://genome.ucsc.edu/"^^xsd:string ; @@ -12184,8 +12284,8 @@ bioregistry:ucsc a bioregistry.schema:0000001 ; bioregistry:unigene a bioregistry.schema:0000001 ; rdfs:label "UniGene" ; dc:description "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UNIGENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UNIGENE, n2t:unigene, fairsharing:FAIRsharing.ge1c3p, prefixcommons:unigene, @@ -12199,8 +12299,8 @@ bioregistry:unigene a bioregistry.schema:0000001 ; bioregistry:unii a bioregistry.schema:0000001 ; rdfs:label "Unique Ingredient Identifier" ; dc:description "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UNII, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UNII, n2t:unii, miriam:unii, cheminf:000563, @@ -12214,8 +12314,8 @@ bioregistry:unii a bioregistry.schema:0000001 ; bioregistry:unimod a bioregistry.schema:0000001 ; rdfs:label "Unimod protein modification database for mass spectrometry" ; dc:description "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:3757, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:3757, biocontext:UNIMOD, n2t:unimod, fairsharing:FAIRsharing.zZHCUQ, @@ -12230,8 +12330,8 @@ bioregistry:unimod a bioregistry.schema:0000001 ; bioregistry:uniparc a bioregistry.schema:0000001 ; rdfs:label "UniProt Archive" ; dc:description "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2392, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2392, biocontext:UNIPARC, go.resource:UniParc, n2t:uniparc, @@ -12246,8 +12346,8 @@ bioregistry:uniparc a bioregistry.schema:0000001 ; bioregistry:unipathway.compound a bioregistry.schema:0000001 ; rdfs:label "UniPathway Compound" ; dc:description "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UNIPATHWAY.COMPOUND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UNIPATHWAY.COMPOUND, n2t:unipathway.compound, miriam:unipathway.compound ; foaf:homepage "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^xsd:string ; @@ -12259,8 +12359,8 @@ bioregistry:unipathway.compound a bioregistry.schema:0000001 ; bioregistry:unipathway.reaction a bioregistry.schema:0000001 ; rdfs:label "UniPathway Reaction" ; dc:description "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:UNIPATHWAY.REACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:UNIPATHWAY.REACTION, n2t:unipathway.reaction, miriam:unipathway.reaction ; foaf:homepage "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^xsd:string ; @@ -12272,8 +12372,8 @@ bioregistry:unipathway.reaction a bioregistry.schema:0000001 ; bioregistry:uniref a bioregistry.schema:0000001 ; rdfs:label "UniRef" ; dc:description "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2346, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2346, miriam:uniref ; foaf:homepage "https://www.uniprot.org/"^^xsd:string ; bioregistry.schema:0000005 "UniRef90_P00750"^^xsd:string ; @@ -12284,8 +12384,8 @@ bioregistry:uniref a bioregistry.schema:0000001 ; bioregistry:unirule a bioregistry.schema:0000001 ; rdfs:label "UniRule" ; dc:description "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:UniRule ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:UniRule ; foaf:homepage "https://www.uniprot.org/unirule/"^^xsd:string ; bioregistry.schema:0000005 "UR000124451"^^xsd:string ; bioregistry.schema:0000006 "https://www.uniprot.org/unirule/$1"^^xsd:string ; @@ -12294,8 +12394,8 @@ bioregistry:unirule a bioregistry.schema:0000001 ; bioregistry:unists a bioregistry.schema:0000001 ; rdfs:label "Database of Sequence Tagged Sites" ; dc:description "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2389, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2389, biocontext:UNISTS, n2t:unists, ncbi.resource:UniSTS, @@ -12310,8 +12410,8 @@ bioregistry:unists a bioregistry.schema:0000001 ; bioregistry:unite a bioregistry.schema:0000001 ; rdfs:label "Molecular database for the identification of fungi" ; dc:description "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2390, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2390, biocontext:UNITE, n2t:unite, ncbi.resource:UNITE, @@ -12324,12 +12424,34 @@ bioregistry:unite a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^UDB\\d{6}$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:upa a bioregistry.schema:0000001 ; + rdfs:label "Unipathway" ; + dc:description "A manually curated resource for the representation and annotation of metabolic pathways"^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:UPA, + edam.data:2645, + obofoundry:upa, + ontobee:UPA, + bioportal:UPA, + biocontext:UNIPATHWAY, + go.resource:UniPathway, + prefixcommons:unipathway, + ols:upa, + uniprot.resource:UniPathway ; + foaf:homepage "https://github.com/geneontology/unipathway"^^xsd:string ; + bioregistry.schema:0000005 "UCR00513"^^xsd:string ; + bioregistry.schema:0000006 "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^xsd:string ; + bioregistry.schema:0000008 "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^xsd:string ; + bioregistry.schema:0000012 true ; + bioregistry.schema:0000017 bioregistry:ro ; + bioregistry.schema:0000019 orcid:0000-0002-1216-2969 . + bioregistry:upheno a bioregistry.schema:0000001 ; rdfs:label "Unified Phenotype Ontology" ; dc:description "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:UPHENO, - obofoundry:UPHENO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:UPHENO, + obofoundry:upheno, ontobee:UPHENO, bioportal:UPHENO, biocontext:UPHENO, @@ -12343,8 +12465,8 @@ bioregistry:upheno a bioregistry.schema:0000001 ; bioregistry:uspto a bioregistry.schema:0000001 ; rdfs:label "United States Patent and Trademark Office" ; dc:description "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:USPTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:USPTO, n2t:uspto, miriam:uspto ; foaf:homepage "http://patft.uspto.gov/netahtml/PTO/index.html"^^xsd:string ; @@ -12356,8 +12478,8 @@ bioregistry:uspto a bioregistry.schema:0000001 ; bioregistry:validatordb a bioregistry.schema:0000001 ; rdfs:label "ValidatorDB" ; dc:description "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VALIDATORDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VALIDATORDB, n2t:validatordb, fairsharing:FAIRsharing.c9psgb, miriam:validatordb ; @@ -12371,8 +12493,8 @@ bioregistry:validatordb a bioregistry.schema:0000001 ; bioregistry:vandf a bioregistry.schema:0000001 ; rdfs:label "Veterans Administration National Drug File" ; dc:description "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VANDF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VANDF, bioportal:VANDF, biolink:VANDF, fairsharing:FAIRsharing.xn3pb3 ; @@ -12384,10 +12506,10 @@ bioregistry:vandf a bioregistry.schema:0000001 ; bioregistry:vario a bioregistry.schema:0000001 ; rdfs:label "Variation Ontology" ; dc:description "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VARIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VARIO, agroportal:VARIO, - obofoundry:VariO, + obofoundry:vario, ontobee:VariO, bioportal:VARIO, biocontext:VARIO, @@ -12405,8 +12527,8 @@ bioregistry:vario a bioregistry.schema:0000001 ; bioregistry:vbase2 a bioregistry.schema:0000001 ; rdfs:label "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" ; dc:description "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VBASE2, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VBASE2, n2t:vbase2, ncbi.resource:VBASE2, fairsharing:FAIRsharing.qvxhb1, @@ -12421,8 +12543,8 @@ bioregistry:vbase2 a bioregistry.schema:0000001 ; bioregistry:vbrc a bioregistry.schema:0000001 ; rdfs:label "Viral Bioinformatics Resource Center" ; dc:description "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VBRC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VBRC, n2t:vbrc, prefixcommons:vbrc, miriam:vbrc ; @@ -12435,8 +12557,8 @@ bioregistry:vbrc a bioregistry.schema:0000001 ; bioregistry:vcell a bioregistry.schema:0000001 ; rdfs:label "VCell Published Models" ; dc:description "Models developed with the Virtual Cell (VCell) software prorgam."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:vcell ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:vcell ; foaf:homepage "https://health.uconn.edu/"^^xsd:string ; bioregistry.schema:0000005 "201022999"^^xsd:string ; bioregistry.schema:0000006 "https://vcell.org/biomodel-$1"^^xsd:string ; @@ -12446,8 +12568,8 @@ bioregistry:vcell a bioregistry.schema:0000001 ; bioregistry:vectorbase a bioregistry.schema:0000001 ; rdfs:label "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" ; dc:description "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VECTORBASE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VECTORBASE, n2t:vectorbase, ncbi.resource:VectorBase, fairsharing:FAIRsharing.3etvdn, @@ -12462,8 +12584,8 @@ bioregistry:vectorbase a bioregistry.schema:0000001 ; bioregistry:vegbank a bioregistry.schema:0000001 ; rdfs:label "VegBank" ; dc:description "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:vegbank ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:vegbank ; foaf:homepage "http://vegbank.org/"^^xsd:string ; bioregistry.schema:0000005 "VB.Ob.3736.GRSM125"^^xsd:string ; bioregistry.schema:0000006 "http://vegbank.org/cite/$1"^^xsd:string ; @@ -12473,8 +12595,8 @@ bioregistry:vegbank a bioregistry.schema:0000001 ; bioregistry:vfb a bioregistry.schema:0000001 ; rdfs:label "Virtual Fly Brain" ; dc:description "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:vfb, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:vfb, fairsharing:FAIRsharing.nzaz6z, miriam:vfb ; foaf:homepage "https://VirtualFlyBrain.org"^^xsd:string ; @@ -12486,8 +12608,8 @@ bioregistry:vfb a bioregistry.schema:0000001 ; bioregistry:vfdb.gene a bioregistry.schema:0000001 ; rdfs:label "VFDB Gene" ; dc:description "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VFDB.GENE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VFDB.GENE, n2t:vfdb.gene, miriam:vfdb.gene ; foaf:homepage "http://www.mgc.ac.cn/VFs/"^^xsd:string ; @@ -12499,8 +12621,8 @@ bioregistry:vfdb.gene a bioregistry.schema:0000001 ; bioregistry:vfdb.genus a bioregistry.schema:0000001 ; rdfs:label "VFDB Genus" ; dc:description "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VFDB.GENUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VFDB.GENUS, n2t:vfdb.genus, miriam:vfdb.genus ; foaf:homepage "http://www.mgc.ac.cn/VFs/"^^xsd:string ; @@ -12512,8 +12634,8 @@ bioregistry:vfdb.genus a bioregistry.schema:0000001 ; bioregistry:vgnc a bioregistry.schema:0000001 ; rdfs:label "Vertebrate Gene Nomenclature Committee" ; dc:description "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:VGNC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:VGNC, ncbi.resource:VGNC, fairsharing:FAIRsharing.5NhJFK, miriam:vgnc, @@ -12526,9 +12648,9 @@ bioregistry:vgnc a bioregistry.schema:0000001 ; bioregistry:vhog a bioregistry.schema:0000001 ; rdfs:label "Vertebrate Homologous Organ Group Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VHOG, - obofoundry:VHOG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VHOG, + obofoundry:vhog, bioportal:VHOG, biocontext:VHOG, prefixcommons:vhog ; @@ -12540,8 +12662,8 @@ bioregistry:vhog a bioregistry.schema:0000001 ; bioregistry:viaf a bioregistry.schema:0000001 ; rdfs:label "Virtual International Authority File" ; dc:description "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:viaf, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:viaf, miriam:viaf ; foaf:homepage "http://viaf.org"^^xsd:string ; bioregistry.schema:0000005 "75121530"^^xsd:string ; @@ -12552,8 +12674,8 @@ bioregistry:viaf a bioregistry.schema:0000001 ; bioregistry:vido a bioregistry.schema:0000001 ; rdfs:label "The Virus Infectious Disease Ontology" ; dc:description "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VIDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VIDO, ontobee:VIDO, bioportal:VIDO, ols:vido ; @@ -12566,8 +12688,8 @@ bioregistry:vido a bioregistry.schema:0000001 ; bioregistry:vipr a bioregistry.schema:0000001 ; rdfs:label "Virus Pathogen Resource" ; dc:description "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VIPR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VIPR, n2t:vipr, ncbi.resource:ViPR, fairsharing:FAIRsharing.2qx8n8, @@ -12581,8 +12703,8 @@ bioregistry:vipr a bioregistry.schema:0000001 ; bioregistry:viralzone a bioregistry.schema:0000001 ; rdfs:label "ViralZone" ; dc:description "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VIRALZONE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VIRALZONE, n2t:viralzone, fairsharing:FAIRsharing.tppk10, miriam:viralzone ; @@ -12595,8 +12717,8 @@ bioregistry:viralzone a bioregistry.schema:0000001 ; bioregistry:virsirna a bioregistry.schema:0000001 ; rdfs:label "VIRsiRNA" ; dc:description "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VIRSIRNA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VIRSIRNA, n2t:virsirna, miriam:virsirna ; foaf:homepage "http://crdd.osdd.net/servers/virsirnadb"^^xsd:string ; @@ -12607,15 +12729,15 @@ bioregistry:virsirna a bioregistry.schema:0000001 ; bioregistry:vmc a bioregistry.schema:0000001 ; rdfs:label "Variation Modelling Collaboration" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:VMC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:VMC ; bioregistry.schema:0000012 true . bioregistry:vmhgene a bioregistry.schema:0000001 ; rdfs:label "VMH Gene" ; dc:description "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:vmhgene ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:vmhgene ; foaf:homepage "https://www.vmh.life/"^^xsd:string ; bioregistry.schema:0000005 "8639.1"^^xsd:string ; bioregistry.schema:0000006 "https://www.vmh.life/#gene/$1"^^xsd:string ; @@ -12625,8 +12747,8 @@ bioregistry:vmhgene a bioregistry.schema:0000001 ; bioregistry:vmhmetabolite a bioregistry.schema:0000001 ; rdfs:label "VMH metabolite" ; dc:description "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VMHMETABOLITE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VMHMETABOLITE, n2t:vmhmetabolite, miriam:vmhmetabolite ; foaf:homepage "https://www.vmh.life/"^^xsd:string ; @@ -12638,8 +12760,8 @@ bioregistry:vmhmetabolite a bioregistry.schema:0000001 ; bioregistry:vmhreaction a bioregistry.schema:0000001 ; rdfs:label "VMH reaction" ; dc:description "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:VMHREACTION, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:VMHREACTION, n2t:vmhreaction, miriam:vmhreaction ; foaf:homepage "https://www.vmh.life/"^^xsd:string ; @@ -12651,9 +12773,9 @@ bioregistry:vmhreaction a bioregistry.schema:0000001 ; bioregistry:vsao a bioregistry.schema:0000001 ; rdfs:label "Vertebrate Skeletal Anatomy Ontology" ; dc:description "Vertebrate skeletal anatomy ontology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VSAO, - obofoundry:VSAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VSAO, + obofoundry:vsao, bioportal:VSAO, biocontext:VSAO ; foaf:homepage "https://www.nescent.org/phenoscape/Main_Page"^^xsd:string ; @@ -12664,8 +12786,8 @@ bioregistry:vsao a bioregistry.schema:0000001 ; bioregistry:vso a bioregistry.schema:0000001 ; rdfs:label "Vital Sign Ontology" ; dc:description "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VSO, bioportal:VSO, fairsharing:FAIRsharing.jjb2p2, prefixcommons:vso ; @@ -12678,9 +12800,9 @@ bioregistry:vso a bioregistry.schema:0000001 ; bioregistry:vto a bioregistry.schema:0000001 ; rdfs:label "Vertebrate Taxonomy Ontology" ; dc:description "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VTO, - obofoundry:VTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VTO, + obofoundry:vto, ontobee:VTO, bioportal:VTO, biocontext:VTO, @@ -12696,8 +12818,8 @@ bioregistry:vto a bioregistry.schema:0000001 ; bioregistry:vz a bioregistry.schema:0000001 ; rdfs:label "ViralZone" ; dc:description "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:VZ, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:VZ, prefixcommons:vz ; foaf:homepage "http://viralzone.expasy.org/"^^xsd:string ; bioregistry.schema:0000005 "886"^^xsd:string ; @@ -12708,8 +12830,8 @@ bioregistry:vz a bioregistry.schema:0000001 ; bioregistry:wb.rnai a bioregistry.schema:0000001 ; rdfs:label "WormBase RNAi" ; dc:description "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WB.RNAI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WB.RNAI, n2t:wb.rnai, miriam:wb.rnai ; foaf:homepage "https://www.wormbase.org/"^^xsd:string ; @@ -12721,9 +12843,9 @@ bioregistry:wb.rnai a bioregistry.schema:0000001 ; bioregistry:wbbt a bioregistry.schema:0000001 ; rdfs:label "C. elegans Gross Anatomy Ontology" ; dc:description "Ontology about the gross anatomy of the C. elegans"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:WBBT, - obofoundry:WBbt, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:WBBT, + obofoundry:wbbt, ontobee:WBbt, bioportal:WB-BT, biocontext:WBbt, @@ -12742,8 +12864,8 @@ bioregistry:wbbt a bioregistry.schema:0000001 ; bioregistry:wgs84 a bioregistry.schema:0000001 ; rdfs:label "WGS84 Geo Positioning" ; dc:description "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:wgs ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:wgs ; foaf:homepage "https://www.w3.org/2003/01/geo/wgs84_pos"^^xsd:string ; bioregistry.schema:0000005 "latitude"^^xsd:string ; bioregistry.schema:0000006 "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^xsd:string ; @@ -12752,8 +12874,8 @@ bioregistry:wgs84 a bioregistry.schema:0000001 ; bioregistry:wicell a bioregistry.schema:0000001 ; rdfs:label "WiCell Research Institute Cell Collection" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:WiCell ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:WiCell ; foaf:homepage "https://www.wicell.org"^^xsd:string ; bioregistry.schema:0000005 "ai10e-kctd13b"^^xsd:string ; bioregistry.schema:0000006 "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^xsd:string ; @@ -12762,8 +12884,8 @@ bioregistry:wicell a bioregistry.schema:0000001 ; bioregistry:wikidata a bioregistry.schema:0000001 ; rdfs:label "Wikidata" ; dc:description "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WIKIDATA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WIKIDATA, biolink:WIKIDATA, cellosaurus.resource:Wikidata, n2t:wikidata, @@ -12780,8 +12902,8 @@ bioregistry:wikidata.property a bioregistry.schema:0000001 ; rdfs:label "Wikidata Property" ; dc:description """Wikidata is a free and open knowledge base that can be read and edited by both humans and machines. Wikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. """^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WD_Prop, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WD_Prop, biolink:WIKIDATA_PROPERTY ; foaf:homepage "https://www.wikidata.org"^^xsd:string ; bioregistry.schema:0000005 "P4355"^^xsd:string ; @@ -12792,8 +12914,8 @@ Wikidata acts as central storage for the structured data of its Wikimedia sister bioregistry:wikigenes a bioregistry.schema:0000001 ; rdfs:label "WikiGenes" ; dc:description "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WIKIGENES, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WIKIGENES, n2t:wikigenes, miriam:wikigenes ; foaf:homepage "http://www.wikigenes.org/"^^xsd:string ; @@ -12807,8 +12929,8 @@ bioregistry:wikipathways a bioregistry.schema:0000001 ; rdfs:label "WikiPathways" ; dc:description """WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r All content is under the Creative Commons Attribution 3.0 Unported license."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:WIKIPATHWAYS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:WIKIPATHWAYS, edam.data:3952, bioportal:WIKIPATHWAYS, biocontext:WIKIPATHWAYS, @@ -12826,8 +12948,8 @@ All content is under the Creative Commons Attribution 3.0 Unported license."""^^ bioregistry:wikipedia.en a bioregistry.schema:0000001 ; rdfs:label "Wikipedia" ; dc:description "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WIKIPEDIA.EN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WIKIPEDIA.EN, go.resource:Wikipedia, n2t:wikipedia.en, prefixcommons:wikipedia, @@ -12841,8 +12963,8 @@ bioregistry:wikipedia.en a bioregistry.schema:0000001 ; bioregistry:worfdb a bioregistry.schema:0000001 ; rdfs:label "C. elegans ORFeome cloning project" ; dc:description "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WORFDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WORFDB, n2t:worfdb, ncbi.resource:WorfDB, prefixcommons:worfdb, @@ -12856,8 +12978,8 @@ bioregistry:worfdb a bioregistry.schema:0000001 ; bioregistry:wormpep a bioregistry.schema:0000001 ; rdfs:label "Wormpep" ; dc:description "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WORMPEP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WORMPEP, n2t:wormpep, prefixcommons:wormpep, miriam:wormpep ; @@ -12870,8 +12992,8 @@ bioregistry:wormpep a bioregistry.schema:0000001 ; bioregistry:worms a bioregistry.schema:0000001 ; rdfs:label "World Register of Marine Species" ; dc:description "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:WORMS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:WORMS, n2t:worms, fairsharing:FAIRsharing.7g1bzj, miriam:worms, @@ -12885,8 +13007,8 @@ bioregistry:worms a bioregistry.schema:0000001 ; bioregistry:xenbase a bioregistry.schema:0000001 ; rdfs:label "Xenbase" ; dc:description "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2738, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2738, biocontext:Xenbase, biolink:Xenbase, go.resource:Xenbase, @@ -12906,8 +13028,8 @@ bioregistry:xenbase a bioregistry.schema:0000001 ; bioregistry:xl a bioregistry.schema:0000001 ; rdfs:label "Cross-linker reagents ontology" ; dc:description "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:XL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:XL, ontobee:XL, biocontext:XL, ols:xl ; @@ -12918,9 +13040,9 @@ bioregistry:xl a bioregistry.schema:0000001 ; bioregistry:xlmod a bioregistry.schema:0000001 ; rdfs:label "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" ; dc:description "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:XLMOD, - obofoundry:XLMOD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:XLMOD, + obofoundry:xlmod, ontobee:XLMOD, bioportal:XLMOD, ols:xlmod ; @@ -12934,8 +13056,8 @@ bioregistry:xlmod a bioregistry.schema:0000001 ; bioregistry:ydpm a bioregistry.schema:0000001 ; rdfs:label "Yeast Deletion and the Mitochondrial Proteomics Project" ; dc:description "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:YDPM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:YDPM, n2t:ydpm, prefixcommons:ydpm, miriam:ydpm ; @@ -12948,8 +13070,8 @@ bioregistry:ydpm a bioregistry.schema:0000001 ; bioregistry:yeastintron a bioregistry.schema:0000001 ; rdfs:label "Yeast Intron Database v4.3" ; dc:description "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:YEASTINTRON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:YEASTINTRON, n2t:yeastintron, miriam:yeastintron ; foaf:homepage "http://intron.ucsc.edu/yeast4.3/"^^xsd:string ; @@ -12961,8 +13083,8 @@ bioregistry:yeastintron a bioregistry.schema:0000001 ; bioregistry:yetfasco a bioregistry.schema:0000001 ; rdfs:label "YeTFasCo" ; dc:description "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:YETFASCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:YETFASCO, n2t:yetfasco, miriam:yetfasco ; foaf:homepage "http://yetfasco.ccbr.utoronto.ca/"^^xsd:string ; @@ -12974,8 +13096,8 @@ bioregistry:yetfasco a bioregistry.schema:0000001 ; bioregistry:yid a bioregistry.schema:0000001 ; rdfs:label "Yeast Intron Database v3" ; dc:description "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:YID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:YID, n2t:yid, miriam:yid ; foaf:homepage "http://compbio.soe.ucsc.edu/yeast_introns.html"^^xsd:string ; @@ -12986,19 +13108,18 @@ bioregistry:yid a bioregistry.schema:0000001 ; bioregistry:ypo a bioregistry.schema:0000001 ; rdfs:label "Yeast phenotypes" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch obofoundry:YPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch obofoundry:ypo, ols:ypo ; foaf:homepage "http://www.yeastgenome.org/"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/YPO_$1"^^xsd:string ; bioregistry.schema:0000012 true ; bioregistry.schema:0000019 orcid:0000-0001-9163-5180 . bioregistry:yrcpdr a bioregistry.schema:0000001 ; rdfs:label "YRC PDR" ; dc:description "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:YRCPDR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:YRCPDR, n2t:yrcpdr, fairsharing:FAIRsharing.karvzj, miriam:yrcpdr ; @@ -13010,9 +13131,9 @@ bioregistry:yrcpdr a bioregistry.schema:0000001 ; bioregistry:zea a bioregistry.schema:0000001 ; rdfs:label "Maize gross anatomy" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ZEA, - obofoundry:ZEA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ZEA, + obofoundry:zea, bioportal:ZEA, biocontext:ZEA, prefixcommons:zea ; @@ -13024,8 +13145,8 @@ bioregistry:zea a bioregistry.schema:0000001 ; bioregistry:zfin a bioregistry.schema:0000001 ; rdfs:label "Zebrafish Information Network Gene" ; dc:description "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ZFIN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ZFIN, go.resource:ZFIN, n2t:zfin, ncbi.resource:ZFIN, @@ -13043,9 +13164,9 @@ bioregistry:zfin a bioregistry.schema:0000001 ; bioregistry:zfs a bioregistry.schema:0000001 ; rdfs:label "Zebrafish developmental stages ontology" ; dc:description "Developmental stages of the Zebrafish"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ZFS, - obofoundry:ZFS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ZFS, + obofoundry:zfs, ontobee:ZFS, bioportal:ZFS, biocontext:ZFS, @@ -13061,8 +13182,8 @@ bioregistry:zfs a bioregistry.schema:0000001 ; bioregistry:zinc a bioregistry.schema:0000001 ; rdfs:label "ZINC is not Commercial" ; dc:description "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ZINC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ZINC, n2t:zinc, miriam:zinc, wikidata:P2084 ; @@ -13201,34 +13322,34 @@ orcid:0000-0002-7440-0467 rdfs:label "Lucas Leclere" . orcid:0000-0002-7509-4802 rdfs:label "Tom Gillespie" . orcid:0000-0002-7509-4805 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.cell . + ns1:contributor bioregistry:nlx.cell . orcid:0000-0002-7509-4806 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.chem . + ns1:contributor bioregistry:nlx.chem . orcid:0000-0002-7509-4808 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.func . + ns1:contributor bioregistry:nlx.func . orcid:0000-0002-7509-4809 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.inv . + ns1:contributor bioregistry:nlx.inv . orcid:0000-0002-7509-4810 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.mol . + ns1:contributor bioregistry:nlx.mol . orcid:0000-0002-7509-4811 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.oen . + ns1:contributor bioregistry:nlx.oen . orcid:0000-0002-7509-4812 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.org . + ns1:contributor bioregistry:nlx.org . orcid:0000-0002-7509-4813 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.qual . + ns1:contributor bioregistry:nlx.qual . orcid:0000-0002-7509-4814 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.res . + ns1:contributor bioregistry:nlx.res . orcid:0000-0002-7509-4815 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.sub . + ns1:contributor bioregistry:nlx.sub . orcid:0000-0002-7558-2880 rdfs:label "Jesualdo Tomás Fernández-Breis" . @@ -13239,7 +13360,7 @@ orcid:0000-0002-8151-7479 rdfs:label "Raymond Lee" . orcid:0000-0002-8374-1941 rdfs:label "Miguel A. Fortuna" . orcid:0000-0002-8424-0604 rdfs:label "Donny Winston" ; - dcterms:contributor bioregistry:nmdc . + ns1:contributor bioregistry:nmdc . orcid:0000-0002-8429-8793 rdfs:label "Pablo Porras Millán" . @@ -13262,7 +13383,7 @@ orcid:0000-0002-9673-1283 rdfs:label "Yuki Yamagata" . orcid:0000-0002-9713-9994 rdfs:label "Mike Tyers" . orcid:0000-0003-0443-9902 rdfs:label "Adriano Rutz" ; - dcterms:contributor bioregistry:coconut, + ns1:contributor bioregistry:coconut, bioregistry:lotus . orcid:0000-0003-0705-9809 rdfs:label "Rahuman Sheriff" . @@ -13278,7 +13399,7 @@ orcid:0000-0003-1613-5981 rdfs:label "Heather Piwowar" . orcid:0000-0003-2338-8872 rdfs:label "Fernanda Farinelli" . orcid:0000-0003-2699-3066 rdfs:label "Meghan Balk" ; - dcterms:contributor bioregistry:col.taiwan, + ns1:contributor bioregistry:col.taiwan, bioregistry:fossilworks.journal, bioregistry:fossilworks.taxon, bioregistry:noaa, @@ -13302,6398 +13423,6402 @@ orcid:0000-0003-4871-5569 rdfs:label "Rebecca Jackson" . orcid:0000-0003-4978-0864 rdfs:label "Lutz Fischer" . -aberowl:ADO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ADO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ADW dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ADW ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AEO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AEO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AERO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AERO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AFO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AFO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AGRO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AGRO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AISM dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AISM ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:AMPHX dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:AMPHX ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:APAONTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:APAONTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:APO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:APO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:APOLLO_SV dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:APOLLO_SV ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ARO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ARO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ATC dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ATC ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ATO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ATO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ATOL dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ATOL ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BCGO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BCGO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BCI-O dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BCI-O ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BCO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BCO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BFO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BFO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BIOLINK dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BIOLINK ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BIRNLEX dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BIRNLEX ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BKO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BKO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BSPO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BSPO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:BTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:BTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CARO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CARO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CCO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CCO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CDAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CDAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CDNO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CDNO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CEPH dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CEPH ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CHEBI dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CHEBI ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CHEMINF dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CHEMINF ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CHIRO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CHIRO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CHMO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CHMO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CIDO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CIDO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CIO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CIO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CL dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CL ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CLAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CLAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CLO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CLO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CLYH dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CLYH ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CMF dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CMF ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CMO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CMO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CMPO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CMPO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:COB dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:COB ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:COLAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:COLAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:COVID19 dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:COVID19 ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CPT dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CPT ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CRISP dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CRISP ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CRO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CRO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CRYOEM dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CRYOEM ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CST dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CST ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CTENO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CTENO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:CVDO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:CVDO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DATACITE dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DATACITE ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DC dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DC ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DCAT dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DCAT ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DDANAT dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DDANAT ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DDPHENO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DDPHENO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DERMO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DERMO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DIDEO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DIDEO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DINTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DINTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DISDRIV dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DISDRIV ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DOID dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DOID ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DPO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DPO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DRON dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DRON ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:DUO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:DUO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ECAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ECAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ECG dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ECG ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ECO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ECO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ECOCORE dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ECOCORE ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ECTO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ECTO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EDAM dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EDAM ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EDDA dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EDDA ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EFO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EFO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EHDA dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EHDA ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EHDAA dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EHDAA ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EHDAA2 dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EHDAA2 ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EMAPA dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EMAPA ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ENM dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ENM ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ENVO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ENVO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EOL dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EOL ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EPIO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EPIO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EPO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EPO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EPSO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EPSO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:ERO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:ERO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EUPATH dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EUPATH ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:EXO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:EXO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:FALDO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:FALDO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:FAO dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:FAO ns1:isPartOf bioregistry.metaresource:aberowl . -aberowl:FB-SP dcterms:isPartOf 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bioregistry.metaresource:bioportal . -bioportal:EHDAA2 dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EHDA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EMAP dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EHDAA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EMAPA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EHDAA2 ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ENM dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EMAP ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ENVO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EMAPA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EOL dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:ENM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EPIO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:ENVO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EPO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EOL ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EPSO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EPIO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ERO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EPO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EUPATH dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EPSO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:EXO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:ERO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:FALDO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EUPATH ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:FAO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:EXO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:FB-BT dcterms:isPartOf 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bioregistry.metaresource:bioportal . -bioportal:FYPO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:FOVT ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GALEN dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:FPLX ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GAZ dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:FYPO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GECKO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GALEN ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GENO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GAZ ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GEO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GECKO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GEXO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GENO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GNO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GEO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GEXO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GRO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GNO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GRO-CPGA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:GSSO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GRO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HANCESTRO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GRO-CPGA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HAO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:GSSO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HCPCS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HANCESTRO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HGNC dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HAO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HOM dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HCPCS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HP_O dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HGNC ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HSAPDV dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HOM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HSO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HP_O ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:HTN dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:HSAPDV ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:IAO dcterms:isPartOf bioregistry.metaresource:bioportal . 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bioregistry.metaresource:bioportal . -bioportal:LBO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:KISAO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:LEPAO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LABO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:LIPRO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LBO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:LOINC dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LEPAO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:LPT dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LIPRO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LOINC ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MAMO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:LPT ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MAT dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MAXO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MAMO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MCCL dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MAT ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MCO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MAXO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MDM dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MCCL ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MEDDRA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MCO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MEDLINEPLUS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:MDM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:MESH dcterms:isPartOf 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bioregistry.metaresource:bioportal . -bioportal:OHD dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OGMS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OHMI dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OGSF ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OHPI dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OHD ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OLATDV dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OHMI ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OM dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OHPI ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMIABIS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OLATDV ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMIM dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMIT dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMIABIS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMIM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMP dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMIT ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:OMRSE dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ONE dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMP ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ONS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:OMRSE ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ONTOAVIDA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:ONE ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:ONTONEO dcterms:isPartOf 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bioregistry.metaresource:bioportal . -bioportal:PO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PLANP ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PORO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PMR ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PPO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PR dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PORO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PROPREO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PPO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PSDO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PR ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PSIMOD dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PROPREO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PSO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PSDO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PTO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PSIMOD ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:PW dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PSO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:QUDT dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PTO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RBO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:PW ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RDFS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:QUDT ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RDO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:RBO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:REPRODUCE-ME dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:RDFS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RETO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:RDO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:REX dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:REPRODUCE-ME ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:REXO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:RETO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RGD dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:REX ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RNAO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:REXO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:RGD ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:RS dcterms:isPartOf bioregistry.metaresource:bioportal . 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-bioportal:STATO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:SOPHARM ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:STY dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:SPD ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:SWEET dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:STATO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:SWO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:STY ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:SYMP dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:SWEET ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TADS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:SWO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TAO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:SYMP ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TAXRANK dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TADS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TEDDY dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TAO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TGMA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TAXRANK ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TRANS dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TEDDY ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TTO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TGMA ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:TXPO dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TRANS ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:UBERON dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TTO ns1:isPartOf bioregistry.metaresource:bioportal . -bioportal:UO dcterms:isPartOf bioregistry.metaresource:bioportal . 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ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:ClinVar dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ChEMBL-Cells ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:ColonAtlas dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ChEMBL-Targets ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Coriell dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ClinVar ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Cosmic dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ColonAtlas ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Cosmic-CLP dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Coriell ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:DGRC dcterms:isPartOf bioregistry.metaresource:cellosaurus . 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bioregistry.metaresource:cellosaurus . +cellosaurus.resource:HIVReagentProgram ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:ICLC dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:HipSci ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:IGRhCellID dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Horizon_Discovery ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:IGSR dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ICLC ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:IHW dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:IGRhCellID ns1:isPartOf bioregistry.metaresource:cellosaurus . - dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:IGSR ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Imanis dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:IHW ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:JCRB dcterms:isPartOf bioregistry.metaresource:cellosaurus . + ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:KCLB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Imanis ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:KYinno dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:JCRB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Kerafast dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:KCLB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:LIMORE dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:KYinno ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:LINCS_LDP dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Kerafast ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:LiGeA dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:LIMORE ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Lonza dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:LINCS_LDP ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:MGI dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:LiGeA ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:MMRRC dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Lonza ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:MeSH dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:MGI ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:MetaboLights dcterms:isPartOf bioregistry.metaresource:cellosaurus . 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bioregistry.metaresource:cellosaurus . +cellosaurus.resource:NHCDR ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Patent dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:ORDO ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:PerkinElmer dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:PRIDE ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:PharmacoDB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Patent ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Progenetix dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:PerkinElmer ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:PubChem dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:PharmacoDB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:PubMed dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Progenetix ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:RCB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:PubChem ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:RGD dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:PubMed ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:SKIP dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:RCB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:SLKBase dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:RGD ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:TCB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:SKIP ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:TKG dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:SLKBase ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:TNGB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:TCB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:TOKU-E dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:TKG ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:UBERON dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:TNGB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:UniProtKB dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:TOKU-E ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:VGNC dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:UBERON ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:WiCell dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:UniProtKB ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Wikidata dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:VGNC ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:Ximbio dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:WiCell ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:dbMHC dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Wikidata ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:dbSNP dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:Ximbio ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:eagle-i dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:dbMHC ns1:isPartOf bioregistry.metaresource:cellosaurus . -cellosaurus.resource:hPSCreg dcterms:isPartOf bioregistry.metaresource:cellosaurus . +cellosaurus.resource:dbSNP ns1:isPartOf bioregistry.metaresource:cellosaurus . -go.resource:AGRICOLA_ID dcterms:isPartOf bioregistry.metaresource:go . +cellosaurus.resource:eagle-i ns1:isPartOf bioregistry.metaresource:cellosaurus . -go.resource:ASAP dcterms:isPartOf bioregistry.metaresource:go . +cellosaurus.resource:hPSCreg ns1:isPartOf bioregistry.metaresource:cellosaurus . -go.resource:AspGD_LOCUS dcterms:isPartOf bioregistry.metaresource:go . +go.resource:AGRICOLA_ID ns1:isPartOf bioregistry.metaresource:go . -go.resource:BFO dcterms:isPartOf bioregistry.metaresource:go . +go.resource:ASAP ns1:isPartOf bioregistry.metaresource:go . -go.resource:BIOMD dcterms:isPartOf bioregistry.metaresource:go . +go.resource:AspGD_LOCUS ns1:isPartOf bioregistry.metaresource:go . -go.resource:BRENDA dcterms:isPartOf bioregistry.metaresource:go . +go.resource:BFO ns1:isPartOf bioregistry.metaresource:go . -go.resource:BTO dcterms:isPartOf bioregistry.metaresource:go . +go.resource:BIOMD ns1:isPartOf bioregistry.metaresource:go . -go.resource:BioCyc dcterms:isPartOf bioregistry.metaresource:go . +go.resource:BRENDA ns1:isPartOf bioregistry.metaresource:go . -go.resource:CARO dcterms:isPartOf bioregistry.metaresource:go . +go.resource:BTO ns1:isPartOf bioregistry.metaresource:go . -go.resource:CAS dcterms:isPartOf bioregistry.metaresource:go . +go.resource:BioCyc ns1:isPartOf bioregistry.metaresource:go . -go.resource:CASSPC dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CARO ns1:isPartOf bioregistry.metaresource:go . -go.resource:CAZY dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CAS ns1:isPartOf bioregistry.metaresource:go . -go.resource:CDD dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CASSPC ns1:isPartOf bioregistry.metaresource:go . -go.resource:CGD dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CAZY ns1:isPartOf bioregistry.metaresource:go . -go.resource:CGSC dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CDD ns1:isPartOf bioregistry.metaresource:go . -go.resource:CHEBI dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CGD ns1:isPartOf bioregistry.metaresource:go . -go.resource:CL dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CGSC ns1:isPartOf bioregistry.metaresource:go . -go.resource:COG_Cluster dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CHEBI ns1:isPartOf bioregistry.metaresource:go . -go.resource:COG_Pathway dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CL ns1:isPartOf bioregistry.metaresource:go . -go.resource:CORIELL dcterms:isPartOf bioregistry.metaresource:go . +go.resource:COG_Cluster ns1:isPartOf bioregistry.metaresource:go . -go.resource:CORUM dcterms:isPartOf bioregistry.metaresource:go . +go.resource:COG_Pathway ns1:isPartOf bioregistry.metaresource:go . -go.resource:ComplexPortal dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CORIELL ns1:isPartOf bioregistry.metaresource:go . -go.resource:DDANAT dcterms:isPartOf bioregistry.metaresource:go . +go.resource:CORUM ns1:isPartOf bioregistry.metaresource:go . -go.resource:DOI dcterms:isPartOf bioregistry.metaresource:go . +go.resource:ComplexPortal ns1:isPartOf bioregistry.metaresource:go . -go.resource:EC dcterms:isPartOf bioregistry.metaresource:go . +go.resource:DDANAT ns1:isPartOf bioregistry.metaresource:go . -go.resource:ECO dcterms:isPartOf bioregistry.metaresource:go . +go.resource:DOI ns1:isPartOf bioregistry.metaresource:go . -go.resource:EMAPA dcterms:isPartOf bioregistry.metaresource:go . +go.resource:EC ns1:isPartOf bioregistry.metaresource:go . -go.resource:ENA dcterms:isPartOf bioregistry.metaresource:go . +go.resource:ECO ns1:isPartOf bioregistry.metaresource:go . -go.resource:ENSEMBL dcterms:isPartOf bioregistry.metaresource:go . +go.resource:EMAPA ns1:isPartOf bioregistry.metaresource:go . -go.resource:EchoBASE dcterms:isPartOf bioregistry.metaresource:go . 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bioregistry.metaresource:n2t . -n2t:img.gene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:igsn ns1:isPartOf bioregistry.metaresource:n2t . -n2t:img.taxon dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:imex ns1:isPartOf bioregistry.metaresource:n2t . -n2t:imgt.hla dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:img.gene ns1:isPartOf bioregistry.metaresource:n2t . -n2t:imgt.ligm dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:img.taxon ns1:isPartOf bioregistry.metaresource:n2t . -n2t:inchi dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:imgt.hla ns1:isPartOf bioregistry.metaresource:n2t . -n2t:inchikey dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:imgt.ligm ns1:isPartOf bioregistry.metaresource:n2t . -n2t:insdc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:inchi ns1:isPartOf bioregistry.metaresource:n2t . -n2t:insdc.cds dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:inchikey ns1:isPartOf bioregistry.metaresource:n2t . -n2t:insdc.gca dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:insdc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:insdc.sra dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:insdc.cds ns1:isPartOf bioregistry.metaresource:n2t . -n2t:intact dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:insdc.gca ns1:isPartOf bioregistry.metaresource:n2t . -n2t:intact.molecule dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:insdc.sra ns1:isPartOf bioregistry.metaresource:n2t . -n2t:interpro dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:intact ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ird.segment dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:intact.molecule ns1:isPartOf bioregistry.metaresource:n2t . -n2t:irefweb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:interpro ns1:isPartOf bioregistry.metaresource:n2t . -n2t:isbn dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ird.segment ns1:isPartOf bioregistry.metaresource:n2t . -n2t:isfinder dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:irefweb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:isni dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:isbn ns1:isPartOf bioregistry.metaresource:n2t . -n2t:issn dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:isfinder ns1:isPartOf bioregistry.metaresource:n2t . -n2t:iuphar.family dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:isni ns1:isPartOf bioregistry.metaresource:n2t . -n2t:iuphar.ligand dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:issn ns1:isPartOf bioregistry.metaresource:n2t . -n2t:iuphar.receptor dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:iuphar.family ns1:isPartOf bioregistry.metaresource:n2t . -n2t:jaxmice dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:iuphar.ligand ns1:isPartOf bioregistry.metaresource:n2t . -n2t:jcggdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:iuphar.receptor ns1:isPartOf bioregistry.metaresource:n2t . -n2t:jcm dcterms:isPartOf bioregistry.metaresource:n2t . 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bioregistry.metaresource:n2t . -n2t:kegg.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:kegg.orthology ns1:isPartOf bioregistry.metaresource:n2t . -n2t:knapsack dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:kegg.pathway ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lei dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:kegg.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lgic dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:knapsack ns1:isPartOf bioregistry.metaresource:n2t . -n2t:licebase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lei ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ligandbook dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lgic ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ligandbox dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:licebase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ligandexpo dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ligandbook ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lincs.cell dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ligandbox ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lincs.data dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ligandexpo ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lincs.protein dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lincs.cell ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lincs.smallmolecule dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lincs.data ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lipidbank dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lincs.protein ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lipidmaps dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lincs.smallmolecule ns1:isPartOf bioregistry.metaresource:n2t . -n2t:lrg dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lipidbank ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ma dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lipidmaps ns1:isPartOf bioregistry.metaresource:n2t . -n2t:macie dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:lrg ns1:isPartOf bioregistry.metaresource:n2t . -n2t:maizegdb.locus dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ma ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mamo dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:macie ns1:isPartOf bioregistry.metaresource:n2t . -n2t:massbank dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:maizegdb.locus ns1:isPartOf bioregistry.metaresource:n2t . -n2t:massive dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mamo ns1:isPartOf bioregistry.metaresource:n2t . -n2t:matrixdb.association dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:massbank ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mdm dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:massive ns1:isPartOf bioregistry.metaresource:n2t . -n2t:meddra dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:matrixdb.association ns1:isPartOf bioregistry.metaresource:n2t . -n2t:medgen dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mdm ns1:isPartOf bioregistry.metaresource:n2t . -n2t:medlineplus dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:meddra ns1:isPartOf bioregistry.metaresource:n2t . -n2t:merops.family dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:medgen ns1:isPartOf bioregistry.metaresource:n2t . -n2t:merops.inhibitor dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:medlineplus ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mesh dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:merops.family ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mesh.2012 dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:merops.inhibitor ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mesh.2013 dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mesh ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metabolights dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mesh.2012 ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metacyc.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mesh.2013 ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metacyc.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metabolights ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metanetx.chemical dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metacyc.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metanetx.compartment dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metacyc.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metanetx.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metanetx.chemical ns1:isPartOf bioregistry.metaresource:n2t . -n2t:metlin dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metanetx.compartment ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mex dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metanetx.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mge dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:metlin ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mgi dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mex ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mgnify.proj dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mge ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mgnify.samp dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mgi ns1:isPartOf bioregistry.metaresource:n2t . -n2t:microscope dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mgnify.proj ns1:isPartOf bioregistry.metaresource:n2t . -n2t:microsporidia dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mgnify.samp ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mim dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:microscope ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mimodb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:microsporidia ns1:isPartOf bioregistry.metaresource:n2t . -n2t:minid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mim ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mint dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mimodb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mipmod dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:minid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mir dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mint ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mirbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mipmod ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mirbase.mature dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mir ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mirex dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mirbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:miriam.collection dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mirbase.mature ns1:isPartOf bioregistry.metaresource:n2t . -n2t:miriam.resource dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mirex ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mirnest dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:miriam.collection ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mirtarbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:miriam.resource ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mmdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mirnest ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mmp.cat dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mirtarbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mmp.db dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mmdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mmp.ref dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mmp.cat ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mmrrc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mmp.db ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mo dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mmp.ref ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mobidb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mmrrc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mod dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mo ns1:isPartOf bioregistry.metaresource:n2t . -n2t:modeldb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mobidb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:molbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mod ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mp dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:modeldb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:mpid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:molbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ms dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mp ns1:isPartOf bioregistry.metaresource:n2t . -n2t:multicellds.cell_line dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mpid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:multicellds.collection dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ms ns1:isPartOf bioregistry.metaresource:n2t . 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bioregistry.metaresource:n2t . -n2t:mzspec dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:myco.tuber ns1:isPartOf bioregistry.metaresource:n2t . -n2t:napdi dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mycobank ns1:isPartOf bioregistry.metaresource:n2t . -n2t:napp dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:mzspec ns1:isPartOf bioregistry.metaresource:n2t . -n2t:narcis dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:napdi ns1:isPartOf bioregistry.metaresource:n2t . -n2t:nasc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:napp ns1:isPartOf bioregistry.metaresource:n2t . -n2t:nbn dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:narcis ns1:isPartOf bioregistry.metaresource:n2t . -n2t:nbrc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:nasc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ncbigene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:nbn ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ncbiprotein dcterms:isPartOf 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bioregistry.metaresource:n2t . +n2t:odor ns1:isPartOf bioregistry.metaresource:n2t . -n2t:oma.protein dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:oid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:omia dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:oma.grp ns1:isPartOf bioregistry.metaresource:n2t . -n2t:omit dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:oma.protein ns1:isPartOf bioregistry.metaresource:n2t . -n2t:opb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:omia ns1:isPartOf bioregistry.metaresource:n2t . -n2t:opm dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:omit ns1:isPartOf bioregistry.metaresource:n2t . -n2t:orcid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:opb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ordb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:opm ns1:isPartOf bioregistry.metaresource:n2t . -n2t:oridb.sacch dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:orcid ns1:isPartOf bioregistry.metaresource:n2t 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bioregistry.metaresource:n2t . -n2t:planttfdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:piroplasma ns1:isPartOf bioregistry.metaresource:n2t . -n2t:plasmodb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pirsf ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pmap.cutdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:planttfdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pmap.substratedb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:plasmodb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pmc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pmap.cutdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pmdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pmap.substratedb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pmp dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pmc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:po dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pmdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pocketome dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pmp ns1:isPartOf bioregistry.metaresource:n2t . -n2t:polbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:po ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pombase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pocketome ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pr dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:polbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pride dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pombase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pride.project dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pr ns1:isPartOf bioregistry.metaresource:n2t . -n2t:prints dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pride ns1:isPartOf bioregistry.metaresource:n2t . -n2t:probonto dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pride.project ns1:isPartOf bioregistry.metaresource:n2t . -n2t:prodom dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:prints ns1:isPartOf bioregistry.metaresource:n2t . -n2t:proglyc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:probonto ns1:isPartOf bioregistry.metaresource:n2t . -n2t:prosite dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:prodom ns1:isPartOf bioregistry.metaresource:n2t . -n2t:protclustdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:proglyc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:proteomicsdb.peptide dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:prosite ns1:isPartOf bioregistry.metaresource:n2t . -n2t:proteomicsdb.protein dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:protclustdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:protonet.cluster dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:proteomicsdb.peptide ns1:isPartOf bioregistry.metaresource:n2t . -n2t:protonet.proteincard dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:proteomicsdb.protein ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pscdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:protonet.cluster ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pseudomonas dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:protonet.proteincard ns1:isPartOf bioregistry.metaresource:n2t . -n2t:psimi dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pscdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:psipar dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pseudomonas ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pubchem.bioassay dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:psimi ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pubchem.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:psipar ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pubchem.substance dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pubchem.bioassay ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pubmed dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pubchem.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:pw dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pubchem.substance ns1:isPartOf bioregistry.metaresource:n2t . -n2t:px dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pubmed ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rbk dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:pw ns1:isPartOf bioregistry.metaresource:n2t . -n2t:reactome dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:px ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rebase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rbk ns1:isPartOf bioregistry.metaresource:n2t . -n2t:refseq dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:reactome ns1:isPartOf bioregistry.metaresource:n2t . -n2t:resid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rebase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rfam dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:refseq ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rgd dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:resid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rgd.qtl dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rfam ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rgd.strain dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rgd ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rhea dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rgd.qtl ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricegap dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rgd.strain ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricenetdb.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rhea ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricenetdb.gene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricegap ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricenetdb.mirna dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricenetdb.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricenetdb.protein dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricenetdb.gene ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ricenetdb.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricenetdb.mirna ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rnacentral dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricenetdb.protein ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rnamods dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ricenetdb.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ro dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rnacentral ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rouge dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rnamods ns1:isPartOf bioregistry.metaresource:n2t . -n2t:rrid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ro ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sabiork.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rouge ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sabiork.ec dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:rrid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sabiork.kineticrecord dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sabiork.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sabiork.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sabiork.ec ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sasbdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sabiork.kineticrecord ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sbo dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sabiork.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:scop dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sasbdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:scretf dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sbo ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sdbs dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:scop ns1:isPartOf bioregistry.metaresource:n2t . -n2t:seed dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:scretf ns1:isPartOf bioregistry.metaresource:n2t . -n2t:seed.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sdbs ns1:isPartOf bioregistry.metaresource:n2t . -n2t:seed.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:seed ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sgd dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:seed.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sgd.pathways dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:seed.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sgn dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sgd ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sheepqtldb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sgd.pathways ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sider.drug dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sgn ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sider.effect dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sheepqtldb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:signaling-gateway dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sider.drug ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sisu dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sider.effect ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sitex dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:signaling-gateway ns1:isPartOf bioregistry.metaresource:n2t . -n2t:smart dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sisu ns1:isPartOf bioregistry.metaresource:n2t . -n2t:smpdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sitex ns1:isPartOf bioregistry.metaresource:n2t . -n2t:snomedct dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:smart ns1:isPartOf bioregistry.metaresource:n2t . -n2t:so dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:smpdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:soybase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:snomedct ns1:isPartOf bioregistry.metaresource:n2t . -n2t:spdx dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:so ns1:isPartOf bioregistry.metaresource:n2t . -n2t:spike.map dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:soybase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:splash dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:spdx ns1:isPartOf bioregistry.metaresource:n2t . -n2t:stap dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:spike.map ns1:isPartOf bioregistry.metaresource:n2t . -n2t:stitch dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:splash ns1:isPartOf bioregistry.metaresource:n2t . -n2t:storedb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:stap ns1:isPartOf bioregistry.metaresource:n2t . -n2t:string dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:stitch ns1:isPartOf bioregistry.metaresource:n2t . -n2t:subtilist dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:storedb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:subtiwiki dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:string ns1:isPartOf bioregistry.metaresource:n2t . -n2t:sugarbind dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:subtilist ns1:isPartOf bioregistry.metaresource:n2t . -n2t:supfam dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:subtiwiki ns1:isPartOf bioregistry.metaresource:n2t . -n2t:swh dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:sugarbind ns1:isPartOf bioregistry.metaresource:n2t . -n2t:swiss-model dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:supfam ns1:isPartOf bioregistry.metaresource:n2t . -n2t:swisslipid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:swh ns1:isPartOf bioregistry.metaresource:n2t . -n2t:swissregulon dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:swiss-model ns1:isPartOf bioregistry.metaresource:n2t . -n2t:t3db dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:swisslipid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tair.gene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:swissregulon ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tair.locus dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:t3db ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tair.protein dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tair.gene ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tarbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tair.locus ns1:isPartOf bioregistry.metaresource:n2t . -n2t:taxonomy dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tair.protein ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tcdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tarbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tgd dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:taxonomy ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tigrfam dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tcdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tissuelist dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tgd ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tol dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tigrfam ns1:isPartOf bioregistry.metaresource:n2t . -n2t:topdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tissuelist ns1:isPartOf bioregistry.metaresource:n2t . -n2t:topfind dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tol ns1:isPartOf bioregistry.metaresource:n2t . -n2t:toxoplasma dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:topdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:treebase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:topfind ns1:isPartOf bioregistry.metaresource:n2t . -n2t:treefam dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:toxoplasma ns1:isPartOf bioregistry.metaresource:n2t . -n2t:trichdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:treebase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:tritrypdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:treefam ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ttd.drug dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:trichdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ttd.target dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:tritrypdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uberon dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ttd.drug ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ubio.namebank dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ttd.target ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umbbd.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uberon ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umbbd.enzyme dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ubio.namebank ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umbbd.pathway dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umbbd.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umbbd.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umbbd.enzyme ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umbbd.rule dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umbbd.pathway ns1:isPartOf bioregistry.metaresource:n2t . -n2t:umls dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umbbd.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unigene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umbbd.rule ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unii dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:umls ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unimod dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unigene ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uniparc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unii ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unipathway.compound dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unimod ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unipathway.reaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uniparc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uniprot dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unipathway.compound ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uniprot.isoform dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unipathway.reaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unists dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uniprot ns1:isPartOf bioregistry.metaresource:n2t . -n2t:unite dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uniprot.isoform ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uo dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unists ns1:isPartOf bioregistry.metaresource:n2t . -n2t:uspto dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:unite ns1:isPartOf bioregistry.metaresource:n2t . -n2t:validatordb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uo ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vario dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:uspto ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vbase2 dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:validatordb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vbrc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vario ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vectorbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vbase2 ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vfb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vbrc ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vfdb.gene dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vectorbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vfdb.genus dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vfb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:viaf dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vfdb.gene ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vipr dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vfdb.genus ns1:isPartOf bioregistry.metaresource:n2t . -n2t:viralzone dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:viaf ns1:isPartOf bioregistry.metaresource:n2t . -n2t:virsirna dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vipr ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vmhmetabolite dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:viralzone ns1:isPartOf bioregistry.metaresource:n2t . -n2t:vmhreaction dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:virsirna ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vmhmetabolite ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wb.rnai dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:vmhreaction ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wikidata dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wikigenes dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wb.rnai ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wikipathways dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wikidata ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wikipedia.en dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wikigenes ns1:isPartOf bioregistry.metaresource:n2t . -n2t:worfdb dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wikipathways ns1:isPartOf bioregistry.metaresource:n2t . -n2t:wormpep dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wikipedia.en ns1:isPartOf bioregistry.metaresource:n2t . -n2t:worms dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:worfdb ns1:isPartOf bioregistry.metaresource:n2t . -n2t:xenbase dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:wormpep ns1:isPartOf bioregistry.metaresource:n2t . -n2t:ydpm dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:worms ns1:isPartOf bioregistry.metaresource:n2t . -n2t:yeastintron dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:xenbase ns1:isPartOf bioregistry.metaresource:n2t . -n2t:yetfasco dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:ydpm ns1:isPartOf bioregistry.metaresource:n2t . -n2t:yid dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:yeastintron ns1:isPartOf bioregistry.metaresource:n2t . -n2t:yrcpdr dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:yetfasco ns1:isPartOf bioregistry.metaresource:n2t . -n2t:zfin dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:yid ns1:isPartOf bioregistry.metaresource:n2t . -n2t:zinc dcterms:isPartOf bioregistry.metaresource:n2t . +n2t:yrcpdr ns1:isPartOf bioregistry.metaresource:n2t . -ncbi.resource:ASAP dcterms:isPartOf bioregistry.metaresource:ncbi . +n2t:zfin ns1:isPartOf bioregistry.metaresource:n2t . -ncbi.resource:ATCC dcterms:isPartOf bioregistry.metaresource:ncbi . +n2t:zinc ns1:isPartOf bioregistry.metaresource:n2t . -ncbi.resource:AntWeb dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ASAP ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ApiDB_PlasmoDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ATCC ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:Araport dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:AntWeb ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:BDGP_EST dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ApiDB_PlasmoDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:BEETLEBASE dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:Araport ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:BOLD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:BDGP_EST ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:CABRI dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:BEETLEBASE ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:CDD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:BOLD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:CGD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:CABRI ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ECOCYC dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:CDD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ENSEMBL dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:CGD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:EPD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ECOCYC ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:EcoGene dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ENSEMBL ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:FBOL dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:EPD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:FLYBASE dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:EcoGene ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:Fungorum dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:FBOL ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GABI dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:FLYBASE ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GO dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:Fungorum ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GOA dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GABI ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GRIN dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GO ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GeneDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GOA ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:GeneID dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GRIN ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:Greengenes dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GeneDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:HGNC dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:GeneID ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:HSSP dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:Greengenes ns1:isPartOf bioregistry.metaresource:ncbi . - dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:HGNC ns1:isPartOf bioregistry.metaresource:ncbi . - dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:HSSP ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ISFinder dcterms:isPartOf bioregistry.metaresource:ncbi . + ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:InterPro dcterms:isPartOf bioregistry.metaresource:ncbi . + ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:JCM dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ISFinder ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:MGI dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:InterPro ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:MIM dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:JCM ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:MaizeGDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:MGI ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:MedGen dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:MIM ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:MycoBank dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:MaizeGDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:NBRC dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:MedGen ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:NextDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:MycoBank ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:PDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:NBRC ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:PFAM dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:NextDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:Phytozome dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:PDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:PomBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:PFAM ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:RFAM dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:Phytozome ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:RGD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:PomBase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:RNAcentral dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:RFAM ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:SEED dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:RGD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:SGD dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:RNAcentral ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:SGN dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:SEED ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:SoyBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:SGD ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:SubtiList dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:SGN ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:TAIR dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:SoyBase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:TIGRFAM dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:SubtiList ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:TubercuList dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:TAIR ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:UNITE dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:TIGRFAM ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:UniProt dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:TubercuList ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:UniSTS dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:UNITE ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:VBASE2 dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:UniProt ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:VGNC dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:UniSTS ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:VectorBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:VBASE2 ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ViPR dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:VGNC ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:WorfDB dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:VectorBase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:WormBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ViPR ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:Xenbase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:WorfDB ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:ZFIN dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:WormBase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:dbEST dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:Xenbase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:dbProbe dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:ZFIN ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:dbSNP dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:dbEST ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:dictyBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:dbProbe ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:miRBase dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:dbSNP ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:niaEST dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:dictyBase ns1:isPartOf bioregistry.metaresource:ncbi . -ncbi.resource:taxon dcterms:isPartOf bioregistry.metaresource:ncbi . +ncbi.resource:miRBase ns1:isPartOf bioregistry.metaresource:ncbi . + +ncbi.resource:niaEST ns1:isPartOf bioregistry.metaresource:ncbi . + +ncbi.resource:taxon ns1:isPartOf bioregistry.metaresource:ncbi . bioregistry:4dn.replicate a bioregistry.schema:0000001 ; rdfs:label "4D Nucleome Data Portal Experiment Replicate" ; dc:description "Database portal containing replicate experiments of different assays and samples"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://data.4dnucleome.org/experiment-set-replicates/"^^xsd:string ; bioregistry.schema:0000005 "4DNESWX1J3QU"^^xsd:string ; bioregistry.schema:0000006 "https://data.4dnucleome.org/experiment-set-replicates/$1"^^xsd:string ; @@ -19701,12 +19826,13 @@ bioregistry:4dn.replicate a bioregistry.schema:0000001 ; bioregistry:ado a bioregistry.schema:0000001 ; rdfs:label "Alzheimer's Disease Ontology" ; - dc:description "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ADO, - obofoundry:ADO, + dc:description "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ADO, + obofoundry:ado, bioportal:ADO, - fairsharing:FAIRsharing.ckd4rf ; + fairsharing:FAIRsharing.ckd4rf, + ols:ado ; foaf:homepage "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"^^xsd:string ; bioregistry.schema:0000005 "0000001"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/ADO_$1"^^xsd:string ; @@ -19717,9 +19843,9 @@ bioregistry:ado a bioregistry.schema:0000001 ; bioregistry:aeo a bioregistry.schema:0000001 ; rdfs:label "Anatomical Entity Ontology" ; dc:description "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AEO, - obofoundry:AEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AEO, + obofoundry:aeo, ontobee:AEO, bioportal:AEO, biocontext:AEO, @@ -19730,13 +19856,12 @@ bioregistry:aeo a bioregistry.schema:0000001 ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/AEO_$1"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; bioregistry.schema:0000012 true ; - bioregistry.schema:0000018 bioregistry:ehdaa2 ; bioregistry.schema:0000019 [ rdfs:label "Jonathan Bard" ] . bioregistry:agilent.probe a bioregistry.schema:0000001 ; rdfs:label "Agilent Probe" ; dc:description "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt"^^xsd:string ; bioregistry.schema:0000005 "A_24_P98555"^^xsd:string ; bioregistry.schema:0000008 "^A_\\d+_.+$"^^xsd:string ; @@ -19755,8 +19880,8 @@ The Alliance of Genome Resources was founded by the following Model Organism dat - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:AGRKB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:AGRKB ; foaf:homepage "https://www.alliancegenome.org"^^xsd:string ; bioregistry.schema:0000005 "100000000000001"^^xsd:string ; bioregistry.schema:0000006 "https://www.alliancegenome.org/accession/$1"^^xsd:string ; @@ -19768,7 +19893,7 @@ The Alliance of Genome Resources was founded by the following Model Organism dat bioregistry:alzforum.mutation a bioregistry.schema:0000001 ; rdfs:label "Alzforum Mutations" ; dc:description "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.alzforum.org/mutations"^^xsd:string ; bioregistry.schema:0000005 "app-d678n-tottori"^^xsd:string ; bioregistry.schema:0000006 "https://www.alzforum.org/mutations/$1"^^xsd:string ; @@ -19777,9 +19902,9 @@ bioregistry:alzforum.mutation a bioregistry.schema:0000001 ; bioregistry:amphx a bioregistry.schema:0000001 ; rdfs:label "The Amphioxus Development and Anatomy Ontology" ; dc:description "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AMPHX, - obofoundry:AMPHX, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AMPHX, + obofoundry:amphx, ontobee:AMPHX, bioportal:AMPHX, ols:amphx ; @@ -19794,9 +19919,9 @@ bioregistry:amphx a bioregistry.schema:0000001 ; bioregistry:apollosv a bioregistry.schema:0000001 ; rdfs:label "Apollo Structured Vocabulary" ; dc:description "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:APOLLO_SV, - obofoundry:APOLLO_SV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:APOLLO_SV, + obofoundry:apollo_sv, ontobee:APOLLO_SV, bioportal:APOLLO-SV, fairsharing:FAIRsharing.ngv2xx, @@ -19812,9 +19937,9 @@ bioregistry:apollosv a bioregistry.schema:0000001 ; bioregistry:aro a bioregistry.schema:0000001 ; rdfs:label "Antibiotic Resistance Ontology" ; dc:description "Antibiotic resistance genes and mutations"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ARO, - obofoundry:ARO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ARO, + obofoundry:aro, ontobee:ARO, bioportal:ARO, biocontext:ARO, @@ -19830,8 +19955,8 @@ bioregistry:aro a bioregistry.schema:0000001 ; bioregistry:asrp a bioregistry.schema:0000001 ; rdfs:label "Arabidopsis Small RNA Project" ; dc:description "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch prefixcommons:asrp ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch prefixcommons:asrp ; foaf:homepage "https://asrp.danforthcenter.org/"^^xsd:string ; bioregistry.schema:0000005 "ASRP1423"^^xsd:string ; bioregistry.schema:0000006 "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^xsd:string ; @@ -19840,8 +19965,8 @@ bioregistry:asrp a bioregistry.schema:0000001 ; bioregistry:bactibase a bioregistry.schema:0000001 ; rdfs:label "Bactibase" ; dc:description "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.5f5mfm, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.5f5mfm, prefixcommons:bactibase ; foaf:homepage "http://bactibase.hammamilab.org"^^xsd:string ; bioregistry.schema:0000005 "BAC045"^^xsd:string ; @@ -19851,18 +19976,18 @@ bioregistry:bactibase a bioregistry.schema:0000001 ; bioregistry:bams a bioregistry.schema:0000001 ; rdfs:label "Brain Architecture Knowledge Management System Neuroanatomical Ontology" ; dc:description "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bams1.org"^^xsd:string ; bioregistry.schema:0000012 true . bioregistry:bco a bioregistry.schema:0000001 ; rdfs:label "Biological Collections Ontology" ; dc:description "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BCO, agroportal:BCO, ecoportal:BCO, - obofoundry:BCO, + obofoundry:bco, ontobee:BCO, bioportal:BCO, biocontext:BCO, @@ -19879,8 +20004,8 @@ bioregistry:bco a bioregistry.schema:0000001 ; bioregistry:bcrc a bioregistry.schema:0000001 ; rdfs:label "BCRC Strain Collection Catalog" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:BCRC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:BCRC ; foaf:homepage "https://catalog.bcrc.firdi.org.tw"^^xsd:string ; bioregistry.schema:0000005 "60316"^^xsd:string ; bioregistry.schema:0000006 "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^xsd:string ; @@ -19890,8 +20015,8 @@ bioregistry:bcrc a bioregistry.schema:0000001 ; bioregistry:beiresources a bioregistry.schema:0000001 ; rdfs:label "BEI Resources" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:BEI_Resources ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:BEI_Resources ; foaf:homepage "https://www.beiresources.org"^^xsd:string ; bioregistry.schema:0000005 "MRA-253"^^xsd:string ; bioregistry.schema:0000006 "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^xsd:string ; @@ -19900,8 +20025,8 @@ bioregistry:beiresources a bioregistry.schema:0000001 ; bioregistry:bel a bioregistry.schema:0000001 ; rdfs:label "Biological Expression Language" ; dc:description "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.dp0jvd ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.dp0jvd ; foaf:homepage "https://biological-expression-language.github.io/"^^xsd:string ; bioregistry.schema:0000005 "9-1-1 Complex"^^xsd:string ; bioregistry.schema:0000012 false . @@ -19909,9 +20034,9 @@ bioregistry:bel a bioregistry.schema:0000001 ; bioregistry:biogrid a bioregistry.schema:0000001 ; rdfs:label "BioGRID" ; dc:description "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^xsd:string ; - dcterms:hasPart bioregistry:biogrid.interaction ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:BIOGRID, + ns1:hasPart bioregistry:biogrid.interaction ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:BIOGRID, n2t:biogrid, fairsharing:FAIRsharing.9d5f5r, prefixcommons:biogrid, @@ -19926,7 +20051,7 @@ bioregistry:biogrid a bioregistry.schema:0000001 ; bioregistry:biolegend a bioregistry.schema:0000001 ; rdfs:label "BioLegend" ; dc:description "BioLegend is a life sciences supply vendor."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.biolegend.com"^^xsd:string ; bioregistry.schema:0000005 "3403"^^xsd:string ; bioregistry.schema:0000006 "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^xsd:string ; @@ -19936,7 +20061,7 @@ bioregistry:biolegend a bioregistry.schema:0000001 ; bioregistry:bioregistry a bioregistry.schema:0000001 ; rdfs:label "Bioregistry" ; dc:description "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bioregistry.io"^^xsd:string ; bioregistry.schema:0000005 "bioregistry"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/registry/$1"^^xsd:string ; @@ -19946,7 +20071,7 @@ bioregistry:bioregistry a bioregistry.schema:0000001 ; bioregistry:bioregistry.collection a bioregistry.schema:0000001 ; rdfs:label "Bioregistry Collections" ; dc:description "Manually curated collections of resources stored in the bioregistry"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bioregistry.io/collection"^^xsd:string ; bioregistry.schema:0000005 "0000001"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/collection/$1"^^xsd:string ; @@ -19957,7 +20082,7 @@ bioregistry:bioregistry.collection a bioregistry.schema:0000001 ; bioregistry:bioregistry.registry a bioregistry.schema:0000001 ; rdfs:label "Bioregistry Metaregistry" ; dc:description "The Bioregistry's meta-registry"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bioregistry.io/metaregistry/"^^xsd:string ; bioregistry.schema:0000005 "miriam"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/$1"^^xsd:string ; @@ -19967,7 +20092,7 @@ bioregistry:bioregistry.registry a bioregistry.schema:0000001 ; bioregistry:bioregistry.schema a bioregistry.schema:0000001 ; rdfs:label "Bioregistry Schema" ; dc:description "Schema for the export of the Bioregistry as RDF"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bioregistry.io/schema"^^xsd:string ; bioregistry.schema:0000005 "0000001"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/schema/#$1"^^xsd:string ; @@ -19978,8 +20103,8 @@ bioregistry:bioregistry.schema a bioregistry.schema:0000001 ; bioregistry:biostudies a bioregistry.schema:0000001 ; rdfs:label "BioStudies database" ; dc:description "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:biostudies, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:biostudies, fairsharing:FAIRsharing.mtjvme, miriam:biostudies ; foaf:homepage "https://www.ebi.ac.uk/biostudies/"^^xsd:string ; @@ -19991,7 +20116,7 @@ bioregistry:biostudies a bioregistry.schema:0000001 ; bioregistry:biozil a bioregistry.schema:0000001 ; rdfs:label "BIOZIL" ; dc:description "Redistributor of bilogics and biomedical supplies"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.biozol.de/en"^^xsd:string ; bioregistry.schema:0000005 "ls-c35719-120"^^xsd:string ; bioregistry.schema:0000006 "https://www.biozol.de/en/product/$1"^^xsd:string ; @@ -20000,8 +20125,8 @@ bioregistry:biozil a bioregistry.schema:0000001 ; bioregistry:bko a bioregistry.schema:0000001 ; rdfs:label "SBGN Bricks data and ontology" ; dc:description "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BKO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BKO, bioportal:BKO ; foaf:homepage "http://www.sbgnbricks.org/"^^xsd:string ; bioregistry.schema:0000005 "0000204"^^xsd:string ; @@ -20014,8 +20139,8 @@ bioregistry:bko a bioregistry.schema:0000001 ; bioregistry:bmrb a bioregistry.schema:0000001 ; rdfs:label "Biological Magnetic Resonance Data Bank" ; dc:description "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.p06nme, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.p06nme, miriam:bmrb, uniprot.resource:BMRB ; foaf:homepage "http://www.bmrb.wisc.edu/"^^xsd:string ; @@ -20027,7 +20152,7 @@ bioregistry:bmrb a bioregistry.schema:0000001 ; bioregistry:bmrb.restraint a bioregistry.schema:0000001 ; rdfs:label "NMR Restraints Grid" ; dc:description "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^xsd:string ; bioregistry.schema:0000005 "28789"^^xsd:string ; bioregistry.schema:0000006 "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^xsd:string ; @@ -20037,7 +20162,7 @@ bioregistry:bmrb.restraint a bioregistry.schema:0000001 ; bioregistry:bpdb a bioregistry.schema:0000001 ; rdfs:label "Bio-Pesticides DataBase" ; dc:description "Database of biopesticides maintained by the University of Hertfordshire "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://sitem.herts.ac.uk/aeru/bpdb/index.htm"^^xsd:string ; bioregistry.schema:0000005 "2404"^^xsd:string ; bioregistry.schema:0000006 "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^xsd:string ; @@ -20047,7 +20172,7 @@ bioregistry:bpdb a bioregistry.schema:0000001 ; bioregistry:brenda.ligand a bioregistry.schema:0000001 ; rdfs:label "BRENDA Ligand" ; dc:description "Information for ligands in the BRENDA database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.brenda-enzymes.de/ligand.php"^^xsd:string ; bioregistry.schema:0000005 "278"^^xsd:string ; bioregistry.schema:0000006 "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^xsd:string ; @@ -20057,7 +20182,7 @@ bioregistry:brenda.ligand a bioregistry.schema:0000001 ; bioregistry:brenda.ligandgroup a bioregistry.schema:0000001 ; rdfs:label "BRENDA Ligand Group" ; dc:description "Information for ligand groups (chemical classes)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.brenda-enzymes.de/ligand.php"^^xsd:string ; bioregistry.schema:0000005 "18030"^^xsd:string ; bioregistry.schema:0000006 "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^xsd:string ; @@ -20067,7 +20192,7 @@ bioregistry:brenda.ligandgroup a bioregistry.schema:0000001 ; bioregistry:bs a bioregistry.schema:0000001 ; rdfs:label "Biosapiens Protein Feature Ontology" ; dc:description "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/The-Sequence-Ontology/SO-Ontologies"^^xsd:string ; bioregistry.schema:0000005 "00042"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -20076,7 +20201,7 @@ bioregistry:bs a bioregistry.schema:0000001 ; bioregistry:caloha a bioregistry.schema:0000001 ; rdfs:label "CALIPHO Group Ontology of Human Anatomy" ; dc:description "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/calipho-sib/controlled-vocabulary"^^xsd:string ; bioregistry.schema:0000005 "TS-0001"^^xsd:string ; bioregistry.schema:0000008 "^TS-\\d+$"^^xsd:string ; @@ -20084,8 +20209,8 @@ bioregistry:caloha a bioregistry.schema:0000001 ; bioregistry:casspc a bioregistry.schema:0000001 ; rdfs:label "Eschmeyer's Catalog of Fishes" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch go.resource:CASSPC ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch go.resource:CASSPC ; foaf:homepage "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"^^xsd:string ; bioregistry.schema:0000005 "5359"^^xsd:string ; bioregistry.schema:0000006 "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^xsd:string ; @@ -20095,9 +20220,9 @@ bioregistry:casspc a bioregistry.schema:0000001 ; bioregistry:cath a bioregistry.schema:0000001 ; rdfs:label "CATH Protein Structural Domain Superfamily" ; dc:description "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^xsd:string ; - dcterms:hasPart bioregistry:cath.superfamily ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2700, + ns1:hasPart bioregistry:cath.superfamily ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2700, biocontext:CATH, n2t:cath, fairsharing:FAIRsharing.xgcyyn, @@ -20112,9 +20237,9 @@ bioregistry:cath a bioregistry.schema:0000001 ; bioregistry:cath.superfamily a bioregistry.schema:0000001 ; rdfs:label "CATH superfamily" ; dc:description "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:cath ; - ns1:exactMatch biocontext:CATH.SUPERFAMILY, + ns2:exactMatch biocontext:CATH.SUPERFAMILY, n2t:cath.superfamily, miriam:cath.superfamily ; foaf:homepage "http://www.cathdb.info/"^^xsd:string ; @@ -20126,9 +20251,9 @@ bioregistry:cath.superfamily a bioregistry.schema:0000001 ; bioregistry:cattleqtldb a bioregistry.schema:0000001 ; rdfs:label "Animal Genome Cattle QTL" ; dc:description "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:qtldb ; - ns1:exactMatch biocontext:CATTLEQTLDB, + ns2:exactMatch biocontext:CATTLEQTLDB, n2t:cattleqtldb, prefixcommons:cattleqtldb, miriam:cattleqtldb ; @@ -20141,7 +20266,7 @@ bioregistry:cattleqtldb a bioregistry.schema:0000001 ; bioregistry:cba a bioregistry.schema:0000001 ; rdfs:label "Chinese Biological Abstracts" ; dc:description "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.cba.ac.cn"^^xsd:string ; bioregistry.schema:0000005 "375364"^^xsd:string ; bioregistry.schema:0000006 "https://europepmc.org/article/CBA/$1"^^xsd:string ; @@ -20151,8 +20276,8 @@ bioregistry:cba a bioregistry.schema:0000001 ; bioregistry:ccrid a bioregistry.schema:0000001 ; rdfs:label "National Experimental Cell Resource Sharing Platform" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CCRID ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CCRID ; foaf:homepage "http://www.cellresource.cn"^^xsd:string ; bioregistry.schema:0000005 "4201PAT-CCTCC00348"^^xsd:string ; bioregistry.schema:0000006 "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^xsd:string ; @@ -20161,7 +20286,7 @@ bioregistry:ccrid a bioregistry.schema:0000001 ; bioregistry:cdt a bioregistry.schema:0000001 ; rdfs:label "Current Dental Terminology" ; dc:description "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ada.org/publications/CDT"^^xsd:string ; bioregistry.schema:0000005 "1000001"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -20171,8 +20296,8 @@ bioregistry:cdt a bioregistry.schema:0000001 ; bioregistry:cellimage a bioregistry.schema:0000001 ; rdfs:label "Cell Image Library" ; dc:description "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CELLIMAGE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CELLIMAGE, n2t:cellimage, fairsharing:FAIRsharing.8t18te, prefixcommons:cellimage, @@ -20186,8 +20311,8 @@ bioregistry:cellimage a bioregistry.schema:0000001 ; bioregistry:cellopub a bioregistry.schema:0000001 ; rdfs:label "Cellosaurus Publication" ; dc:description "Cellosaurus identifeirs for publications, like Pubmed"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:CelloPub ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:CelloPub ; foaf:homepage "https://web.expasy.org/cellosaurus/"^^xsd:string ; bioregistry.schema:0000005 "CLPUB00496"^^xsd:string ; bioregistry.schema:0000006 "https://web.expasy.org/cellosaurus/cellopub/$1"^^xsd:string ; @@ -20196,8 +20321,8 @@ bioregistry:cellopub a bioregistry.schema:0000001 ; bioregistry:cellosaurus a bioregistry.schema:0000001 ; rdfs:label "Cellosaurus" ; dc:description "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:CELLOSAURUS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:CELLOSAURUS, cellosaurus.resource:Cellosaurus, n2t:cellosaurus, fairsharing:FAIRsharing.hkk309, @@ -20212,7 +20337,7 @@ bioregistry:cellosaurus a bioregistry.schema:0000001 ; bioregistry:cellosaurus.resource a bioregistry.schema:0000001 ; rdfs:label "Cellosaurus Registry" ; dc:description "The set of prefixes used in the Cellosaurus resource"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://web.expasy.org/cellosaurus/"^^xsd:string ; bioregistry.schema:0000005 "4DN"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/cellosaurus/$1"^^xsd:string ; @@ -20221,8 +20346,8 @@ bioregistry:cellosaurus.resource a bioregistry.schema:0000001 ; bioregistry:cgnc a bioregistry.schema:0000001 ; rdfs:label "Chicken Gene Nomenclature Consortium" ; dc:description "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch prefixcommons:cgnc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch prefixcommons:cgnc ; foaf:homepage "http://birdgenenames.org/cgnc/"^^xsd:string ; bioregistry.schema:0000005 "10087"^^xsd:string ; bioregistry.schema:0000006 "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^xsd:string ; @@ -20232,9 +20357,9 @@ bioregistry:cgnc a bioregistry.schema:0000001 ; bioregistry:chembl.compound a bioregistry.schema:0000001 ; rdfs:label "ChEMBL" ; dc:description "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:chembl ; - ns1:exactMatch edam.data:2646, + ns2:exactMatch edam.data:2646, biocontext:CHEMBL.COMPOUND, n2t:chembl.compound, miriam:chembl.compound, @@ -20248,9 +20373,9 @@ bioregistry:chembl.compound a bioregistry.schema:0000001 ; bioregistry:chembl.target a bioregistry.schema:0000001 ; rdfs:label "ChEMBL target" ; dc:description "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:chembl ; - ns1:exactMatch biocontext:CHEMBL.TARGET, + ns2:exactMatch biocontext:CHEMBL.TARGET, cellosaurus.resource:ChEMBL-Targets, n2t:chembl.target, miriam:chembl.target ; @@ -20263,8 +20388,8 @@ bioregistry:chembl.target a bioregistry.schema:0000001 ; bioregistry:chemidplus a bioregistry.schema:0000001 ; rdfs:label "ChemIDplus" ; dc:description "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2658, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2658, biocontext:CHEMIDPLUS, n2t:chemidplus, fairsharing:FAIRsharing.5949vn, @@ -20279,9 +20404,9 @@ bioregistry:chemidplus a bioregistry.schema:0000001 ; bioregistry:cheminf a bioregistry.schema:0000001 ; rdfs:label "Chemical Information Ontology" ; dc:description "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CHEMINF, - obofoundry:CHEMINF, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CHEMINF, + obofoundry:cheminf, ontobee:CHEMINF, bioportal:CHEMINF, biocontext:CHEMINF, @@ -20298,9 +20423,9 @@ bioregistry:cheminf a bioregistry.schema:0000001 ; bioregistry:chickenqtldb a bioregistry.schema:0000001 ; rdfs:label "Animal Genome Chicken QTL" ; dc:description "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:qtldb ; - ns1:exactMatch biocontext:CHICKENQTLDB, + ns2:exactMatch biocontext:CHICKENQTLDB, n2t:chickenqtldb, prefixcommons:chickenqtldb, miriam:chickenqtldb ; @@ -20313,8 +20438,8 @@ bioregistry:chickenqtldb a bioregistry.schema:0000001 ; bioregistry:citexplore a bioregistry.schema:0000001 ; rdfs:label "CiteXplore" ; dc:description "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.619eqr, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.619eqr, prefixcommons:citexplore ; foaf:homepage "https://www.ebi.ac.uk/citexplore/"^^xsd:string ; bioregistry.schema:0000005 "C6155"^^xsd:string ; @@ -20324,9 +20449,9 @@ bioregistry:citexplore a bioregistry.schema:0000001 ; bioregistry:clao a bioregistry.schema:0000001 ; rdfs:label "Collembola Anatomy Ontology" ; dc:description "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CLAO, - obofoundry:CLAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CLAO, + obofoundry:clao, ontobee:CLAO, bioportal:CLAO, ols:clao ; @@ -20341,7 +20466,7 @@ bioregistry:clao a bioregistry.schema:0000001 ; bioregistry:cmecs a bioregistry.schema:0000001 ; rdfs:label "Costal and Marine Ecological Classification Standard" ; dc:description "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://cmecscatalog.org/cmecs"^^xsd:string ; bioregistry.schema:0000005 "595"^^xsd:string ; bioregistry.schema:0000006 "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^xsd:string ; @@ -20351,9 +20476,9 @@ bioregistry:cmecs a bioregistry.schema:0000001 ; bioregistry:cmo a bioregistry.schema:0000001 ; rdfs:label "Clinical measurement ontology" ; dc:description "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CMO, - obofoundry:CMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CMO, + obofoundry:cmo, ontobee:CMO, bioportal:CMO, biocontext:CMO, @@ -20370,7 +20495,7 @@ bioregistry:cmo a bioregistry.schema:0000001 ; bioregistry:coconut a bioregistry.schema:0000001 ; rdfs:label "COlleCtion of Open Natural ProdUcTs" ; dc:description "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://coconut.naturalproducts.net"^^xsd:string ; bioregistry.schema:0000005 "CNP0171505"^^xsd:string ; bioregistry.schema:0000006 "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^xsd:string ; @@ -20381,7 +20506,7 @@ bioregistry:coconut a bioregistry.schema:0000001 ; bioregistry:codelink a bioregistry.schema:0000001 ; rdfs:label "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" ; dc:description "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"^^xsd:string ; bioregistry.schema:0000005 "GE86325"^^xsd:string ; bioregistry.schema:0000008 "^GE\\d+$"^^xsd:string ; @@ -20390,9 +20515,9 @@ bioregistry:codelink a bioregistry.schema:0000001 ; bioregistry:cog.pathway a bioregistry.schema:0000001 ; rdfs:label "COG Pathways" ; dc:description "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:cog ; - ns1:exactMatch go.resource:COG_Pathway ; + ns2:exactMatch go.resource:COG_Pathway ; foaf:homepage "https://www.ncbi.nlm.nih.gov/research/cog/pathways"^^xsd:string ; bioregistry.schema:0000005 "NAD%20biosynthesis"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^xsd:string ; @@ -20402,15 +20527,15 @@ bioregistry:cog.pathway a bioregistry.schema:0000001 ; bioregistry:cohd a bioregistry.schema:0000001 ; rdfs:label "MIMIC III Database" ; dc:description "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/MIT-LCP/mimic-omop"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:col.taiwan a bioregistry.schema:0000001 ; rdfs:label "Catalogue of Life in Taiwan" ; dc:description "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P3088 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P3088 ; foaf:homepage "http://taibnet.sinica.edu.tw/home.php"^^xsd:string ; bioregistry.schema:0000005 "431472"^^xsd:string ; bioregistry.schema:0000006 "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^xsd:string ; @@ -20421,8 +20546,8 @@ bioregistry:col.taiwan a bioregistry.schema:0000001 ; bioregistry:complexportal a bioregistry.schema:0000001 ; rdfs:label "Complex Portal" ; dc:description "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:COMPLEXPORTAL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:COMPLEXPORTAL, go.resource:ComplexPortal, n2t:complexportal, miriam:complexportal, @@ -20437,7 +20562,7 @@ bioregistry:complexportal a bioregistry.schema:0000001 ; bioregistry:conso a bioregistry.schema:0000001 ; rdfs:label "Curation of Neurodegeneration Supporting Ontology" ; dc:description "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://pharmacome.github.io/conso/"^^xsd:string ; bioregistry.schema:0000005 "CONSO00010"^^xsd:string ; bioregistry.schema:0000006 "https://pharmacome.github.io/conso/$1"^^xsd:string ; @@ -20447,7 +20572,7 @@ bioregistry:conso a bioregistry.schema:0000001 ; bioregistry:cordis.article a bioregistry.schema:0000001 ; rdfs:label "CORDIS Article" ; dc:description "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://cordis.europa.eu/"^^xsd:string ; bioregistry.schema:0000005 "436605"^^xsd:string ; bioregistry.schema:0000006 "https://cordis.europa.eu/article/id/$1"^^xsd:string ; @@ -20457,7 +20582,7 @@ bioregistry:cordis.article a bioregistry.schema:0000001 ; bioregistry:cordis.project a bioregistry.schema:0000001 ; rdfs:label "CORDIS Project" ; dc:description "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://cordis.europa.eu/"^^xsd:string ; bioregistry.schema:0000005 "817732"^^xsd:string ; bioregistry.schema:0000006 "https://cordis.europa.eu/project/id/$1"^^xsd:string ; @@ -20468,8 +20593,8 @@ bioregistry:cordis.project a bioregistry.schema:0000001 ; bioregistry:cosmic.cell a bioregistry.schema:0000001 ; rdfs:label "COSMIC Cell Lines" ; dc:description "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Cosmic-CLP ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Cosmic-CLP ; foaf:homepage "https://cancer.sanger.ac.uk/cell_lines/"^^xsd:string ; bioregistry.schema:0000005 "906801"^^xsd:string ; bioregistry.schema:0000006 "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^xsd:string ; @@ -20478,15 +20603,15 @@ bioregistry:cosmic.cell a bioregistry.schema:0000001 ; bioregistry:cp a bioregistry.schema:0000001 ; rdfs:label "Cellular Phenotypes" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true ; bioregistry.schema:0000018 bioregistry:cl . bioregistry:cpt a bioregistry.schema:0000001 ; rdfs:label "Current Procedural Terminology" ; dc:description "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CPT, bioportal:CPT, biolink:CPT, fairsharing:FAIRsharing.wpxab1 ; @@ -20500,7 +20625,7 @@ bioregistry:cpt a bioregistry.schema:0000001 ; bioregistry:credit a bioregistry.schema:0000001 ; rdfs:label "CASRAI Contributor Roles Taxonomy" ; dc:description "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://casrai.org/credit/"^^xsd:string ; bioregistry.schema:0000005 "Software"^^xsd:string ; bioregistry.schema:0000012 false . @@ -20508,9 +20633,9 @@ bioregistry:credit a bioregistry.schema:0000001 ; bioregistry:ctd.chemical a bioregistry.schema:0000001 ; rdfs:label "CTD Chemical" ; dc:description "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ctd ; - ns1:exactMatch biocontext:CTD.CHEMICAL, + ns2:exactMatch biocontext:CTD.CHEMICAL, biolink:CTD.CHEMICAL, n2t:ctd.chemical, miriam:ctd.chemical ; @@ -20524,9 +20649,9 @@ bioregistry:ctd.chemical a bioregistry.schema:0000001 ; bioregistry:ctd.disease a bioregistry.schema:0000001 ; rdfs:label "CTD Disease" ; dc:description "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ctd ; - ns1:exactMatch biocontext:CTD.DISEASE, + ns2:exactMatch biocontext:CTD.DISEASE, biolink:CTD.DISEASE, n2t:ctd.disease, miriam:ctd.disease ; @@ -20540,9 +20665,9 @@ bioregistry:ctd.disease a bioregistry.schema:0000001 ; bioregistry:ctd.gene a bioregistry.schema:0000001 ; rdfs:label "CTD Gene" ; dc:description "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ctd ; - ns1:exactMatch biocontext:CTD.GENE, + ns2:exactMatch biocontext:CTD.GENE, biolink:CTD.GENE, n2t:ctd.gene, miriam:ctd.gene ; @@ -20553,15 +20678,15 @@ bioregistry:ctd.gene a bioregistry.schema:0000001 ; bioregistry.schema:0000011 bioregistry:ncbigene ; bioregistry.schema:0000012 false . -bioregistry:datanator dcterms:hasPart bioregistry:datanator.gene, +bioregistry:datanator ns1:hasPart bioregistry:datanator.gene, bioregistry:datanator.metabolite . bioregistry:datanator.gene a bioregistry.schema:0000001 ; rdfs:label "Datanator Gene" ; dc:description "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:datanator ; - ns1:exactMatch miriam:datanator.gene ; + ns2:exactMatch miriam:datanator.gene ; foaf:homepage "https://datanator.info/"^^xsd:string ; bioregistry.schema:0000005 "K00973"^^xsd:string ; bioregistry.schema:0000006 "https://www.datanator.info/gene/$1"^^xsd:string ; @@ -20571,9 +20696,9 @@ bioregistry:datanator.gene a bioregistry.schema:0000001 ; bioregistry:datanator.metabolite a bioregistry.schema:0000001 ; rdfs:label "Datanator Metabolite" ; dc:description "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:datanator ; - ns1:exactMatch miriam:datanator.metabolite ; + ns2:exactMatch miriam:datanator.metabolite ; foaf:homepage "https://datanator.info/"^^xsd:string ; bioregistry.schema:0000005 "OUYCCCASQSFEME-MRVPVSSYSA-N"^^xsd:string ; bioregistry.schema:0000006 "https://www.datanator.info/metabolite/$1"^^xsd:string ; @@ -20583,8 +20708,8 @@ bioregistry:datanator.metabolite a bioregistry.schema:0000001 ; bioregistry:dbest a bioregistry.schema:0000001 ; rdfs:label "EST database maintained at the NCBI." ; dc:description "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1105, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1105, biocontext:DBEST, n2t:dbest, ncbi.resource:dbEST, @@ -20600,8 +20725,8 @@ bioregistry:dbest a bioregistry.schema:0000001 ; bioregistry:dbsnp a bioregistry.schema:0000001 ; rdfs:label "NCBI dbSNP" ; dc:description "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1106, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1106, biocontext:dbSNP, cellosaurus.resource:dbSNP, go.resource:dbSNP, @@ -20620,7 +20745,7 @@ bioregistry:dbsnp a bioregistry.schema:0000001 ; bioregistry:dbvar.study a bioregistry.schema:0000001 ; rdfs:label "Database of Genomic Structural Variation - Study" ; dc:description "Studies in dbVar."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/dbvar"^^xsd:string ; bioregistry.schema:0000005 "nstd102"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^xsd:string ; @@ -20629,7 +20754,7 @@ bioregistry:dbvar.study a bioregistry.schema:0000001 ; bioregistry:dbvar.variant a bioregistry.schema:0000001 ; rdfs:label "Database of Genomic Structural Variation - Variant" ; dc:description "Variants in dbVar."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/dbvar"^^xsd:string ; bioregistry.schema:0000005 "nsv3875336"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^xsd:string ; @@ -20638,8 +20763,8 @@ bioregistry:dbvar.variant a bioregistry.schema:0000001 ; bioregistry:dc a bioregistry.schema:0000001 ; rdfs:label "Dublin Core" ; dc:description "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DC, bioportal:DC, biocontext:dc, fairsharing:FAIRsharing.3nx7t ; @@ -20652,8 +20777,8 @@ bioregistry:dc a bioregistry.schema:0000001 ; bioregistry:dcat a bioregistry.schema:0000001 ; rdfs:label "Data Catalog" ; dc:description "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DCAT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DCAT, bioportal:DCAT, biocontext:dcat, biolink:dcat, @@ -20666,8 +20791,8 @@ bioregistry:dcat a bioregistry.schema:0000001 ; bioregistry:dctypes a bioregistry.schema:0000001 ; rdfs:label "Dublin Core Types" ; dc:description "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:dctypes ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:dctypes ; foaf:homepage "https://dublincore.org/specifications/dublin-core/dcmi-terms/"^^xsd:string ; bioregistry.schema:0000005 "Collection"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/dc/dcmitype/$1"^^xsd:string ; @@ -20676,7 +20801,7 @@ bioregistry:dctypes a bioregistry.schema:0000001 ; bioregistry:debio a bioregistry.schema:0000001 ; rdfs:label "Decentralized Biomedical Ontology" ; dc:description "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://biopragmatics.github.io/debio"^^xsd:string ; bioregistry.schema:0000005 "0000001"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/debio/$1"^^xsd:string ; @@ -20687,8 +20812,8 @@ bioregistry:debio a bioregistry.schema:0000001 ; bioregistry:decipher a bioregistry.schema:0000001 ; rdfs:label "DECIPHER CNV Syndromes" ; dc:description "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:DECIPHER, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:DECIPHER, fairsharing:FAIRsharing.l8Sf5x ; foaf:homepage "https://www.deciphergenomics.org/"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; @@ -20699,9 +20824,9 @@ bioregistry:decipher a bioregistry.schema:0000001 ; bioregistry:dictybase.est a bioregistry.schema:0000001 ; rdfs:label "dictyBase Expressed Sequence Tag" ; dc:description "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dictybase ; - ns1:exactMatch biocontext:DICTYBASE.EST, + ns2:exactMatch biocontext:DICTYBASE.EST, n2t:dictybase.est, miriam:dictybase.est ; foaf:homepage "http://dictybase.org/"^^xsd:string ; @@ -20713,9 +20838,9 @@ bioregistry:dictybase.est a bioregistry.schema:0000001 ; bioregistry:dictybase.gene a bioregistry.schema:0000001 ; rdfs:label "Dictybase Gene" ; dc:description "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dictybase ; - ns1:exactMatch biocontext:DICTYBASE.GENE, + ns2:exactMatch biocontext:DICTYBASE.GENE, n2t:dictybase.gene, miriam:dictybase.gene ; foaf:homepage "http://dictybase.org/"^^xsd:string ; @@ -20727,21 +20852,21 @@ bioregistry:dictybase.gene a bioregistry.schema:0000001 ; bioregistry:diseaseclass a bioregistry.schema:0000001 ; rdfs:label "Disease Class" ; dc:description "Legacy disease classes that later became MONDO"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000005 "0000598"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; bioregistry.schema:0000012 true ; bioregistry.schema:0000018 bioregistry:efo . -bioregistry:dlx dcterms:hasPart bioregistry:dlxb, +bioregistry:dlx ns1:hasPart bioregistry:dlxb, bioregistry:dlxc . bioregistry:dlxb a bioregistry.schema:0000001 ; rdfs:label "Linear double stranded DNA sequences" ; dc:description "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dlx ; - ns1:exactMatch miriam:dlxb ; + ns2:exactMatch miriam:dlxb ; foaf:homepage "https://doulix.com"^^xsd:string ; bioregistry.schema:0000005 "6VDC956"^^xsd:string ; bioregistry.schema:0000006 "https://doulix.com/biomodules/$1"^^xsd:string ; @@ -20751,24 +20876,24 @@ bioregistry:dlxb a bioregistry.schema:0000001 ; bioregistry:dlxc a bioregistry.schema:0000001 ; rdfs:label "Circular double stranded DNA sequences composed" ; dc:description "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dlx ; - ns1:exactMatch miriam:dlxc ; + ns2:exactMatch miriam:dlxc ; foaf:homepage "https://doulix.com"^^xsd:string ; bioregistry.schema:0000005 "M77F7JM"^^xsd:string ; bioregistry.schema:0000006 "https://doulix.com/constructs/$1"^^xsd:string ; bioregistry.schema:0000008 "^[A-Z0-9]{6,7}$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:doqcs dcterms:hasPart bioregistry:doqcs.model, +bioregistry:doqcs ns1:hasPart bioregistry:doqcs.model, bioregistry:doqcs.pathway . bioregistry:doqcs.model a bioregistry.schema:0000001 ; rdfs:label "Database of Quantitative Cellular Signaling: Model" ; dc:description "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:doqcs ; - ns1:exactMatch biocontext:DOQCS.MODEL, + ns2:exactMatch biocontext:DOQCS.MODEL, n2t:doqcs.model, prefixcommons:doqcs.model, miriam:doqcs.model ; @@ -20781,9 +20906,9 @@ bioregistry:doqcs.model a bioregistry.schema:0000001 ; bioregistry:doqcs.pathway a bioregistry.schema:0000001 ; rdfs:label "Database of Quantitative Cellular Signaling: Pathway" ; dc:description "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:doqcs ; - ns1:exactMatch biocontext:DOQCS.PATHWAY, + ns2:exactMatch biocontext:DOQCS.PATHWAY, n2t:doqcs.pathway, prefixcommons:doqcs.pathway, miriam:doqcs.pathway ; @@ -20796,10 +20921,10 @@ bioregistry:doqcs.pathway a bioregistry.schema:0000001 ; bioregistry:dpo a bioregistry.schema:0000001 ; rdfs:label "Drosophila Phenotype Ontology" ; dc:description "An ontology for the description of Drosophila melanogaster phenotypes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:fbcv ; - ns1:exactMatch aberowl:DPO, - obofoundry:FBcv, + ns2:exactMatch aberowl:DPO, + obofoundry:dpo, ontobee:DPO, bioportal:DPO, ols:dpo ; @@ -20811,9 +20936,9 @@ bioregistry:dpo a bioregistry.schema:0000001 ; bioregistry:dragondb.allele a bioregistry.schema:0000001 ; rdfs:label "DragonDB Allele" ; dc:description "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dragondb ; - ns1:exactMatch biocontext:DRAGONDB.ALLELE, + ns2:exactMatch biocontext:DRAGONDB.ALLELE, n2t:dragondb.allele, miriam:dragondb.allele ; foaf:homepage "http://www.antirrhinum.net/"^^xsd:string ; @@ -20825,9 +20950,9 @@ bioregistry:dragondb.allele a bioregistry.schema:0000001 ; bioregistry:dragondb.dna a bioregistry.schema:0000001 ; rdfs:label "DragonDB DNA" ; dc:description "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dragondb ; - ns1:exactMatch biocontext:DRAGONDB.DNA, + ns2:exactMatch biocontext:DRAGONDB.DNA, n2t:dragondb.dna, miriam:dragondb.dna ; foaf:homepage "http://www.antirrhinum.net/"^^xsd:string ; @@ -20839,9 +20964,9 @@ bioregistry:dragondb.dna a bioregistry.schema:0000001 ; bioregistry:dragondb.locus a bioregistry.schema:0000001 ; rdfs:label "DragonDB Locus" ; dc:description "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dragondb ; - ns1:exactMatch biocontext:DRAGONDB.LOCUS, + ns2:exactMatch biocontext:DRAGONDB.LOCUS, n2t:dragondb.locus, miriam:dragondb.locus ; foaf:homepage "http://www.antirrhinum.net/"^^xsd:string ; @@ -20853,9 +20978,9 @@ bioregistry:dragondb.locus a bioregistry.schema:0000001 ; bioregistry:dragondb.protein a bioregistry.schema:0000001 ; rdfs:label "DragonDB Protein" ; dc:description "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:dragondb ; - ns1:exactMatch biocontext:DRAGONDB.PROTEIN, + ns2:exactMatch biocontext:DRAGONDB.PROTEIN, n2t:dragondb.protein, miriam:dragondb.protein ; foaf:homepage "http://www.antirrhinum.net/"^^xsd:string ; @@ -20867,9 +20992,9 @@ bioregistry:dragondb.protein a bioregistry.schema:0000001 ; bioregistry:dron a bioregistry.schema:0000001 ; rdfs:label "The Drug Ontology" ; dc:description "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DRON, - obofoundry:DRON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DRON, + obofoundry:dron, ontobee:DRON, bioportal:DRON, biocontext:DRON, @@ -20886,9 +21011,9 @@ bioregistry:dron a bioregistry.schema:0000001 ; bioregistry:drugbank.salt a bioregistry.schema:0000001 ; rdfs:label "DrugBank Salts" ; dc:description "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:drugbank ; - ns1:exactMatch biocontext:DRUGBANK.TARGET ; + ns2:exactMatch biocontext:DRUGBANK.TARGET ; foaf:homepage "http://www.drugbank.ca"^^xsd:string ; bioregistry.schema:0000005 "DBSALT001211"^^xsd:string ; bioregistry.schema:0000006 "https://go.drugbank.com/salts/$1"^^xsd:string ; @@ -20898,9 +21023,9 @@ bioregistry:drugbank.salt a bioregistry.schema:0000001 ; bioregistry:drugbankv4.target a bioregistry.schema:0000001 ; rdfs:label "DrugBank Target v4" ; dc:description "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:drugbank ; - ns1:exactMatch biocontext:DRUGBANKV4.TARGET, + ns2:exactMatch biocontext:DRUGBANKV4.TARGET, n2t:drugbankv4.target, miriam:drugbankv4.target ; foaf:homepage "http://www.drugbank.ca/targets"^^xsd:string ; @@ -20912,8 +21037,8 @@ bioregistry:drugbankv4.target a bioregistry.schema:0000001 ; bioregistry:dsmz a bioregistry.schema:0000001 ; rdfs:label "Deutsche Sammlung von Mikroorganismen und Zellkulturen" ; dc:description "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:DSMZ ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:DSMZ ; foaf:homepage "https://www.dsmz.de"^^xsd:string ; bioregistry.schema:0000005 "ACC-1"^^xsd:string ; bioregistry.schema:0000006 "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^xsd:string ; @@ -20922,8 +21047,8 @@ bioregistry:dsmz a bioregistry.schema:0000001 ; bioregistry:eaglei a bioregistry.schema:0000001 ; rdfs:label "eagle-i" ; dc:description "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:eagle-i ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:eagle-i ; foaf:homepage "https://hawaii.eagle-i.net"^^xsd:string ; bioregistry.schema:0000005 "0000012b-5661-2f63-2f73-b43980000000"^^xsd:string ; bioregistry.schema:0000006 "http://hawaii.eagle-i.net/i/$1"^^xsd:string ; @@ -20932,7 +21057,7 @@ bioregistry:eaglei a bioregistry.schema:0000001 ; bioregistry:easychair.cfp a bioregistry.schema:0000001 ; rdfs:label "EasyChair Call for Paper" ; dc:description "Conferences in EasyChair"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://easychair.org/cfp/"^^xsd:string ; bioregistry.schema:0000005 "SysBioCancer2022"^^xsd:string ; bioregistry.schema:0000006 "https://easychair.org/cfp/$1"^^xsd:string ; @@ -20941,7 +21066,7 @@ bioregistry:easychair.cfp a bioregistry.schema:0000001 ; bioregistry:easychair.topic a bioregistry.schema:0000001 ; rdfs:label "EasyChair Topic" ; dc:description "Call for paper topics in EasyChair"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://easychair.org/cfp/"^^xsd:string ; bioregistry.schema:0000005 "27106865"^^xsd:string ; bioregistry.schema:0000006 "https://easychair.org/cfp/topic.cgi?tid=$1"^^xsd:string ; @@ -20951,7 +21076,7 @@ bioregistry:easychair.topic a bioregistry.schema:0000001 ; bioregistry:ecolexicon a bioregistry.schema:0000001 ; rdfs:label "EcoLexicon" ; dc:description "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://ecolexicon.ugr.es/en/index.htm"^^xsd:string ; bioregistry.schema:0000005 "canal"^^xsd:string ; bioregistry.schema:0000012 false . @@ -20959,9 +21084,9 @@ bioregistry:ecolexicon a bioregistry.schema:0000001 ; bioregistry:ecyano.entity a bioregistry.schema:0000001 ; rdfs:label "E-cyanobacterium entity" ; dc:description "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ecyano ; - ns1:exactMatch biocontext:ECYANO.ENTITY, + ns2:exactMatch biocontext:ECYANO.ENTITY, n2t:ecyano.entity, miriam:ecyano.entity ; foaf:homepage "http://www.e-cyanobacterium.org/bcs/entity/"^^xsd:string ; @@ -20973,9 +21098,9 @@ bioregistry:ecyano.entity a bioregistry.schema:0000001 ; bioregistry:ecyano.experiment a bioregistry.schema:0000001 ; rdfs:label "E-cyanobacterium Experimental Data" ; dc:description "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ecyano ; - ns1:exactMatch miriam:ecyano.experiment ; + ns2:exactMatch miriam:ecyano.experiment ; foaf:homepage "https://www.e-cyanobacterium.org/experiments-repository/"^^xsd:string ; bioregistry.schema:0000005 "18"^^xsd:string ; bioregistry.schema:0000006 "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^xsd:string ; @@ -20985,9 +21110,9 @@ bioregistry:ecyano.experiment a bioregistry.schema:0000001 ; bioregistry:ecyano.rule a bioregistry.schema:0000001 ; rdfs:label "E-cyanobacterium rule" ; dc:description "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ecyano ; - ns1:exactMatch biocontext:ECYANO.RULE, + ns2:exactMatch biocontext:ECYANO.RULE, n2t:ecyano.rule, miriam:ecyano.rule ; foaf:homepage "http://www.e-cyanobacterium.org/bcs/rule/"^^xsd:string ; @@ -20999,8 +21124,8 @@ bioregistry:ecyano.rule a bioregistry.schema:0000001 ; bioregistry:ega.dataset a bioregistry.schema:0000001 ; rdfs:label "European Genome-phenome Archive Dataset" ; dc:description "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EGA.DATASET, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EGA.DATASET, n2t:ega.dataset, fairsharing:FAIRsharing.mya1ff, miriam:ega.dataset ; @@ -21013,8 +21138,8 @@ bioregistry:ega.dataset a bioregistry.schema:0000001 ; bioregistry:ega.study a bioregistry.schema:0000001 ; rdfs:label "European Genome-phenome Archive Study" ; dc:description "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:EGA.STUDY, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:EGA.STUDY, n2t:ega.study, miriam:ega.study ; foaf:homepage "https://www.ebi.ac.uk/ega/studies"^^xsd:string ; @@ -21026,8 +21151,8 @@ bioregistry:ega.study a bioregistry.schema:0000001 ; bioregistry:emdb a bioregistry.schema:0000001 ; rdfs:label "Electron Microscopy Data Bank" ; dc:description "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1146, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1146, biocontext:EMDB, n2t:emdb, fairsharing:FAIRsharing.651n9j, @@ -21041,7 +21166,7 @@ bioregistry:emdb a bioregistry.schema:0000001 ; bioregistry:emolecules a bioregistry.schema:0000001 ; rdfs:label "Reaxys eMolecules" ; dc:description "Catalog of purchasable reagents and building blocks"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://reaxys.emolecules.com"^^xsd:string ; bioregistry.schema:0000005 "491187"^^xsd:string ; bioregistry.schema:0000006 "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^xsd:string ; @@ -21051,8 +21176,8 @@ bioregistry:emolecules a bioregistry.schema:0000001 ; bioregistry:empiar a bioregistry.schema:0000001 ; rdfs:label "Electron Microscopy Public Image Archive" ; dc:description "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.dff3ef ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.dff3ef ; foaf:homepage "https://www.ebi.ac.uk/pdbe/emdb"^^xsd:string ; bioregistry.schema:0000005 "10595"^^xsd:string ; bioregistry.schema:0000006 "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^xsd:string ; @@ -21062,8 +21187,8 @@ bioregistry:empiar a bioregistry.schema:0000001 ; bioregistry:ena.embl a bioregistry.schema:0000001 ; rdfs:label "European Nucleotide Archive" ; dc:description "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:ENA.EMBL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:ENA.EMBL, go.resource:ENA, n2t:ena.embl, fairsharing:FAIRsharing.dj8nt8, @@ -21078,36 +21203,17 @@ bioregistry:ena.embl a bioregistry.schema:0000001 ; bioregistry:enzo a bioregistry.schema:0000001 ; rdfs:label "Enzo Life Sciences" ; dc:description "Enzo Life Sciences is an antibody vendor."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.enzolifesciences.com"^^xsd:string ; bioregistry.schema:0000005 "ALX-210-175"^^xsd:string ; bioregistry.schema:0000006 "https://www.enzolifesciences.com/$1"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:eo a bioregistry.schema:0000001 ; - rdfs:label "Plant Environment Ontology" ; - dc:description "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EO, - agroportal:EO, - obofoundry:EO, - biocontext:EO, - n2t:eo, - prefixcommons:eo, - miriam:eo ; - foaf:homepage "http://planteome.org/"^^xsd:string ; - bioregistry.schema:0000005 "0007404"^^xsd:string ; - bioregistry.schema:0000006 "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000018 bioregistry:foodon ; - bioregistry.schema:0000019 orcid:0000-0002-1005-8383 . - bioregistry:eol a bioregistry.schema:0000001 ; rdfs:label "Environment Ontology for Livestock" ; dc:description "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EOL, agroportal:EOL, bioportal:EOL, fairsharing:FAIRsharing.w7bw2y, @@ -21120,8 +21226,8 @@ bioregistry:eol a bioregistry.schema:0000001 ; bioregistry:eolife a bioregistry.schema:0000001 ; rdfs:label "Encyclopedia of Life" ; dc:description "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.3J6NYn, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.3J6NYn, wikidata:P830 ; foaf:homepage "https://eol.org"^^xsd:string ; bioregistry.schema:0000005 "1044544"^^xsd:string ; @@ -21132,16 +21238,16 @@ bioregistry:eolife a bioregistry.schema:0000001 ; bioregistry:epcc a bioregistry.schema:0000001 ; rdfs:label "European Paediatric Cardiac Codes" ; dc:description "Collection of European paediatric cardiac coding files"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.aepc.org/european-paediatric-cardiac-coding"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:epio a bioregistry.schema:0000001 ; rdfs:label "Epilepsy Ontology" ; dc:description "A application driven Epilepsy Ontology with official terms from the ILAE."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EPIO, - obofoundry:EPIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EPIO, + obofoundry:epio, ontobee:EPIO, bioportal:EPIO ; foaf:homepage "https://github.com/SCAI-BIO/EpilepsyOntology"^^xsd:string ; @@ -21155,9 +21261,9 @@ bioregistry:epio a bioregistry.schema:0000001 ; bioregistry:eupath a bioregistry.schema:0000001 ; rdfs:label "VEuPathDB ontology" ; dc:description "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EUPATH, - obofoundry:EUPATH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EUPATH, + obofoundry:eupath, ontobee:EUPATH, bioportal:EUPATH, biocontext:EUPATH, @@ -21173,14 +21279,14 @@ bioregistry:eupath a bioregistry.schema:0000001 ; bioregistry:evm a bioregistry.schema:0000001 ; rdfs:label "eVOC mouse development stage" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true . bioregistry:faldo a bioregistry.schema:0000001 ; rdfs:label "Feature Annotation Location Description Ontology " ; dc:description "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FALDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FALDO, agroportal:FALDO, bioportal:FALDO, biocontext:faldo, @@ -21193,10 +21299,10 @@ bioregistry:faldo a bioregistry.schema:0000001 ; bioregistry:fbbt a bioregistry.schema:0000001 ; rdfs:label "Drosophila gross anatomy" ; dc:description "An ontology of Drosophila melanogaster anatomy."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:flybase ; - ns1:exactMatch aberowl:FBBT, - obofoundry:FBbt, + ns2:exactMatch aberowl:FBBT, + obofoundry:fbbt, ontobee:FBBT, bioportal:FB-BT, biocontext:FBbt, @@ -21213,7 +21319,7 @@ bioregistry:fbbt a bioregistry.schema:0000001 ; bioregistry:fbql a bioregistry.schema:0000001 ; rdfs:label "FlyBase Qualifiers" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000005 "00005254"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 true . @@ -21221,10 +21327,10 @@ bioregistry:fbql a bioregistry.schema:0000001 ; bioregistry:fbsp a bioregistry.schema:0000001 ; rdfs:label "Fly taxonomy" ; dc:description "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:flybase ; - ns1:exactMatch aberowl:FB-SP, - obofoundry:FBSP, + ns2:exactMatch aberowl:FB-SP, + obofoundry:fbsp, bioportal:FB-SP, biocontext:FBSP ; foaf:homepage "http://www.flybase.org/"^^xsd:string ; @@ -21237,8 +21343,8 @@ bioregistry:fbsp a bioregistry.schema:0000001 ; bioregistry:fcsfree a bioregistry.schema:0000001 ; rdfs:label "Fetal Calf Serum-Free Database" ; dc:description "Cell line databases/resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:FCS-free ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:FCS-free ; foaf:homepage "https://fcs-free.org"^^xsd:string ; bioregistry.schema:0000005 "240-17-488-3-4-12"^^xsd:string ; bioregistry.schema:0000006 "https://fcs-free.org/fcs-database?$1"^^xsd:string ; @@ -21247,8 +21353,8 @@ bioregistry:fcsfree a bioregistry.schema:0000001 ; bioregistry:fivestars a bioregistry.schema:0000001 ; rdfs:label "Five Stars of Online Research Articles Ontology" ; dc:description "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.6dfe9b ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.6dfe9b ; foaf:homepage "http://www.sparontologies.net/ontologies/fivestars"^^xsd:string ; bioregistry.schema:0000005 "hasOpenAccessRating"^^xsd:string ; bioregistry.schema:0000012 false . @@ -21256,10 +21362,10 @@ bioregistry:fivestars a bioregistry.schema:0000001 ; bioregistry:fix a bioregistry.schema:0000001 ; rdfs:label "Physico-chemical methods and properties" ; dc:description "An ontology of physico-chemical methods and properties."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:chebi ; - ns1:exactMatch aberowl:FIX, - obofoundry:FIX, + ns2:exactMatch aberowl:FIX, + obofoundry:fix, ontobee:FIX, bioportal:FIX, biocontext:FIX, @@ -21276,7 +21382,7 @@ bioregistry:fix a bioregistry.schema:0000001 ; bioregistry:flybrain.ndb a bioregistry.schema:0000001 ; rdfs:label "FlyBrain Neuron Database" ; dc:description "A database of fly neurons and pathways with an associated 3D viewer."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://flybrain-ndb.virtualflybrain.org"^^xsd:string ; bioregistry.schema:0000005 "10531"^^xsd:string ; bioregistry.schema:0000006 "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^xsd:string ; @@ -21286,8 +21392,8 @@ bioregistry:flybrain.ndb a bioregistry.schema:0000001 ; bioregistry:foaf a bioregistry.schema:0000001 ; rdfs:label "Friend of a Friend" ; dc:description "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:foaf, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:foaf, bioportal:FOAF, biocontext:foaf, biolink:foaf ; @@ -21299,22 +21405,22 @@ bioregistry:foaf a bioregistry.schema:0000001 ; bioregistry:foodb.food a bioregistry.schema:0000001 ; rdfs:label "FooDB Food" ; dc:description "Foods in FooDB"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:foodb.food ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:foodb.food ; foaf:homepage "https://foodb.ca/foods"^^xsd:string ; bioregistry.schema:0000005 "FOOD00020"^^xsd:string ; bioregistry.schema:0000006 "https://foodb.ca/foods/$1"^^xsd:string ; bioregistry.schema:0000008 "^FOOD\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:fossilworks dcterms:hasPart bioregistry:fossilworks.journal, +bioregistry:fossilworks ns1:hasPart bioregistry:fossilworks.journal, bioregistry:fossilworks.taxon . bioregistry:fr a bioregistry.schema:0000001 ; rdfs:label "FAIR* Reviews Ontology" ; dc:description "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.e7e609 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.e7e609 ; foaf:homepage "http://www.sparontologies.net/ontologies/fr"^^xsd:string ; bioregistry.schema:0000005 "ReviewVersion"^^xsd:string ; bioregistry.schema:0000012 false . @@ -21322,8 +21428,8 @@ bioregistry:fr a bioregistry.schema:0000001 ; bioregistry:frbr a bioregistry.schema:0000001 ; rdfs:label "Functional Requirements for Bibliographic Records" ; dc:description "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.b34b43 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.b34b43 ; foaf:homepage "http://www.sparontologies.net/ontologies/frbr"^^xsd:string ; bioregistry.schema:0000005 "Expression"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/vocab/frbr/core#$1"^^xsd:string ; @@ -21332,7 +21438,7 @@ bioregistry:frbr a bioregistry.schema:0000001 ; bioregistry:ftt a bioregistry.schema:0000001 ; rdfs:label "Feature Type Thesaurus" ; dc:description "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^xsd:string ; bioregistry.schema:0000005 "273"^^xsd:string ; bioregistry.schema:0000006 "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^xsd:string ; @@ -21342,8 +21448,8 @@ bioregistry:ftt a bioregistry.schema:0000001 ; bioregistry:fungorum a bioregistry.schema:0000001 ; rdfs:label "Index Fungorum" ; dc:description "identifier for a fungus taxon in Index Fungorum"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ncbi.resource:Fungorum, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ncbi.resource:Fungorum, wikidata:P1391 ; foaf:homepage "http://www.indexfungorum.org"^^xsd:string ; bioregistry.schema:0000005 "154022"^^xsd:string ; @@ -21354,8 +21460,8 @@ bioregistry:fungorum a bioregistry.schema:0000001 ; bioregistry:fyeco a bioregistry.schema:0000001 ; rdfs:label "Fission Yeast Experimental Conditions Ontology" ; dc:description "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:FYECO ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:FYECO ; foaf:homepage "https://github.com/pombase/fypo"^^xsd:string ; bioregistry.schema:0000005 "0000003"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -21366,36 +21472,16 @@ bioregistry:fyeco a bioregistry.schema:0000001 ; bioregistry:fyler a bioregistry.schema:0000001 ; rdfs:label "Fyler" ; dc:description "A hierarchical classification of congenital heart disease "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906"^^xsd:string ; bioregistry.schema:0000005 "4447"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:gaz a bioregistry.schema:0000001 ; - rdfs:label "Gazetteer" ; - dc:description "A gazetteer constructed on ontological principles"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GAZ, - obofoundry:GAZ, - ontobee:GAZ, - bioportal:GAZ, - biocontext:GAZ, - fairsharing:FAIRsharing.wkdjpb, - ols:gaz, - wikidata:P6778 ; - foaf:homepage "http://environmentontology.github.io/gaz/"^^xsd:string ; - bioregistry.schema:0000005 "00620027"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/GAZ_$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{8}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000018 bioregistry:scdo ; - bioregistry.schema:0000019 orcid:0000-0001-8910-9851 . - bioregistry:gc a bioregistry.schema:0000001 ; rdfs:label "Genetic Code" ; dc:description "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"^^xsd:string ; bioregistry.schema:0000005 "11"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^xsd:string ; @@ -21405,8 +21491,8 @@ bioregistry:gc a bioregistry.schema:0000001 ; bioregistry:gemet a bioregistry.schema:0000001 ; rdfs:label "General Multilingual Environmental Thesaurus" ; dc:description "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch agroportal:GEMET ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch agroportal:GEMET ; foaf:homepage "https://www.eionet.europa.eu/gemet/en/themes/"^^xsd:string ; bioregistry.schema:0000005 "627"^^xsd:string ; bioregistry.schema:0000006 "https://www.eionet.europa.eu/gemet/en/concept/$1"^^xsd:string ; @@ -21416,8 +21502,8 @@ bioregistry:gemet a bioregistry.schema:0000001 ; bioregistry:genbank a bioregistry.schema:0000001 ; rdfs:label "GenBank" ; dc:description "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2292, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2292, biocontext:GenBank, go.resource:GenBank, fairsharing:FAIRsharing.9kahy4, @@ -21432,8 +21518,8 @@ bioregistry:genbank a bioregistry.schema:0000001 ; bioregistry:geo a bioregistry.schema:0000001 ; rdfs:label "NCBI Gene Expression Omnibus" ; dc:description "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GEO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GEO, edam.data:1147, biocontext:GEO, cellosaurus.resource:GEO, @@ -21451,8 +21537,8 @@ bioregistry:geo a bioregistry.schema:0000001 ; bioregistry:geonames a bioregistry.schema:0000001 ; rdfs:label "GeoNames" ; dc:description "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.56a0Uj ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.56a0Uj ; foaf:homepage "https://www.geonames.org"^^xsd:string ; bioregistry.schema:0000005 "3532759"^^xsd:string ; bioregistry.schema:0000006 "https://www.geonames.org/$1"^^xsd:string ; @@ -21462,7 +21548,7 @@ bioregistry:geonames a bioregistry.schema:0000001 ; bioregistry:geonames.feature a bioregistry.schema:0000001 ; rdfs:label "GeoNames Feature Code" ; dc:description "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.geonames.org/export/codes.html"^^xsd:string ; bioregistry.schema:0000005 "ADM1"^^xsd:string ; bioregistry.schema:0000006 "https://www.geonames.org/recent-changes/featurecode/$1/"^^xsd:string ; @@ -21471,7 +21557,7 @@ bioregistry:geonames.feature a bioregistry.schema:0000001 ; bioregistry:ghr a bioregistry.schema:0000001 ; rdfs:label "Genetics Home Reference" ; dc:description "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://medlineplus.gov/genetics/condition"^^xsd:string ; bioregistry.schema:0000005 "saddan"^^xsd:string ; bioregistry.schema:0000006 "https://medlineplus.gov/genetics/condition/$1"^^xsd:string ; @@ -21480,7 +21566,7 @@ bioregistry:ghr a bioregistry.schema:0000001 ; bioregistry:github.issue a bioregistry.schema:0000001 ; rdfs:label "GitHub Issue" ; dc:description "An issue in any public repository on GitHub."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/"^^xsd:string ; bioregistry.schema:0000005 "biopragmatics/bioregistry/424"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/resolve/github/issue/$1"^^xsd:string ; @@ -21489,7 +21575,7 @@ bioregistry:github.issue a bioregistry.schema:0000001 ; bioregistry:github.pull a bioregistry.schema:0000001 ; rdfs:label "GitHub Pull Request" ; dc:description "A pull request in any public repository on GitHub."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/"^^xsd:string ; bioregistry.schema:0000005 "biopragmatics/bioregistry/416"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/resolve/github/pull/$1"^^xsd:string ; @@ -21498,8 +21584,8 @@ bioregistry:github.pull a bioregistry.schema:0000001 ; bioregistry:glytoucan a bioregistry.schema:0000001 ; rdfs:label "GlyTouCan" ; dc:description "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GLYTOUCAN, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GLYTOUCAN, n2t:glytoucan, miriam:glytoucan ; foaf:homepage "https://glytoucan.org"^^xsd:string ; @@ -21511,7 +21597,7 @@ bioregistry:glytoucan a bioregistry.schema:0000001 ; bioregistry:go.resource a bioregistry.schema:0000001 ; rdfs:label "Gene Ontology Registry" ; dc:description "A database-specific registry supporting curation in the Gene Ontology"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://geneontology.org/"^^xsd:string ; bioregistry.schema:0000005 "CHEBI"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/go/$1"^^xsd:string ; @@ -21520,7 +21606,7 @@ bioregistry:go.resource a bioregistry.schema:0000001 ; bioregistry:goche a bioregistry.schema:0000001 ; rdfs:label "GO Chemicals" ; dc:description "Represent chemical entities having particular CHEBI roles"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/geneontology/go-ontology"^^xsd:string ; bioregistry.schema:0000005 "25512"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -21529,7 +21615,7 @@ bioregistry:goche a bioregistry.schema:0000001 ; bioregistry:goeco a bioregistry.schema:0000001 ; rdfs:label "GO Evidence Code" ; dc:description "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://geneontology.org/docs/guide-go-evidence-codes/"^^xsd:string ; bioregistry.schema:0000005 "IPI"^^xsd:string ; bioregistry.schema:0000012 false . @@ -21537,8 +21623,8 @@ bioregistry:goeco a bioregistry.schema:0000001 ; bioregistry:google.patent a bioregistry.schema:0000001 ; rdfs:label "Google Patents" ; dc:description "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:GOOGLE.PATENT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:GOOGLE.PATENT, cellosaurus.resource:Patent, n2t:google.patent, miriam:google.patent ; @@ -21551,7 +21637,7 @@ bioregistry:google.patent a bioregistry.schema:0000001 ; bioregistry:graingenes.reference a bioregistry.schema:0000001 ; rdfs:label "GrainGenes" ; dc:description "A database for Triticeae and Avena references."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://wheat.pw.usda.gov"^^xsd:string ; bioregistry.schema:0000005 "WGS-95-1333"^^xsd:string ; bioregistry.schema:0000006 "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^xsd:string ; @@ -21560,7 +21646,7 @@ bioregistry:graingenes.reference a bioregistry.schema:0000001 ; bioregistry:graingenes.symbol a bioregistry.schema:0000001 ; rdfs:label "GrainGenes" ; dc:description "A database for Triticeae and Avena gene symbols."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://wheat.pw.usda.gov"^^xsd:string ; bioregistry.schema:0000005 "1-FEH+w3"^^xsd:string ; bioregistry.schema:0000006 "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^xsd:string ; @@ -21569,7 +21655,7 @@ bioregistry:graingenes.symbol a bioregistry.schema:0000001 ; bioregistry:gramene.reference a bioregistry.schema:0000001 ; rdfs:label "Gramene Reference" ; dc:description "Literature references in Gramene"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.gramene.org"^^xsd:string ; bioregistry.schema:0000005 "6200"^^xsd:string ; bioregistry.schema:0000006 "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^xsd:string ; @@ -21579,8 +21665,8 @@ bioregistry:gramene.reference a bioregistry.schema:0000001 ; bioregistry:grassbase a bioregistry.schema:0000001 ; rdfs:label "GrassBase" ; dc:description "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P1832 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P1832 ; foaf:homepage "https://www.kew.org/data/grasses-syn/index.htm"^^xsd:string ; bioregistry.schema:0000005 "imp10873"^^xsd:string ; bioregistry.schema:0000006 "https://www.kew.org/data/grasses-db/www/$1"^^xsd:string ; @@ -21590,7 +21676,7 @@ bioregistry:grassbase a bioregistry.schema:0000001 ; bioregistry:gsfa a bioregistry.schema:0000001 ; rdfs:label "General Standard for Food Additives Online Database" ; dc:description "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.fao.org/gsfaonline"^^xsd:string ; bioregistry.schema:0000005 "174"^^xsd:string ; bioregistry.schema:0000006 "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^xsd:string ; @@ -21600,7 +21686,7 @@ bioregistry:gsfa a bioregistry.schema:0000001 ; bioregistry:gtr a bioregistry.schema:0000001 ; rdfs:label "Genetic Testing Registry" ; dc:description "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/gtr/"^^xsd:string ; bioregistry.schema:0000005 "AN0097748"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^xsd:string ; @@ -21610,8 +21696,8 @@ bioregistry:gtr a bioregistry.schema:0000001 ; bioregistry:hgnc.genegroup a bioregistry.schema:0000001 ; rdfs:label "HGNC Gene Group" ; dc:description "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:hgnc.genegroup ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:hgnc.genegroup ; foaf:homepage "https://www.genenames.org"^^xsd:string ; bioregistry.schema:0000005 "141"^^xsd:string ; bioregistry.schema:0000006 "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^xsd:string ; @@ -21621,8 +21707,8 @@ bioregistry:hgnc.genegroup a bioregistry.schema:0000001 ; bioregistry:hgnc.symbol a bioregistry.schema:0000001 ; rdfs:label "HGNC Symbol" ; dc:description "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:HGNC.SYMBOL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:HGNC.SYMBOL, n2t:hgnc.symbol, miriam:hgnc.symbol ; foaf:homepage "https://www.genenames.org/"^^xsd:string ; @@ -21634,8 +21720,8 @@ bioregistry:hgnc.symbol a bioregistry.schema:0000001 ; bioregistry:hmdb a bioregistry.schema:0000001 ; rdfs:label "Human Metabolome Database" ; dc:description "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2622, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2622, biocontext:HMDB, n2t:hmdb, fairsharing:FAIRsharing.sye5js, @@ -21652,7 +21738,7 @@ bioregistry:hmdb a bioregistry.schema:0000001 ; bioregistry:hms.lincs.compound a bioregistry.schema:0000001 ; rdfs:label "HMS LINCS Compound" ; dc:description "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://lincs.hms.harvard.edu/db/sm/"^^xsd:string ; bioregistry.schema:0000005 "10001-101"^^xsd:string ; bioregistry.schema:0000006 "https://lincs.hms.harvard.edu/db/sm/$1"^^xsd:string ; @@ -21661,7 +21747,7 @@ bioregistry:hms.lincs.compound a bioregistry.schema:0000001 ; bioregistry:hog a bioregistry.schema:0000001 ; rdfs:label "Homologous Organ Groups" ; dc:description "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships"^^xsd:string ; bioregistry.schema:0000005 "0000255"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -21670,8 +21756,8 @@ bioregistry:hog a bioregistry.schema:0000001 ; bioregistry:icd10 a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases, 10th Revision" ; dc:description "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICD10, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICD10, edam.data:2611, bioportal:ICD10, biocontext:ICD, @@ -21690,8 +21776,8 @@ bioregistry:icd10 a bioregistry.schema:0000001 ; bioregistry:icd10cm a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases, 10th Revision, Clinical Modification" ; dc:description "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICD10CM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICD10CM, bioportal:ICD10CM, fairsharing:FAIRsharing.hpvbxb, wikidata:P4229 ; @@ -21705,8 +21791,8 @@ bioregistry:icd10pcs a bioregistry.schema:0000001 ; dc:description """ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. ICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICD10PCS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICD10PCS, bioportal:ICD10PCS, fairsharing:FAIRsharing.85k1jm, wikidata:P1690 ; @@ -21718,8 +21804,8 @@ ICD-10-PCS will be the official system of assigning codes to procedures associat bioregistry:icd11 a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases, 11th Revision" ; dc:description "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.97805c, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.97805c, wikidata:P7807 ; foaf:homepage "https://icd.who.int/"^^xsd:string ; bioregistry.schema:0000005 "RA01.0"^^xsd:string ; @@ -21729,8 +21815,8 @@ bioregistry:icd11 a bioregistry.schema:0000001 ; bioregistry:icd9 a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases, 9th Revision" ; dc:description "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:ICD9, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:ICD9, wikidata:P493 ; foaf:homepage "https://www.cdc.gov/nchs/icd/icd9.htm"^^xsd:string ; bioregistry.schema:0000005 "277.9"^^xsd:string ; @@ -21740,8 +21826,8 @@ bioregistry:icd9 a bioregistry.schema:0000001 ; bioregistry:icd9cm a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases, 9th Revision, Clinical Modification" ; dc:description "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICD9CM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICD9CM, bioportal:ICD9CM, fairsharing:FAIRsharing.10zsxb, wikidata:P1692 ; @@ -21754,8 +21840,8 @@ bioregistry:icd9cm a bioregistry.schema:0000001 ; bioregistry:icdo a bioregistry.schema:0000001 ; rdfs:label "International Classification of Diseases for Oncology" ; dc:description "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICDO, prefixcommons:icdo, wikidata:P563 ; foaf:homepage "https://www.who.int/classifications/icd/adaptations/oncology/en/"^^xsd:string ; @@ -21767,7 +21853,7 @@ bioregistry:icdo a bioregistry.schema:0000001 ; bioregistry:icepo a bioregistry.schema:0000001 ; rdfs:label "Ion Channel Electrophysiology Ontology" ; dc:description "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://download.nextprot.org/pub/current_release/controlled_vocabularies/"^^xsd:string ; bioregistry.schema:0000005 "0000002"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -21776,9 +21862,9 @@ bioregistry:icepo a bioregistry.schema:0000001 ; bioregistry:ico a bioregistry.schema:0000001 ; rdfs:label "Informed Consent Ontology" ; dc:description "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ICO, - obofoundry:ICO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ICO, + obofoundry:ico, ontobee:ICO, bioportal:ICO, biocontext:ICO, @@ -21795,9 +21881,9 @@ bioregistry:ico a bioregistry.schema:0000001 ; bioregistry:ido a bioregistry.schema:0000001 ; rdfs:label "Infectious Disease Ontology" ; dc:description "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:IDO, - obofoundry:IDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:IDO, + obofoundry:ido, ontobee:IDO, bioportal:IDO, biocontext:IDO, @@ -21813,30 +21899,11 @@ bioregistry:ido a bioregistry.schema:0000001 ; bioregistry.schema:0000018 bioregistry:scdo ; bioregistry.schema:0000019 orcid:0000-0003-1617-8244 . -bioregistry:idomal a bioregistry.schema:0000001 ; - rdfs:label "Malaria Ontology" ; - dc:description "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:IDOMAL, - obofoundry:IDOMAL, - ontobee:IDOMAL, - bioportal:IDOMAL, - biocontext:IDOMAL, - fairsharing:FAIRsharing.2q8c28, - ols:idomal ; - foaf:homepage "https://www.vectorbase.org/ontology-browser"^^xsd:string ; - bioregistry.schema:0000005 "0002350"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/IDOMAL_$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000018 bioregistry:scdo ; - bioregistry.schema:0000019 [ rdfs:label "Pantelis Topalis" ] . - bioregistry:idot a bioregistry.schema:0000001 ; rdfs:label "Identifiers.org Terms" ; dc:description "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:idot, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:idot, n2t:idot, miriam:idot ; foaf:homepage "http://biomodels.net/vocab/idot.rdf"^^xsd:string ; @@ -21848,7 +21915,7 @@ bioregistry:idot a bioregistry.schema:0000001 ; bioregistry:idpo a bioregistry.schema:0000001 ; rdfs:label "Intrinsically Disordered Proteins Ontology" ; dc:description "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.disprot.org/ontology"^^xsd:string ; bioregistry.schema:0000005 "00056"^^xsd:string ; bioregistry.schema:0000006 "https://www.disprot.org/idpo/IDPO:$1"^^xsd:string ; @@ -21859,8 +21926,8 @@ bioregistry:idpo a bioregistry.schema:0000001 ; bioregistry:idr a bioregistry.schema:0000001 ; rdfs:label "Image Data Resource" ; dc:description "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.6wf1zw, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.6wf1zw, miriam:idr ; foaf:homepage "https://idr.openmicroscopy.org"^^xsd:string ; bioregistry.schema:0000005 "0001"^^xsd:string ; @@ -21871,7 +21938,7 @@ bioregistry:idr a bioregistry.schema:0000001 ; bioregistry:illumina.probe a bioregistry.schema:0000001 ; rdfs:label "Illumina Probe Identifier" ; dc:description "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt"^^xsd:string ; bioregistry.schema:0000005 "ILMN_129894"^^xsd:string ; bioregistry.schema:0000008 "^ILMN_\\d+$"^^xsd:string ; @@ -21880,15 +21947,15 @@ bioregistry:illumina.probe a bioregistry.schema:0000001 ; bioregistry:imdrf a bioregistry.schema:0000001 ; rdfs:label "International Medical Device Regulators Forum" ; dc:description "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.imdrf.org/"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:inaturalist.taxon a bioregistry.schema:0000001 ; rdfs:label "iNaturalist Taxonomy" ; dc:description "Identifier for a species in iNaturalist"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P3151 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P3151 ; foaf:homepage "https://www.inaturalist.org/taxa"^^xsd:string ; bioregistry.schema:0000005 "21723"^^xsd:string ; bioregistry.schema:0000006 "https://www.inaturalist.org/taxa/$1"^^xsd:string ; @@ -21898,16 +21965,16 @@ bioregistry:inaturalist.taxon a bioregistry.schema:0000001 ; bioregistry:inhand a bioregistry.schema:0000001 ; rdfs:label "The International Harmonization of Nomenclature and Diagnostic criteria" ; dc:description "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.9gqfpm ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.9gqfpm ; foaf:homepage "https://www.goreni.org/gr3_nomenclature.php"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:insdc a bioregistry.schema:0000001 ; rdfs:label "Nucleotide Sequence Database" ; dc:description "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INSDC, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INSDC, n2t:insdc, prefixcommons:insdc, miriam:insdc ; @@ -21920,7 +21987,7 @@ bioregistry:insdc a bioregistry.schema:0000001 ; bioregistry:insdc.run a bioregistry.schema:0000001 ; rdfs:label "International Nucleotide Sequence Database Collaboration (INSDC) Run" ; dc:description "An experimental run, served thrugh the ENA"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.insdc.org/"^^xsd:string ; bioregistry.schema:0000005 "ERR436051"^^xsd:string ; bioregistry.schema:0000006 "https://www.ebi.ac.uk/ena/browser/view/$1"^^xsd:string ; @@ -21932,8 +21999,8 @@ bioregistry:insdc.run a bioregistry.schema:0000001 ; bioregistry:insdc.sra a bioregistry.schema:0000001 ; rdfs:label "Sequence Read Archive" ; dc:description "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:INSDC.SRA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:INSDC.SRA, n2t:insdc.sra, fairsharing:FAIRsharing.g7t2hv, miriam:insdc.sra ; @@ -21945,7 +22012,7 @@ bioregistry:insdc.sra a bioregistry.schema:0000001 ; bioregistry:iro a bioregistry.schema:0000001 ; rdfs:label "Insect Resistance Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000005 "0000008"^^xsd:string ; bioregistry.schema:0000006 "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -21954,8 +22021,8 @@ bioregistry:iro a bioregistry.schema:0000001 ; bioregistry:jcrb a bioregistry.schema:0000001 ; rdfs:label "JRBC Cell Bank" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:JCRB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:JCRB ; foaf:homepage "https://cellbank.nibiohn.go.jp"^^xsd:string ; bioregistry.schema:0000005 "JCRB1355"^^xsd:string ; bioregistry.schema:0000006 "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^xsd:string ; @@ -21964,8 +22031,8 @@ bioregistry:jcrb a bioregistry.schema:0000001 ; bioregistry:kclb a bioregistry.schema:0000001 ; rdfs:label "Korean Cell Line Bank" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:KCLB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:KCLB ; foaf:homepage "https://cellbank.snu.ac.kr/english"^^xsd:string ; bioregistry.schema:0000005 "10020.2"^^xsd:string ; bioregistry.schema:0000006 "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^xsd:string ; @@ -21974,9 +22041,9 @@ bioregistry:kclb a bioregistry.schema:0000001 ; bioregistry:kegg.disease a bioregistry.schema:0000001 ; rdfs:label "KEGG Disease" ; dc:description "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.DISEASE, + ns2:exactMatch biocontext:KEGG.DISEASE, n2t:kegg.disease, prefixcommons:kegg.disease, miriam:kegg.disease ; @@ -21989,9 +22056,9 @@ bioregistry:kegg.disease a bioregistry.schema:0000001 ; bioregistry:kegg.environ a bioregistry.schema:0000001 ; rdfs:label "KEGG Environ" ; dc:description "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.ENVIRON, + ns2:exactMatch biocontext:KEGG.ENVIRON, n2t:kegg.environ, miriam:kegg.environ ; foaf:homepage "http://www.genome.jp/kegg/drug/environ.html"^^xsd:string ; @@ -22003,9 +22070,9 @@ bioregistry:kegg.environ a bioregistry.schema:0000001 ; bioregistry:kegg.enzyme a bioregistry.schema:0000001 ; rdfs:label "KEGG Enzyme" ; dc:description "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biolink:KEGG.ENZYME, + ns2:exactMatch biolink:KEGG.ENZYME, go.resource:KEGG_ENZYME ; foaf:homepage "http://www.genome.jp/dbget-bin/www_bfind?enzyme"^^xsd:string ; bioregistry.schema:0000006 "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^xsd:string ; @@ -22015,9 +22082,9 @@ bioregistry:kegg.enzyme a bioregistry.schema:0000001 ; bioregistry:kegg.genes a bioregistry.schema:0000001 ; rdfs:label "KEGG Genes" ; dc:description "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.GENES, + ns2:exactMatch biocontext:KEGG.GENES, biolink:KEGG.GENE, n2t:kegg.genes, miriam:kegg.genes, @@ -22031,9 +22098,9 @@ bioregistry:kegg.genes a bioregistry.schema:0000001 ; bioregistry:kegg.genome a bioregistry.schema:0000001 ; rdfs:label "KEGG Genome" ; dc:description "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.GENOME, + ns2:exactMatch biocontext:KEGG.GENOME, n2t:kegg.genome, prefixcommons:kegg.genome, miriam:kegg.genome, @@ -22046,9 +22113,9 @@ bioregistry:kegg.genome a bioregistry.schema:0000001 ; bioregistry:kegg.ligand a bioregistry.schema:0000001 ; rdfs:label "KEGG LIGAND" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch go.resource:KEGG_LIGAND ; + ns2:exactMatch go.resource:KEGG_LIGAND ; foaf:homepage "http://www.genome.ad.jp/kegg/docs/upd_ligand.html"^^xsd:string ; bioregistry.schema:0000006 "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^xsd:string ; bioregistry.schema:0000012 true . @@ -22056,9 +22123,9 @@ bioregistry:kegg.ligand a bioregistry.schema:0000001 ; bioregistry:kegg.metagenome a bioregistry.schema:0000001 ; rdfs:label "KEGG Metagenome" ; dc:description "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.METAGENOME, + ns2:exactMatch biocontext:KEGG.METAGENOME, n2t:kegg.metagenome, prefixcommons:kegg.metagenome, miriam:kegg.metagenome ; @@ -22071,9 +22138,9 @@ bioregistry:kegg.metagenome a bioregistry.schema:0000001 ; bioregistry:kegg.module a bioregistry.schema:0000001 ; rdfs:label "KEGG Module" ; dc:description "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.MODULE, + ns2:exactMatch biocontext:KEGG.MODULE, n2t:kegg.module, miriam:kegg.module ; foaf:homepage "http://www.kegg.jp/kegg/module.html"^^xsd:string ; @@ -22085,9 +22152,9 @@ bioregistry:kegg.module a bioregistry.schema:0000001 ; bioregistry:kegg.orthology a bioregistry.schema:0000001 ; rdfs:label "KEGG Orthology" ; dc:description "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biocontext:KEGG.ORTHOLOGY, + ns2:exactMatch biocontext:KEGG.ORTHOLOGY, n2t:kegg.orthology, prefixcommons:kegg.orthology, miriam:kegg.orthology ; @@ -22100,9 +22167,9 @@ bioregistry:kegg.orthology a bioregistry.schema:0000001 ; bioregistry:kegg.pathway a bioregistry.schema:0000001 ; rdfs:label "KEGG Pathways Database" ; dc:description "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch edam.data:2343, + ns2:exactMatch edam.data:2343, biocontext:KEGG.PATHWAY, biolink:KEGG.PATHWAY, go.resource:KEGG_PATHWAY, @@ -22119,9 +22186,9 @@ bioregistry:kegg.pathway a bioregistry.schema:0000001 ; bioregistry:kegg.reaction a bioregistry.schema:0000001 ; rdfs:label "KEGG Reaction" ; dc:description "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch edam.data:2608, + ns2:exactMatch edam.data:2608, biocontext:KEGG.REACTION, go.resource:KEGG_REACTION, n2t:kegg.reaction, @@ -22138,8 +22205,8 @@ bioregistry:knapsack a bioregistry.schema:0000001 ; rdfs:label "KNApSAcK" ; dc:description """KNApSAcK provides information on metabolites and the taxonomic class with which they are associated."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:KNAPSACK, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:KNAPSACK, n2t:knapsack, miriam:knapsack, wikidata:P2064 ; @@ -22151,7 +22218,7 @@ taxonomic class with which they are associated."""^^xsd:string ; bioregistry:kupo a bioregistry.schema:0000001 ; rdfs:label "Kidney and Urinary Pathway Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.kupkb.org/"^^xsd:string ; bioregistry.schema:0000005 "0001009"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -22161,8 +22228,8 @@ bioregistry:kupo a bioregistry.schema:0000001 ; bioregistry:lincs.smallmolecule a bioregistry.schema:0000001 ; rdfs:label "LINCS Small Molecule" ; dc:description "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:LINCS.SMALLMOLECULE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:LINCS.SMALLMOLECULE, n2t:lincs.smallmolecule, miriam:lincs.smallmolecule ; foaf:homepage "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^xsd:string ; @@ -22174,8 +22241,8 @@ bioregistry:lincs.smallmolecule a bioregistry.schema:0000001 ; bioregistry:lipidmaps a bioregistry.schema:0000001 ; rdfs:label "LIPID MAPS" ; dc:description "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2625, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2625, biocontext:LIPIDMAPS, n2t:lipidmaps, fairsharing:FAIRsharing.cpneh8, @@ -22192,8 +22259,8 @@ bioregistry:lipidmaps a bioregistry.schema:0000001 ; bioregistry:lncipedia a bioregistry.schema:0000001 ; rdfs:label "LNCipedia" ; dc:description "A comprehensive compendium of human long non-coding RNAs"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.84c1a7 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.84c1a7 ; foaf:homepage "https://lncipedia.org"^^xsd:string ; bioregistry.schema:0000005 "SNHG3"^^xsd:string ; bioregistry.schema:0000012 false . @@ -22201,8 +22268,8 @@ bioregistry:lncipedia a bioregistry.schema:0000001 ; bioregistry:lonza a bioregistry.schema:0000001 ; rdfs:label "Lonza" ; dc:description "Contains information about cells and data sheets related to transfection."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Lonza ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Lonza ; foaf:homepage "https://knowledge.lonza.com"^^xsd:string ; bioregistry.schema:0000005 "968"^^xsd:string ; bioregistry.schema:0000006 "https://knowledge.lonza.com/cell?id=$1"^^xsd:string ; @@ -22212,7 +22279,7 @@ bioregistry:lonza a bioregistry.schema:0000001 ; bioregistry:lotus a bioregistry.schema:0000001 ; rdfs:label "LOTUS Initiative for Open Natural Products Research" ; dc:description "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://lotus.naturalproducts.net"^^xsd:string ; bioregistry.schema:0000005 "LTS0004651"^^xsd:string ; bioregistry.schema:0000006 "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^xsd:string ; @@ -22224,8 +22291,8 @@ bioregistry:lotus a bioregistry.schema:0000001 ; bioregistry:lpt a bioregistry.schema:0000001 ; rdfs:label "Livestock Product Trait Ontology" ; dc:description "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LPT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LPT, agroportal:LPT, bioportal:LPT, biocontext:LPT, @@ -22240,7 +22307,7 @@ bioregistry:lpt a bioregistry.schema:0000001 ; bioregistry:lspci a bioregistry.schema:0000001 ; rdfs:label "Laboratory of Systems Pharmacology Compound" ; dc:description "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://labsyspharm.github.io/lspci/"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; bioregistry.schema:0000006 "https://labsyspharm.github.io/lspci/$1"^^xsd:string ; @@ -22250,7 +22317,7 @@ bioregistry:lspci a bioregistry.schema:0000001 ; bioregistry:lter a bioregistry.schema:0000001 ; rdfs:label "Long Term Ecological Research Controlled Vocabulary" ; dc:description "Ecological terms"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://vocab.lternet.edu/vocab/vocab/index.php"^^xsd:string ; bioregistry.schema:0000005 "182"^^xsd:string ; bioregistry.schema:0000006 "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^xsd:string ; @@ -22260,8 +22327,8 @@ bioregistry:lter a bioregistry.schema:0000001 ; bioregistry:massive a bioregistry.schema:0000001 ; rdfs:label "MassIVE" ; dc:description "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:MASSIVE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:MASSIVE, n2t:massive, fairsharing:FAIRsharing.LYsiMd, miriam:massive, @@ -22275,8 +22342,8 @@ bioregistry:massive a bioregistry.schema:0000001 ; bioregistry:matrixdb a bioregistry.schema:0000001 ; rdfs:label "MatrixDB" ; dc:description "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.91yrz6, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.91yrz6, prefixcommons:matrixdb ; foaf:homepage "http://matrixdb.univ-lyon1.fr/"^^xsd:string ; bioregistry.schema:0000005 "MULT_4_VAR1_bovine"^^xsd:string ; @@ -22284,15 +22351,15 @@ bioregistry:matrixdb a bioregistry.schema:0000001 ; bioregistry.schema:0000012 false ; bioregistry.schema:0000018 bioregistry:complexportal . -bioregistry:merops dcterms:hasPart bioregistry:merops.clan, +bioregistry:merops ns1:hasPart bioregistry:merops.clan, bioregistry:merops.family . bioregistry:merops.family a bioregistry.schema:0000001 ; rdfs:label "MEROPS Family" ; dc:description "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:merops ; - ns1:exactMatch biocontext:MEROPS.FAMILY, + ns2:exactMatch biocontext:MEROPS.FAMILY, n2t:merops.family, miriam:merops.family ; foaf:homepage "http://merops.sanger.ac.uk/index.htm"^^xsd:string ; @@ -22304,8 +22371,8 @@ bioregistry:merops.family a bioregistry.schema:0000001 ; bioregistry:metacyc.compound a bioregistry.schema:0000001 ; rdfs:label "Metabolic Encyclopedia of metabolic and other pathways" ; dc:description "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:METACYC.COMPOUND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:METACYC.COMPOUND, biolink:MetaCyc, go.resource:MetaCyc, n2t:metacyc.compound, @@ -22320,9 +22387,9 @@ bioregistry:metacyc.compound a bioregistry.schema:0000001 ; bioregistry:mfmo a bioregistry.schema:0000001 ; rdfs:label "Mammalian Feeding Muscle Ontology" ; dc:description "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MFMO, - obofoundry:MFMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MFMO, + obofoundry:mfmo, ontobee:MFMO, bioportal:MFMO, biocontext:MFMO, @@ -22339,7 +22406,7 @@ bioregistry:mfmo a bioregistry.schema:0000001 ; bioregistry:mgnify.analysis a bioregistry.schema:0000001 ; rdfs:label "MGnify Analysis" ; dc:description "Analyses of microbiome data within MGnify"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ebi.ac.uk/metagenomics/"^^xsd:string ; bioregistry.schema:0000005 "MGYA00002270"^^xsd:string ; bioregistry.schema:0000006 "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^xsd:string ; @@ -22348,15 +22415,15 @@ bioregistry:mgnify.analysis a bioregistry.schema:0000001 ; bioregistry:miaa a bioregistry.schema:0000001 ; rdfs:label "Minimal Information About Anatomy ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true . bioregistry:micro a bioregistry.schema:0000001 ; rdfs:label "Ontology of Prokaryotic Phenotypic and Metabolic Characters" ; dc:description "An ontology of prokaryotic phenotypic and metabolic characters"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MICRO, - obofoundry:MICRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MICRO, + obofoundry:micro, ontobee:MicrO, biocontext:MICRO, fairsharing:FAIRsharing.brhpb0, @@ -22372,7 +22439,7 @@ bioregistry:micro a bioregistry.schema:0000001 ; bioregistry:mirbase.family a bioregistry.schema:0000001 ; rdfs:label "miRBase Families" ; dc:description "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.mirbase.org/"^^xsd:string ; bioregistry.schema:0000005 "MIPF0000002"^^xsd:string ; bioregistry.schema:0000006 "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^xsd:string ; @@ -22381,7 +22448,7 @@ bioregistry:mirbase.family a bioregistry.schema:0000001 ; bioregistry:mirte a bioregistry.schema:0000001 ; rdfs:label "miRNA Target Prediction at EMBL" ; dc:description "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.russelllab.org/miRNAs/"^^xsd:string ; bioregistry.schema:0000005 "miR-1"^^xsd:string ; bioregistry.schema:0000012 false . @@ -22389,7 +22456,7 @@ bioregistry:mirte a bioregistry.schema:0000001 ; bioregistry:mmsl a bioregistry.schema:0000001 ; rdfs:label "Multum MediSource Lexicon" ; dc:description "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html"^^xsd:string ; bioregistry.schema:0000005 "3355"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -22398,9 +22465,9 @@ bioregistry:mmsl a bioregistry.schema:0000001 ; bioregistry:multicellds.cell_line a bioregistry.schema:0000001 ; rdfs:label "MultiCellDS Digital Cell Line" ; dc:description "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:multicellds ; - ns1:exactMatch biocontext:MULTICELLDS.CELL_LINE, + ns2:exactMatch biocontext:MULTICELLDS.CELL_LINE, n2t:multicellds.cell_line, miriam:multicellds.cell_line ; foaf:homepage "http://multicellds.org/MultiCellDB.php"^^xsd:string ; @@ -22412,9 +22479,9 @@ bioregistry:multicellds.cell_line a bioregistry.schema:0000001 ; bioregistry:multicellds.collection a bioregistry.schema:0000001 ; rdfs:label "MultiCellDS collection" ; dc:description "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:multicellds ; - ns1:exactMatch biocontext:MULTICELLDS.COLLECTION, + ns2:exactMatch biocontext:MULTICELLDS.COLLECTION, n2t:multicellds.collection, miriam:multicellds.collection ; foaf:homepage "http://multicellds.org/MultiCellDB.php"^^xsd:string ; @@ -22426,9 +22493,9 @@ bioregistry:multicellds.collection a bioregistry.schema:0000001 ; bioregistry:multicellds.snapshot a bioregistry.schema:0000001 ; rdfs:label "MultiCellDS Digital snapshot" ; dc:description "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:multicellds ; - ns1:exactMatch biocontext:MULTICELLDS.SNAPSHOT, + ns2:exactMatch biocontext:MULTICELLDS.SNAPSHOT, n2t:multicellds.snapshot, miriam:multicellds.snapshot ; foaf:homepage "http://multicellds.org/MultiCellDB.php"^^xsd:string ; @@ -22440,7 +22507,7 @@ bioregistry:multicellds.snapshot a bioregistry.schema:0000001 ; bioregistry:n2t a bioregistry.schema:0000001 ; rdfs:label "Name-to-Thing" ; dc:description "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://n2t.net"^^xsd:string ; bioregistry.schema:0000005 "chebi"^^xsd:string ; bioregistry.schema:0000006 "https://n2t.net/$1:"^^xsd:string ; @@ -22449,7 +22516,7 @@ bioregistry:n2t a bioregistry.schema:0000001 ; bioregistry:namerxn a bioregistry.schema:0000001 ; rdfs:label "NameRXN" ; dc:description "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.nextmovesoftware.com/namerxn.html"^^xsd:string ; bioregistry.schema:0000005 "4.2.78"^^xsd:string ; bioregistry.schema:0000012 false . @@ -22457,8 +22524,8 @@ bioregistry:namerxn a bioregistry.schema:0000001 ; bioregistry:ncats.bioplanet a bioregistry.schema:0000001 ; rdfs:label "National Center for Advancing Translation Sciences BioPlanet" ; dc:description "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:ncats.bioplanet ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:ncats.bioplanet ; foaf:homepage "https://tripod.nih.gov/bioplanet/"^^xsd:string ; bioregistry.schema:0000005 "3"^^xsd:string ; bioregistry.schema:0000006 "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^xsd:string ; @@ -22475,8 +22542,8 @@ bioregistry:ncats.drug a bioregistry.schema:0000001 ; - Marketed Drugs - Investigational Drugs - Other Substances"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:ncats.drug ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:ncats.drug ; foaf:homepage "https://drugs.ncats.io/"^^xsd:string ; bioregistry.schema:0000005 "44259"^^xsd:string ; bioregistry.schema:0000006 "https://drugs.ncats.io/drug/$1"^^xsd:string ; @@ -22485,8 +22552,8 @@ bioregistry:ncats.drug a bioregistry.schema:0000001 ; bioregistry:ncbi.genome a bioregistry.schema:0000001 ; rdfs:label "NCBI Genome" ; dc:description "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2787, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2787, biocontext:NCBIGenome ; foaf:homepage "https://www.ncbi.nlm.nih.gov/genome"^^xsd:string ; bioregistry.schema:0000005 "51"^^xsd:string ; @@ -22497,7 +22564,7 @@ bioregistry:ncbi.genome a bioregistry.schema:0000001 ; bioregistry:ncbi.resource a bioregistry.schema:0000001 ; rdfs:label "NCBI Registry" ; dc:description "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"^^xsd:string ; bioregistry.schema:0000005 "ECOCYC"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/ncbi/$1"^^xsd:string ; @@ -22506,7 +22573,7 @@ bioregistry:ncbi.resource a bioregistry.schema:0000001 ; bioregistry:ncbibook a bioregistry.schema:0000001 ; rdfs:label "NCBI Bookshelf" ; dc:description "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ncbi.nlm.nih.gov/books"^^xsd:string ; bioregistry.schema:0000005 "NBK331"^^xsd:string ; bioregistry.schema:0000006 "https://www.ncbi.nlm.nih.gov/books/$1"^^xsd:string ; @@ -22516,8 +22583,8 @@ bioregistry:ncbibook a bioregistry.schema:0000001 ; bioregistry:ndex a bioregistry.schema:0000001 ; rdfs:label "Network Data Exchange" ; dc:description "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.8nq9t6 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.8nq9t6 ; foaf:homepage "https://www.ndexbio.org"^^xsd:string ; bioregistry.schema:0000005 "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^xsd:string ; bioregistry.schema:0000006 "https://www.ndexbio.org/viewer/networks/$1"^^xsd:string ; @@ -22526,9 +22593,9 @@ bioregistry:ndex a bioregistry.schema:0000001 ; bioregistry:neurolex a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Neurolex" ; dc:description "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch biocontext:NEUROLEX, + ns2:exactMatch biocontext:NEUROLEX, n2t:neurolex, prefixcommons:neurolex, miriam:neurolex ; @@ -22543,7 +22610,7 @@ bioregistry:nextprot.family a bioregistry.schema:0000001 ; rdfs:label "neXtProt family" ; dc:description """NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. (Developed by the SIB Swiss Institute of Bioinformatics)"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.nextprot.org/"^^xsd:string ; bioregistry.schema:0000005 "01406"^^xsd:string ; bioregistry.schema:0000006 "https://www.nextprot.org/term/FA-$1"^^xsd:string ; @@ -22553,10 +22620,10 @@ bioregistry:nextprot.family a bioregistry.schema:0000001 ; bioregistry:nif.cell a bioregistry.schema:0000001 ; rdfs:label "NIF Cell" ; dc:description "Neuronal cell types"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch aberowl:NIFCELL, - obofoundry:NIF_CELL, + ns2:exactMatch aberowl:NIFCELL, + obofoundry:nif_cell, bioportal:NIFCELL, biocontext:NIF_CELL ; foaf:homepage "http://neuinfo.org/"^^xsd:string ; @@ -22566,9 +22633,9 @@ bioregistry:nif.cell a bioregistry.schema:0000001 ; bioregistry:nif.dysfunction a bioregistry.schema:0000001 ; rdfs:label "NIF Dysfunction" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch obofoundry:NIF_DYSFUNCTION, + ns2:exactMatch obofoundry:nif_dysfunction, biocontext:NIF_DYSFUNCTION ; foaf:homepage "http://neuinfo.org/"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^xsd:string ; @@ -22577,9 +22644,9 @@ bioregistry:nif.dysfunction a bioregistry.schema:0000001 ; bioregistry:nif.grossanatomy a bioregistry.schema:0000001 ; rdfs:label "NIF Gross Anatomy" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch obofoundry:NIF_GROSSANATOMY, + ns2:exactMatch obofoundry:nif_grossanatomy, biocontext:NIF_GROSSANATOMY ; foaf:homepage "http://neuinfo.org/"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^xsd:string ; @@ -22589,7 +22656,7 @@ bioregistry:nif.grossanatomy a bioregistry.schema:0000001 ; bioregistry:nihreporter.project a bioregistry.schema:0000001 ; rdfs:label "NIH RePORTER" ; dc:description "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://reporter.nih.gov/"^^xsd:string ; bioregistry.schema:0000005 "10343835"^^xsd:string ; bioregistry.schema:0000006 "https://reporter.nih.gov/project-details/$1"^^xsd:string ; @@ -22600,15 +22667,15 @@ bioregistry:nihreporter.project a bioregistry.schema:0000001 ; bioregistry:nist a bioregistry.schema:0000001 ; rdfs:label "NIST Chemistry WebBook" ; dc:description "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://webbook.nist.gov/chemistry/"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:nmdc a bioregistry.schema:0000001 ; rdfs:label "National Microbiome Data Collaborative" ; dc:description "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:nmdc ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:nmdc ; foaf:homepage "https://microbiomedata.org/"^^xsd:string ; bioregistry.schema:0000005 "y3ax-8bq3-60"^^xsd:string ; bioregistry.schema:0000006 "https://drs.microbiomedata.org/objects/$1"^^xsd:string ; @@ -22620,8 +22687,8 @@ bioregistry:nmdc a bioregistry.schema:0000001 ; bioregistry:noaa a bioregistry.schema:0000001 ; rdfs:label "NOAA Fisheries Species Directory" ; dc:description "Identifier for a species on the noaa fisheries website"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P6049 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P6049 ; foaf:homepage "https://www.fisheries.noaa.gov/species-directory"^^xsd:string ; bioregistry.schema:0000005 "long-finned-pilot-whale"^^xsd:string ; bioregistry.schema:0000006 "https://www.fisheries.noaa.gov/species/$1"^^xsd:string ; @@ -22632,7 +22699,7 @@ bioregistry:noaa a bioregistry.schema:0000001 ; bioregistry:novus a bioregistry.schema:0000001 ; rdfs:label "Novus Biologicals" ; dc:description "A vendor of antibodies and other biologics"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.novusbio.com"^^xsd:string ; bioregistry.schema:0000005 "nb100-56351"^^xsd:string ; bioregistry.schema:0000006 "https://www.novusbio.com/products/$1"^^xsd:string ; @@ -22642,7 +22709,7 @@ bioregistry:npass a bioregistry.schema:0000001 ; rdfs:label "Natural Product Activity and Species Source Database" ; dc:description """Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. """^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://bidd.group/NPASS/"^^xsd:string ; bioregistry.schema:0000005 "NPC139585"^^xsd:string ; bioregistry.schema:0000008 "^NPC\\d+$"^^xsd:string ; @@ -22651,8 +22718,8 @@ bioregistry:npass a bioregistry.schema:0000001 ; bioregistry:oa a bioregistry.schema:0000001 ; rdfs:label "Web Annotation Ontology" ; dc:description "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OA, bioportal:OA, biocontext:oa ; foaf:homepage "http://www.w3.org/ns/oa"^^xsd:string ; @@ -22663,9 +22730,9 @@ bioregistry:oa a bioregistry.schema:0000001 ; bioregistry:oba a bioregistry.schema:0000001 ; rdfs:label "Ontology of Biological Attributes" ; dc:description "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OBA, - obofoundry:OBA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OBA, + obofoundry:oba, ontobee:OBA, bioportal:OBA, biocontext:OBA, @@ -22682,8 +22749,8 @@ bioregistry:oba a bioregistry.schema:0000001 ; bioregistry:oboinowl a bioregistry.schema:0000001 ; rdfs:label "OBO in OWL" ; dc:description "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:oboInOwl, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:oboInOwl, biolink:oboformat ; foaf:homepage "https://github.com/geneontology/go-ontology/tree/master/contrib"^^xsd:string ; bioregistry.schema:0000005 "hasDbXref"^^xsd:string ; @@ -22693,9 +22760,9 @@ bioregistry:oboinowl a bioregistry.schema:0000001 ; bioregistry:ohd a bioregistry.schema:0000001 ; rdfs:label "Oral Health and Disease Ontology" ; dc:description "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OHD, - obofoundry:OHD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OHD, + obofoundry:ohd, ontobee:OHD, bioportal:OHD, biocontext:OHD, @@ -22708,30 +22775,12 @@ bioregistry:ohd a bioregistry.schema:0000001 ; bioregistry.schema:0000012 false ; bioregistry.schema:0000019 orcid:0000-0001-9625-1899 . -bioregistry:omiabis a bioregistry.schema:0000001 ; - rdfs:label "Ontologized MIABIS" ; - dc:description "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMIABIS, - obofoundry:OMIABIS, - ontobee:OMIABIS, - bioportal:OMIABIS, - biocontext:OMIABIS, - ols:omiabis ; - foaf:homepage "https://github.com/OMIABIS/omiabis-dev"^^xsd:string ; - bioregistry.schema:0000005 "0001079"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/OMIABIS_$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000018 bioregistry:labo ; - bioregistry.schema:0000019 orcid:0000-0003-1834-3856 . - bioregistry:omim a bioregistry.schema:0000001 ; rdfs:label "Online Mendelian Inheritance in Man" ; dc:description "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^xsd:string ; - dcterms:hasPart bioregistry:omim.ps ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMIM, + ns1:hasPart bioregistry:omim.ps ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMIM, edam.data:1153, bioportal:OMIM, biocontext:OMIM, @@ -22753,9 +22802,9 @@ bioregistry:omim a bioregistry.schema:0000001 ; bioregistry:omit a bioregistry.schema:0000001 ; rdfs:label "Ontology for MicroRNA Target" ; dc:description "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMIT, - obofoundry:OMIT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMIT, + obofoundry:omit, ontobee:OMIT, bioportal:OMIT, biocontext:OMIT, @@ -22774,9 +22823,9 @@ bioregistry:omit a bioregistry.schema:0000001 ; bioregistry:omo a bioregistry.schema:0000001 ; rdfs:label "OBO Metadata Ontology" ; dc:description "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMO, - obofoundry:OMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMO, + obofoundry:omo, ontobee:OMO, bioportal:OMO, ols:omo ; @@ -22789,16 +22838,16 @@ bioregistry:omo a bioregistry.schema:0000001 ; bioregistry:omop a bioregistry.schema:0000001 ; rdfs:label "Observational Medical Outcomes Partnership" ; dc:description "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.ohdsi.org/data-standardization/the-common-data-model/"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:omp a bioregistry.schema:0000001 ; rdfs:label "Ontology of Microbial Phenotypes" ; dc:description "An ontology of phenotypes covering microbes"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMP, - obofoundry:OMP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMP, + obofoundry:omp, ontobee:OMP, bioportal:OMP, biocontext:OMP, @@ -22815,9 +22864,9 @@ bioregistry:omp a bioregistry.schema:0000001 ; bioregistry:omrse a bioregistry.schema:0000001 ; rdfs:label "Ontology of Medically Related Social Entities" ; dc:description "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OMRSE, - obofoundry:OMRSE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OMRSE, + obofoundry:omrse, ontobee:OMRSE, bioportal:OMRSE, biocontext:OMRSE, @@ -22834,7 +22883,7 @@ bioregistry:omrse a bioregistry.schema:0000001 ; bioregistry:oncotree a bioregistry.schema:0000001 ; rdfs:label "OncoTree" ; dc:description "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://oncotree.mskcc.org"^^xsd:string ; bioregistry.schema:0000005 "BLL"^^xsd:string ; bioregistry.schema:0000006 "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^xsd:string ; @@ -22844,7 +22893,7 @@ bioregistry:oncotree a bioregistry.schema:0000001 ; bioregistry:openalex a bioregistry.schema:0000001 ; rdfs:label "OpenAlex" ; dc:description "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://openalex.org/"^^xsd:string ; bioregistry.schema:0000005 "W2741809807"^^xsd:string ; bioregistry.schema:0000006 "https://openalex.org/$1"^^xsd:string ; @@ -22856,8 +22905,8 @@ bioregistry:openalex a bioregistry.schema:0000001 ; bioregistry:otol a bioregistry.schema:0000001 ; rdfs:label "Open Tree of Life" ; dc:description "Identifier for an entity in open tree of life"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P9157 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P9157 ; foaf:homepage "https://tree.opentreeoflife.org"^^xsd:string ; bioregistry.schema:0000005 "3905431"^^xsd:string ; bioregistry.schema:0000006 "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^xsd:string ; @@ -22868,8 +22917,8 @@ bioregistry:otol a bioregistry.schema:0000001 ; bioregistry:owl a bioregistry.schema:0000001 ; rdfs:label "Web Ontology Language" ; dc:description "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:owl, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:owl, fairsharing:FAIRsharing.atygwy ; foaf:homepage "https://www.w3.org/TR/owl-features/"^^xsd:string ; bioregistry.schema:0000005 "Ontology"^^xsd:string ; @@ -22879,8 +22928,8 @@ bioregistry:owl a bioregistry.schema:0000001 ; bioregistry:panorama a bioregistry.schema:0000001 ; rdfs:label "Panorama Public" ; dc:description "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.uBpQ1q ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.uBpQ1q ; foaf:homepage "https://panoramaweb.org"^^xsd:string ; bioregistry.schema:0000005 "FxnI151FMs"^^xsd:string ; bioregistry.schema:0000006 "https://panoramaweb.org/$1.url"^^xsd:string ; @@ -22889,9 +22938,9 @@ bioregistry:panorama a bioregistry.schema:0000001 ; bioregistry:panther.family a bioregistry.schema:0000001 ; rdfs:label "Protein ANalysis THrough Evolutionary Relationships Classification System" ; dc:description "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:panther ; - ns1:exactMatch biocontext:PANTHER.FAMILY, + ns2:exactMatch biocontext:PANTHER.FAMILY, biolink:PANTHER.FAMILY, go.resource:PANTHER, n2t:panther.family, @@ -22905,9 +22954,9 @@ bioregistry:panther.family a bioregistry.schema:0000001 ; bioregistry:panther.node a bioregistry.schema:0000001 ; rdfs:label "PANTHER Node" ; dc:description "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:panther ; - ns1:exactMatch biocontext:PANTHER.NODE, + ns2:exactMatch biocontext:PANTHER.NODE, n2t:panther.node, miriam:panther.node ; foaf:homepage "http://pantree.org/"^^xsd:string ; @@ -22919,9 +22968,9 @@ bioregistry:panther.node a bioregistry.schema:0000001 ; bioregistry:panther.pathway a bioregistry.schema:0000001 ; rdfs:label "PANTHER Pathway" ; dc:description "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:panther ; - ns1:exactMatch edam.data:1161, + ns2:exactMatch edam.data:1161, biocontext:PANTHER.PATHWAY, n2t:panther.pathway, miriam:panther.pathway ; @@ -22935,9 +22984,9 @@ bioregistry:panther.pthcmp a bioregistry.schema:0000001 ; rdfs:label "PANTHER Pathway Component" ; dc:description """The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:panther ; - ns1:exactMatch biocontext:PANTHER.PTHCMP, + ns2:exactMatch biocontext:PANTHER.PTHCMP, n2t:panther.pthcmp, miriam:panther.pthcmp ; foaf:homepage "http://www.pantherdb.org/"^^xsd:string ; @@ -22949,8 +22998,8 @@ components may be proteins, genes/DNA, RNA, or simple molecules. Where the ident bioregistry:pathbank a bioregistry.schema:0000001 ; rdfs:label "PathBank" ; dc:description "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.3xwMon ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.3xwMon ; foaf:homepage "https://pathbank.org"^^xsd:string ; bioregistry.schema:0000005 "SMP0000219"^^xsd:string ; bioregistry.schema:0000006 "https://pathbank.org/view/$1"^^xsd:string ; @@ -22960,8 +23009,8 @@ bioregistry:pathbank a bioregistry.schema:0000001 ; bioregistry:pav a bioregistry.schema:0000001 ; rdfs:label "Provenance, Authoring, and Versioning Vocabulary" ; dc:description "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PAV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PAV, bioportal:PAV, biocontext:pav, biolink:pav, @@ -22976,8 +23025,8 @@ bioregistry:pav a bioregistry.schema:0000001 ; bioregistry:pdb-ccd a bioregistry.schema:0000001 ; rdfs:label "Chemical Component Dictionary" ; dc:description "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PDB-CCD, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PDB-CCD, n2t:pdb-ccd, miriam:pdb-ccd ; foaf:homepage "https://www.ebi.ac.uk/pdbe-srv/pdbechem/"^^xsd:string ; @@ -22990,8 +23039,8 @@ bioregistry:pdb-ccd a bioregistry.schema:0000001 ; bioregistry:pdb.ligand a bioregistry.schema:0000001 ; rdfs:label "Protein Data Bank Ligand" ; dc:description "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:PDB.LIGAND, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:PDB.LIGAND, n2t:pdb.ligand, prefixcommons:pdbligand, miriam:pdb.ligand, @@ -23005,7 +23054,7 @@ bioregistry:pdb.ligand a bioregistry.schema:0000001 ; bioregistry:pdc.study a bioregistry.schema:0000001 ; rdfs:label "Proteomic Data Commons" ; dc:description "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://pdc.cancer.gov/pdc"^^xsd:string ; bioregistry.schema:0000005 "PDC000351"^^xsd:string ; bioregistry.schema:0000006 "https://pdc.cancer.gov/pdc/study/$1"^^xsd:string ; @@ -23016,9 +23065,9 @@ bioregistry:pdc.study a bioregistry.schema:0000001 ; bioregistry:ped a bioregistry.schema:0000001 ; rdfs:label "Protein Ensemble Database" ; dc:description "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^xsd:string ; - dcterms:hasPart bioregistry:ped.ensemble ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.31385c, + ns1:hasPart bioregistry:ped.ensemble ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.31385c, miriam:ped ; foaf:homepage "https://proteinensemble.org/"^^xsd:string ; bioregistry.schema:0000005 "PED00037"^^xsd:string ; @@ -23029,9 +23078,9 @@ bioregistry:ped a bioregistry.schema:0000001 ; bioregistry:ped.ensemble a bioregistry.schema:0000001 ; rdfs:label "Protein Ensemble Database ensemble" ; dc:description "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:ped ; - ns1:exactMatch miriam:ped.ensemble ; + ns2:exactMatch miriam:ped.ensemble ; foaf:homepage "https://proteinensemble.org/"^^xsd:string ; bioregistry.schema:0000005 "PED00017e001"^^xsd:string ; bioregistry.schema:0000006 "https://proteinensemble.org/$1"^^xsd:string ; @@ -23040,7 +23089,7 @@ bioregistry:ped.ensemble a bioregistry.schema:0000001 ; bioregistry:peff a bioregistry.schema:0000001 ; rdfs:label "PSI Extended File Format" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.psidev.info/peff"^^xsd:string ; bioregistry.schema:0000005 "0001011"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -23049,8 +23098,8 @@ bioregistry:peff a bioregistry.schema:0000001 ; bioregistry:peptideatlas.dataset a bioregistry.schema:0000001 ; rdfs:label "PeptideAtlas Dataset" ; dc:description "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch n2t:peptideatlas.dataset, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch n2t:peptideatlas.dataset, miriam:peptideatlas.dataset ; foaf:homepage "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^xsd:string ; bioregistry.schema:0000005 "PASS01237"^^xsd:string ; @@ -23061,8 +23110,8 @@ bioregistry:peptideatlas.dataset a bioregistry.schema:0000001 ; bioregistry:pfam.clan a bioregistry.schema:0000001 ; rdfs:label "Pfam Clans" ; dc:description "Higher order grouping of Pfam families"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2758 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2758 ; foaf:homepage "https://pfam.xfam.org"^^xsd:string ; bioregistry.schema:0000005 "CL0192"^^xsd:string ; bioregistry.schema:0000006 "https://pfam.xfam.org/clan/$1"^^xsd:string ; @@ -23072,8 +23121,8 @@ bioregistry:pfam.clan a bioregistry.schema:0000001 ; bioregistry:pfr a bioregistry.schema:0000001 ; rdfs:label "Proteoform Atlas" ; dc:description "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.wqsxtg ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.wqsxtg ; foaf:homepage "http://repository.topdownproteomics.org/proteoforms"^^xsd:string ; bioregistry.schema:0000005 "1001"^^xsd:string ; bioregistry.schema:0000006 "http://repository.topdownproteomics.org/proteoforms/$1"^^xsd:string ; @@ -23083,7 +23132,7 @@ bioregistry:pfr a bioregistry.schema:0000001 ; bioregistry:pharmacodb.dataset a bioregistry.schema:0000001 ; rdfs:label "PharmacoDB Datasets" ; dc:description "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://pharmacodb.ca/datasets"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; bioregistry.schema:0000006 "https://pharmacodb.ca/datasets/$1"^^xsd:string ; @@ -23093,7 +23142,7 @@ bioregistry:pharmacodb.dataset a bioregistry.schema:0000001 ; bioregistry:pharmacodb.tissue a bioregistry.schema:0000001 ; rdfs:label "PharmacoDB Tissues" ; dc:description "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://pharmacodb.ca/tissues"^^xsd:string ; bioregistry.schema:0000005 "13"^^xsd:string ; bioregistry.schema:0000006 "https://pharmacodb.ca/tissues/$1"^^xsd:string ; @@ -23103,9 +23152,9 @@ bioregistry:pharmacodb.tissue a bioregistry.schema:0000001 ; bioregistry:phipo a bioregistry.schema:0000001 ; rdfs:label "Pathogen Host Interaction Phenotype Ontology" ; dc:description "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PHIPO, - obofoundry:PHIPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PHIPO, + obofoundry:phipo, ontobee:PHIPO, bioportal:PHIPO, ols:phipo ; @@ -23120,7 +23169,7 @@ bioregistry:phipo a bioregistry.schema:0000001 ; bioregistry:phosphosite.sitegroup a bioregistry.schema:0000001 ; rdfs:label "PhosphoSite Site Group" ; dc:description "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.phosphosite.org"^^xsd:string ; bioregistry.schema:0000005 "447860"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -23129,7 +23178,7 @@ bioregistry:phosphosite.sitegroup a bioregistry.schema:0000001 ; bioregistry:pictar a bioregistry.schema:0000001 ; rdfs:label "PicTar" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://pictar.mdc-berlin.de/"^^xsd:string ; bioregistry.schema:0000005 "hsa-let-7a"^^xsd:string ; bioregistry.schema:0000012 true . @@ -23137,9 +23186,9 @@ bioregistry:pictar a bioregistry.schema:0000001 ; bioregistry:pigqtldb a bioregistry.schema:0000001 ; rdfs:label "Animal Genome Pig QTL" ; dc:description "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:qtldb ; - ns1:exactMatch biocontext:PIGQTLDB, + ns2:exactMatch biocontext:PIGQTLDB, n2t:pigqtldb, prefixcommons:pigqtldb, miriam:pigqtldb ; @@ -23152,8 +23201,8 @@ bioregistry:pigqtldb a bioregistry.schema:0000001 ; bioregistry:ppdb a bioregistry.schema:0000001 ; rdfs:label "Pesticide Properties DataBase" ; dc:description "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.7k8zh0 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.7k8zh0 ; foaf:homepage "https://sitem.herts.ac.uk/aeru/ppdb/"^^xsd:string ; bioregistry.schema:0000005 "1484"^^xsd:string ; bioregistry.schema:0000006 "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^xsd:string ; @@ -23163,7 +23212,7 @@ bioregistry:ppdb a bioregistry.schema:0000001 ; bioregistry:ppr a bioregistry.schema:0000001 ; rdfs:label "Europe PMC Preprints" ; dc:description "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://europepmc.org"^^xsd:string ; bioregistry.schema:0000005 "ppr103739"^^xsd:string ; bioregistry.schema:0000006 "https://europepmc.org/article/ppr/$1"^^xsd:string ; @@ -23172,7 +23221,7 @@ bioregistry:ppr a bioregistry.schema:0000001 ; bioregistry:prefixcommons a bioregistry.schema:0000001 ; rdfs:label "Prefix Commons" ; dc:description "A registry of life science prefxes"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://prefixcommons.org"^^xsd:string ; bioregistry.schema:0000005 "ChEBI"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/prefixcommons/$1"^^xsd:string ; @@ -23181,8 +23230,8 @@ bioregistry:prefixcommons a bioregistry.schema:0000001 ; bioregistry:pride a bioregistry.schema:0000001 ; rdfs:label "PRIDE Controlled Vocabulary" ; dc:description "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PRIDE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PRIDE, biocontext:PRIDE, cellosaurus.resource:PRIDE, n2t:pride, @@ -23200,8 +23249,8 @@ bioregistry:pride a bioregistry.schema:0000001 ; bioregistry:prov a bioregistry.schema:0000001 ; rdfs:label "PROV Namespace" ; dc:description "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PROV, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PROV, biocontext:prov, biolink:prov, ols:prov ; @@ -23213,16 +23262,16 @@ bioregistry:prov a bioregistry.schema:0000001 ; bioregistry:pspub a bioregistry.schema:0000001 ; rdfs:label "Phenoscape Publication" ; dc:description "Documentation of the Phenoscape Curation Workflow"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://wiki.phenoscape.org/wiki/Curation_workflow"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:pubchem.bioassay a bioregistry.schema:0000001 ; rdfs:label "NCBI PubChem database of bioassay records" ; dc:description "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; - ns1:exactMatch edam.data:2638, + ns2:exactMatch edam.data:2638, biocontext:PUBCHEM.BIOASSAY, go.resource:PubChem_BioAssay, n2t:pubchem.bioassay, @@ -23237,9 +23286,9 @@ bioregistry:pubchem.bioassay a bioregistry.schema:0000001 ; bioregistry:pubchem.compound a bioregistry.schema:0000001 ; rdfs:label "PubChem CID" ; dc:description "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; - ns1:exactMatch edam.data:2639, + ns2:exactMatch edam.data:2639, biocontext:PUBCHEM.COMPOUND, biolink:CID, cellosaurus.resource:PubChem, @@ -23259,9 +23308,9 @@ bioregistry:pubchem.compound a bioregistry.schema:0000001 ; bioregistry:pubchem.substance a bioregistry.schema:0000001 ; rdfs:label "PubChem Substance ID (SID)" ; dc:description "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; - ns1:exactMatch biocontext:PUBCHEM.SUBSTANCE, + ns2:exactMatch biocontext:PUBCHEM.SUBSTANCE, go.resource:PubChem_Substance, n2t:pubchem.substance, prefixcommons:pubchem.substance, @@ -23277,8 +23326,8 @@ bioregistry:pubchem.substance a bioregistry.schema:0000001 ; bioregistry:rcb a bioregistry.schema:0000001 ; rdfs:label "RIKEN Bioresource Center Cell Bank" ; dc:description "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:RCB ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:RCB ; foaf:homepage "https://cell.brc.riken.jp/en/rcb"^^xsd:string ; bioregistry.schema:0000005 "RCB0002"^^xsd:string ; bioregistry.schema:0000006 "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^xsd:string ; @@ -23288,8 +23337,8 @@ bioregistry:rcb a bioregistry.schema:0000001 ; bioregistry:rdf a bioregistry.schema:0000001 ; rdfs:label "Resource Description Framework" ; dc:description "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:rdf, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:rdf, fairsharing:FAIRsharing.p77ph9 ; foaf:homepage "http://www.w3.org/1999/02/22-rdf-syntax-ns"^^xsd:string ; bioregistry.schema:0000005 "RDF"^^xsd:string ; @@ -23299,8 +23348,8 @@ bioregistry:rdf a bioregistry.schema:0000001 ; bioregistry:rdfs a bioregistry.schema:0000001 ; rdfs:label "RDF Schema" ; dc:description "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RDFS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RDFS, bioportal:RDFS, biocontext:rdfs, fairsharing:FAIRsharing.v9n3gk ; @@ -23312,7 +23361,7 @@ bioregistry:rdfs a bioregistry.schema:0000001 ; bioregistry:receptome.family a bioregistry.schema:0000001 ; rdfs:label "Human Plasma Membrane Receptome Families" ; dc:description "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.receptome.org"^^xsd:string ; bioregistry.schema:0000005 "5.1"^^xsd:string ; bioregistry.schema:0000006 "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^xsd:string ; @@ -23321,8 +23370,8 @@ bioregistry:receptome.family a bioregistry.schema:0000001 ; bioregistry:reo a bioregistry.schema:0000001 ; rdfs:label "Reagent Ontology" ; dc:description "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch ontobee:REO ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch ontobee:REO ; foaf:homepage "https://github.com/tis-lab/reagent-ontology"^^xsd:string ; bioregistry.schema:0000005 "0000079"^^xsd:string ; bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; @@ -23332,9 +23381,9 @@ bioregistry:reo a bioregistry.schema:0000001 ; bioregistry:resid a bioregistry.schema:0000001 ; rdfs:label "Protein covalent bond" ; dc:description "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2619, - obofoundry:RESID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2619, + obofoundry:resid, biocontext:RESID, go.resource:RESID, n2t:resid, @@ -23350,10 +23399,10 @@ bioregistry:resid a bioregistry.schema:0000001 ; bioregistry:rex a bioregistry.schema:0000001 ; rdfs:label "Physico-chemical process" ; dc:description "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:chebi ; - ns1:exactMatch aberowl:REX, - obofoundry:REX, + ns2:exactMatch aberowl:REX, + obofoundry:rex, ontobee:REX, bioportal:REX, biocontext:REX, @@ -23369,7 +23418,7 @@ bioregistry:rex a bioregistry.schema:0000001 ; bioregistry:rnamod a bioregistry.schema:0000001 ; rdfs:label "The RNA Modification Database" ; dc:description "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://rna.rega.kuleuven.be/rnamods/"^^xsd:string ; bioregistry.schema:0000005 "051"^^xsd:string ; bioregistry.schema:0000006 "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^xsd:string ; @@ -23378,13 +23427,13 @@ bioregistry:rnamod a bioregistry.schema:0000001 ; bioregistry:sael a bioregistry.schema:0000001 ; rdfs:label "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true . bioregistry:salk a bioregistry.schema:0000001 ; rdfs:label "Salk Institute for Biological Studies" ; dc:description "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.salk.edu/"^^xsd:string ; bioregistry.schema:0000005 "037727"^^xsd:string ; bioregistry.schema:0000006 "https://abrc.osu.edu/stocks/number/SALK_$1"^^xsd:string ; @@ -23395,7 +23444,7 @@ bioregistry:salk a bioregistry.schema:0000001 ; bioregistry:schem a bioregistry.schema:0000001 ; rdfs:label "Selventa Chemicals" ; dc:description "Selventa legacy chemical namespace used with the Biological Expression Language"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt"^^xsd:string ; bioregistry.schema:0000005 "A0001"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/providers/schem/$1"^^xsd:string ; @@ -23405,8 +23454,8 @@ bioregistry:schem a bioregistry.schema:0000001 ; bioregistry:schema a bioregistry.schema:0000001 ; rdfs:label "Schema.org" ; dc:description "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SCHEMA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SCHEMA, bioportal:SCHEMA, biolink:schema ; foaf:homepage "https://schema.org"^^xsd:string ; @@ -23417,7 +23466,7 @@ bioregistry:schema a bioregistry.schema:0000001 ; bioregistry:scholia.resource a bioregistry.schema:0000001 ; rdfs:label "Scholia Registry" ; dc:description "A frontend to Wikidata"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://scholia.toolforge.org/"^^xsd:string ; bioregistry.schema:0000005 "doi"^^xsd:string ; bioregistry.schema:0000006 "https://bioregistry.io/metaregistry/scholia/$1"^^xsd:string ; @@ -23426,7 +23475,7 @@ bioregistry:scholia.resource a bioregistry.schema:0000001 ; bioregistry:scomp a bioregistry.schema:0000001 ; rdfs:label "Selventa Complexes" ; dc:description "Selventa legacy complex namespace used with the Biological Expression Language"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^xsd:string ; bioregistry.schema:0000005 "C0001"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/providers/scomp/$1"^^xsd:string ; @@ -23436,7 +23485,7 @@ bioregistry:scomp a bioregistry.schema:0000001 ; bioregistry:scr a bioregistry.schema:0000001 ; rdfs:label "SciCrunch Registry" ; dc:description "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://scicrunch.org/browse/resourcedashboard"^^xsd:string ; bioregistry.schema:0000005 "003070"^^xsd:string ; bioregistry.schema:0000006 "http://scicrunch.org/resolver/SCR_$1"^^xsd:string ; @@ -23446,7 +23495,7 @@ bioregistry:scr a bioregistry.schema:0000001 ; bioregistry:sdis a bioregistry.schema:0000001 ; rdfs:label "Selventa Diseases" ; dc:description "Selventa legacy disease namespace used with the Biological Expression Language"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt"^^xsd:string ; bioregistry.schema:0000005 "D0001"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/providers/sdis/$1"^^xsd:string ; @@ -23456,7 +23505,7 @@ bioregistry:sdis a bioregistry.schema:0000001 ; bioregistry:sfam a bioregistry.schema:0000001 ; rdfs:label "Selventa Families" ; dc:description "Selventa legacy protein family namespace used with the Biological Expression Language"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt"^^xsd:string ; bioregistry.schema:0000005 "F0001"^^xsd:string ; bioregistry.schema:0000006 "https://biopragmatics.github.io/providers/sfam/$1"^^xsd:string ; @@ -23466,9 +23515,9 @@ bioregistry:sfam a bioregistry.schema:0000001 ; bioregistry:sheepqtldb a bioregistry.schema:0000001 ; rdfs:label "Animal Genome Sheep QTL" ; dc:description "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:qtldb ; - ns1:exactMatch biocontext:SHEEPQTLDB, + ns2:exactMatch biocontext:SHEEPQTLDB, n2t:sheepqtldb, prefixcommons:sheepqtldb, miriam:sheepqtldb ; @@ -23481,7 +23530,7 @@ bioregistry:sheepqtldb a bioregistry.schema:0000001 ; bioregistry:sigmaaldrich a bioregistry.schema:0000001 ; rdfs:label "Sigma Aldrich" ; dc:description "Sigma Aldrich is a life sciences supply vendor."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.sigmaaldrich.com"^^xsd:string ; bioregistry.schema:0000005 "HPA000698"^^xsd:string ; bioregistry.schema:0000006 "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^xsd:string ; @@ -23490,9 +23539,9 @@ bioregistry:sigmaaldrich a bioregistry.schema:0000001 ; bioregistry:signor a bioregistry.schema:0000001 ; rdfs:label "Signaling Network Open Resource" ; dc:description "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^xsd:string ; - dcterms:hasPart bioregistry:signor.relation ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.ss78t4, + ns1:hasPart bioregistry:signor.relation ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.ss78t4, miriam:signor, uniprot.resource:SIGNOR ; foaf:homepage "https://signor.uniroma2.it/"^^xsd:string ; @@ -23504,8 +23553,8 @@ bioregistry:signor a bioregistry.schema:0000001 ; bioregistry:skos a bioregistry.schema:0000001 ; rdfs:label "Simple Knowledge Organization System" ; dc:description "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:skos, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:skos, biocontext:skos ; foaf:homepage "https://www.w3.org/2004/02/skos/"^^xsd:string ; bioregistry.schema:0000005 "prefLabel"^^xsd:string ; @@ -23515,8 +23564,8 @@ bioregistry:skos a bioregistry.schema:0000001 ; bioregistry:snap a bioregistry.schema:0000001 ; rdfs:label "Snapshot" ; dc:description "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch prefixcommons:snap ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch prefixcommons:snap ; foaf:homepage "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^xsd:string ; bioregistry.schema:0000005 "Quality"^^xsd:string ; bioregistry.schema:0000006 "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^xsd:string ; @@ -23527,7 +23576,7 @@ bioregistry:snornabase a bioregistry.schema:0000001 ; dc:description """A comprehensive database of human H/ACA and C/D box snoRNAs."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www-snorna.biotoul.fr/"^^xsd:string ; bioregistry.schema:0000005 "SR0000178"^^xsd:string ; bioregistry.schema:0000012 false . @@ -23535,10 +23584,10 @@ human H/ACA and C/D box snoRNAs."""^^xsd:string ; bioregistry:so a bioregistry.schema:0000001 ; rdfs:label "Sequence types and features ontology" ; dc:description "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SO, agroportal:SO, - obofoundry:SO, + obofoundry:so, ontobee:SO, bioportal:SO, biocontext:SO, @@ -23559,15 +23608,15 @@ bioregistry:so a bioregistry.schema:0000001 ; bioregistry:span a bioregistry.schema:0000001 ; rdfs:label "Span" ; dc:description "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:sprint a bioregistry.schema:0000001 ; rdfs:label "Search PRINTS-S" ; dc:description "SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch prefixcommons:sprint ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch prefixcommons:sprint ; foaf:homepage "http://130.88.97.239/dbbrowser/sprint/"^^xsd:string ; bioregistry.schema:0000005 "PR00001"^^xsd:string ; bioregistry.schema:0000006 "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"^^xsd:string ; @@ -23577,8 +23626,8 @@ bioregistry:sprint a bioregistry.schema:0000001 ; bioregistry:ssbd.dataset a bioregistry.schema:0000001 ; rdfs:label "System Science of Biological Dynamics dataset" ; dc:description "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.we2r5a ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.we2r5a ; foaf:homepage "https://ssbd.riken.jp"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; bioregistry.schema:0000006 "https://ssbd.riken.jp/database/dataset/$1"^^xsd:string ; @@ -23588,9 +23637,9 @@ bioregistry:ssbd.dataset a bioregistry.schema:0000001 ; bioregistry:symp a bioregistry.schema:0000001 ; rdfs:label "Symptom Ontology" ; dc:description "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SYMP, - obofoundry:SYMP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SYMP, + obofoundry:symp, ontobee:SYMP, bioportal:SYMP, biocontext:SYMP, @@ -23607,12 +23656,12 @@ bioregistry:symp a bioregistry.schema:0000001 ; bioregistry:syoid a bioregistry.schema:0000001 ; rdfs:label "Gemina Symptom Ontology" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true . bioregistry:tgn a bioregistry.schema:0000001 ; rdfs:label "Getty Thesaurus of Geographic Names" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.getty.edu/research/tools/vocabularies/tgn/"^^xsd:string ; bioregistry.schema:0000005 "1023371"^^xsd:string ; bioregistry.schema:0000006 "http://vocab.getty.edu/page/tgn/$1"^^xsd:string ; @@ -23622,7 +23671,7 @@ bioregistry:tgn a bioregistry.schema:0000001 ; bioregistry:th a bioregistry.schema:0000001 ; rdfs:label "Terminologia Histologica" ; dc:description "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://ifaa.unifr.ch/"^^xsd:string ; bioregistry.schema:0000005 "H3.03.00.0.00007"^^xsd:string ; bioregistry.schema:0000012 false . @@ -23630,7 +23679,7 @@ bioregistry:th a bioregistry.schema:0000001 ; bioregistry:thermofisher a bioregistry.schema:0000001 ; rdfs:label "Thermo Fisher Scientific" ; dc:description "ThermoFisher is a life sciences supply vendor."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.thermofisher.com"^^xsd:string ; bioregistry.schema:0000005 "OSR00185W"^^xsd:string ; bioregistry.schema:0000006 "https://www.thermofisher.com/antibody/product/$1"^^xsd:string ; @@ -23639,8 +23688,8 @@ bioregistry:thermofisher a bioregistry.schema:0000001 ; bioregistry:tkg a bioregistry.schema:0000001 ; rdfs:label "Tohoku University cell line catalog" ; dc:description "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:TKG ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:TKG ; foaf:homepage "http://www2.idac.tohoku.ac.jp/dep/ccr/"^^xsd:string ; bioregistry.schema:0000005 "0221"^^xsd:string ; bioregistry.schema:0000006 "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^xsd:string ; @@ -23650,10 +23699,10 @@ bioregistry:tkg a bioregistry.schema:0000001 ; bioregistry:to a bioregistry.schema:0000001 ; rdfs:label "Plant Trait Ontology" ; dc:description "A controlled vocabulary to describe phenotypic traits in plants."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:TO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:TO, agroportal:TO, - obofoundry:TO, + obofoundry:to, ontobee:TO, bioportal:PTO, biocontext:TO, @@ -23669,15 +23718,15 @@ bioregistry:to a bioregistry.schema:0000001 ; bioregistry:ubprop a bioregistry.schema:0000001 ; rdfs:label "Uberon Property" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true . bioregistry:umbbd.enzyme a bioregistry.schema:0000001 ; rdfs:label "EAWAG Biocatalysis/Biodegradation Database" ; dc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:umbbd ; - ns1:exactMatch biocontext:UMBBD.ENZYME, + ns2:exactMatch biocontext:UMBBD.ENZYME, go.resource:UM-BBD_enzymeID, n2t:umbbd.enzyme, miriam:umbbd.enzyme ; @@ -23690,9 +23739,9 @@ bioregistry:umbbd.enzyme a bioregistry.schema:0000001 ; bioregistry:umbbd.pathway a bioregistry.schema:0000001 ; rdfs:label "EAWAG Biocatalysis/Biodegradation Database" ; dc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:umbbd ; - ns1:exactMatch biocontext:UMBBD.PATHWAY, + ns2:exactMatch biocontext:UMBBD.PATHWAY, go.resource:UM-BBD_pathwayID, n2t:umbbd.pathway, miriam:umbbd.pathway ; @@ -23705,9 +23754,9 @@ bioregistry:umbbd.pathway a bioregistry.schema:0000001 ; bioregistry:umbbd.reaction a bioregistry.schema:0000001 ; rdfs:label "EAWAG Biocatalysis/Biodegradation Database" ; dc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:umbbd ; - ns1:exactMatch biocontext:UMBBD.REACTION, + ns2:exactMatch biocontext:UMBBD.REACTION, go.resource:UM-BBD_reactionID, n2t:umbbd.reaction, miriam:umbbd.reaction ; @@ -23720,9 +23769,9 @@ bioregistry:umbbd.reaction a bioregistry.schema:0000001 ; bioregistry:umbbd.rule a bioregistry.schema:0000001 ; rdfs:label "EAWAG Biocatalysis/Biodegradation Database" ; dc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:umbbd ; - ns1:exactMatch biocontext:UMBBD.RULE, + ns2:exactMatch biocontext:UMBBD.RULE, go.resource:UM-BBD_ruleID, n2t:umbbd.rule, miriam:umbbd.rule ; @@ -23735,8 +23784,8 @@ bioregistry:umbbd.rule a bioregistry.schema:0000001 ; bioregistry:umls a bioregistry.schema:0000001 ; rdfs:label "Unified Medical Language System Concept Unique Identifier" ; dc:description "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1181, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1181, biocontext:UMLS, n2t:umls, miriam:umls, @@ -23750,7 +23799,7 @@ bioregistry:umls a bioregistry.schema:0000001 ; bioregistry:umls.aui a bioregistry.schema:0000001 ; rdfs:label "Unified Medical Language System Atomic Unique Identifier" ; dc:description "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.nlm.nih.gov/research/umls"^^xsd:string ; bioregistry.schema:0000005 "A0118748"^^xsd:string ; bioregistry.schema:0000008 "^A\\d+$"^^xsd:string ; @@ -23759,9 +23808,9 @@ bioregistry:umls.aui a bioregistry.schema:0000001 ; bioregistry:uniprot.chain a bioregistry.schema:0000001 ; rdfs:label "UniProt Chain" ; dc:description "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch miriam:uniprot.chain ; + ns2:exactMatch miriam:uniprot.chain ; foaf:homepage "https://www.uniprot.org"^^xsd:string ; bioregistry.schema:0000005 "PRO_0000016681"^^xsd:string ; bioregistry.schema:0000006 "http://purl.uniprot.org/annotation/$1"^^xsd:string ; @@ -23771,9 +23820,9 @@ bioregistry:uniprot.chain a bioregistry.schema:0000001 ; bioregistry:uniprot.isoform a bioregistry.schema:0000001 ; rdfs:label "UniProt Isoform" ; dc:description "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch biocontext:UNIPROT.ISOFORM, + ns2:exactMatch biocontext:UNIPROT.ISOFORM, n2t:uniprot.isoform, miriam:uniprot.isoform ; foaf:homepage "http://www.uniprot.org/"^^xsd:string ; @@ -23785,8 +23834,8 @@ bioregistry:uniprot.isoform a bioregistry.schema:0000001 ; bioregistry:uniprot.journal a bioregistry.schema:0000001 ; rdfs:label "UniProt journal ID" ; dc:description "identifier for a scientific journal, in the UniProt database"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P4616 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P4616 ; foaf:homepage "https://www.uniprot.org/journals"^^xsd:string ; bioregistry.schema:0000005 "3546"^^xsd:string ; bioregistry.schema:0000006 "https://www.uniprot.org/journals/$1"^^xsd:string ; @@ -23796,9 +23845,9 @@ bioregistry:uniprot.journal a bioregistry.schema:0000001 ; bioregistry:uniprot.keyword a bioregistry.schema:0000001 ; rdfs:label "UniProt Keywords" ; dc:description "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch go.resource:UniProtKB-KW, + ns2:exactMatch go.resource:UniProtKB-KW, prefixcommons:uniprot.kw ; foaf:homepage "http://www.uniprot.org/keywords/"^^xsd:string ; bioregistry.schema:0000005 "KW-1273"^^xsd:string ; @@ -23809,9 +23858,9 @@ bioregistry:uniprot.keyword a bioregistry.schema:0000001 ; bioregistry:uniprot.location a bioregistry.schema:0000001 ; rdfs:label "UniProt Subcellular Locations" ; dc:description "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch go.resource:UniProtKB-SubCell ; + ns2:exactMatch go.resource:UniProtKB-SubCell ; foaf:homepage "https://www.uniprot.org/locations/"^^xsd:string ; bioregistry.schema:0000005 "SL-0002"^^xsd:string ; bioregistry.schema:0000006 "https://www.uniprot.org/locations/$1"^^xsd:string ; @@ -23821,9 +23870,9 @@ bioregistry:uniprot.location a bioregistry.schema:0000001 ; bioregistry:uniprot.tissue a bioregistry.schema:0000001 ; rdfs:label "Tissue List" ; dc:description "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch biocontext:TISSUELIST, + ns2:exactMatch biocontext:TISSUELIST, n2t:tissuelist, miriam:tissuelist ; foaf:homepage "https://www.uniprot.org/docs/tisslist.txt"^^xsd:string ; @@ -23834,37 +23883,15 @@ bioregistry:uniprot.tissue a bioregistry.schema:0000001 ; bioregistry:unpd a bioregistry.schema:0000001 ; rdfs:label "Universal Natural Products Database" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://pkuxxj.pku.edu.cn/UNPD/"^^xsd:string ; bioregistry.schema:0000012 true . -bioregistry:upa a bioregistry.schema:0000001 ; - rdfs:label "Unipathway" ; - dc:description "A manually curated resource for the representation and annotation of metabolic pathways"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:UPA, - edam.data:2645, - obofoundry:UPA, - ontobee:UPA, - bioportal:UPA, - biocontext:UNIPATHWAY, - go.resource:UniPathway, - prefixcommons:unipathway, - ols:upa, - uniprot.resource:UniPathway ; - foaf:homepage "https://github.com/geneontology/unipathway"^^xsd:string ; - bioregistry.schema:0000005 "UCR00513"^^xsd:string ; - bioregistry.schema:0000006 "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^xsd:string ; - bioregistry.schema:0000008 "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000017 bioregistry:ro ; - bioregistry.schema:0000019 orcid:0000-0002-1216-2969 . - bioregistry:vega a bioregistry.schema:0000001 ; rdfs:label "Vertebrate Genome Annotation Database" ; dc:description "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.mr293q, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.mr293q, prefixcommons:vega ; foaf:homepage "https://vega.archive.ensembl.org/index.html"^^xsd:string ; bioregistry.schema:0000005 "OTTHUMG00000169812"^^xsd:string ; @@ -23874,9 +23901,9 @@ bioregistry:vega a bioregistry.schema:0000001 ; bioregistry:vo a bioregistry.schema:0000001 ; rdfs:label "Vaccine Ontology" ; dc:description "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VO, - obofoundry:VO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VO, + obofoundry:vo, ontobee:VO, bioportal:VO, biocontext:VO, @@ -23894,8 +23921,8 @@ bioregistry:vo a bioregistry.schema:0000001 ; bioregistry:void a bioregistry.schema:0000001 ; rdfs:label "Vocabulary of Interlinked Datasets" ; dc:description "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:void ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:void ; foaf:homepage "http://vocab.deri.ie/void"^^xsd:string ; bioregistry.schema:0000005 "feature"^^xsd:string ; bioregistry.schema:0000006 "http://rdfs.org/ns/void#$1"^^xsd:string ; @@ -23904,7 +23931,7 @@ bioregistry:void a bioregistry.schema:0000001 ; bioregistry:vsdb a bioregistry.schema:0000001 ; rdfs:label "Veterinary Substances DataBase" ; dc:description "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://sitem.herts.ac.uk/aeru/vsdb"^^xsd:string ; bioregistry.schema:0000005 "1868"^^xsd:string ; bioregistry.schema:0000006 "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^xsd:string ; @@ -23914,10 +23941,10 @@ bioregistry:vsdb a bioregistry.schema:0000001 ; bioregistry:vt a bioregistry.schema:0000001 ; rdfs:label "Vertebrate trait ontology" ; dc:description "An ontology of traits covering vertebrates"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:VT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:VT, agroportal:VT, - obofoundry:VT, + obofoundry:vt, ontobee:VT, bioportal:VT, biocontext:VT, @@ -23935,7 +23962,7 @@ bioregistry:vt a bioregistry.schema:0000001 ; bioregistry:vuid a bioregistry.schema:0000001 ; rdfs:label "Veterans Health Administration (VHA) unique identifier" ; dc:description "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.va.gov/health"^^xsd:string ; bioregistry.schema:0000005 "4007166"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -23944,10 +23971,10 @@ bioregistry:vuid a bioregistry.schema:0000001 ; bioregistry:wbls a bioregistry.schema:0000001 ; rdfs:label "C. elegans development ontology" ; dc:description "Ontology about the development and life stages of the C. elegans"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:wormbase ; - ns1:exactMatch aberowl:WBLS, - obofoundry:WBls, + ns2:exactMatch aberowl:WBLS, + obofoundry:wbls, ontobee:WBLS, bioportal:WB-LS, biocontext:WBLS, @@ -23966,10 +23993,10 @@ bioregistry:wbls a bioregistry.schema:0000001 ; bioregistry:wbphenotype a bioregistry.schema:0000001 ; rdfs:label "C. elegans phenotype" ; dc:description "Ontology about C. elegans and other nematode phenotypes"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:wormbase ; - ns1:exactMatch aberowl:WBPHENOTYPE, - obofoundry:WBPhenotype, + ns2:exactMatch aberowl:WBPHENOTYPE, + obofoundry:wbphenotype, ontobee:WBPhenotype, bioportal:WB-PHENOTYPE, biocontext:WBPhenotype, @@ -23987,8 +24014,8 @@ bioregistry:wbphenotype a bioregistry.schema:0000001 ; bioregistry:wwf.ecoregion a bioregistry.schema:0000001 ; rdfs:label "World Wildlife Fund Ecoregion" ; dc:description "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P1294 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P1294 ; foaf:homepage "https://www.worldwildlife.org/biomes"^^xsd:string ; bioregistry.schema:0000005 "AT1402"^^xsd:string ; bioregistry.schema:0000006 "https://www.worldwildlife.org/ecoregions/$1"^^xsd:string ; @@ -23999,9 +24026,9 @@ bioregistry:wwf.ecoregion a bioregistry.schema:0000001 ; bioregistry:xao a bioregistry.schema:0000001 ; rdfs:label "Xenopus Anatomy Ontology" ; dc:description "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:XAO, - obofoundry:XAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:XAO, + obofoundry:xao, ontobee:XAO, bioportal:XAO, biocontext:XAO, @@ -24019,8 +24046,8 @@ bioregistry:xao a bioregistry.schema:0000001 ; bioregistry:ximbio a bioregistry.schema:0000001 ; rdfs:label "Ximbio" ; dc:description "Cell line collections"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch cellosaurus.resource:Ximbio ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch cellosaurus.resource:Ximbio ; foaf:homepage "https://ximbio.com"^^xsd:string ; bioregistry.schema:0000005 "151022"^^xsd:string ; bioregistry.schema:0000006 "https://ximbio.com/reagent/$1"^^xsd:string ; @@ -24030,7 +24057,7 @@ bioregistry:ximbio a bioregistry.schema:0000001 ; bioregistry:xmetdb a bioregistry.schema:0000001 ; rdfs:label "Xenobiotics Metabolism Database" ; dc:description "Metabolites in the Xenobiotics Metabolism Database."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://xmetdb.org"^^xsd:string ; bioregistry.schema:0000005 "171"^^xsd:string ; bioregistry.schema:0000006 "http://www.xmetdb.org/xmetdb/protocol/$1"^^xsd:string ; @@ -24040,8 +24067,8 @@ bioregistry:xmetdb a bioregistry.schema:0000001 ; bioregistry:xml a bioregistry.schema:0000001 ; rdfs:label "Extensible Markup Language" ; dc:description "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:xml ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:xml ; foaf:homepage "https://www.w3.org/TR/xml/"^^xsd:string ; bioregistry.schema:0000005 "lang"^^xsd:string ; bioregistry.schema:0000006 "http://www.w3.org/XML/1998/namespace#$1"^^xsd:string ; @@ -24050,8 +24077,8 @@ bioregistry:xml a bioregistry.schema:0000001 ; bioregistry:xsd a bioregistry.schema:0000001 ; rdfs:label "XML Schema Definition" ; dc:description "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:xsd ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:xsd ; foaf:homepage "http://www.w3.org/2001/XMLSchema"^^xsd:string ; bioregistry.schema:0000005 "decimal"^^xsd:string ; bioregistry.schema:0000006 "http://www.w3.org/2001/XMLSchema#$1"^^xsd:string ; @@ -24059,16 +24086,16 @@ bioregistry:xsd a bioregistry.schema:0000001 ; bioregistry:xuo a bioregistry.schema:0000001 ; rdfs:label "XUO" ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; bioregistry.schema:0000012 true ; bioregistry.schema:0000018 bioregistry:hsapdv . bioregistry:zeco a bioregistry.schema:0000001 ; rdfs:label "Zebrafish Experimental Conditions Ontology" ; dc:description "Ontology of Zebrafish Experimental Conditions"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ZECO, - obofoundry:ZECO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ZECO, + obofoundry:zeco, ontobee:ZECO, bioportal:ZECO, biocontext:ZECO, @@ -24085,8 +24112,8 @@ bioregistry:zeco a bioregistry.schema:0000001 ; bioregistry:zenodo.record a bioregistry.schema:0000001 ; rdfs:label "Zenodo" ; dc:description "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch wikidata:P4901 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch wikidata:P4901 ; foaf:homepage "https://zenodo.org"^^xsd:string ; bioregistry.schema:0000005 "4390079"^^xsd:string ; bioregistry.schema:0000006 "https://zenodo.org/record/$1"^^xsd:string ; @@ -24097,9 +24124,9 @@ bioregistry:zenodo.record a bioregistry.schema:0000001 ; bioregistry:zfa a bioregistry.schema:0000001 ; rdfs:label "Zebrafish anatomy and development ontology" ; dc:description "ZFA description."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ZFA, - obofoundry:ZFA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ZFA, + obofoundry:zfa, ontobee:ZFA, bioportal:ZFA, biocontext:ZFA, @@ -24114,1121 +24141,1121 @@ bioregistry:zfa a bioregistry.schema:0000001 ; bioregistry.schema:0000018 bioregistry:zp ; bioregistry.schema:0000019 orcid:0000-0002-2244-7917 . -fairsharing:FAIRsharing.0a2576 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.0a2576 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.0a674c dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.0a674c ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.0pUMYW dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.0pUMYW ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.10gr18 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.10gr18 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.10zsxb dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.10zsxb ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1414v8 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1414v8 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.162003 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.162003 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.17zapb dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.17zapb ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1a27h8 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1a27h8 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1c1738 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1c1738 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1fbc5y dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1fbc5y ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1gr4tz dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1gr4tz ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1rj558 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.1rj558 ns1:isPartOf bioregistry.metaresource:fairsharing . -fairsharing:FAIRsharing.1tbrdz dcterms:isPartOf bioregistry.metaresource:fairsharing . 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bioregistry.metaresource:wikidata . -wikidata:P938 dcterms:isPartOf bioregistry.metaresource:wikidata . +wikidata:P9157 ns1:isPartOf bioregistry.metaresource:wikidata . -obofoundry:FBcv dcterms:isPartOf bioregistry.metaresource:obofoundry . +wikidata:P932 ns1:isPartOf bioregistry.metaresource:wikidata . -biocontext:GEO dcterms:isPartOf bioregistry.metaresource:biocontext . +wikidata:P938 ns1:isPartOf bioregistry.metaresource:wikidata . + +biocontext:GEO ns1:isPartOf bioregistry.metaresource:biocontext . bioregistry:ac a bioregistry.schema:0000001 ; rdfs:label "Activity Streams" ; dc:description "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.w3.org/ns/activitystreams"^^xsd:string ; bioregistry.schema:0000005 "Add"^^xsd:string ; bioregistry.schema:0000006 "http://www.w3.org/ns/activitystreams#$1"^^xsd:string ; @@ -28548,8 +28577,8 @@ bioregistry:ac a bioregistry.schema:0000001 ; bioregistry:bido a bioregistry.schema:0000001 ; rdfs:label "Bibliometric Data Ontology" ; dc:description "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.d7f0a9 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.d7f0a9 ; foaf:homepage "http://www.sparontologies.net/ontologies/bido"^^xsd:string ; bioregistry.schema:0000005 "CategorialBibliometricData"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/bido/$1"^^xsd:string ; @@ -28558,9 +28587,9 @@ bioregistry:bido a bioregistry.schema:0000001 ; bioregistry:biogrid.interaction a bioregistry.schema:0000001 ; rdfs:label "BioGRID Interactions" ; dc:description "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:biogrid ; - ns1:exactMatch edam.data:2628 ; + ns2:exactMatch edam.data:2628 ; foaf:homepage "https://thebiogrid.org/"^^xsd:string ; bioregistry.schema:0000005 "2649230"^^xsd:string ; bioregistry.schema:0000006 "https://thebiogrid.org/interaction/$1"^^xsd:string ; @@ -28571,8 +28600,8 @@ bioregistry:biogrid.interaction a bioregistry.schema:0000001 ; bioregistry:biro a bioregistry.schema:0000001 ; rdfs:label "Bibliographic Reference Ontology" ; dc:description "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.99da5f ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.99da5f ; foaf:homepage "http://www.sparontologies.net/ontologies/biro"^^xsd:string ; bioregistry.schema:0000005 "BibliographicRecord"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/biro/$1"^^xsd:string ; @@ -28581,8 +28610,8 @@ bioregistry:biro a bioregistry.schema:0000001 ; bioregistry:c4o a bioregistry.schema:0000001 ; rdfs:label "Citation Counting and Context Characterisation Ontology" ; dc:description "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.beb855 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.beb855 ; foaf:homepage "http://www.sparontologies.net/ontologies/c4o"^^xsd:string ; bioregistry.schema:0000005 "InTextReferencePointer"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/c4o/$1"^^xsd:string ; @@ -28591,9 +28620,9 @@ bioregistry:c4o a bioregistry.schema:0000001 ; bioregistry:chembl.cell a bioregistry.schema:0000001 ; rdfs:label "ChEMBL database of bioactive drug-like small molecules - Cell lines section" ; dc:description "Chemistry resources"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:chembl ; - ns1:exactMatch cellosaurus.resource:ChEMBL-Cells ; + ns2:exactMatch cellosaurus.resource:ChEMBL-Cells ; foaf:homepage "https://www.ebi.ac.uk/chembldb"^^xsd:string ; bioregistry.schema:0000005 "CHEMBL3307800"^^xsd:string ; bioregistry.schema:0000006 "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^xsd:string ; @@ -28602,9 +28631,9 @@ bioregistry:chembl.cell a bioregistry.schema:0000001 ; bioregistry:chmo a bioregistry.schema:0000001 ; rdfs:label "Chemical Methods Ontology" ; dc:description "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CHMO, - obofoundry:CHMO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CHMO, + obofoundry:chmo, ontobee:CHMO, bioportal:CHMO, biocontext:CHMO, @@ -28622,8 +28651,8 @@ bioregistry:chmo a bioregistry.schema:0000001 ; bioregistry:cito a bioregistry.schema:0000001 ; rdfs:label "Citation Typing Ontology" ; dc:description "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.b220d4 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.b220d4 ; foaf:homepage "http://www.sparontologies.net/ontologies/cito"^^xsd:string ; bioregistry.schema:0000005 "sharesAuthorInstitutionWith"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/cito/$1"^^xsd:string ; @@ -28632,10 +28661,10 @@ bioregistry:cito a bioregistry.schema:0000001 ; bioregistry:cog a bioregistry.schema:0000001 ; rdfs:label "Cluster of orthologous genes" ; dc:description "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^xsd:string ; - dcterms:hasPart bioregistry:cog.category, + ns1:hasPart bioregistry:cog.category, bioregistry:cog.pathway ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biolink:COG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biolink:COG, go.resource:COG_Cluster, fairsharing:FAIRsharing.djsbw2, prefixcommons:cog ; @@ -28649,7 +28678,7 @@ bioregistry:cog a bioregistry.schema:0000001 ; bioregistry:cog.category a bioregistry.schema:0000001 ; rdfs:label "COG Categories" ; dc:description "Higher-level classifications of COG Pathways"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:cog ; foaf:homepage "https://www.ncbi.nlm.nih.gov/research/cog/"^^xsd:string ; bioregistry.schema:0000005 "K"^^xsd:string ; @@ -28660,23 +28689,23 @@ bioregistry:cog.category a bioregistry.schema:0000001 ; bioregistry:come a bioregistry.schema:0000001 ; rdfs:label "The Bioinorganic Motif Database" ; dc:description "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch prefixcommons:come ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch prefixcommons:come ; foaf:homepage "https://www.flymine.org/come"^^xsd:string ; bioregistry.schema:0000005 "MOL000160"^^xsd:string ; bioregistry.schema:0000006 "https://www.flymine.org/come/entry?gn=$1"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:ctd dcterms:hasPart bioregistry:ctd.chemical, +bioregistry:ctd ns1:hasPart bioregistry:ctd.chemical, bioregistry:ctd.disease, bioregistry:ctd.gene . bioregistry:cteno a bioregistry.schema:0000001 ; rdfs:label "Ctenophore Ontology" ; dc:description "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CTENO, - obofoundry:CTENO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CTENO, + obofoundry:cteno, ontobee:CTENO, bioportal:CTENO, biocontext:CTENO, @@ -28694,8 +28723,8 @@ bioregistry:cteno a bioregistry.schema:0000001 ; bioregistry:datacite a bioregistry.schema:0000001 ; rdfs:label "DataCite Ontology" ; dc:description "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DATACITE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DATACITE, bioportal:DATACITE, fairsharing:FAIRsharing.c06f1e ; foaf:homepage "http://www.sparontologies.net/ontologies/datacite"^^xsd:string ; @@ -28706,8 +28735,8 @@ bioregistry:datacite a bioregistry.schema:0000001 ; bioregistry:dcterms a bioregistry.schema:0000001 ; rdfs:label "Dublin Core Metadata Vocabulary" ; dc:description "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:dcterms, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:dcterms, bioportal:DCTERMS, biocontext:dcterms, biolink:dct, @@ -28720,8 +28749,8 @@ bioregistry:dcterms a bioregistry.schema:0000001 ; bioregistry:deo a bioregistry.schema:0000001 ; rdfs:label "Discourse Elements Ontology" ; dc:description "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.39fd58 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.39fd58 ; foaf:homepage "http://www.sparontologies.net/ontologies/deo"^^xsd:string ; bioregistry.schema:0000005 "Reference"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/deo/$1"^^xsd:string ; @@ -28730,7 +28759,7 @@ bioregistry:deo a bioregistry.schema:0000001 ; bioregistry:dhba a bioregistry.schema:0000001 ; rdfs:label "Developing Human Brain Atlas" ; dc:description "A controlled vocabulary to support the study of transcription in the developing human brain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.brainspan.org/"^^xsd:string ; bioregistry.schema:0000005 "10153"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -28739,10 +28768,10 @@ bioregistry:dhba a bioregistry.schema:0000001 ; bioregistry:dictybase a bioregistry.schema:0000001 ; rdfs:label "dictyBase" ; dc:description "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^xsd:string ; - dcterms:hasPart bioregistry:dictybase.est, + ns1:hasPart bioregistry:dictybase.est, bioregistry:dictybase.gene ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:dictyBase, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:dictyBase, go.resource:dictyBase, ncbi.resource:dictyBase, fairsharing:FAIRsharing.4shj9c, @@ -28756,7 +28785,7 @@ bioregistry:dictybase a bioregistry.schema:0000001 ; bioregistry:dmba a bioregistry.schema:0000001 ; rdfs:label "Developing Mouse Brain Atlas" ; dc:description "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://developingmouse.brain-map.org/"^^xsd:string ; bioregistry.schema:0000005 "688"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -28765,8 +28794,8 @@ bioregistry:dmba a bioregistry.schema:0000001 ; bioregistry:doco a bioregistry.schema:0000001 ; rdfs:label "Document Components Ontology" ; dc:description "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.162003 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.162003 ; foaf:homepage "http://www.sparontologies.net/ontologies/doco"^^xsd:string ; bioregistry.schema:0000005 "Paragraph"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/doco/$1"^^xsd:string ; @@ -28775,9 +28804,9 @@ bioregistry:doco a bioregistry.schema:0000001 ; bioregistry:doid a bioregistry.schema:0000001 ; rdfs:label "Human Disease Ontology" ; dc:description "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DOID, - obofoundry:DOID, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DOID, + obofoundry:doid, ontobee:DOID, bioportal:DOID, biocontext:DOID, @@ -28799,7 +28828,7 @@ bioregistry:doid a bioregistry.schema:0000001 ; bioregistry:drugbank.category a bioregistry.schema:0000001 ; rdfs:label "DrugBank Drug Category" ; dc:description "Close to 5K Categorizations for drugs, similar to ATCC."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:drugbank ; foaf:homepage "https://go.drugbank.com/categories"^^xsd:string ; bioregistry.schema:0000005 "DBCAT000600"^^xsd:string ; @@ -28810,8 +28839,8 @@ bioregistry:drugbank.category a bioregistry.schema:0000001 ; bioregistry:eccode a bioregistry.schema:0000001 ; rdfs:label "Enzyme Commission Code" ; dc:description "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1011, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1011, biocontext:EC-CODE, go.resource:EC, n2t:ec-code, @@ -28828,23 +28857,23 @@ bioregistry:eccode a bioregistry.schema:0000001 ; bioregistry:ecmdb a bioregistry.schema:0000001 ; rdfs:label "E. coli Metabolite Database" ; dc:description "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://ecmdb.ca"^^xsd:string ; bioregistry.schema:0000005 "ECMDB00005"^^xsd:string ; bioregistry.schema:0000006 "http://ecmdb.ca/compounds/$1"^^xsd:string ; bioregistry.schema:0000008 "^ECMDB\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:ecyano dcterms:hasPart bioregistry:ecyano.entity, +bioregistry:ecyano ns1:hasPart bioregistry:ecyano.entity, bioregistry:ecyano.experiment, bioregistry:ecyano.rule . bioregistry:edam.data a bioregistry.schema:0000001 ; rdfs:label "EDAM Data" ; dc:description "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:edam ; - ns1:exactMatch biolink:EDAM-DATA ; + ns2:exactMatch biolink:EDAM-DATA ; foaf:homepage "http://edamontology.org"^^xsd:string ; bioregistry.schema:0000005 "1664"^^xsd:string ; bioregistry.schema:0000006 "http://edamontology.org/data_$1"^^xsd:string ; @@ -28855,9 +28884,9 @@ bioregistry:edam.data a bioregistry.schema:0000001 ; bioregistry:edam.format a bioregistry.schema:0000001 ; rdfs:label "EDAM Format" ; dc:description "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:edam ; - ns1:exactMatch biolink:EDAM-FORMAT ; + ns2:exactMatch biolink:EDAM-FORMAT ; foaf:homepage "http://edamontology.org"^^xsd:string ; bioregistry.schema:0000005 "1915"^^xsd:string ; bioregistry.schema:0000006 "http://edamontology.org/format_$1"^^xsd:string ; @@ -28868,9 +28897,9 @@ bioregistry:edam.format a bioregistry.schema:0000001 ; bioregistry:edam.operation a bioregistry.schema:0000001 ; rdfs:label "EDAM Operation" ; dc:description "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:edam ; - ns1:exactMatch biolink:EDAM-OPERATION ; + ns2:exactMatch biolink:EDAM-OPERATION ; foaf:homepage "http://edamontology.org"^^xsd:string ; bioregistry.schema:0000005 "0004"^^xsd:string ; bioregistry.schema:0000006 "http://edamontology.org/operation_$1"^^xsd:string ; @@ -28881,9 +28910,9 @@ bioregistry:edam.operation a bioregistry.schema:0000001 ; bioregistry:edam.topic a bioregistry.schema:0000001 ; rdfs:label "EDAM Topic" ; dc:description "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:edam ; - ns1:exactMatch biolink:EDAM-TOPIC ; + ns2:exactMatch biolink:EDAM-TOPIC ; foaf:homepage "http://edamontology.org"^^xsd:string ; bioregistry.schema:0000005 "0003"^^xsd:string ; bioregistry.schema:0000006 "http://edamontology.org/topic_$1"^^xsd:string ; @@ -28894,16 +28923,16 @@ bioregistry:edam.topic a bioregistry.schema:0000001 ; bioregistry:eurofir a bioregistry.schema:0000001 ; rdfs:label "European Food Information Resource Network" ; dc:description "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.eurofir.org"^^xsd:string ; bioregistry.schema:0000012 false . bioregistry:exo a bioregistry.schema:0000001 ; rdfs:label "Exposure ontology" ; dc:description "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EXO, - obofoundry:ExO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EXO, + obofoundry:exo, ontobee:ExO, bioportal:EXO, biocontext:EXO, @@ -28922,8 +28951,8 @@ bioregistry:exo a bioregistry.schema:0000001 ; bioregistry:fabio a bioregistry.schema:0000001 ; rdfs:label "FaBiO, the FRBR-aligned Bibliographic Ontology" ; dc:description "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FaBiO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FaBiO, biolink:fabio, fairsharing:FAIRsharing.2f3180 ; foaf:homepage "https://github.com/sparontologies/fabio"^^xsd:string ; @@ -28934,7 +28963,7 @@ bioregistry:fabio a bioregistry.schema:0000001 ; bioregistry:fbrf a bioregistry.schema:0000001 ; rdfs:label "FlyBase Reference Report" ; dc:description "FlyBase internal citation identifiers"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:flybase ; foaf:homepage "https://flybase.org"^^xsd:string ; bioregistry.schema:0000005 "0187632"^^xsd:string ; @@ -28945,7 +28974,7 @@ bioregistry:fbrf a bioregistry.schema:0000001 ; bioregistry:fbtc a bioregistry.schema:0000001 ; rdfs:label "Flybase Cell Line" ; dc:description "The cell line vocabulary inside FlyBase"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:flybase ; foaf:homepage "https://flybase.org"^^xsd:string ; bioregistry.schema:0000005 "0000190"^^xsd:string ; @@ -28956,10 +28985,10 @@ bioregistry:fbtc a bioregistry.schema:0000001 ; bioregistry:fobi a bioregistry.schema:0000001 ; rdfs:label "Food-Biomarker Ontology" ; dc:description "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FOBI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FOBI, agroportal:FOBI, - obofoundry:FOBI, + obofoundry:fobi, ontobee:FOBI, bioportal:FOBI, ols:fobi ; @@ -28975,9 +29004,9 @@ bioregistry:fobi a bioregistry.schema:0000001 ; bioregistry:fossilworks.journal a bioregistry.schema:0000001 ; rdfs:label "Fossilworks Journal" ; dc:description "Identifier for a journal article in the fossilworks website"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:fossilworks ; - ns1:exactMatch wikidata:P7720 ; + ns2:exactMatch wikidata:P7720 ; foaf:homepage "http://fossilworks.org"^^xsd:string ; bioregistry.schema:0000005 "61467"^^xsd:string ; bioregistry.schema:0000006 "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^xsd:string ; @@ -28988,9 +29017,9 @@ bioregistry:fossilworks.journal a bioregistry.schema:0000001 ; bioregistry:fossilworks.taxon a bioregistry.schema:0000001 ; rdfs:label "Fossilworks Taxon" ; dc:description "Identifier for an animal, plant, or microorganism from the fossilworks website"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:fossilworks ; - ns1:exactMatch wikidata:P842 ; + ns2:exactMatch wikidata:P842 ; foaf:homepage "http://www.fossilworks.org"^^xsd:string ; bioregistry.schema:0000005 "40565"^^xsd:string ; bioregistry.schema:0000006 "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^xsd:string ; @@ -29001,8 +29030,8 @@ bioregistry:fossilworks.taxon a bioregistry.schema:0000001 ; bioregistry:frapo a bioregistry.schema:0000001 ; rdfs:label "Funding, Research Administration and Projects Ontology" ; dc:description "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FRAPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FRAPO, fairsharing:FAIRsharing.0a2576 ; foaf:homepage "http://www.sparontologies.net/ontologies/frapo"^^xsd:string ; bioregistry.schema:0000005 "Grant"^^xsd:string ; @@ -29012,9 +29041,9 @@ bioregistry:frapo a bioregistry.schema:0000001 ; bioregistry:gsso a bioregistry.schema:0000001 ; rdfs:label "Gender, Sex, and Sexual Orientation Ontology" ; dc:description "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GSSO, - obofoundry:GSSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GSSO, + obofoundry:gsso, ontobee:GSSO, bioportal:GSSO, miriam:gsso, @@ -29031,7 +29060,7 @@ bioregistry:gsso a bioregistry.schema:0000001 ; bioregistry:hba a bioregistry.schema:0000001 ; rdfs:label "Human Brain Atlas" ; dc:description "A controlled vocabulary to support the study of transcription in the human brain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://human.brain-map.org"^^xsd:string ; bioregistry.schema:0000005 "4005"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -29040,9 +29069,9 @@ bioregistry:hba a bioregistry.schema:0000001 ; bioregistry:hp a bioregistry.schema:0000001 ; rdfs:label "Human Phenotype Ontology" ; dc:description "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HP_O, - obofoundry:HP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HP_O, + obofoundry:hp, ontobee:HP, bioportal:HP_O, biocontext:HPO, @@ -29063,9 +29092,9 @@ bioregistry:hp a bioregistry.schema:0000001 ; bioregistry:hsapdv a bioregistry.schema:0000001 ; rdfs:label "Human Developmental Stages" ; dc:description "Life cycle stages for Human"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HSAPDV, - obofoundry:HsapDv, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HSAPDV, + obofoundry:hsapdv, ontobee:HSAPDV, bioportal:HSAPDV, biocontext:HSAPDV, @@ -29083,9 +29112,9 @@ bioregistry:hsapdv a bioregistry.schema:0000001 ; bioregistry:kegg.compound a bioregistry.schema:0000001 ; rdfs:label "KEGG Compound" ; dc:description "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch edam.data:2605, + ns2:exactMatch edam.data:2605, biocontext:KEGG.COMPOUND, n2t:kegg.compound, prefixcommons:kegg.compound, @@ -29108,9 +29137,9 @@ bioregistry:kegg.dgroup a bioregistry.schema:0000001 ; Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters Chemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biolink:KEGG.DGROUP ; + ns2:exactMatch biolink:KEGG.DGROUP ; foaf:homepage "http://www.genome.jp/kegg/reaction/"^^xsd:string ; bioregistry.schema:0000005 "DG00301"^^xsd:string ; bioregistry.schema:0000008 "^DG\\d+$"^^xsd:string ; @@ -29119,9 +29148,9 @@ Chemical groups are often used for identifying essentially the same active ingre bioregistry:kegg.drug a bioregistry.schema:0000001 ; rdfs:label "KEGG Drug" ; dc:description "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch edam.data:2609, + ns2:exactMatch edam.data:2609, biocontext:KEGG.DRUG, n2t:kegg.drug, prefixcommons:kegg.drug, @@ -29136,9 +29165,9 @@ bioregistry:kegg.drug a bioregistry.schema:0000001 ; bioregistry:kegg.glycan a bioregistry.schema:0000001 ; rdfs:label "KEGG Glycan" ; dc:description "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch edam.data:2613, + ns2:exactMatch edam.data:2613, biocontext:KEGG.GLYCAN, n2t:kegg.glycan, prefixcommons:kegg.glycan, @@ -29152,9 +29181,9 @@ bioregistry:kegg.glycan a bioregistry.schema:0000001 ; bioregistry:kegg.rclass a bioregistry.schema:0000001 ; rdfs:label "KEGG Reaction Class" ; dc:description "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:kegg ; - ns1:exactMatch biolink:KEGG.RCLASS ; + ns2:exactMatch biolink:KEGG.RCLASS ; foaf:homepage "http://www.genome.jp/kegg/reaction/"^^xsd:string ; bioregistry.schema:0000005 "RC00001"^^xsd:string ; bioregistry.schema:0000008 "^RC\\d+$"^^xsd:string ; @@ -29163,7 +29192,7 @@ bioregistry:kegg.rclass a bioregistry.schema:0000001 ; bioregistry:mba a bioregistry.schema:0000001 ; rdfs:label "Mouse Brain Atlas" ; dc:description "A controlled vocabulary to support the study of transcription in the mouse brain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://mouse.brain-map.org"^^xsd:string ; bioregistry.schema:0000005 "688"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -29172,7 +29201,7 @@ bioregistry:mba a bioregistry.schema:0000001 ; bioregistry:merops.clan a bioregistry.schema:0000001 ; rdfs:label "MEROPS Clan" ; dc:description "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:merops ; foaf:homepage "https://www.ebi.ac.uk/merops"^^xsd:string ; bioregistry.schema:0000005 "IA"^^xsd:string ; @@ -29182,8 +29211,8 @@ bioregistry:merops.clan a bioregistry.schema:0000001 ; bioregistry:mesh a bioregistry.schema:0000001 ; rdfs:label "Medical Subject Headings" ; dc:description "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MESH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MESH, edam.data:1177, bioportal:MESH, biocontext:MESH, @@ -29204,7 +29233,7 @@ bioregistry:mesh a bioregistry.schema:0000001 ; bioregistry:molbase.sheffield a bioregistry.schema:0000001 ; rdfs:label "MolBase" ; dc:description "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://winter.group.shef.ac.uk/molbase/"^^xsd:string ; bioregistry.schema:0000005 "1868"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -29213,9 +29242,9 @@ bioregistry:molbase.sheffield a bioregistry.schema:0000001 ; bioregistry:mondo a bioregistry.schema:0000001 ; rdfs:label "Monarch Disease Ontology" ; dc:description "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MONDO, - obofoundry:MONDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MONDO, + obofoundry:mondo, ontobee:MONDO, bioportal:MONDO, biocontext:MONDO, @@ -29232,9 +29261,9 @@ bioregistry:mondo a bioregistry.schema:0000001 ; bioregistry:mp a bioregistry.schema:0000001 ; rdfs:label "Mammalian Phenotype Ontology" ; dc:description "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MP, - obofoundry:MP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MP, + obofoundry:mp, ontobee:MP, bioportal:MP, biocontext:MP, @@ -29255,9 +29284,9 @@ bioregistry:mp a bioregistry.schema:0000001 ; bioregistry:ms a bioregistry.schema:0000001 ; rdfs:label "Mass spectrometry ontology" ; dc:description "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MS, - obofoundry:MS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MS, + obofoundry:ms, ontobee:MS, bioportal:MS, biocontext:MS, @@ -29276,8 +29305,8 @@ bioregistry:ms a bioregistry.schema:0000001 ; bioregistry:ncbigene a bioregistry.schema:0000001 ; rdfs:label "Entrez Gene" ; dc:description "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1027, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1027, biocontext:NCBIGene, biolink:NCBIGene, go.resource:NCBIGene, @@ -29296,8 +29325,8 @@ bioregistry:ncbigene a bioregistry.schema:0000001 ; bioregistry:ncbiprotein a bioregistry.schema:0000001 ; rdfs:label "NCBI Protein" ; dc:description "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:NCBIProtein, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:NCBIProtein, go.resource:NCBI_NP, n2t:ncbiprotein, prefixcommons:ncbi.protein, @@ -29311,7 +29340,7 @@ bioregistry:ncbiprotein a bioregistry.schema:0000001 ; bioregistry:nif.ext a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: External" ; dc:description "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "7123"^^xsd:string ; @@ -29324,9 +29353,9 @@ bioregistry:nif.ext a bioregistry.schema:0000001 ; bioregistry:nif.std a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology" ; dc:description "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch aberowl:NIFSTD, + ns2:exactMatch aberowl:NIFSTD, bioportal:NIFSTD, fairsharing:FAIRsharing.vgw1m6 ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; @@ -29340,7 +29369,7 @@ bioregistry:nif.std a bioregistry.schema:0000001 ; bioregistry:nlx.anat a bioregistry.schema:0000001 ; rdfs:label "NeuroLex Anatomy" ; dc:description "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://scicrunch.org/scicrunch/interlex/dashboard"^^xsd:string ; bioregistry.schema:0000005 "090201"^^xsd:string ; @@ -29353,7 +29382,7 @@ bioregistry:nlx.anat a bioregistry.schema:0000001 ; bioregistry:nlx.br a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Brain Regions" ; dc:description "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "145"^^xsd:string ; @@ -29366,7 +29395,7 @@ bioregistry:nlx.br a bioregistry.schema:0000001 ; bioregistry:nlx.cell a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Cell Types" ; dc:description "NLXCELL conatins cell types with a focus on neuron types."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "91005"^^xsd:string ; @@ -29379,7 +29408,7 @@ bioregistry:nlx.cell a bioregistry.schema:0000001 ; bioregistry:nlx.chem a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Chemical" ; dc:description "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "90801"^^xsd:string ; @@ -29392,7 +29421,7 @@ bioregistry:nlx.chem a bioregistry.schema:0000001 ; bioregistry:nlx.dys a bioregistry.schema:0000001 ; rdfs:label "NeuroLex Dysfunction" ; dc:description "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://scicrunch.org/scicrunch/interlex/dashboard"^^xsd:string ; bioregistry.schema:0000005 "20090303"^^xsd:string ; @@ -29406,7 +29435,7 @@ bioregistry:nlx.dys a bioregistry.schema:0000001 ; bioregistry:nlx.func a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Cognitive Function" ; dc:description "NLXFUNC covers terms for cognitive function."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "90801"^^xsd:string ; @@ -29419,7 +29448,7 @@ bioregistry:nlx.func a bioregistry.schema:0000001 ; bioregistry:nlx.inv a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Investigations" ; dc:description "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "90901"^^xsd:string ; @@ -29431,7 +29460,7 @@ bioregistry:nlx.inv a bioregistry.schema:0000001 ; bioregistry:nlx.mol a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Molecules" ; dc:description "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "90806"^^xsd:string ; @@ -29444,7 +29473,7 @@ bioregistry:nlx.mol a bioregistry.schema:0000001 ; bioregistry:nlx.oen a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: OEN Terms in Neurolex" ; dc:description "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "0001000"^^xsd:string ; @@ -29457,7 +29486,7 @@ bioregistry:nlx.oen a bioregistry.schema:0000001 ; bioregistry:nlx.org a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Organisms" ; dc:description "NLXORG covers organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "090701"^^xsd:string ; @@ -29470,7 +29499,7 @@ bioregistry:nlx.org a bioregistry.schema:0000001 ; bioregistry:nlx.qual a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Qualities" ; dc:description "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "100810"^^xsd:string ; @@ -29483,7 +29512,7 @@ bioregistry:nlx.qual a bioregistry.schema:0000001 ; bioregistry:nlx.res a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Digital Resources" ; dc:description "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "090924"^^xsd:string ; @@ -29496,9 +29525,9 @@ bioregistry:nlx.res a bioregistry.schema:0000001 ; bioregistry:nlx.sub a bioregistry.schema:0000001 ; rdfs:label "NIF Standard Ontology: Subcellular Entities" ; dc:description "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:nif ; - ns1:exactMatch go.resource:NIF_Subcellular ; + ns2:exactMatch go.resource:NIF_Subcellular ; foaf:homepage "https://github.com/SciCrunch/NIF-Ontology"^^xsd:string ; bioregistry.schema:0000005 "090803"^^xsd:string ; bioregistry.schema:0000006 "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^xsd:string ; @@ -29512,9 +29541,9 @@ bioregistry:ogms a bioregistry.schema:0000001 ; dc:description """The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OGMS, - obofoundry:OGMS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OGMS, + obofoundry:ogms, ontobee:OGMS, bioportal:OGMS, biocontext:OGMS, @@ -29532,9 +29561,9 @@ OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagn bioregistry:omim.ps a bioregistry.schema:0000001 ; rdfs:label "OMIM Phenotypic Series" ; dc:description "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:omim ; - ns1:exactMatch biolink:OMIM.PS ; + ns2:exactMatch biolink:OMIM.PS ; foaf:homepage "https://www.omim.org/phenotypicSeriesTitles/all"^^xsd:string ; bioregistry.schema:0000005 "PS214100"^^xsd:string ; bioregistry.schema:0000006 "https://omim.org/phenotypicSeries/$1"^^xsd:string ; @@ -29545,9 +29574,9 @@ bioregistry:omim.ps a bioregistry.schema:0000001 ; bioregistry:opmi a bioregistry.schema:0000001 ; rdfs:label "Ontology of Precision Medicine and Investigation" ; dc:description "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OPMI, - obofoundry:OPMI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OPMI, + obofoundry:opmi, ontobee:OPMI, bioportal:OPMI, ols:opmi ; @@ -29563,7 +29592,7 @@ bioregistry:opmi a bioregistry.schema:0000001 ; bioregistry:pba a bioregistry.schema:0000001 ; rdfs:label "Primate Brain Atlas" ; dc:description "A controlled vocabulary to support the study of transcription in the primate brain"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.blueprintnhpatlas.org/"^^xsd:string ; bioregistry.schema:0000005 "128011350"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; @@ -29572,10 +29601,10 @@ bioregistry:pba a bioregistry.schema:0000001 ; bioregistry:peco a bioregistry.schema:0000001 ; rdfs:label "Plant Experimental Conditions Ontology" ; dc:description "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PECO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PECO, agroportal:PECO, - obofoundry:PECO, + obofoundry:peco, ontobee:PECO, bioportal:PECO, biocontext:PECO, @@ -29593,7 +29622,7 @@ bioregistry:peco a bioregistry.schema:0000001 ; bioregistry:pesticides a bioregistry.schema:0000001 ; rdfs:label "Alan Wood's Pesticides" ; dc:description "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "http://www.alanwood.net/pesticides"^^xsd:string ; bioregistry.schema:0000005 "derivatives%2Fthiocyclam%20hydrochloride"^^xsd:string ; bioregistry.schema:0000006 "http://www.alanwood.net/pesticides/$1.html"^^xsd:string ; @@ -29602,9 +29631,9 @@ bioregistry:pesticides a bioregistry.schema:0000001 ; bioregistry:poro a bioregistry.schema:0000001 ; rdfs:label "Porifera Ontology" ; dc:description "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PORO, - obofoundry:PORO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PORO, + obofoundry:poro, ontobee:PORO, bioportal:PORO, biocontext:PORO, @@ -29622,9 +29651,9 @@ bioregistry:poro a bioregistry.schema:0000001 ; bioregistry:pso a bioregistry.schema:0000001 ; rdfs:label "Plant Stress Ontology" ; dc:description "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PSO, - obofoundry:PSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PSO, + obofoundry:pso, ontobee:PSO, bioportal:PSO, fairsharing:FAIRsharing.dyj433, @@ -29640,7 +29669,7 @@ bioregistry:pso a bioregistry.schema:0000001 ; bioregistry:pubchem.cell a bioregistry.schema:0000001 ; rdfs:label "PubChem Cell Line" ; dc:description "Cell Lines in PubChem"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; foaf:homepage "https://pubchem.ncbi.nlm.nih.gov"^^xsd:string ; bioregistry.schema:0000005 "31"^^xsd:string ; @@ -29651,7 +29680,7 @@ bioregistry:pubchem.cell a bioregistry.schema:0000001 ; bioregistry:pubchem.classification a bioregistry.schema:0000001 ; rdfs:label "PubChem Classification" ; dc:description "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; foaf:homepage "https://pubchem.ncbi.nlm.nih.gov/classification/"^^xsd:string ; bioregistry.schema:0000005 "87"^^xsd:string ; @@ -29662,7 +29691,7 @@ bioregistry:pubchem.classification a bioregistry.schema:0000001 ; bioregistry:pubchem.element a bioregistry.schema:0000001 ; rdfs:label "PubChem Element" ; dc:description "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:pubchem ; foaf:homepage "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; @@ -29673,8 +29702,8 @@ bioregistry:pubchem.element a bioregistry.schema:0000001 ; bioregistry:puro a bioregistry.schema:0000001 ; rdfs:label "Publishing Roles Ontology" ; dc:description "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.3e88d6 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.3e88d6 ; foaf:homepage "http://www.sparontologies.net/ontologies/pro"^^xsd:string ; bioregistry.schema:0000005 "RoleInTime"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/pro/$1"^^xsd:string ; @@ -29683,8 +29712,8 @@ bioregistry:puro a bioregistry.schema:0000001 ; bioregistry:pwo a bioregistry.schema:0000001 ; rdfs:label "Publishing Workflow Ontology" ; dc:description "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.c4e46c ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.c4e46c ; foaf:homepage "http://www.sparontologies.net/ontologies/pwo"^^xsd:string ; bioregistry.schema:0000005 "Workflow"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/pwo/$1"^^xsd:string ; @@ -29693,9 +29722,9 @@ bioregistry:pwo a bioregistry.schema:0000001 ; bioregistry:sbo a bioregistry.schema:0000001 ; rdfs:label "Systems Biology Ontology" ; dc:description "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SBO, - obofoundry:SBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SBO, + obofoundry:sbo, ontobee:SBO, bioportal:SBO, biocontext:SBO, @@ -29716,8 +29745,8 @@ bioregistry:sbo a bioregistry.schema:0000001 ; bioregistry:scoro a bioregistry.schema:0000001 ; rdfs:label "Scholarly Contributions and Roles Ontology" ; dc:description "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.c86b48 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.c86b48 ; foaf:homepage "http://www.sparontologies.net/ontologies/scoro"^^xsd:string ; bioregistry.schema:0000005 "IntellectualContribution"^^xsd:string ; bioregistry.schema:0000006 "http://purl.org/spar/scoro/$1"^^xsd:string ; @@ -29726,7 +29755,7 @@ bioregistry:scoro a bioregistry.schema:0000001 ; bioregistry:signor.relation a bioregistry.schema:0000001 ; rdfs:label "SIGNOR Relation" ; dc:description "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:signor ; foaf:homepage "https://signor.uniroma2.it"^^xsd:string ; bioregistry.schema:0000005 "SIGNOR-252737"^^xsd:string ; @@ -29737,7 +29766,7 @@ bioregistry:signor.relation a bioregistry.schema:0000001 ; bioregistry:smid a bioregistry.schema:0000001 ; rdfs:label "C. elegans Small Molecule Identifier Database" ; dc:description "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://smid-db.org/"^^xsd:string ; bioregistry.schema:0000005 "137"^^xsd:string ; bioregistry.schema:0000006 "https://smid-db.org/smid/$1"^^xsd:string ; @@ -29747,7 +29776,7 @@ bioregistry:smid a bioregistry.schema:0000001 ; bioregistry:ssbd.project a bioregistry.schema:0000001 ; rdfs:label "System Science of Biological Dynamics project" ; dc:description "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://ssbd.riken.jp"^^xsd:string ; bioregistry.schema:0000005 "1"^^xsd:string ; bioregistry.schema:0000006 "https://ssbd.riken.jp/database/project/$1"^^xsd:string ; @@ -29757,7 +29786,7 @@ bioregistry:ssbd.project a bioregistry.schema:0000001 ; bioregistry:storedb.dataset a bioregistry.schema:0000001 ; rdfs:label "STOREDB at University of Cambridge" ; dc:description "Datasets inside StoreDB"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:storedb ; foaf:homepage "https://www.storedb.org/"^^xsd:string ; bioregistry.schema:0000005 "1251"^^xsd:string ; @@ -29768,7 +29797,7 @@ bioregistry:storedb.dataset a bioregistry.schema:0000001 ; bioregistry:storedb.file a bioregistry.schema:0000001 ; rdfs:label "STOREDB at University of Cambridge" ; dc:description "File inside StoreDB"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:storedb ; foaf:homepage "https://www.storedb.org/"^^xsd:string ; bioregistry.schema:0000005 "12929"^^xsd:string ; @@ -29779,7 +29808,7 @@ bioregistry:storedb.file a bioregistry.schema:0000001 ; bioregistry:storedb.study a bioregistry.schema:0000001 ; rdfs:label "STOREDB at University of Cambridge" ; dc:description "Study inside StoreDB"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:storedb ; foaf:homepage "https://www.storedb.org/"^^xsd:string ; bioregistry.schema:0000005 "1174"^^xsd:string ; @@ -29790,9 +29819,9 @@ bioregistry:storedb.study a bioregistry.schema:0000001 ; bioregistry:umbbd.compound a bioregistry.schema:0000001 ; rdfs:label "UM-BBD Compound" ; dc:description "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:umbbd ; - ns1:exactMatch biocontext:UMBBD.COMPOUND, + ns2:exactMatch biocontext:UMBBD.COMPOUND, n2t:umbbd.compound, miriam:umbbd.compound, wikidata:P8121 ; @@ -29805,9 +29834,9 @@ bioregistry:umbbd.compound a bioregistry.schema:0000001 ; bioregistry:uniprot.disease a bioregistry.schema:0000001 ; rdfs:label "UniProt Diseases" ; dc:description "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; - ns1:exactMatch biolink:SPDI ; + ns2:exactMatch biolink:SPDI ; foaf:homepage "https://www.uniprot.org/diseases/"^^xsd:string ; bioregistry.schema:0000005 "DI-04240"^^xsd:string ; bioregistry.schema:0000006 "https://www.uniprot.org/diseases/$1"^^xsd:string ; @@ -29817,7 +29846,7 @@ bioregistry:uniprot.disease a bioregistry.schema:0000001 ; bioregistry:uniprot.ptm a bioregistry.schema:0000001 ; rdfs:label "UniProt Post-Translational Modification" ; dc:description "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; foaf:homepage "https://www.uniprot.org/docs/ptmlist"^^xsd:string ; bioregistry.schema:0000005 "PTM-0450"^^xsd:string ; @@ -29828,7 +29857,7 @@ bioregistry:uniprot.ptm a bioregistry.schema:0000001 ; bioregistry:uniprot.resource a bioregistry.schema:0000001 ; rdfs:label "UniProt Resource" ; dc:description "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; foaf:homepage "https://www.uniprot.org/database/"^^xsd:string ; bioregistry.schema:0000005 "DB-0174"^^xsd:string ; @@ -29839,7 +29868,7 @@ bioregistry:uniprot.resource a bioregistry.schema:0000001 ; bioregistry:uniprot.var a bioregistry.schema:0000001 ; rdfs:label "UniProt Variants" ; dc:description "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:uniprot ; foaf:homepage "https://web.expasy.org/variant_pages"^^xsd:string ; bioregistry.schema:0000005 "068078"^^xsd:string ; @@ -29850,7 +29879,7 @@ bioregistry:uniprot.var a bioregistry.schema:0000001 ; bioregistry:webelements a bioregistry.schema:0000001 ; rdfs:label "Web Elements" ; dc:description "Browser for the periodic table of the elements"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; foaf:homepage "https://www.webelements.com/"^^xsd:string ; bioregistry.schema:0000005 "chromium"^^xsd:string ; bioregistry.schema:0000006 "https://www.webelements.com/$1"^^xsd:string ; @@ -29860,10 +29889,10 @@ bioregistry:webelements a bioregistry.schema:0000001 ; bioregistry:wormbase a bioregistry.schema:0000001 ; rdfs:label "WormBase database of nematode biology" ; dc:description "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^xsd:string ; - dcterms:hasPart bioregistry:wbls, + ns1:hasPart bioregistry:wbls, bioregistry:wbphenotype ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1805, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1805, biocontext:WormBase, biolink:WBVocab, go.resource:WB_REF, @@ -29883,9 +29912,9 @@ bioregistry:wormbase a bioregistry.schema:0000001 ; bioregistry:xco a bioregistry.schema:0000001 ; rdfs:label "Experimental condition ontology" ; dc:description "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:XCO, - obofoundry:XCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:XCO, + obofoundry:xco, ontobee:XCO, bioportal:XCO, biocontext:XCO, @@ -29904,8 +29933,8 @@ bioregistry:xco a bioregistry.schema:0000001 ; bioregistry:ymdb a bioregistry.schema:0000001 ; rdfs:label "Yeast Metabolome Database" ; dc:description "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.tawpg2 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.tawpg2 ; foaf:homepage "http://www.ymdb.ca"^^xsd:string ; bioregistry.schema:0000005 "YMDB00001"^^xsd:string ; bioregistry.schema:0000006 "http://www.ymdb.ca/compounds/$1"^^xsd:string ; @@ -29915,7 +29944,7 @@ bioregistry:ymdb a bioregistry.schema:0000001 ; orcid:0000-0001-5208-3432 rdfs:label "Nicole Vasilevsky" . orcid:0000-0001-6330-7526 rdfs:label "Val Wood" ; - dcterms:contributor bioregistry:fyeco . + ns1:contributor bioregistry:fyeco . orcid:0000-0001-8815-0078 rdfs:label "Ramona Walls" . @@ -29939,17 +29968,14 @@ orcid:0000-0002-5640-5491 rdfs:label "Matt Yoder" . orcid:0000-0002-6443-9376 rdfs:label "Jennifer Smith" . orcid:0000-0002-7509-4804 rdfs:label "Tom Gillespie" ; - dcterms:contributor bioregistry:nlx.br . + ns1:contributor bioregistry:nlx.br . orcid:0000-0002-8457-6693 rdfs:label "Bjoern Peters" . -orcid:0000-0002-9881-1017 rdfs:label "Bill Hogan", - "William Hogan" . - bioregistry.metaresource:ecoportal a bioregistry.schema:0000002 ; rdfs:label "EcoPortal" ; dc:description "The LifeWatch ERIC repository of semantic resources for the ecological domain." ; - dcterms:hasPart ecoportal:AGROVOC, + ns1:hasPart ecoportal:AGROVOC, ecoportal:BCO, ecoportal:PCO, ecoportal:STY ; @@ -29961,11 +29987,11 @@ bioregistry.metaresource:ecoportal a bioregistry.schema:0000002 ; bioregistry:chembl a bioregistry.schema:0000001 ; rdfs:label "ChEMBL" ; dc:description "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^xsd:string ; - dcterms:hasPart bioregistry:chembl.cell, + ns1:hasPart bioregistry:chembl.cell, bioregistry:chembl.compound, bioregistry:chembl.target ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.m3jtpg, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.m3jtpg, prefixcommons:chembl, miriam:chembl, cheminf:000412, @@ -29979,9 +30005,9 @@ bioregistry:chembl a bioregistry.schema:0000001 ; bioregistry:clyh a bioregistry.schema:0000001 ; rdfs:label "Clytia hemisphaerica Development and Anatomy Ontology" ; dc:description "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CLYH, - obofoundry:CLYH, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CLYH, + obofoundry:clyh, ontobee:CLYH, bioportal:CLYH, ols:clyh ; @@ -29995,7 +30021,7 @@ bioregistry:clyh a bioregistry.schema:0000001 ; bioregistry:uberon ; bioregistry.schema:0000019 orcid:0000-0002-7440-0467 . -bioregistry:dragondb dcterms:hasPart bioregistry:dragondb.allele, +bioregistry:dragondb ns1:hasPart bioregistry:dragondb.allele, bioregistry:dragondb.dna, bioregistry:dragondb.locus, bioregistry:dragondb.protein . @@ -30003,9 +30029,9 @@ bioregistry:dragondb dcterms:hasPart bioregistry:dragondb.allele, bioregistry:duo a bioregistry.schema:0000001 ; rdfs:label "Data Use Ontology" ; dc:description "DUO is an ontology which represent data use conditions."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:DUO, - obofoundry:DUO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:DUO, + obofoundry:duo, ontobee:DUO, bioportal:DUO, biocontext:DUO, @@ -30024,9 +30050,9 @@ bioregistry:duo a bioregistry.schema:0000001 ; bioregistry:ecao a bioregistry.schema:0000001 ; rdfs:label "The Echinoderm Anatomy and Development Ontology" ; dc:description "None"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ECAO, - obofoundry:ECAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ECAO, + obofoundry:ecao, ontobee:ECAO, bioportal:ECAO, ols:ecao ; @@ -30043,8 +30069,8 @@ bioregistry:ecao a bioregistry.schema:0000001 ; bioregistry:efo a bioregistry.schema:0000001 ; rdfs:label "Experimental Factor Ontology" ; dc:description "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EFO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EFO, agroportal:EFO, ontobee:EFO, bioportal:EFO, @@ -30062,35 +30088,14 @@ bioregistry:efo a bioregistry.schema:0000001 ; bioregistry.schema:0000012 false ; bioregistry.schema:0000019 orcid:0000-0002-3458-4839 . -bioregistry:ehdaa2 a bioregistry.schema:0000001 ; - rdfs:label "Human developmental anatomy, abstract" ; - dc:description "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EHDAA2, - obofoundry:EHDAA2, - ontobee:EHDAA2, - bioportal:EHDAA2, - biocontext:EHDAA2, - fairsharing:FAIRsharing.7zxrs6, - ols:ehdaa2 ; - foaf:homepage "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^xsd:string ; - bioregistry.schema:0000005 "0000000"^^xsd:string ; - bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/EHDAA2_$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{7}$"^^xsd:string ; - bioregistry.schema:0000012 true ; - bioregistry.schema:0000017 bioregistry:aeo, - bioregistry:caro, - bioregistry:cl ; - bioregistry.schema:0000019 [ rdfs:label "Jonathan Bard" ] . - bioregistry:fbcv a bioregistry.schema:0000001 ; rdfs:label "FlyBase Controlled Vocabulary" ; dc:description "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^xsd:string ; - dcterms:hasPart bioregistry:dpo ; - dcterms:isPartOf bioregistry.metaresource:bioregistry, + ns1:hasPart bioregistry:dpo ; + ns1:isPartOf bioregistry.metaresource:bioregistry, bioregistry:flybase ; - ns1:exactMatch aberowl:FBCV, - obofoundry:FBcv, + ns2:exactMatch aberowl:FBCV, + obofoundry:fbcv, ontobee:FBCV, bioportal:FB-CV, biocontext:FBcv, @@ -30108,9 +30113,9 @@ bioregistry:fbcv a bioregistry.schema:0000001 ; bioregistry:nbo a bioregistry.schema:0000001 ; rdfs:label "Neuro Behavior Ontology" ; dc:description "An ontology of human and animal behaviours and behavioural phenotypes"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NBO, - obofoundry:NBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NBO, + obofoundry:nbo, ontobee:NBO, bioportal:NBO, biocontext:NBO, @@ -30129,9 +30134,9 @@ bioregistry:nbo a bioregistry.schema:0000001 ; bioregistry:one a bioregistry.schema:0000001 ; rdfs:label "Ontology for Nutritional Epidemiology" ; dc:description "An ontology to standardize research output of nutritional epidemiologic studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ONE, - obofoundry:ONE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ONE, + obofoundry:one, ontobee:ONE, bioportal:ONE, fairsharing:FAIRsharing.USxx0K, @@ -30146,7 +30151,7 @@ bioregistry:one a bioregistry.schema:0000001 ; bioregistry:ons ; bioregistry.schema:0000019 orcid:0000-0001-9202-5309 . -bioregistry:panther dcterms:hasPart bioregistry:panther.family, +bioregistry:panther ns1:hasPart bioregistry:panther.family, bioregistry:panther.node, bioregistry:panther.pathway, bioregistry:panther.pthcmp . @@ -30154,8 +30159,8 @@ bioregistry:panther dcterms:hasPart bioregistry:panther.family, bioregistry:pdb a bioregistry.schema:0000001 ; rdfs:label "PDB Structure" ; dc:description "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1127, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1127, biocontext:PDB, go.resource:PDB, n2t:pdb, @@ -30174,9 +30179,9 @@ bioregistry:pdb a bioregistry.schema:0000001 ; bioregistry:plana a bioregistry.schema:0000001 ; rdfs:label "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" ; dc:description "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PLANA, - obofoundry:PLANA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PLANA, + obofoundry:plana, ontobee:PLANA, bioportal:PLANA, biocontext:PLANA, @@ -30195,9 +30200,9 @@ bioregistry:plana a bioregistry.schema:0000001 ; bioregistry:stato a bioregistry.schema:0000001 ; rdfs:label "The Statistical Methods Ontology" ; dc:description "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:STATO, - obofoundry:STATO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:STATO, + obofoundry:stato, ontobee:STATO, bioportal:STATO, biocontext:STATO, @@ -30216,11 +30221,11 @@ bioregistry:stato a bioregistry.schema:0000001 ; bioregistry:storedb a bioregistry.schema:0000001 ; rdfs:label "Store DB" ; dc:description "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^xsd:string ; - dcterms:hasPart bioregistry:storedb.dataset, + ns1:hasPart bioregistry:storedb.dataset, bioregistry:storedb.file, bioregistry:storedb.study ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:STOREDB, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:STOREDB, n2t:storedb, fairsharing:FAIRsharing.6h8d2r, miriam:storedb ; @@ -30234,16 +30239,19 @@ orcid:0000-0001-5985-7429 rdfs:label "Colin Batchelor" . orcid:0000-0002-8688-6599 rdfs:label "Jim Balhoff" . +orcid:0000-0002-9881-1017 rdfs:label "Bill Hogan", + "William Hogan" . + orcid:0000-0003-1834-3856 rdfs:label "Mathias Brochhausen" . bioregistry:drugbank a bioregistry.schema:0000001 ; rdfs:label "DrugBank" ; dc:description "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^xsd:string ; - dcterms:hasPart bioregistry:drugbank.category, + ns1:hasPart bioregistry:drugbank.category, bioregistry:drugbank.salt, bioregistry:drugbankv4.target ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:2326, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:2326, biocontext:DrugBank, cellosaurus.resource:DrugBank, n2t:drugbank, @@ -30262,12 +30270,12 @@ bioregistry:drugbank a bioregistry.schema:0000001 ; bioregistry:edam a bioregistry.schema:0000001 ; rdfs:label "Bioinformatics operations, data types, formats, identifiers and topics" ; dc:description "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^xsd:string ; - dcterms:hasPart bioregistry:edam.data, + ns1:hasPart bioregistry:edam.data, bioregistry:edam.format, bioregistry:edam.operation, bioregistry:edam.topic ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:EDAM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:EDAM, agroportal:EDAM, ontobee:EDAM, bioportal:EDAM, @@ -30287,11 +30295,11 @@ bioregistry:edam a bioregistry.schema:0000001 ; bioregistry:multicellds a bioregistry.schema:0000001 ; rdfs:label "MultiCellDS" ; dc:description "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^xsd:string ; - dcterms:hasPart bioregistry:multicellds.cell_line, + ns1:hasPart bioregistry:multicellds.cell_line, bioregistry:multicellds.collection, bioregistry:multicellds.snapshot ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch fairsharing:FAIRsharing.pqzyd5 ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch fairsharing:FAIRsharing.pqzyd5 ; foaf:homepage "http://multicellds.org/MultiCellDB.php"^^xsd:string ; bioregistry.schema:0000005 "MCDS_S_0000000001"^^xsd:string ; bioregistry.schema:0000006 "http://multicellds.org/MultiCellDB/$1"^^xsd:string ; @@ -30300,9 +30308,9 @@ bioregistry:multicellds a bioregistry.schema:0000001 ; bioregistry:ncit a bioregistry.schema:0000001 ; rdfs:label "NCI Thesaurus" ; dc:description "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NCIT, - obofoundry:NCIT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NCIT, + obofoundry:ncit, ontobee:NCIT, bioportal:NCIT, biocontext:NCIT, @@ -30327,9 +30335,9 @@ bioregistry:ncit a bioregistry.schema:0000001 ; bioregistry:planp a bioregistry.schema:0000001 ; rdfs:label "Planarian Phenotype Ontology" ; dc:description "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PLANP, - obofoundry:PLANP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PLANP, + obofoundry:planp, ontobee:PLANP, bioportal:PLANP, ols:planp ; @@ -30347,11 +30355,11 @@ bioregistry:planp a bioregistry.schema:0000001 ; bioregistry:po a bioregistry.schema:0000001 ; rdfs:label "Plant Ontology" ; dc:description "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PO, agroportal:PO, edam.data:1180, - obofoundry:PO, + obofoundry:po, ontobee:PO, bioportal:PO, biocontext:PO, @@ -30375,9 +30383,9 @@ bioregistry:po a bioregistry.schema:0000001 ; bioregistry:psdo a bioregistry.schema:0000001 ; rdfs:label "Performance Summary Display Ontology" ; dc:description "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PSDO, - obofoundry:PSDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PSDO, + obofoundry:psdo, ontobee:PSDO, bioportal:PSDO, ols:psdo ; @@ -30395,19 +30403,19 @@ bioregistry:psdo a bioregistry.schema:0000001 ; bioregistry:qtldb a bioregistry.schema:0000001 ; rdfs:label "Animal Genome QTL" ; dc:description "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^xsd:string ; - dcterms:hasPart bioregistry:cattleqtldb, + ns1:hasPart bioregistry:cattleqtldb, bioregistry:chickenqtldb, bioregistry:pigqtldb, bioregistry:sheepqtldb ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch miriam:qtldb ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch miriam:qtldb ; foaf:homepage "https://www.animalgenome.org/QTLdb"^^xsd:string ; bioregistry.schema:0000005 "4685"^^xsd:string ; bioregistry.schema:0000006 "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:umbbd dcterms:hasPart bioregistry:umbbd.compound, +bioregistry:umbbd ns1:hasPart bioregistry:umbbd.compound, bioregistry:umbbd.enzyme, bioregistry:umbbd.pathway, bioregistry:umbbd.reaction, @@ -30416,9 +30424,9 @@ bioregistry:umbbd dcterms:hasPart bioregistry:umbbd.compound, bioregistry:uo a bioregistry.schema:0000001 ; rdfs:label "Units of measurement ontology" ; dc:description "Ontology of standardized units"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:UO, - obofoundry:UO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:UO, + obofoundry:uo, ontobee:UO, bioportal:UO, biocontext:UO, @@ -30444,14 +30452,14 @@ orcid:0000-0002-1005-8383 rdfs:label "Pankaj Jaiswal" . orcid:0000-0002-1373-1705 rdfs:label "Clare Pilgrim" . -wikidata:P7001 dcterms:isPartOf bioregistry.metaresource:wikidata . +wikidata:P7001 ns1:isPartOf bioregistry.metaresource:wikidata . bioregistry:bspo a bioregistry.schema:0000001 ; rdfs:label "Biological Spatial Ontology" ; dc:description "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BSPO, - obofoundry:BSPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BSPO, + obofoundry:bspo, ontobee:BSPO, bioportal:BSPO, biocontext:BSPO, @@ -30472,9 +30480,9 @@ bioregistry:bspo a bioregistry.schema:0000001 ; bioregistry:caro a bioregistry.schema:0000001 ; rdfs:label "Common Anatomy Reference Ontology" ; dc:description "None"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CARO, - obofoundry:CARO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CARO, + obofoundry:caro, ontobee:CARO, bioportal:CARO, biocontext:CARO, @@ -30488,7 +30496,6 @@ bioregistry:caro a bioregistry.schema:0000001 ; bioregistry.schema:0000012 false ; bioregistry.schema:0000018 bioregistry:aism, bioregistry:colao, - bioregistry:ehdaa2, bioregistry:lepao, bioregistry:pco ; bioregistry.schema:0000019 orcid:0000-0001-9114-8737 . @@ -30496,9 +30503,9 @@ bioregistry:caro a bioregistry.schema:0000001 ; bioregistry:cdno a bioregistry.schema:0000001 ; rdfs:label "Compositional Dietary Nutrition Ontology" ; dc:description "None"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CDNO, - obofoundry:CDNO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CDNO, + obofoundry:cdno, ontobee:CDNO, bioportal:CDNO, ols:cdno ; @@ -30517,9 +30524,9 @@ bioregistry:cdno a bioregistry.schema:0000001 ; bioregistry:clo a bioregistry.schema:0000001 ; rdfs:label "Cell Line Ontology" ; dc:description "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CLO, - obofoundry:CLO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CLO, + obofoundry:clo, ontobee:CLO, bioportal:CLO, biocontext:CLO, @@ -30543,13 +30550,13 @@ bioregistry:clo a bioregistry.schema:0000001 ; bioregistry:flybase a bioregistry.schema:0000001 ; rdfs:label "FlyBase Gene" ; dc:description "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^xsd:string ; - dcterms:hasPart bioregistry:fbbt, + ns1:hasPart bioregistry:fbbt, bioregistry:fbcv, bioregistry:fbrf, bioregistry:fbsp, bioregistry:fbtc ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch edam.data:1089, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch edam.data:1089, biocontext:FlyBase, cellosaurus.resource:FlyBase, go.resource:FB, @@ -30569,9 +30576,9 @@ bioregistry:flybase a bioregistry.schema:0000001 ; bioregistry:genepio a bioregistry.schema:0000001 ; rdfs:label "Genomic Epidemiology Ontology" ; dc:description "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GENEPIO, - obofoundry:GENEPIO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GENEPIO, + obofoundry:genepio, ontobee:GENEPIO, biocontext:GENEPIO, fairsharing:FAIRsharing.y1mmbv, @@ -30591,9 +30598,9 @@ bioregistry:genepio a bioregistry.schema:0000001 ; bioregistry:hso a bioregistry.schema:0000001 ; rdfs:label "Health Surveillance Ontology" ; dc:description "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:HSO, - obofoundry:HSO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:HSO, + obofoundry:hso, ontobee:HSO, bioportal:HSO, ols:hso ; @@ -30618,9 +30625,9 @@ The lack of a clearly defined vocabulary makes biologists feel reluctant to embr OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). More information can be found at https://obofoundry.org/ontology/ontoavida.html"""^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ONTOAVIDA, - obofoundry:ONTOAVIDA, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ONTOAVIDA, + obofoundry:ontoavida, ontobee:ONTOAVIDA, bioportal:ONTOAVIDA, ols:ontoavida ; @@ -30636,7 +30643,7 @@ More information can be found at https://obofoundry.org/ontology/ontoavida.html" bioregistry:stato ; bioregistry.schema:0000019 orcid:0000-0002-8374-1941 . -bioregistry:pubchem dcterms:hasPart bioregistry:pubchem.bioassay, +bioregistry:pubchem ns1:hasPart bioregistry:pubchem.bioassay, bioregistry:pubchem.cell, bioregistry:pubchem.classification, bioregistry:pubchem.compound, @@ -30650,9 +30657,9 @@ orcid:0000-0002-2999-0103 rdfs:label "Jie Zheng" . bioregistry:labo a bioregistry.schema:0000001 ; rdfs:label "clinical LABoratory Ontology" ; dc:description "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LABO, - obofoundry:LABO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LABO, + obofoundry:labo, ontobee:LABO, bioportal:LABO, ols:labo ; @@ -30664,7 +30671,6 @@ bioregistry:labo a bioregistry.schema:0000001 ; bioregistry.schema:0000017 bioregistry:iao, bioregistry:obi, bioregistry:ogms, - bioregistry:omiabis, bioregistry:omrse, bioregistry:opmi ; bioregistry.schema:0000019 orcid:0000-0002-3336-2476 . @@ -30672,10 +30678,10 @@ bioregistry:labo a bioregistry.schema:0000001 ; bioregistry:pr a bioregistry.schema:0000001 ; rdfs:label "Protein Ontology" ; dc:description "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PR, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PR, agroportal:PR, - obofoundry:PR, + obofoundry:pr, ontobee:PR, bioportal:PR, biocontext:PR, @@ -30701,11 +30707,12 @@ bioregistry:pr a bioregistry.schema:0000001 ; bioregistry:proco a bioregistry.schema:0000001 ; rdfs:label "Process Chemistry Ontology" ; - dc:description "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PROCO, - obofoundry:PROCO, - ontobee:PROCO ; + dc:description "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^xsd:string ; + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PROCO, + obofoundry:proco, + ontobee:PROCO, + ols:proco ; foaf:homepage "https://github.com/proco-ontology/PROCO"^^xsd:string ; bioregistry.schema:0000005 "0000001"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/PROCO_$1"^^xsd:string ; @@ -30721,14 +30728,14 @@ bioregistry:proco a bioregistry.schema:0000001 ; orcid:0000-0002-9415-5104 rdfs:label "Frederic Bastian", "Frédéric Bastian" . -wikidata:P665 dcterms:isPartOf bioregistry.metaresource:wikidata . +wikidata:P665 ns1:isPartOf bioregistry.metaresource:wikidata . bioregistry:chiro a bioregistry.schema:0000001 ; rdfs:label "ChEBI Integrated Role Ontology" ; dc:description "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CHIRO, - obofoundry:CHIRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CHIRO, + obofoundry:chiro, ontobee:CHIRO, bioportal:CHIRO, ols:chiro ; @@ -30747,9 +30754,9 @@ bioregistry:chiro a bioregistry.schema:0000001 ; bioregistry:colao a bioregistry.schema:0000001 ; rdfs:label "Coleoptera Anatomy Ontology" ; dc:description "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:COLAO, - obofoundry:COLAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:COLAO, + obofoundry:colao, ontobee:COLAO, bioportal:COLAO, ols:colao ; @@ -30770,9 +30777,9 @@ bioregistry:colao a bioregistry.schema:0000001 ; bioregistry:lepao a bioregistry.schema:0000001 ; rdfs:label "Lepidoptera Anatomy Ontology" ; dc:description "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:LEPAO, - obofoundry:LEPAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:LEPAO, + obofoundry:lepao, bioportal:LEPAO, ols:lepao ; foaf:homepage "https://github.com/insect-morphology/lepao"^^xsd:string ; @@ -30792,9 +30799,9 @@ bioregistry:lepao a bioregistry.schema:0000001 ; bioregistry:maxo a bioregistry.schema:0000001 ; rdfs:label "Medical Action Ontology" ; dc:description "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MAXO, - obofoundry:MAXO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MAXO, + obofoundry:maxo, ontobee:MAXO, bioportal:MAXO, biolink:MAXO, @@ -30816,9 +30823,9 @@ bioregistry:maxo a bioregistry.schema:0000001 ; bioregistry:rbo a bioregistry.schema:0000001 ; rdfs:label "Radiation Biology Ontology" ; dc:description "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RBO, - obofoundry:RBO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RBO, + obofoundry:rbo, ontobee:RBO, bioportal:RBO, ols:rbo ; @@ -30839,9 +30846,9 @@ bioregistry:rbo a bioregistry.schema:0000001 ; bioregistry:zp a bioregistry.schema:0000001 ; rdfs:label "Zebrafish Phenotype Ontology" ; dc:description "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ZP, - obofoundry:ZP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ZP, + obofoundry:zp, ontobee:ZP, bioportal:ZP, biocontext:ZP, @@ -30863,9 +30870,9 @@ bioregistry:zp a bioregistry.schema:0000001 ; bioregistry:aism a bioregistry.schema:0000001 ; rdfs:label "Ontology for the Anatomy of the Insect SkeletoMuscular system" ; dc:description "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AISM, - obofoundry:AISM, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AISM, + obofoundry:aism, ontobee:AISM, bioportal:AISM, ols:aism ; @@ -30887,9 +30894,9 @@ bioregistry:aism a bioregistry.schema:0000001 ; bioregistry:fovt a bioregistry.schema:0000001 ; rdfs:label "FuTRES Ontology of Vertebrate Traits" ; dc:description "None"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FOVT, - obofoundry:FOVT, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FOVT, + obofoundry:fovt, ontobee:FOVT, bioportal:FOVT, ols:fovt ; @@ -30911,9 +30918,9 @@ bioregistry:fovt a bioregistry.schema:0000001 ; bioregistry:xpo a bioregistry.schema:0000001 ; rdfs:label "Xenopus Phenotype Ontology" ; dc:description "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:XPO, - obofoundry:XPO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:XPO, + obofoundry:xpo, ontobee:XPO, bioportal:XPO, biolink:XPO, @@ -30936,9 +30943,9 @@ bioregistry:xpo a bioregistry.schema:0000001 ; bioregistry:ons a bioregistry.schema:0000001 ; rdfs:label "Ontology for Nutritional Studies" ; dc:description "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ONS, - obofoundry:ONS, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ONS, + obofoundry:ons, ontobee:ONS, bioportal:ONS, fairsharing:FAIRsharing.rfec93, @@ -30965,9 +30972,9 @@ orcid:0000-0001-9189-9661 rdfs:label "Yongqun Oliver He", bioregistry:ecocore a bioregistry.schema:0000001 ; rdfs:label "An ontology of core ecological entities" ; dc:description "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ECOCORE, - obofoundry:ECOCORE, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ECOCORE, + obofoundry:ecocore, ontobee:ECOCORE, bioportal:ECOCORE, biocontext:ECOCORE, @@ -30992,9 +30999,9 @@ bioregistry:ecocore a bioregistry.schema:0000001 ; bioregistry:obi a bioregistry.schema:0000001 ; rdfs:label "Ontology for Biomedical Investigations" ; dc:description "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:OBI, - obofoundry:OBI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:OBI, + obofoundry:obi, ontobee:OBI, bioportal:OBI, biocontext:OBI, @@ -31024,11 +31031,11 @@ bioregistry:obi a bioregistry.schema:0000001 ; bioregistry:pco a bioregistry.schema:0000001 ; rdfs:label "Population and Community Ontology" ; dc:description "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PCO, agroportal:PCO, ecoportal:PCO, - obofoundry:PCO, + obofoundry:pco, ontobee:PCO, bioportal:PCO, biocontext:PCO, @@ -31054,9 +31061,9 @@ bioregistry:pco a bioregistry.schema:0000001 ; bioregistry:iao a bioregistry.schema:0000001 ; rdfs:label "Information Artifact Ontology" ; dc:description "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:IAO, - obofoundry:IAO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:IAO, + obofoundry:iao, ontobee:IAO, bioportal:IAO, biocontext:IAO, @@ -31084,15 +31091,15 @@ bioregistry:iao a bioregistry.schema:0000001 ; bioregistry.schema:0000019 orcid:0000-0002-2999-0103 . orcid:0000-0002-6601-2165 rdfs:label "Chris Mungall" ; - dcterms:contributor bioregistry:insdc.run, + ns1:contributor bioregistry:insdc.run, bioregistry:wwf.ecoregion . bioregistry:pcl a bioregistry.schema:0000001 ; rdfs:label "Provisional Cell Ontology" ; dc:description "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PCL, - obofoundry:PCL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PCL, + obofoundry:pcl, ontobee:PCL, bioportal:PCL, ols:pcl ; @@ -31118,9 +31125,9 @@ bioregistry:pcl a bioregistry.schema:0000001 ; bioregistry:ecto a bioregistry.schema:0000001 ; rdfs:label "Environmental conditions, treatments and exposures ontology" ; dc:description "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ECTO, - obofoundry:ECTO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ECTO, + obofoundry:ecto, ontobee:ECTO, bioportal:ECTO, biolink:ECTO, @@ -31148,7 +31155,7 @@ bioregistry:ecto a bioregistry.schema:0000001 ; bioregistry.metaresource:cheminf a bioregistry.schema:0000002 ; rdfs:label "Chemical Information Ontology" ; dc:description "Contains entries for various database identifiers" ; - dcterms:hasPart cheminf:000140, + ns1:hasPart cheminf:000140, cheminf:000141, cheminf:000302, cheminf:000304, @@ -31171,10 +31178,10 @@ bioregistry.metaresource:cheminf a bioregistry.schema:0000002 ; bioregistry:agro a bioregistry.schema:0000001 ; rdfs:label "Agronomy Ontology" ; dc:description "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:AGRO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:AGRO, agroportal:AGRO, - obofoundry:AGRO, + obofoundry:agro, ontobee:AGRO, bioportal:AGRO, biocontext:AGRO, @@ -31204,10 +31211,10 @@ bioregistry:agro a bioregistry.schema:0000001 ; bioregistry:foodon a bioregistry.schema:0000001 ; rdfs:label "The Food Ontology" ; dc:description "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:FOODON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:FOODON, agroportal:FOODON, - obofoundry:FOODON, + obofoundry:foodon, ontobee:FOODON, bioportal:FOODON, biocontext:FOODON, @@ -31223,7 +31230,6 @@ bioregistry:foodon a bioregistry.schema:0000001 ; bioregistry.schema:0000017 bioregistry:bfo, bioregistry:chebi, bioregistry:envo, - bioregistry:eo, bioregistry:ncbitaxon, bioregistry:obi, bioregistry:ro, @@ -31239,9 +31245,9 @@ bioregistry:foodon a bioregistry.schema:0000001 ; bioregistry:mco a bioregistry.schema:0000001 ; rdfs:label "Microbial Conditions Ontology" ; dc:description "Microbial Conditions Ontology is an ontology..."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:MCO, - obofoundry:MCO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:MCO, + obofoundry:mco, ontobee:MCO, bioportal:MCO, ols:mco ; @@ -31269,11 +31275,11 @@ bioregistry:mco a bioregistry.schema:0000001 ; bioregistry:ncbitaxon a bioregistry.schema:0000001 ; rdfs:label "NCBI Taxonomy" ; dc:description "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:NCBITAXON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:NCBITAXON, agroportal:NCBITAXON, edam.data:1179, - obofoundry:NCBITaxon, + obofoundry:ncbitaxon, ontobee:NCBITaxon, bioportal:NCBITAXON, biocontext:TAXONOMY, @@ -31310,7 +31316,7 @@ bioregistry:ncbitaxon a bioregistry.schema:0000001 ; bioregistry:kegg a bioregistry.schema:0000001 ; rdfs:label "Kyoto Encyclopedia of Genes and Genomes" ; dc:description "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^xsd:string ; - dcterms:hasPart bioregistry:kegg.compound, + ns1:hasPart bioregistry:kegg.compound, bioregistry:kegg.dgroup, bioregistry:kegg.disease, bioregistry:kegg.drug, @@ -31326,8 +31332,8 @@ bioregistry:kegg a bioregistry.schema:0000001 ; bioregistry:kegg.pathway, bioregistry:kegg.rclass, bioregistry:kegg.reaction ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch biocontext:KEGG, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch biocontext:KEGG, go.resource:KEGG, n2t:kegg, miriam:kegg, @@ -31342,10 +31348,10 @@ bioregistry:kegg a bioregistry.schema:0000001 ; bioregistry:envo a bioregistry.schema:0000001 ; rdfs:label "Environment Ontology" ; dc:description "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:ENVO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:ENVO, agroportal:ENVO, - obofoundry:ENVO, + obofoundry:envo, ontobee:ENVO, bioportal:ENVO, biocontext:ENVO, @@ -31380,11 +31386,11 @@ bioregistry:envo a bioregistry.schema:0000001 ; bioregistry:go a bioregistry.schema:0000001 ; rdfs:label "Gene Ontology" ; dc:description "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:GO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:GO, agroportal:GO, edam.data:1176, - obofoundry:GO, + obofoundry:go, ontobee:GO, bioportal:GO, biocontext:GO, @@ -31424,10 +31430,10 @@ bioregistry:go a bioregistry.schema:0000001 ; bioregistry:cl a bioregistry.schema:0000001 ; rdfs:label "Cell Ontology" ; dc:description "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CL, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CL, agroportal:CL, - obofoundry:CL, + obofoundry:cl, ontobee:CL, bioportal:CL, biocontext:CL, @@ -31453,7 +31459,6 @@ bioregistry:cl a bioregistry.schema:0000001 ; bioregistry:uberon ; bioregistry.schema:0000018 bioregistry:clo, bioregistry:ecao, - bioregistry:ehdaa2, bioregistry:go, bioregistry:mco, bioregistry:pcl, @@ -31461,7 +31466,7 @@ bioregistry:cl a bioregistry.schema:0000001 ; bioregistry:xpo ; bioregistry.schema:0000019 orcid:0000-0001-9990-8331 . -bioregistry:nif dcterms:hasPart bioregistry:neurolex, +bioregistry:nif ns1:hasPart bioregistry:neurolex, bioregistry:nif.cell, bioregistry:nif.dysfunction, bioregistry:nif.ext, @@ -31484,10 +31489,10 @@ bioregistry:nif dcterms:hasPart bioregistry:neurolex, bioregistry:pato a bioregistry.schema:0000001 ; rdfs:label "Phenotype And Trait Ontology" ; dc:description "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:PATO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:PATO, agroportal:PATO, - obofoundry:PATO, + obofoundry:pato, ontobee:PATO, bioportal:PATO, biocontext:PATO, @@ -31526,10 +31531,10 @@ bioregistry:pato a bioregistry.schema:0000001 ; bioregistry:bfo a bioregistry.schema:0000001 ; rdfs:label "Basic Formal Ontology" ; dc:description "The upper level ontology upon which OBO Foundry ontologies are built."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:BFO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:BFO, agroportal:BFO, - obofoundry:BFO, + obofoundry:bfo, ontobee:BFO, bioportal:BFO, biocontext:BFO, @@ -31566,12 +31571,12 @@ bioregistry:bfo a bioregistry.schema:0000001 ; bioregistry:chebi a bioregistry.schema:0000001 ; rdfs:label "Chemical Entities of Biological Interest" ; dc:description "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^xsd:string ; - dcterms:hasPart bioregistry:fix, + ns1:hasPart bioregistry:fix, bioregistry:rex ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:CHEBI, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:CHEBI, edam.data:1174, - obofoundry:CHEBI, + obofoundry:chebi, ontobee:CHEBI, bioportal:CHEBI, biocontext:CHEBI, @@ -31611,7 +31616,7 @@ bioregistry:chebi a bioregistry.schema:0000001 ; bioregistry:uniprot a bioregistry.schema:0000001 ; rdfs:label "UniProt Protein" ; dc:description "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^xsd:string ; - dcterms:hasPart bioregistry:uniprot.chain, + ns1:hasPart bioregistry:uniprot.chain, bioregistry:uniprot.disease, bioregistry:uniprot.isoform, bioregistry:uniprot.keyword, @@ -31620,8 +31625,8 @@ bioregistry:uniprot a bioregistry.schema:0000001 ; bioregistry:uniprot.resource, bioregistry:uniprot.tissue, bioregistry:uniprot.var ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:UP, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:UP, edam.data:3021, biocontext:UniProtKB, cellosaurus.resource:UniProtKB, @@ -31641,9 +31646,9 @@ bioregistry:uniprot a bioregistry.schema:0000001 ; bioregistry:uberon a bioregistry.schema:0000001 ; rdfs:label "Uber Anatomy Ontology" ; dc:description "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:UBERON, - obofoundry:UBERON, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:UBERON, + obofoundry:uberon, ontobee:UBERON, bioportal:UBERON, biocontext:UBERON, @@ -31694,7 +31699,7 @@ bioregistry:uberon a bioregistry.schema:0000001 ; bioregistry.metaresource:cropoct a bioregistry.schema:0000002 ; rdfs:label "Crop Ontology Curation Tool" ; dc:description "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" ; - dcterms:hasPart cropoct:CO_320, + ns1:hasPart cropoct:CO_320, cropoct:CO_321, cropoct:CO_322, cropoct:CO_323, @@ -31734,9 +31739,9 @@ bioregistry.metaresource:cropoct a bioregistry.schema:0000002 ; bioregistry:scdo a bioregistry.schema:0000001 ; rdfs:label "Sickle Cell Disease Ontology" ; dc:description "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:SCDO, - obofoundry:SCDO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:SCDO, + obofoundry:scdo, ontobee:SCDO, bioportal:SCDO, fairsharing:FAIRsharing.kkq6pw, @@ -31757,13 +31762,11 @@ bioregistry:scdo a bioregistry.schema:0000001 ; bioregistry:envo, bioregistry:eupath, bioregistry:exo, - bioregistry:gaz, bioregistry:gsso, bioregistry:hp, bioregistry:hsapdv, bioregistry:ico, bioregistry:ido, - bioregistry:idomal, bioregistry:mp, bioregistry:nbo, bioregistry:ncit, @@ -31782,10 +31785,10 @@ bioregistry:scdo a bioregistry.schema:0000001 ; bioregistry:ro a bioregistry.schema:0000001 ; rdfs:label "Relation Ontology" ; dc:description "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - ns1:exactMatch aberowl:RO, + ns1:isPartOf bioregistry.metaresource:bioregistry ; + ns2:exactMatch aberowl:RO, agroportal:RO, - obofoundry:RO, + obofoundry:ro, ontobee:RO, bioportal:OBOREL, biocontext:RO, @@ -31832,13 +31835,12 @@ bioregistry:ro a bioregistry.schema:0000001 ; bioregistry:psdo, bioregistry:pso, bioregistry:rbo, - bioregistry:upa, bioregistry:xpo, bioregistry:zp ; bioregistry.schema:0000019 orcid:0000-0002-6601-2165 . orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; - dcterms:contributor bioregistry:4dn.replicate, + ns1:contributor bioregistry:4dn.replicate, bioregistry:ac, bioregistry:agilent.probe, bioregistry:alzforum.mutation, @@ -32055,7 +32057,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry.metaresource:agroportal a bioregistry.schema:0000002 ; rdfs:label "AgroPortal" ; dc:description "A vocabulary and ontology repository for agronomy and related domains." ; - dcterms:hasPart agroportal:AGRO, + ns1:hasPart agroportal:AGRO, agroportal:AGROVOC, agroportal:ATOL, agroportal:BCO, @@ -32130,7 +32132,7 @@ bioregistry.metaresource:agroportal a bioregistry.schema:0000002 ; bioregistry.metaresource:ncbi a bioregistry.schema:0000002 ; rdfs:label "National Center for Biotechnology Information Registry" ; dc:description "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" ; - dcterms:hasPart ncbi.resource:ASAP, + ns1:hasPart ncbi.resource:ASAP, ncbi.resource:ATCC, ncbi.resource:AntWeb, ncbi.resource:ApiDB_PlasmoDB, @@ -32209,7 +32211,7 @@ bioregistry.metaresource:ncbi a bioregistry.schema:0000002 ; bioregistry.metaresource:biolink a bioregistry.schema:0000002 ; rdfs:label "Biolink Model Registry" ; dc:description "A modeling paradigm-specific registry of prefixes and their URL expansions" ; - dcterms:hasPart biolink:AGRKB, + ns1:hasPart biolink:AGRKB, biolink:CAID, biolink:CID, biolink:CLINVAR, @@ -32309,7 +32311,7 @@ bioregistry.metaresource:biolink a bioregistry.schema:0000002 ; bioregistry.metaresource:uniprot a bioregistry.schema:0000002 ; rdfs:label "UniProt Cross-ref database" ; dc:description "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." ; - dcterms:hasPart uniprot.resource:ABCD, + ns1:hasPart uniprot.resource:ABCD, uniprot.resource:Allergome, uniprot.resource:ArachnoServer, uniprot.resource:Araport, @@ -32412,7 +32414,7 @@ bioregistry.metaresource:uniprot a bioregistry.schema:0000002 ; bioregistry.metaresource:cellosaurus a bioregistry.schema:0000002 ; rdfs:label "Cellosaurus Registry" ; dc:description "The set of prefixes used in the Cellosaurus resource" ; - dcterms:hasPart cellosaurus.resource:4DN, + ns1:hasPart cellosaurus.resource:4DN, cellosaurus.resource:ABCD, cellosaurus.resource:ABM, cellosaurus.resource:ATCC, @@ -32518,7 +32520,7 @@ bioregistry.metaresource:cellosaurus a bioregistry.schema:0000002 ; bioregistry.metaresource:edam a bioregistry.schema:0000002 ; rdfs:label "EDAM Ontology" ; dc:description "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." ; - dcterms:hasPart edam.data:1002, + ns1:hasPart edam.data:1002, edam.data:1003, edam.data:1004, edam.data:1011, @@ -32637,7 +32639,7 @@ bioregistry.metaresource:edam a bioregistry.schema:0000002 ; bioregistry.metaresource:wikidata a bioregistry.schema:0000002 ; rdfs:label "Wikidata Property" ; dc:description "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." ; - dcterms:hasPart wikidata:P1294, + ns1:hasPart wikidata:P1294, wikidata:P1391, wikidata:P1550, wikidata:P1554, @@ -32761,7 +32763,7 @@ bioregistry.metaresource:wikidata a bioregistry.schema:0000002 ; bioregistry.metaresource:go a bioregistry.schema:0000002 ; rdfs:label "Gene Ontology Registry" ; dc:description "A database-specific registry supporting curation in the Gene Ontology" ; - dcterms:hasPart go.resource:AGRICOLA_ID, + ns1:hasPart go.resource:AGRICOLA_ID, go.resource:ASAP, go.resource:AspGD_LOCUS, go.resource:BFO, @@ -32908,7 +32910,7 @@ bioregistry.metaresource:go a bioregistry.schema:0000002 ; bioregistry.metaresource:ontobee a bioregistry.schema:0000002 ; rdfs:label "OntoBee" ; dc:description "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." ; - dcterms:hasPart ontobee:AEO, + ns1:hasPart ontobee:AEO, ontobee:AGRO, ontobee:AISM, ontobee:AMPHX, @@ -33132,257 +33134,258 @@ bioregistry.metaresource:ontobee a bioregistry.schema:0000002 ; bioregistry.metaresource:obofoundry a bioregistry.schema:0000002 ; rdfs:label "OBO Foundry" ; dc:description "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." ; - dcterms:hasPart obofoundry:AAO, - obofoundry:ADO, - obofoundry:ADW, - obofoundry:AEO, - obofoundry:AERO, - obofoundry:AGRO, - obofoundry:AISM, - obofoundry:AMPHX, - obofoundry:APO, - obofoundry:APOLLO_SV, - obofoundry:ARO, - obofoundry:ATO, - obofoundry:BCGO, - obofoundry:BCO, - obofoundry:BFO, - obofoundry:BILA, - obofoundry:BOOTSTREP, - obofoundry:BSPO, - obofoundry:BTO, - obofoundry:CARO, - obofoundry:CDAO, - obofoundry:CDNO, - obofoundry:CEPH, - obofoundry:CHEBI, - obofoundry:CHEMINF, - obofoundry:CHIRO, - obofoundry:CHMO, - obofoundry:CIDO, - obofoundry:CIO, - obofoundry:CL, - obofoundry:CLAO, - obofoundry:CLO, - obofoundry:CLYH, - obofoundry:CMF, - obofoundry:CMO, - obofoundry:COB, - obofoundry:COLAO, - obofoundry:CRO, - obofoundry:CTENO, - obofoundry:CTO, - obofoundry:CVDO, - obofoundry:DC_CL, - obofoundry:DDANAT, - obofoundry:DDPHENO, - obofoundry:DIDEO, - obofoundry:DINTO, - obofoundry:DISDRIV, - obofoundry:DOID, - obofoundry:DRON, - obofoundry:DUO, - obofoundry:ECAO, - obofoundry:ECO, - obofoundry:ECOCORE, - obofoundry:ECTO, - obofoundry:EHDA, - obofoundry:EHDAA, - obofoundry:EHDAA2, - obofoundry:EMAP, - obofoundry:EMAPA, - obofoundry:ENVO, - obofoundry:EO, - obofoundry:EPIO, - obofoundry:EPO, - obofoundry:ERO, - obofoundry:EUPATH, - obofoundry:EV, - obofoundry:ExO, - obofoundry:FAO, - obofoundry:FBSP, - obofoundry:FBbi, - obofoundry:FBbt, - obofoundry:FBcv, - obofoundry:FBdv, - obofoundry:FIDEO, - obofoundry:FIX, - obofoundry:FLOPO, - obofoundry:FLU, - obofoundry:FMA, - obofoundry:FOBI, - obofoundry:FOODON, - obofoundry:FOVT, - obofoundry:FYPO, - obofoundry:GAZ, - obofoundry:GECKO, - obofoundry:GENEPIO, - obofoundry:GENO, - obofoundry:GEO, - obofoundry:GNO, - obofoundry:GO, - obofoundry:GRO, - obofoundry:GSSO, - obofoundry:HABRONATTUS, - obofoundry:HANCESTRO, - obofoundry:HAO, - obofoundry:HOM, - obofoundry:HP, - obofoundry:HSO, - obofoundry:HTN, - obofoundry:HsapDv, - obofoundry:IAO, - obofoundry:ICEO, - obofoundry:ICO, - obofoundry:IDO, - obofoundry:IDOMAL, - obofoundry:IEV, - obofoundry:IMR, - obofoundry:INO, - obofoundry:IPR, - obofoundry:KISAO, - obofoundry:LABO, - obofoundry:LEPAO, - obofoundry:LIPRO, - obofoundry:LOGGERHEAD, - obofoundry:MA, - obofoundry:MAMO, - obofoundry:MAO, - obofoundry:MAT, - obofoundry:MAXO, - obofoundry:MCO, - obofoundry:MF, - obofoundry:MFMO, - obofoundry:MFO, - obofoundry:MFOEM, - obofoundry:MFOMD, - obofoundry:MI, - obofoundry:MIAPA, - obofoundry:MICRO, - obofoundry:MIRNAO, - obofoundry:MIRO, - obofoundry:MMO, - obofoundry:MO, - obofoundry:MOD, - obofoundry:MONDO, - obofoundry:MOP, - obofoundry:MP, - obofoundry:MPATH, - obofoundry:MPIO, - obofoundry:MRO, - obofoundry:MS, - obofoundry:MmusDv, - obofoundry:NBO, - obofoundry:NCBITaxon, - obofoundry:NCIT, - obofoundry:NCRO, - obofoundry:NIF_CELL, - obofoundry:NIF_DYSFUNCTION, - obofoundry:NIF_GROSSANATOMY, - obofoundry:NMR, - obofoundry:NOMEN, - obofoundry:OAE, - obofoundry:OARCS, - obofoundry:OBA, - obofoundry:OBCS, - obofoundry:OBI, - obofoundry:OBIB, - obofoundry:OGG, - obofoundry:OGI, - obofoundry:OGMS, - obofoundry:OGSF, - obofoundry:OHD, - obofoundry:OHMI, - obofoundry:OHPI, - obofoundry:OMIABIS, - obofoundry:OMIT, - obofoundry:OMO, - obofoundry:OMP, - obofoundry:OMRSE, - obofoundry:ONE, - obofoundry:ONS, - obofoundry:ONTOAVIDA, - obofoundry:ONTONEO, - obofoundry:OOSTT, - obofoundry:OPL, - obofoundry:OPMI, - obofoundry:ORNASEQ, - obofoundry:OVAE, - obofoundry:OlatDv, - obofoundry:PAO, - obofoundry:PATO, - obofoundry:PCL, - obofoundry:PCO, - obofoundry:PDRO, - obofoundry:PD_ST, - obofoundry:PECO, - obofoundry:PGDSO, - obofoundry:PHIPO, - obofoundry:PLANA, - obofoundry:PLANP, - obofoundry:PLO, - obofoundry:PO, - obofoundry:PORO, - obofoundry:PPO, - obofoundry:PR, - obofoundry:PROCO, - obofoundry:PROPREO, - obofoundry:PSDO, - obofoundry:PSO, - obofoundry:PW, - obofoundry:PdumDv, - obofoundry:RBO, - obofoundry:RESID, - obofoundry:REX, - obofoundry:RNAO, - obofoundry:RO, - obofoundry:RS, - obofoundry:RXNO, - obofoundry:SAO, - obofoundry:SBO, - obofoundry:SCDO, - obofoundry:SEP, - obofoundry:SEPIO, - obofoundry:SIBO, - obofoundry:SO, - obofoundry:SOPHARM, - obofoundry:SPD, - obofoundry:STATO, - obofoundry:SWO, - obofoundry:SYMP, - obofoundry:TADS, - obofoundry:TAHE, - obofoundry:TAHH, - obofoundry:TAO, - obofoundry:TAXRANK, - obofoundry:TGMA, - obofoundry:TO, - obofoundry:TRANS, - obofoundry:TTO, - obofoundry:TXPO, - obofoundry:UBERON, - obofoundry:UO, - obofoundry:UPA, - obofoundry:UPHENO, - obofoundry:VHOG, - obofoundry:VO, - obofoundry:VSAO, - obofoundry:VT, - obofoundry:VTO, - obofoundry:VariO, - obofoundry:WBPhenotype, - obofoundry:WBbt, - obofoundry:WBls, - obofoundry:XAO, - obofoundry:XCO, - obofoundry:XLMOD, - obofoundry:XPO, - obofoundry:YPO, - obofoundry:ZEA, - obofoundry:ZECO, - obofoundry:ZFA, - obofoundry:ZFS, - obofoundry:ZP ; + ns1:hasPart obofoundry:aao, + obofoundry:ado, + obofoundry:adw, + obofoundry:aeo, + obofoundry:aero, + obofoundry:agro, + obofoundry:aism, + obofoundry:amphx, + obofoundry:apo, + obofoundry:apollo_sv, + obofoundry:aro, + obofoundry:ato, + obofoundry:bcgo, + obofoundry:bco, + obofoundry:bfo, + obofoundry:bila, + obofoundry:bootstrep, + obofoundry:bspo, + obofoundry:bto, + obofoundry:caro, + obofoundry:cdao, + obofoundry:cdno, + obofoundry:ceph, + obofoundry:chebi, + obofoundry:cheminf, + obofoundry:chiro, + obofoundry:chmo, + obofoundry:cido, + obofoundry:cio, + obofoundry:cl, + obofoundry:clao, + obofoundry:clo, + obofoundry:clyh, + obofoundry:cmf, + obofoundry:cmo, + obofoundry:cob, + obofoundry:colao, + obofoundry:cro, + obofoundry:cteno, + obofoundry:cto, + obofoundry:cvdo, + obofoundry:dc_cl, + obofoundry:ddanat, + obofoundry:ddpheno, + obofoundry:dideo, + obofoundry:dinto, + obofoundry:disdriv, + obofoundry:doid, + obofoundry:dpo, + obofoundry:dron, + obofoundry:duo, + obofoundry:ecao, + obofoundry:eco, + obofoundry:ecocore, + obofoundry:ecto, + obofoundry:ehda, + obofoundry:ehdaa, + obofoundry:ehdaa2, + obofoundry:emap, + obofoundry:emapa, + obofoundry:envo, + obofoundry:eo, + obofoundry:epio, + obofoundry:epo, + obofoundry:ero, + obofoundry:eupath, + obofoundry:ev, + obofoundry:exo, + obofoundry:fao, + obofoundry:fbbi, + obofoundry:fbbt, + obofoundry:fbcv, + obofoundry:fbdv, + obofoundry:fbsp, + obofoundry:fideo, + obofoundry:fix, + obofoundry:flopo, + obofoundry:flu, + obofoundry:fma, + obofoundry:fobi, + obofoundry:foodon, + obofoundry:fovt, + obofoundry:fypo, + obofoundry:gaz, + obofoundry:gecko, + obofoundry:genepio, + obofoundry:geno, + obofoundry:geo, + obofoundry:gno, + obofoundry:go, + obofoundry:gro, + obofoundry:gsso, + obofoundry:habronattus, + obofoundry:hancestro, + obofoundry:hao, + obofoundry:hom, + obofoundry:hp, + obofoundry:hsapdv, + obofoundry:hso, + obofoundry:htn, + obofoundry:iao, + obofoundry:iceo, + obofoundry:ico, + obofoundry:ido, + obofoundry:idomal, + obofoundry:iev, + obofoundry:imr, + obofoundry:ino, + obofoundry:ipr, + obofoundry:kisao, + obofoundry:labo, + obofoundry:lepao, + obofoundry:lipro, + obofoundry:loggerhead, + obofoundry:ma, + obofoundry:mamo, + obofoundry:mao, + obofoundry:mat, + obofoundry:maxo, + obofoundry:mco, + obofoundry:mf, + obofoundry:mfmo, + obofoundry:mfo, + obofoundry:mfoem, + obofoundry:mfomd, + obofoundry:mi, + obofoundry:miapa, + obofoundry:micro, + obofoundry:mirnao, + obofoundry:miro, + obofoundry:mmo, + obofoundry:mmusdv, + obofoundry:mo, + obofoundry:mod, + obofoundry:mondo, + obofoundry:mop, + obofoundry:mp, + obofoundry:mpath, + obofoundry:mpio, + obofoundry:mro, + obofoundry:ms, + obofoundry:nbo, + obofoundry:ncbitaxon, + obofoundry:ncit, + obofoundry:ncro, + obofoundry:nif_cell, + obofoundry:nif_dysfunction, + obofoundry:nif_grossanatomy, + obofoundry:nmr, + obofoundry:nomen, + obofoundry:oae, + obofoundry:oarcs, + obofoundry:oba, + obofoundry:obcs, + obofoundry:obi, + obofoundry:obib, + obofoundry:ogg, + obofoundry:ogi, + obofoundry:ogms, + obofoundry:ogsf, + obofoundry:ohd, + obofoundry:ohmi, + obofoundry:ohpi, + obofoundry:olatdv, + obofoundry:omiabis, + obofoundry:omit, + obofoundry:omo, + obofoundry:omp, + obofoundry:omrse, + obofoundry:one, + obofoundry:ons, + obofoundry:ontoavida, + obofoundry:ontoneo, + obofoundry:oostt, + obofoundry:opl, + obofoundry:opmi, + obofoundry:ornaseq, + obofoundry:ovae, + obofoundry:pao, + obofoundry:pato, + obofoundry:pcl, + obofoundry:pco, + obofoundry:pd_st, + obofoundry:pdro, + obofoundry:pdumdv, + obofoundry:peco, + obofoundry:pgdso, + obofoundry:phipo, + obofoundry:plana, + obofoundry:planp, + obofoundry:plo, + obofoundry:po, + obofoundry:poro, + obofoundry:ppo, + obofoundry:pr, + obofoundry:proco, + obofoundry:propreo, + obofoundry:psdo, + obofoundry:pso, + obofoundry:pw, + obofoundry:rbo, + obofoundry:resid, + obofoundry:rex, + obofoundry:rnao, + obofoundry:ro, + obofoundry:rs, + obofoundry:rxno, + obofoundry:sao, + obofoundry:sbo, + obofoundry:scdo, + obofoundry:sep, + obofoundry:sepio, + obofoundry:sibo, + obofoundry:so, + obofoundry:sopharm, + obofoundry:spd, + obofoundry:stato, + obofoundry:swo, + obofoundry:symp, + obofoundry:tads, + obofoundry:tahe, + obofoundry:tahh, + obofoundry:tao, + obofoundry:taxrank, + obofoundry:tgma, + obofoundry:to, + obofoundry:trans, + obofoundry:tto, + obofoundry:txpo, + obofoundry:uberon, + obofoundry:uo, + obofoundry:upa, + obofoundry:upheno, + obofoundry:vario, + obofoundry:vhog, + obofoundry:vo, + obofoundry:vsao, + obofoundry:vt, + obofoundry:vto, + obofoundry:wbbt, + obofoundry:wbls, + obofoundry:wbphenotype, + obofoundry:xao, + obofoundry:xco, + obofoundry:xlmod, + obofoundry:xpo, + obofoundry:ypo, + obofoundry:zea, + obofoundry:zeco, + obofoundry:zfa, + obofoundry:zfs, + obofoundry:zp ; foaf:homepage "http://www.obofoundry.org/" ; bioregistry.schema:0000005 "chebi" ; bioregistry.schema:0000006 "http://www.obofoundry.org/ontology/$1" ; @@ -33392,7 +33395,8 @@ bioregistry.metaresource:obofoundry a bioregistry.schema:0000002 ; bioregistry.metaresource:ols a bioregistry.schema:0000002 ; rdfs:label "Ontology Lookup Service" ; dc:description "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " ; - dcterms:hasPart ols:aeo, + ns1:hasPart ols:ado, + ols:aeo, ols:afo, ols:agro, ols:aism, @@ -33605,6 +33609,7 @@ bioregistry.metaresource:ols a bioregistry.schema:0000002 ; ols:pr, ols:pride, ols:probonto, + ols:proco, ols:prov, ols:psdo, ols:pso, @@ -33670,7 +33675,7 @@ bioregistry.metaresource:ols a bioregistry.schema:0000002 ; bioregistry.metaresource:bioportal a bioregistry.schema:0000002 ; rdfs:label "BioPortal Prefixes" ; dc:description "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" ; - dcterms:hasPart bioportal:ADO, + ns1:hasPart bioportal:ADO, bioportal:ADW, bioportal:AEO, bioportal:AERO, @@ -33992,7 +33997,7 @@ bioregistry.metaresource:bioportal a bioregistry.schema:0000002 ; bioregistry.metaresource:aberowl a bioregistry.schema:0000002 ; rdfs:label "AberOWL" ; dc:description "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." ; - dcterms:hasPart aberowl:ADO, + ns1:hasPart aberowl:ADO, aberowl:ADW, aberowl:AEO, aberowl:AERO, @@ -34320,7 +34325,7 @@ bioregistry.metaresource:aberowl a bioregistry.schema:0000002 ; bioregistry.metaresource:prefixcommons a bioregistry.schema:0000002 ; rdfs:label "Prefix Commons" ; dc:description "A registry of commonly used prefixes in the life sciences and linked data" ; - dcterms:hasPart prefixcommons:3dmet, + ns1:hasPart prefixcommons:3dmet, prefixcommons:4dn, prefixcommons:aao, prefixcommons:abs, @@ -34659,7 +34664,7 @@ bioregistry.metaresource:prefixcommons a bioregistry.schema:0000002 ; bioregistry.metaresource:fairsharing a bioregistry.schema:0000002 ; rdfs:label "FAIRSharing" ; dc:description "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." ; - dcterms:hasPart fairsharing:FAIRsharing.0a2576, + ns1:hasPart fairsharing:FAIRsharing.0a2576, fairsharing:FAIRsharing.0a674c, fairsharing:FAIRsharing.0pUMYW, fairsharing:FAIRsharing.10gr18, @@ -35225,7 +35230,7 @@ bioregistry.metaresource:fairsharing a bioregistry.schema:0000002 ; bioregistry.metaresource:n2t a bioregistry.schema:0000002 ; rdfs:label "Name-to-Thing" ; dc:description "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" ; - dcterms:hasPart n2t:3dmet, + ns1:hasPart n2t:3dmet, n2t:abs, n2t:aceview.worm, n2t:addgene, @@ -35909,7 +35914,7 @@ bioregistry.metaresource:n2t a bioregistry.schema:0000002 ; bioregistry.metaresource:miriam a bioregistry.schema:0000002 ; rdfs:label "Identifiers.org" ; dc:description "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." ; - dcterms:hasPart miriam:3dmet, + ns1:hasPart miriam:3dmet, miriam:4dn, miriam:abs, miriam:aceview.worm, @@ -36686,7 +36691,7 @@ bioregistry.metaresource:miriam a bioregistry.schema:0000002 ; bioregistry.metaresource:biocontext a bioregistry.schema:0000002 ; rdfs:label "BioContext" ; dc:description "BioContext contains modular JSON-LD contexts for bioinformatics data." ; - dcterms:hasPart biocontext:3DMET, + ns1:hasPart biocontext:3DMET, biocontext:AAO, biocontext:ABS, biocontext:ACEVIEW.WORM, @@ -37530,7 +37535,7 @@ bioregistry.metaresource:biocontext a bioregistry.schema:0000002 ; bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; rdfs:label "Bioregistry" ; dc:description "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." ; - dcterms:hasPart bioregistry:3dmet, + ns1:hasPart bioregistry:3dmet, bioregistry:4dn.biosource, bioregistry:4dn.replicate, bioregistry:aao, diff --git a/exports/rdf/schema.jsonld b/exports/rdf/schema.jsonld index c0760df9b..4ac5443ba 100644 --- a/exports/rdf/schema.jsonld +++ b/exports/rdf/schema.jsonld @@ -13,13 +13,29 @@ }, "@graph": [ { - "@id": "https://bioregistry.io/schema/#0000001", + "@id": "https://bioregistry.io/schema/#0000008", + "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", + "http://purl.org/dc/terms/description": { + "@value": "The pattern for identifiers in the given resource" + }, + "http://www.w3.org/2000/01/rdf-schema#domain": { + "@id": "https://bioregistry.io/schema/#0000001" + }, + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "has pattern" + }, + "http://www.w3.org/2000/01/rdf-schema#range": { + "@id": "http://www.w3.org/2001/XMLSchema#string" + } + }, + { + "@id": "https://bioregistry.io/schema/#0000020", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's registry." + "@value": "A person" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Resource" + "@value": "Person" } }, { @@ -39,225 +55,209 @@ } }, { - "@id": "https://bioregistry.io/schema/#0000016", + "@id": "https://bioregistry.io/schema/#0000011", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" + "@value": "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has canonical" + "@value": "provides for" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000011", + "@id": "https://bioregistry.io/schema/#0000016", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." + "@value": "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "provides for" + "@value": "has canonical" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000020", + "@id": "https://bioregistry.io/schema/#0000003", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A person" + "@value": "A type for entries in the Bioregistry's collections" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Person" + "@value": "Collection" } }, { - "@id": "https://bioregistry.io/schema/#0000021", + "@id": "https://bioregistry.io/schema/#0000010", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The reviewer of a prefix" + "@value": "A download link for the given resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has reviewer" + "@value": "has download URL" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000008", + "@id": "https://bioregistry.io/schema/#0000019", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The pattern for identifiers in the given resource" + "@value": "The responsible person for a resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has pattern" + "@value": "has responsible" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" - } - }, - { - "@id": "https://bioregistry.io/schema/#0000002", - "@type": "http://www.w3.org/2000/01/rdf-schema#Class", - "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's metaregistry." - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Registry" + "@id": "https://bioregistry.io/schema/#0000020" } }, { - "@id": "https://bioregistry.io/schema/#0000006", + "@id": "https://bioregistry.io/schema/#0000017", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." + "@value": "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has provider formatter" + "@value": "depends on" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000018", + "@id": "https://bioregistry.io/schema/#0000021", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "Terms from the source appear in the target resource" + "@value": "The reviewer of a prefix" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "appears in" + "@value": "has reviewer" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "https://bioregistry.io/schema/#0000020" } }, { - "@id": "https://bioregistry.io/schema/#0000012", + "@id": "https://bioregistry.io/schema/#0000006", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." + "@value": "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "is deprecated" + "@value": "has provider formatter" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#boolean" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000019", + "@id": "https://bioregistry.io/schema/#0000005", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The responsible person for a resource" + "@value": "An identifier for a resource or metaresource." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has responsible" + "@value": "has example" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000010", + "@id": "https://bioregistry.io/schema/#0000018", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A download link for the given resource" + "@value": "Terms from the source appear in the target resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has download URL" + "@value": "appears in" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000003", + "@id": "https://bioregistry.io/schema/#0000002", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's collections" + "@value": "A type for entries in the Bioregistry's metaregistry." }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Collection" + "@value": "Registry" } }, { - "@id": "https://bioregistry.io/schema/#0000017", + "@id": "https://bioregistry.io/schema/#0000012", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" + "@value": "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "depends on" + "@value": "is deprecated" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "http://www.w3.org/2001/XMLSchema#boolean" } }, { - "@id": "https://bioregistry.io/schema/#0000005", + "@id": "https://bioregistry.io/schema/#0000007", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "An identifier for a resource or metaresource." + "@value": "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." }, "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "https://bioregistry.io/schema/#0000002" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has example" + "@value": "has resolver formatter" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000007", - "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", + "@id": "https://bioregistry.io/schema/#0000001", + "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." - }, - "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000002" + "@value": "A type for entries in the Bioregistry's registry." }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has resolver formatter" - }, - "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@value": "Resource" } } ] diff --git a/exports/rdf/schema.nt b/exports/rdf/schema.nt index d2d256318..65a85c8ea 100644 --- a/exports/rdf/schema.nt +++ b/exports/rdf/schema.nt @@ -1,77 +1,77 @@ - "depends on" . - "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . - "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . - . - . - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + . . - . - . - "Person" . - "is deprecated" . + . . - "provides for" . - . - . - "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - "has provider formatter" . - . - "has pattern" . - "A person" . - . - . + "has example" . + . + . + . "A type for entries in the Bioregistry's metaregistry." . - "The reviewer of a prefix" . - . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . - . - "has resolver formatter" . - "A type for entries in the Bioregistry's registry." . - . - . - . + "has canonical" . . - "The responsible person for a resource" . - . - "Registry" . - . - . - "A download link for the given resource" . + "Terms from the source appear in the target resource" . + . + . + "has responsible" . + "A type for entries in the Bioregistry's registry." . + . "has responsible" . - "Collection" . - . - . + . + "The reviewer of a prefix" . + "An identifier for a resource or metaresource." . + . "Resource" . - . - . - . - "has example" . + "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . + "has resolver formatter" . + . . - . + . + "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . + "appears in" . + "has provider formatter" . + "is deprecated" . + . + "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . + . . - "Terms from the source appear in the target resource" . - . - "The main contact person for a registry" . - "The pattern for identifiers in the given resource" . - . - . - . - . . - . - . - . - "has canonical" . - . - "A type for entries in the Bioregistry's collections" . - . + . + "The responsible person for a resource" . + . + . . - . + "A type for entries in the Bioregistry's collections" . + "The main contact person for a registry" . + . + "A person" . + "A download link for the given resource" . + . + . + . + . "has reviewer" . - "An identifier for a resource or metaresource." . - . - "appears in" . - "has responsible" . + . + "provides for" . + "depends on" . + . + "Collection" . + "has pattern" . + . + . + "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . + . "has download URL" . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + . + "The pattern for identifiers in the given resource" . + . + . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + "Registry" . + . + "Person" . + . + . + . + . + . diff --git a/exports/registry/registry.json b/exports/registry/registry.json index 05dd391fa..b019d4803 100644 --- a/exports/registry/registry.json +++ b/exports/registry/registry.json @@ -62,7 +62,7 @@ "mappings": { "biocontext": "AAO", "fairsharing": "FAIRsharing.mxx5rp", - "obofoundry": "AAO", + "obofoundry": "aao", "prefixcommons": "aao" }, "name": "Amphibian gross anatomy", @@ -176,7 +176,7 @@ "depends_on": [ "bfo" ], - "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.", + "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", "download_owl": "http://purl.obolibrary.org/obo/ado.owl", "example": "0000001", "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", @@ -185,12 +185,14 @@ "aberowl": "ADO", "bioportal": "ADO", "fairsharing": "FAIRsharing.ckd4rf", - "obofoundry": "ADO" + "obofoundry": "ado", + "ols": "ado" }, "name": "Alzheimer's Disease Ontology", "preferred_prefix": "ADO", "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", - "uri_format": "http://purl.obolibrary.org/obo/ADO_$1" + "uri_format": "http://purl.obolibrary.org/obo/ADO_$1", + "version": "2.0.0" }, "adw": { "contact": { @@ -211,7 +213,7 @@ "fairsharing": "FAIRsharing.t9fvdn", "miriam": "adw", "n2t": "adw", - "obofoundry": "ADW" + "obofoundry": "adw" }, "name": "Animal natural history and life history", "pattern": "^[A-Z_a-z]+$", @@ -219,9 +221,6 @@ "uri_format": "https://animaldiversity.org/accounts/$1" }, "aeo": { - "appears_in": [ - "ehdaa2" - ], "contact": { "email": "J.Bard@ed.ac.uk", "github": null, @@ -240,7 +239,7 @@ "biocontext": "AEO", "bioportal": "AEO", "fairsharing": "FAIRsharing.93ee19", - "obofoundry": "AEO", + "obofoundry": "aeo", "ols": "aeo", "ontobee": "AEO" }, @@ -272,7 +271,7 @@ "biocontext": "AERO", "bioportal": "AERO", "fairsharing": "FAIRsharing.rycy2x", - "obofoundry": "AERO" + "obofoundry": "aero" }, "name": "Adverse Event Reporting Ontology", "pattern": "^\\d{7}$", @@ -432,7 +431,7 @@ "biocontext": "AGRO", "bioportal": "AGRO", "fairsharing": "FAIRsharing.m40bhw", - "obofoundry": "AGRO", + "obofoundry": "agro", "ols": "agro", "ontobee": "AGRO" }, @@ -491,7 +490,7 @@ "mappings": { "aberowl": "AISM", "bioportal": "AISM", - "obofoundry": "AISM", + "obofoundry": "aism", "ols": "aism", "ontobee": "AISM" }, @@ -571,7 +570,7 @@ "mappings": { "aberowl": "AMPHX", "bioportal": "AMPHX", - "obofoundry": "AMPHX", + "obofoundry": "amphx", "ols": "amphx", "ontobee": "AMPHX" }, @@ -747,7 +746,7 @@ "biocontext": "YPO", "bioportal": "APO", "fairsharing": "FAIRsharing.dyqz3y", - "obofoundry": "APO", + "obofoundry": "apo", "ols": "apo", "ontobee": "APO" }, @@ -777,7 +776,7 @@ "aberowl": "APOLLO_SV", "bioportal": "APOLLO-SV", "fairsharing": "FAIRsharing.ngv2xx", - "obofoundry": "APOLLO_SV", + "obofoundry": "apollo_sv", "ols": "apollo_sv", "ontobee": "APOLLO_SV" }, @@ -867,7 +866,7 @@ "aberowl": "ARO", "biocontext": "ARO", "bioportal": "ARO", - "obofoundry": "ARO", + "obofoundry": "aro", "ols": "aro", "ontobee": "ARO" }, @@ -1148,7 +1147,7 @@ "biocontext": "ATO", "bioportal": "ATO", "fairsharing": "FAIRsharing.ayjdsm", - "obofoundry": "ATO" + "obofoundry": "ato" }, "name": "Amphibian taxonomy", "pattern": "^\\d{7}$", @@ -1328,7 +1327,7 @@ "biocontext": "BCGO", "bioportal": "BCGO", "cellosaurus": "BCGO", - "obofoundry": "BCGO", + "obofoundry": "bcgo", "ontobee": "BCGO" }, "name": "Beta Cell Genomics Ontology", @@ -1373,7 +1372,7 @@ "bioportal": "BCO", "ecoportal": "BCO", "fairsharing": "FAIRsharing.8ktkqy", - "obofoundry": "BCO", + "obofoundry": "bco", "ols": "bco", "ontobee": "BCO" }, @@ -1568,7 +1567,7 @@ "bioportal": "BFO", "fairsharing": "FAIRsharing.wcpd6f", "go": "BFO", - "obofoundry": "BFO", + "obofoundry": "bfo", "ols": "bfo", "ontobee": "BFO" }, @@ -1710,12 +1709,21 @@ "uri_format": "http://bigg.ucsd.edu/models/universal/reactions/$1" }, "bila": { + "contact": { + "email": "henrich@embl.de", + "github": null, + "name": "Thorsten Heinrich", + "orcid": null + }, "deprecated": true, "description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.", + "download_owl": "http://purl.obolibrary.org/obo/bila.owl", + "example": "0000000", + "homepage": "http://4dx.embl.de/4DXpress", "mappings": { "biocontext": "BILA", "fairsharing": "FAIRsharing.eqgjeq", - "obofoundry": "BILA" + "obofoundry": "bila" }, "name": "Bilateria anatomy", "preferred_prefix": "BILA", @@ -1927,7 +1935,7 @@ "fairsharing": "FAIRsharing.jcg19w", "miriam": "biomodels.kisao", "n2t": "biomodels.kisao", - "obofoundry": "KISAO", + "obofoundry": "kisao", "ols": "kisao", "ontobee": "KISAO", "prefixcommons": "kisao" @@ -2440,7 +2448,7 @@ "homepage": "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html", "mappings": { "biocontext": "BOOTSTREP", - "obofoundry": "BOOTSTREP" + "obofoundry": "bootstrep" }, "name": "Gene Regulation Ontology", "preferred_prefix": "BOOTSTREP", @@ -2565,7 +2573,7 @@ "biocontext": "BSPO", "bioportal": "BSPO", "fairsharing": "FAIRsharing.newa3z", - "obofoundry": "BSPO", + "obofoundry": "bspo", "ols": "bspo", "ontobee": "BSPO" }, @@ -2600,7 +2608,7 @@ "go": "BTO", "miriam": "bto", "n2t": "bto", - "obofoundry": "BTO", + "obofoundry": "bto", "ols": "bto", "ontobee": "BTO", "prefixcommons": "bto", @@ -2771,7 +2779,6 @@ "appears_in": [ "aism", "colao", - "ehdaa2", "lepao", "pco" ], @@ -2792,7 +2799,7 @@ "bioportal": "CARO", "fairsharing": "FAIRsharing.3kcgmr", "go": "CARO", - "obofoundry": "CARO", + "obofoundry": "caro", "ols": "caro", "ontobee": "CARO" }, @@ -3069,7 +3076,7 @@ "biocontext": "CDAO", "bioportal": "CDAO", "fairsharing": "FAIRsharing.kay31r", - "obofoundry": "CDAO", + "obofoundry": "cdao", "ols": "cdao", "ontobee": "CDAO" }, @@ -3123,7 +3130,7 @@ "mappings": { "aberowl": "CDNO", "bioportal": "CDNO", - "obofoundry": "CDNO", + "obofoundry": "cdno", "ols": "cdno", "ontobee": "CDNO" }, @@ -3300,7 +3307,7 @@ "biocontext": "CEPH", "bioportal": "CEPH", "fairsharing": "FAIRsharing.p58bm4", - "obofoundry": "CEPH", + "obofoundry": "ceph", "ols": "ceph", "ontobee": "CEPH" }, @@ -3438,7 +3445,7 @@ "go": "CHEBI", "miriam": "chebi", "n2t": "chebi", - "obofoundry": "CHEBI", + "obofoundry": "chebi", "ols": "chebi", "ontobee": "CHEBI", "prefixcommons": "chebi", @@ -3632,7 +3639,7 @@ "biocontext": "CHEMINF", "bioportal": "CHEMINF", "fairsharing": "FAIRsharing.sjhvyy", - "obofoundry": "CHEMINF", + "obofoundry": "cheminf", "ols": "cheminf", "ontobee": "CHEMINF" }, @@ -3706,7 +3713,7 @@ "mappings": { "aberowl": "CHIRO", "bioportal": "CHIRO", - "obofoundry": "CHIRO", + "obofoundry": "chiro", "ols": "chiro", "ontobee": "CHIRO" }, @@ -3738,7 +3745,7 @@ "biocontext": "CHMO", "bioportal": "CHMO", "fairsharing": "FAIRsharing.9j4wh2", - "obofoundry": "CHMO", + "obofoundry": "chmo", "ols": "chmo", "ontobee": "CHMO" }, @@ -3765,7 +3772,7 @@ "aberowl": "CIDO", "bioportal": "CIDO", "fairsharing": "FAIRsharing.aVmpKl", - "obofoundry": "CIDO", + "obofoundry": "cido", "ols": "cido", "ontobee": "CIDO" }, @@ -3794,7 +3801,7 @@ "biocontext": "CIO", "bioportal": "CIO", "fairsharing": "FAIRsharing.e3t0yw", - "obofoundry": "CIO", + "obofoundry": "cio", "ols": "cio", "ontobee": "CIO" }, @@ -3875,7 +3882,6 @@ "appears_in": [ "clo", "ecao", - "ehdaa2", "go", "mco", "pcl", @@ -3914,7 +3920,7 @@ "go": "CL", "miriam": "cl", "n2t": "cl", - "obofoundry": "CL", + "obofoundry": "cl", "ols": "cl", "ontobee": "CL", "prefixcommons": "cl", @@ -3947,7 +3953,7 @@ "mappings": { "aberowl": "CLAO", "bioportal": "CLAO", - "obofoundry": "CLAO", + "obofoundry": "clao", "ols": "clao", "ontobee": "CLAO" }, @@ -4102,7 +4108,7 @@ "bioportal": "CLO", "cellosaurus": "CLO", "fairsharing": "FAIRsharing.4dvtcz", - "obofoundry": "CLO", + "obofoundry": "clo", "ols": "clo", "ontobee": "CLO", "prefixcommons": "clo", @@ -4150,7 +4156,7 @@ "mappings": { "aberowl": "CLYH", "bioportal": "CLYH", - "obofoundry": "CLYH", + "obofoundry": "clyh", "ols": "clyh", "ontobee": "CLYH" }, @@ -4192,7 +4198,7 @@ "mappings": { "aberowl": "CMF", "biocontext": "CMF", - "obofoundry": "CMF", + "obofoundry": "cmf", "ontobee": "CMF" }, "name": "CranioMaxilloFacial ontology", @@ -4220,7 +4226,7 @@ "biocontext": "CMO", "bioportal": "CMO", "fairsharing": "FAIRsharing.dq78pn", - "obofoundry": "CMO", + "obofoundry": "cmo", "ols": "cmo", "ontobee": "CMO" }, @@ -4789,7 +4795,7 @@ "mappings": { "aberowl": "COB", "bioportal": "COB", - "obofoundry": "COB", + "obofoundry": "cob", "ols": "cob", "ontobee": "COB" }, @@ -4967,7 +4973,7 @@ "mappings": { "aberowl": "COLAO", "bioportal": "COLAO", - "obofoundry": "COLAO", + "obofoundry": "colao", "ols": "colao", "ontobee": "COLAO" }, @@ -5293,15 +5299,15 @@ "orcid": null }, "deprecated": true, + "description": "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology.", "homepage": "http://www.gramene.org/plant_ontology/", "mappings": { "biocontext": "gro.cpga", "bioportal": "GRO-CPGA", - "obofoundry": "GRO" + "obofoundry": "gro" }, "name": "Cereal Plant Gross Anatomy", - "preferred_prefix": "GRO", - "uri_format": "http://purl.obolibrary.org/obo/GRO_$1" + "preferred_prefix": "GRO" }, "cpt": { "contributor": { @@ -5379,7 +5385,7 @@ "aberowl": "CRO", "biocontext": "CRO", "bioportal": "CRO", - "obofoundry": "CRO", + "obofoundry": "cro", "ols": "cro", "ontobee": "CRO" }, @@ -5572,7 +5578,7 @@ "biocontext": "CTENO", "bioportal": "CTENO", "fairsharing": "FAIRsharing.mgxgza", - "obofoundry": "CTENO", + "obofoundry": "cteno", "ols": "cteno", "ontobee": "CTENO" }, @@ -5599,7 +5605,7 @@ "aberowl": "CTO", "bioportal": "CTO", "fairsharing": "FAIRsharing.qp211a", - "obofoundry": "CTO", + "obofoundry": "cto", "ols": "cto", "ontobee": "CTO" }, @@ -5643,7 +5649,7 @@ "biocontext": "CVDO", "bioportal": "CVDO", "fairsharing": "FAIRsharing.2basyz", - "obofoundry": "CVDO", + "obofoundry": "cvdo", "ols": "cvdo", "ontobee": "CVDO" }, @@ -6017,7 +6023,7 @@ "homepage": "http://www.dukeontologygroup.org/Projects.html", "mappings": { "biocontext": "DC_CL", - "obofoundry": "DC_CL" + "obofoundry": "dc_cl" }, "name": "Dendritic cell", "pattern": "^\\d{7}$", @@ -6089,7 +6095,7 @@ "bioportal": "DDANAT", "fairsharing": "FAIRsharing.z656ab", "go": "DDANAT", - "obofoundry": "DDANAT", + "obofoundry": "ddanat", "ols": "ddanat", "ontobee": "DDANAT", "prefixcommons": "ddanat" @@ -6119,7 +6125,7 @@ "biocontext": "DDPHENO", "bioportal": "DDPHENO", "fairsharing": "FAIRsharing.9c1p18", - "obofoundry": "DDPHENO", + "obofoundry": "ddpheno", "ols": "ddpheno", "ontobee": "DDPHENO" }, @@ -6457,7 +6463,7 @@ "biocontext": "DIDEO", "bioportal": "DIDEO", "fairsharing": "FAIRsharing.9y8f0n", - "obofoundry": "DIDEO", + "obofoundry": "dideo", "ols": "dideo", "ontobee": "DIDEO" }, @@ -6484,7 +6490,7 @@ "aberowl": "DINTO", "biocontext": "DINTO", "bioportal": "DINTO", - "obofoundry": "DINTO", + "obofoundry": "dinto", "ontobee": "DINTO" }, "name": "The Drug-Drug Interactions Ontology", @@ -6536,7 +6542,7 @@ "mappings": { "aberowl": "DISDRIV", "bioportal": "DISDRIV", - "obofoundry": "DISDRIV", + "obofoundry": "disdriv", "ols": "disdriv" }, "name": "Disease Drivers Ontology", @@ -6743,7 +6749,7 @@ "fairsharing": "FAIRsharing.8b6wfq", "miriam": "doid", "n2t": "doid", - "obofoundry": "DOID", + "obofoundry": "doid", "ols": "doid", "ontobee": "DOID", "prefixcommons": "do", @@ -6847,7 +6853,7 @@ "mappings": { "aberowl": "DPO", "bioportal": "DPO", - "obofoundry": "FBcv", + "obofoundry": "dpo", "ols": "dpo", "ontobee": "DPO" }, @@ -6961,7 +6967,7 @@ "biocontext": "DRON", "bioportal": "DRON", "fairsharing": "FAIRsharing.w5ntfd", - "obofoundry": "DRON", + "obofoundry": "dron", "ols": "dron", "ontobee": "DRON" }, @@ -7134,7 +7140,7 @@ "biocontext": "DUO", "bioportal": "DUO", "fairsharing": "FAIRsharing.5dnjs2", - "obofoundry": "DUO", + "obofoundry": "duo", "ols": "duo", "ontobee": "DUO" }, @@ -7235,7 +7241,7 @@ "mappings": { "aberowl": "ECAO", "bioportal": "ECAO", - "obofoundry": "ECAO", + "obofoundry": "ecao", "ols": "ecao", "ontobee": "ECAO" }, @@ -7385,7 +7391,7 @@ "go": "ECO", "miriam": "eco", "n2t": "eco", - "obofoundry": "ECO", + "obofoundry": "eco", "ols": "eco", "ontobee": "ECO", "prefixcommons": "eco" @@ -7427,7 +7433,7 @@ "aberowl": "ECOCORE", "biocontext": "ECOCORE", "bioportal": "ECOCORE", - "obofoundry": "ECOCORE", + "obofoundry": "ecocore", "ols": "ecocore", "ontobee": "ECOCORE" }, @@ -7531,7 +7537,7 @@ "aberowl": "ECTO", "biolink": "ECTO", "bioportal": "ECTO", - "obofoundry": "ECTO", + "obofoundry": "ecto", "ols": "ecto", "ontobee": "ECTO" }, @@ -7871,7 +7877,7 @@ "aberowl": "EHDA", "biocontext": "EHDA", "bioportal": "EHDA", - "obofoundry": "EHDA", + "obofoundry": "ehda", "prefixcommons": "ehda" }, "name": "Human developmental anatomy, timed version", @@ -7893,7 +7899,7 @@ "aberowl": "EHDAA", "biocontext": "EHDAA", "bioportal": "EHDAA", - "obofoundry": "EHDAA", + "obofoundry": "ehdaa", "prefixcommons": "ehdaa" }, "name": "Human developmental anatomy, abstract version", @@ -7925,7 +7931,7 @@ "biocontext": "EHDAA2", "bioportal": "EHDAA2", "fairsharing": "FAIRsharing.7zxrs6", - "obofoundry": "EHDAA2", + "obofoundry": "ehdaa2", "ols": "ehdaa2", "ontobee": "EHDAA2" }, @@ -7972,7 +7978,7 @@ "mappings": { "biocontext": "EMAP", "bioportal": "EMAP", - "obofoundry": "EMAP" + "obofoundry": "emap" }, "name": "Mouse gross anatomy and development, timed", "pattern": "^\\d+$", @@ -7998,7 +8004,7 @@ "bioportal": "EMAPA", "fairsharing": "FAIRsharing.j0fa1d", "go": "EMAPA", - "obofoundry": "EMAPA", + "obofoundry": "emapa", "ols": "emapa", "ontobee": "EMAPA" }, @@ -8344,7 +8350,7 @@ "fairsharing": "FAIRsharing.azqskx", "miriam": "envo", "n2t": "envo", - "obofoundry": "ENVO", + "obofoundry": "envo", "ols": "envo", "ontobee": "ENVO" }, @@ -8397,7 +8403,7 @@ "biocontext": "EO", "miriam": "eo", "n2t": "eo", - "obofoundry": "EO", + "obofoundry": "eo", "prefixcommons": "eo" }, "name": "Plant Environment Ontology", @@ -8501,7 +8507,7 @@ "mappings": { "aberowl": "EPIO", "bioportal": "EPIO", - "obofoundry": "EPIO", + "obofoundry": "epio", "ontobee": "EPIO" }, "name": "Epilepsy Ontology", @@ -8519,7 +8525,7 @@ "aberowl": "EPO", "biocontext": "EPO", "bioportal": "EPO", - "obofoundry": "EPO", + "obofoundry": "epo", "ontobee": "EPO" }, "name": "Epidemiology Ontology", @@ -8572,7 +8578,7 @@ "biocontext": "ERO", "bioportal": "ERO", "fairsharing": "FAIRsharing.nwgynk", - "obofoundry": "ERO", + "obofoundry": "ero", "ols": "ero", "ontobee": "ERO" }, @@ -8658,7 +8664,7 @@ "biocontext": "EUPATH", "bioportal": "EUPATH", "fairsharing": "FAIRsharing.9rhr9j", - "obofoundry": "EUPATH", + "obofoundry": "eupath", "ols": "eupath", "ontobee": "EUPATH" }, @@ -8696,7 +8702,7 @@ "homepage": "http://www.evocontology.org/", "mappings": { "biocontext": "EV", - "obofoundry": "EV" + "obofoundry": "ev" }, "name": "eVOC (Expressed Sequence Annotation for Humans)", "preferred_prefix": "EV", @@ -8784,7 +8790,7 @@ "biolink": "ExO", "bioportal": "EXO", "fairsharing": "FAIRsharing.6hna78", - "obofoundry": "ExO", + "obofoundry": "exo", "ols": "exo", "ontobee": "ExO" }, @@ -8892,7 +8898,7 @@ "biocontext": "FAO", "bioportal": "FAO", "fairsharing": "FAIRsharing.xs6t67", - "obofoundry": "FAO", + "obofoundry": "fao", "ols": "fao", "ontobee": "FAO", "prefixcommons": "fao" @@ -8922,7 +8928,7 @@ "biocontext": "FBbi", "bioportal": "FBbi", "fairsharing": "FAIRsharing.ny3z9j", - "obofoundry": "FBbi", + "obofoundry": "fbbi", "ols": "fbbi", "ontobee": "FBBI", "prefixcommons": "fbbi" @@ -8957,7 +8963,7 @@ "bioportal": "FB-BT", "fairsharing": "FAIRsharing.y2qkst", "go": "FBbt", - "obofoundry": "FBbt", + "obofoundry": "fbbt", "ols": "fbbt", "ontobee": "FBBT", "prefixcommons": "fbbt" @@ -8996,7 +9002,7 @@ "biocontext": "FBcv", "bioportal": "FB-CV", "fairsharing": "FAIRsharing.6tgyxf", - "obofoundry": "FBcv", + "obofoundry": "fbcv", "ols": "fbcv", "ontobee": "FBCV", "prefixcommons": "fbcv" @@ -9031,7 +9037,7 @@ "biocontext": "FBdv", "bioportal": "FB-DV", "fairsharing": "FAIRsharing.p52pzj", - "obofoundry": "FBdv", + "obofoundry": "fbdv", "ols": "fbdv", "ontobee": "FBdv", "prefixcommons": "fbdv" @@ -9109,7 +9115,7 @@ "aberowl": "FB-SP", "biocontext": "FBSP", "bioportal": "FB-SP", - "obofoundry": "FBSP" + "obofoundry": "fbsp" }, "name": "Fly taxonomy", "part_of": "flybase", @@ -9177,7 +9183,7 @@ "mappings": { "aberowl": "FIDEO", "bioportal": "FIDEO", - "obofoundry": "FIDEO", + "obofoundry": "fideo", "ols": "fideo", "ontobee": "FIDEO" }, @@ -9236,7 +9242,7 @@ "biocontext": "FIX", "bioportal": "FIX", "fairsharing": "FAIRsharing.wwy1ns", - "obofoundry": "FIX", + "obofoundry": "fix", "ols": "fix", "ontobee": "FIX", "prefixcommons": "fix" @@ -9266,7 +9272,7 @@ "biocontext": "FLOPO", "bioportal": "FLOPO", "fairsharing": "FAIRsharing.ny9vnm", - "obofoundry": "FLOPO", + "obofoundry": "flopo", "ols": "flopo", "ontobee": "FLOPO" }, @@ -9306,7 +9312,7 @@ "aberowl": "FLU", "biocontext": "FLU", "bioportal": "FLU", - "obofoundry": "FLU" + "obofoundry": "flu" }, "name": "Influenza Ontology", "pattern": "^\\d{7}$", @@ -9393,7 +9399,7 @@ "go": "FMA", "miriam": "fma", "n2t": "fma", - "obofoundry": "FMA", + "obofoundry": "fma", "ols": "fma", "ontobee": "FMA", "prefixcommons": "fma" @@ -9445,7 +9451,7 @@ "aberowl": "FOBI", "agroportal": "FOBI", "bioportal": "FOBI", - "obofoundry": "FOBI", + "obofoundry": "fobi", "ols": "fobi", "ontobee": "FOBI" }, @@ -9511,7 +9517,6 @@ "bfo", "chebi", "envo", - "eo", "ncbitaxon", "obi", "ro", @@ -9530,7 +9535,7 @@ "fairsharing": "FAIRsharing.dzxae", "miriam": "foodon", "n2t": "foodon", - "obofoundry": "FOODON", + "obofoundry": "foodon", "ols": "foodon", "ontobee": "FOODON" }, @@ -9618,7 +9623,7 @@ "mappings": { "aberowl": "FOVT", "bioportal": "FOVT", - "obofoundry": "FOVT", + "obofoundry": "fovt", "ols": "fovt", "ontobee": "FOVT" }, @@ -9907,7 +9912,7 @@ "bioportal": "FYPO", "fairsharing": "FAIRsharing.4vr0ys", "go": "FYPO", - "obofoundry": "FYPO", + "obofoundry": "fypo", "ols": "fypo", "ontobee": "FYPO" }, @@ -10010,7 +10015,7 @@ "biocontext": "GAZ", "bioportal": "GAZ", "fairsharing": "FAIRsharing.wkdjpb", - "obofoundry": "GAZ", + "obofoundry": "gaz", "ols": "gaz", "ontobee": "GAZ", "wikidata": "P6778" @@ -10113,7 +10118,7 @@ "aberowl": "GECKO", "bioportal": "GECKO", "fairsharing": "FAIRsharing.3da56b", - "obofoundry": "GECKO", + "obofoundry": "gecko", "ols": "gecko", "ontobee": "GECKO" }, @@ -10254,7 +10259,7 @@ "aberowl": "GENEPIO", "biocontext": "GENEPIO", "fairsharing": "FAIRsharing.y1mmbv", - "obofoundry": "GENEPIO", + "obofoundry": "genepio", "ols": "genepio", "ontobee": "GENEPIO" }, @@ -10315,7 +10320,7 @@ "biocontext": "GENO", "bioportal": "GENO", "fairsharing": "FAIRsharing.kpbna7", - "obofoundry": "GENO", + "obofoundry": "geno", "ols": "geno", "ontobee": "GENO" }, @@ -10381,9 +10386,9 @@ "banana_peel": "_", "contact": { "email": "hoganwr@gmail.com", - "github": null, + "github": "hoganwr", "name": "Bill Hogan", - "orcid": null + "orcid": "0000-0002-9881-1017" }, "description": "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\".", "download_owl": "http://purl.obolibrary.org/obo/geo.owl", @@ -10394,7 +10399,7 @@ "biocontext": "GEO", "bioportal": "GEO", "miriam": "geogeo", - "obofoundry": "GEO", + "obofoundry": "geo", "ols": "geo", "ontobee": "GEO" }, @@ -10765,7 +10770,7 @@ "mappings": { "aberowl": "GNO", "bioportal": "GNO", - "obofoundry": "GNO", + "obofoundry": "gno", "ols": "gno", "ontobee": "GNO" }, @@ -10838,7 +10843,7 @@ "miriam": "go", "n2t": "go", "ncbi": "GO", - "obofoundry": "GO", + "obofoundry": "go", "ols": "go", "ontobee": "GO", "prefixcommons": "go", @@ -11371,7 +11376,7 @@ "aberowl": "GSSO", "bioportal": "GSSO", "miriam": "gsso", - "obofoundry": "GSSO", + "obofoundry": "gsso", "ols": "gsso", "ontobee": "GSSO" }, @@ -11524,7 +11529,7 @@ "homepage": "http://www.mesquiteproject.org/ontology/Habronattus/index.html", "mappings": { "biocontext": "HABRONATTUS", - "obofoundry": "HABRONATTUS" + "obofoundry": "habronattus" }, "name": "Habronattus courtship", "preferred_prefix": "HABRONATTUS", @@ -11566,7 +11571,7 @@ "biolink": "HANCESTRO", "bioportal": "HANCESTRO", "fairsharing": "FAIRsharing.rja8qp", - "obofoundry": "HANCESTRO", + "obofoundry": "hancestro", "ols": "hancestro", "ontobee": "HANCESTRO" }, @@ -11595,7 +11600,7 @@ "biocontext": "HAO", "bioportal": "HAO", "fairsharing": "FAIRsharing.kj3m5n", - "obofoundry": "HAO", + "obofoundry": "hao", "ols": "hao", "ontobee": "HAO" }, @@ -11956,7 +11961,7 @@ "biocontext": "HOM", "bioportal": "HOM", "fairsharing": "FAIRsharing.efv7gw", - "obofoundry": "HOM", + "obofoundry": "hom", "ols": "hom", "ontobee": "HOM" }, @@ -12075,7 +12080,7 @@ "fairsharing": "FAIRsharing.kbtt7f", "miriam": "hp", "n2t": "hp", - "obofoundry": "HP", + "obofoundry": "hp", "ols": "hp", "ontobee": "HP", "wikidata": "P3841" @@ -12207,7 +12212,7 @@ "biolink": "HsapDv", "bioportal": "HSAPDV", "fairsharing": "FAIRsharing.c6vhm3", - "obofoundry": "HsapDv", + "obofoundry": "hsapdv", "ols": "hsapdv", "ontobee": "HSAPDV" }, @@ -12255,7 +12260,7 @@ "mappings": { "aberowl": "HSO", "bioportal": "HSO", - "obofoundry": "HSO", + "obofoundry": "hso", "ols": "hso", "ontobee": "HSO" }, @@ -12306,7 +12311,7 @@ "mappings": { "aberowl": "HTN", "bioportal": "HTN", - "obofoundry": "HTN", + "obofoundry": "htn", "ols": "htn", "ontobee": "HTN" }, @@ -12367,7 +12372,7 @@ "go": "IAO", "miriam": "iao", "n2t": "iao", - "obofoundry": "IAO", + "obofoundry": "iao", "ols": "iao", "ontobee": "IAO" }, @@ -12570,7 +12575,7 @@ "mappings": { "aberowl": "ICEO", "bioportal": "ICEO", - "obofoundry": "ICEO", + "obofoundry": "iceo", "ols": "iceo", "ontobee": "ICEO" }, @@ -12630,7 +12635,7 @@ "biocontext": "ICO", "bioportal": "ICO", "fairsharing": "FAIRsharing.b9znd5", - "obofoundry": "ICO", + "obofoundry": "ico", "ols": "ico", "ontobee": "ICO" }, @@ -12679,7 +12684,7 @@ "fairsharing": "FAIRsharing.aae3v6", "miriam": "ido", "n2t": "ido", - "obofoundry": "IDO", + "obofoundry": "ido", "ols": "ido", "ontobee": "IDO" }, @@ -12751,7 +12756,7 @@ "biocontext": "IDOMAL", "bioportal": "IDOMAL", "fairsharing": "FAIRsharing.2q8c28", - "obofoundry": "IDOMAL", + "obofoundry": "idomal", "ols": "idomal", "ontobee": "IDOMAL" }, @@ -12842,7 +12847,7 @@ "homepage": "http://www.inoh.org", "mappings": { "biocontext": "IEV", - "obofoundry": "IEV", + "obofoundry": "iev", "prefixcommons": "iev" }, "name": "Event (INOH pathway ontology)", @@ -13057,7 +13062,7 @@ "homepage": "http://www.inoh.org", "mappings": { "biocontext": "IMR", - "obofoundry": "IMR", + "obofoundry": "imr", "prefixcommons": "imr" }, "name": "Molecule role (INOH Protein name/family name ontology)", @@ -13195,7 +13200,7 @@ "biolink": "INO", "bioportal": "INO", "fairsharing": "FAIRsharing.mm72as", - "obofoundry": "INO", + "obofoundry": "ino", "ols": "ino", "ontobee": "INO" }, @@ -13422,7 +13427,7 @@ "miriam": "interpro", "n2t": "interpro", "ncbi": "InterPro", - "obofoundry": "IPR", + "obofoundry": "ipr", "prefixcommons": "interpro", "uniprot": "InterPro", "wikidata": "P2926" @@ -14223,7 +14228,6 @@ "iao", "obi", "ogms", - "omiabis", "omrse", "opmi" ], @@ -14235,7 +14239,7 @@ "mappings": { "aberowl": "LABO", "bioportal": "LABO", - "obofoundry": "LABO", + "obofoundry": "labo", "ols": "labo", "ontobee": "LABO" }, @@ -14308,7 +14312,7 @@ "mappings": { "aberowl": "LEPAO", "bioportal": "LEPAO", - "obofoundry": "LEPAO", + "obofoundry": "lepao", "ols": "lepao" }, "name": "Lepidoptera Anatomy Ontology", @@ -14585,7 +14589,7 @@ "aberowl": "LIPRO", "biocontext": "LIPRO", "bioportal": "LIPRO", - "obofoundry": "LIPRO" + "obofoundry": "lipro" }, "name": "Lipid Ontology", "preferred_prefix": "LIPRO", @@ -14618,7 +14622,7 @@ "homepage": "http://www.mesquiteproject.org/ontology/Loggerhead/index.html", "mappings": { "biocontext": "LOGGERHEAD", - "obofoundry": "LOGGERHEAD" + "obofoundry": "loggerhead" }, "name": "Loggerhead nesting", "preferred_prefix": "LOGGERHEAD", @@ -14814,7 +14818,7 @@ "go": "MA", "miriam": "ma", "n2t": "ma", - "obofoundry": "MA", + "obofoundry": "ma", "ols": "ma", "ontobee": "MA", "prefixcommons": "ma" @@ -14882,7 +14886,7 @@ "fairsharing": "FAIRsharing.kbz5jh", "miriam": "mamo", "n2t": "mamo", - "obofoundry": "MAMO", + "obofoundry": "mamo", "ols": "mamo", "ontobee": "MAMO" }, @@ -14904,7 +14908,7 @@ "homepage": "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html", "mappings": { "biocontext": "MAO", - "obofoundry": "MAO", + "obofoundry": "mao", "prefixcommons": "mao" }, "name": "Multiple alignment", @@ -14975,7 +14979,7 @@ "aberowl": "MAT", "biocontext": "MAT", "bioportal": "MAT", - "obofoundry": "MAT" + "obofoundry": "mat" }, "name": "Minimal Anatomical Terminology", "pattern": "^\\d{7}$", @@ -15046,7 +15050,7 @@ "aberowl": "MAXO", "biolink": "MAXO", "bioportal": "MAXO", - "obofoundry": "MAXO", + "obofoundry": "maxo", "ols": "maxo", "ontobee": "MAXO" }, @@ -15112,7 +15116,7 @@ "mappings": { "aberowl": "MCO", "bioportal": "MCO", - "obofoundry": "MCO", + "obofoundry": "mco", "ols": "mco", "ontobee": "MCO" }, @@ -15487,7 +15491,7 @@ "biocontext": "MF", "bioportal": "MF", "fairsharing": "FAIRsharing.4gm9gt", - "obofoundry": "MF", + "obofoundry": "mf", "ols": "mf", "ontobee": "MF" }, @@ -15518,7 +15522,7 @@ "biocontext": "MFMO", "bioportal": "MFMO", "fairsharing": "FAIRsharing.669cnk", - "obofoundry": "MFMO", + "obofoundry": "mfmo", "ols": "mfmo", "ontobee": "MFMO" }, @@ -15544,7 +15548,7 @@ "aberowl": "MFO", "biocontext": "MFO", "bioportal": "MFO", - "obofoundry": "MFO", + "obofoundry": "mfo", "prefixcommons": "mfo" }, "name": "Medaka fish anatomy and development", @@ -15568,7 +15572,7 @@ "biocontext": "MFOEM", "bioportal": "MFOEM", "fairsharing": "FAIRsharing.dx30m8", - "obofoundry": "MFOEM", + "obofoundry": "mfoem", "ols": "mfoem", "ontobee": "MFOEM" }, @@ -15596,7 +15600,7 @@ "biocontext": "MFOMD", "bioportal": "MFOMD", "fairsharing": "FAIRsharing.q053vb", - "obofoundry": "MFOMD", + "obofoundry": "mfomd", "ols": "mfomd", "ontobee": "MFOMD" }, @@ -15729,7 +15733,7 @@ "go": "PSI-MI", "miriam": "mi", "n2t": "psimi", - "obofoundry": "MI", + "obofoundry": "mi", "ols": "mi", "ontobee": "MI", "prefixcommons": "psi.mi" @@ -15776,7 +15780,7 @@ "biocontext": "MIAPA", "bioportal": "MIAPA", "fairsharing": "FAIRsharing.ca48xs", - "obofoundry": "MIAPA", + "obofoundry": "miapa", "ols": "miapa", "ontobee": "MIAPA" }, @@ -15806,7 +15810,7 @@ "aberowl": "MICRO", "biocontext": "MICRO", "fairsharing": "FAIRsharing.brhpb0", - "obofoundry": "MICRO", + "obofoundry": "micro", "ols": "micro", "ontobee": "MicrO" }, @@ -16093,7 +16097,7 @@ "aberowl": "MIRNAO", "biocontext": "MIRNAO", "bioportal": "MIRNAO", - "obofoundry": "MIRNAO", + "obofoundry": "mirnao", "ontobee": "miRNAO" }, "name": "microRNA Ontology", @@ -16134,7 +16138,7 @@ "biocontext": "MIRO", "bioportal": "MIRO", "fairsharing": "FAIRsharing.sjf113", - "obofoundry": "MIRO", + "obofoundry": "miro", "ols": "miro", "ontobee": "MIRO" }, @@ -16237,7 +16241,7 @@ "biocontext": "MMO", "bioportal": "MMO", "fairsharing": "FAIRsharing.bgkyd7", - "obofoundry": "MMO", + "obofoundry": "mmo", "ols": "mmo", "ontobee": "MMO" }, @@ -16354,7 +16358,7 @@ "biolink": "MmusDv", "bioportal": "MMUSDV", "fairsharing": "FAIRsharing.zchb68", - "obofoundry": "MmusDv", + "obofoundry": "mmusdv", "ols": "mmusdv", "ontobee": "MMUSDV" }, @@ -16386,7 +16390,7 @@ "bioportal": "MO", "miriam": "mo", "n2t": "mo", - "obofoundry": "MO" + "obofoundry": "mo" }, "name": "Microarray experimental conditions", "pattern": "^\\w+$", @@ -16441,7 +16445,7 @@ "go": "PSI-MOD", "miriam": "mod", "n2t": "mod", - "obofoundry": "MOD", + "obofoundry": "mod", "ols": "mod", "ontobee": "MOD", "prefixcommons": "psi.mod" @@ -16534,7 +16538,7 @@ "biocontext": "MONDO", "bioportal": "MONDO", "fairsharing": "FAIRsharing.b2979t", - "obofoundry": "MONDO", + "obofoundry": "mondo", "ols": "mondo", "ontobee": "MONDO", "wikidata": "P5270" @@ -16564,7 +16568,7 @@ "biocontext": "MOP", "bioportal": "MOP", "fairsharing": "FAIRsharing.mct09a", - "obofoundry": "MOP", + "obofoundry": "mop", "ols": "mop", "ontobee": "MOP" }, @@ -16613,7 +16617,7 @@ "fairsharing": "FAIRsharing.kg1x4z", "miriam": "mp", "n2t": "mp", - "obofoundry": "MP", + "obofoundry": "mp", "ols": "mp", "ontobee": "MP", "prefixcommons": "mp" @@ -16643,7 +16647,7 @@ "biocontext": "MPATH", "bioportal": "MPATH", "fairsharing": "FAIRsharing.3wbgm0", - "obofoundry": "MPATH", + "obofoundry": "mpath", "ols": "mpath", "ontobee": "MPATH", "prefixcommons": "mpath" @@ -16701,7 +16705,7 @@ "aberowl": "MPIO", "biocontext": "MPIO", "bioportal": "MPIO", - "obofoundry": "MPIO", + "obofoundry": "mpio", "ols": "mpio", "ontobee": "MPIO" }, @@ -16729,7 +16733,7 @@ "biocontext": "MRO", "bioportal": "MRO", "fairsharing": "FAIRsharing.k893xa", - "obofoundry": "MRO", + "obofoundry": "mro", "ols": "mro", "ontobee": "MRO" }, @@ -16764,7 +16768,7 @@ "bioportal": "MS", "miriam": "ms", "n2t": "ms", - "obofoundry": "MS", + "obofoundry": "ms", "ols": "ms", "ontobee": "MS" }, @@ -17143,7 +17147,7 @@ "biocontext": "NBO", "bioportal": "NBO", "fairsharing": "FAIRsharing.pktgc6", - "obofoundry": "NBO", + "obofoundry": "nbo", "ols": "nbo", "ontobee": "NBO" }, @@ -17398,7 +17402,7 @@ "miriam": "taxonomy", "n2t": "taxonomy", "ncbi": "taxon", - "obofoundry": "NCBITaxon", + "obofoundry": "ncbitaxon", "ols": "ncbitaxon", "ontobee": "NCBITaxon", "prefixcommons": "uniprot.taxonomy", @@ -17493,7 +17497,7 @@ "fairsharing": "FAIRsharing.4cvwxa", "miriam": "ncit", "n2t": "ncit", - "obofoundry": "NCIT", + "obofoundry": "ncit", "ols": "ncit", "ontobee": "NCIT", "prefixcommons": "ncit", @@ -17535,7 +17539,7 @@ "biocontext": "NCRO", "bioportal": "NCRO", "fairsharing": "FAIRsharing.vppyga", - "obofoundry": "NCRO", + "obofoundry": "ncro", "ols": "ncro", "ontobee": "NCRO" }, @@ -17853,7 +17857,7 @@ "aberowl": "NIFCELL", "biocontext": "NIF_CELL", "bioportal": "NIFCELL", - "obofoundry": "NIF_CELL" + "obofoundry": "nif_cell" }, "name": "NIF Cell", "part_of": "nif", @@ -17871,7 +17875,7 @@ "homepage": "http://neuinfo.org/", "mappings": { "biocontext": "NIF_DYSFUNCTION", - "obofoundry": "NIF_DYSFUNCTION" + "obofoundry": "nif_dysfunction" }, "name": "NIF Dysfunction", "part_of": "nif", @@ -17922,7 +17926,7 @@ "homepage": "http://neuinfo.org/", "mappings": { "biocontext": "NIF_GROSSANATOMY", - "obofoundry": "NIF_GROSSANATOMY" + "obofoundry": "nif_grossanatomy" }, "name": "NIF Gross Anatomy", "part_of": "nif", @@ -18487,7 +18491,7 @@ "bioportal": "NMR", "miriam": "nmr", "n2t": "nmr", - "obofoundry": "NMR", + "obofoundry": "nmr", "ols": "nmrcv", "prefixcommons": "nmr" }, @@ -18553,7 +18557,7 @@ "mappings": { "aberowl": "NOMEN", "bioportal": "NOMEN", - "obofoundry": "NOMEN", + "obofoundry": "nomen", "ols": "nomen", "ontobee": "NOMEN" }, @@ -18727,7 +18731,7 @@ "biocontext": "OAE", "bioportal": "OAE", "fairsharing": "FAIRsharing.tw4q8x", - "obofoundry": "OAE", + "obofoundry": "oae", "ols": "oae", "ontobee": "OAE" }, @@ -18755,7 +18759,7 @@ "biocontext": "OARCS", "bioportal": "OARCS", "fairsharing": "FAIRsharing.yqn857", - "obofoundry": "OARCS", + "obofoundry": "oarcs", "ols": "oarcs", "ontobee": "OARCS" }, @@ -18787,7 +18791,7 @@ "biocontext": "OBA", "bioportal": "OBA", "fairsharing": "FAIRsharing.mp0rwf", - "obofoundry": "OBA", + "obofoundry": "oba", "ols": "oba", "ontobee": "OBA" }, @@ -18815,7 +18819,7 @@ "biocontext": "OBCS", "bioportal": "OBCS", "fairsharing": "FAIRsharing.5p12xh", - "obofoundry": "OBCS", + "obofoundry": "obcs", "ols": "obcs", "ontobee": "OBCS" }, @@ -18861,7 +18865,7 @@ "go": "OBI", "miriam": "obi", "n2t": "obi", - "obofoundry": "OBI", + "obofoundry": "obi", "ols": "obi", "ontobee": "OBI", "prefixcommons": "obi" @@ -18891,7 +18895,7 @@ "biocontext": "OBIB", "bioportal": "OBIB", "fairsharing": "FAIRsharing.bxc508", - "obofoundry": "OBIB", + "obofoundry": "obib", "ols": "obib", "ontobee": "OBIB" }, @@ -19054,7 +19058,7 @@ "biocontext": "OGG", "bioportal": "OGG", "fairsharing": "FAIRsharing.zmx7nn", - "obofoundry": "OGG", + "obofoundry": "ogg", "ols": "ogg", "ontobee": "OGG" }, @@ -19081,7 +19085,7 @@ "aberowl": "OGI", "biocontext": "OGI", "bioportal": "OGI", - "obofoundry": "OGI", + "obofoundry": "ogi", "ols": "ogi", "ontobee": "OGI" }, @@ -19115,7 +19119,7 @@ "biocontext": "OGMS", "bioportal": "OGMS", "fairsharing": "FAIRsharing.rvz0m9", - "obofoundry": "OGMS", + "obofoundry": "ogms", "ols": "ogms", "ontobee": "OGMS" }, @@ -19146,7 +19150,7 @@ "biocontext": "OGSF", "bioportal": "OGSF", "fairsharing": "FAIRsharing.egv2cz", - "obofoundry": "OGSF", + "obofoundry": "ogsf", "ols": "ogsf", "ontobee": "OGSF" }, @@ -19174,7 +19178,7 @@ "biocontext": "OHD", "bioportal": "OHD", "fairsharing": "FAIRsharing.bg7bb6", - "obofoundry": "OHD", + "obofoundry": "ohd", "ols": "ohd", "ontobee": "OHD" }, @@ -19202,7 +19206,7 @@ "biocontext": "OHMI", "bioportal": "OHMI", "fairsharing": "FAIRsharing.cz9cnp", - "obofoundry": "OHMI", + "obofoundry": "ohmi", "ols": "ohmi", "ontobee": "OHMI" }, @@ -19229,7 +19233,7 @@ "aberowl": "OHPI", "bioportal": "OHPI", "fairsharing": "FAIRsharing.vxpUJ6", - "obofoundry": "OHPI", + "obofoundry": "ohpi", "ols": "ohpi", "ontobee": "OHPI" }, @@ -19271,7 +19275,7 @@ "biocontext": "OLATDV", "bioportal": "OLATDV", "fairsharing": "FAIRsharing.c86z66", - "obofoundry": "OlatDv", + "obofoundry": "olatdv", "ols": "olatdv", "ontobee": "OLATDV" }, @@ -19378,7 +19382,7 @@ "aberowl": "OMIABIS", "biocontext": "OMIABIS", "bioportal": "OMIABIS", - "obofoundry": "OMIABIS", + "obofoundry": "omiabis", "ols": "omiabis", "ontobee": "OMIABIS" }, @@ -19485,7 +19489,7 @@ "fairsharing": "FAIRsharing.mf91p5", "miriam": "omit", "n2t": "omit", - "obofoundry": "OMIT", + "obofoundry": "omit", "ols": "omit", "ontobee": "OMIT" }, @@ -19516,7 +19520,7 @@ "mappings": { "aberowl": "OMO", "bioportal": "OMO", - "obofoundry": "OMO", + "obofoundry": "omo", "ols": "omo", "ontobee": "OMO" }, @@ -19564,7 +19568,7 @@ "biocontext": "OMP", "bioportal": "OMP", "fairsharing": "FAIRsharing.cc3f2x", - "obofoundry": "OMP", + "obofoundry": "omp", "ols": "omp", "ontobee": "OMP" }, @@ -19596,7 +19600,7 @@ "biocontext": "OMRSE", "bioportal": "OMRSE", "fairsharing": "FAIRsharing.z0p37e", - "obofoundry": "OMRSE", + "obofoundry": "omrse", "ols": "omrse", "ontobee": "OMRSE" }, @@ -19645,7 +19649,7 @@ "aberowl": "ONE", "bioportal": "ONE", "fairsharing": "FAIRsharing.USxx0K", - "obofoundry": "ONE", + "obofoundry": "one", "ols": "one", "ontobee": "ONE" }, @@ -19684,7 +19688,7 @@ "aberowl": "ONS", "bioportal": "ONS", "fairsharing": "FAIRsharing.rfec93", - "obofoundry": "ONS", + "obofoundry": "ons", "ols": "ons", "ontobee": "ONS" }, @@ -19718,7 +19722,7 @@ "mappings": { "aberowl": "ONTOAVIDA", "bioportal": "ONTOAVIDA", - "obofoundry": "ONTOAVIDA", + "obofoundry": "ontoavida", "ols": "ontoavida", "ontobee": "ONTOAVIDA" }, @@ -19746,7 +19750,7 @@ "biocontext": "ONTONEO", "bioportal": "ONTONEO", "fairsharing": "FAIRsharing.5a4y1y", - "obofoundry": "ONTONEO", + "obofoundry": "ontoneo", "ols": "ontoneo", "ontobee": "ONTONEO" }, @@ -19774,7 +19778,7 @@ "biocontext": "OOSTT", "bioportal": "OOSTT", "fairsharing": "FAIRsharing.b4sa0w", - "obofoundry": "OOSTT", + "obofoundry": "oostt", "ols": "oostt", "ontobee": "OOSTT" }, @@ -19850,7 +19854,7 @@ "biocontext": "OPL", "bioportal": "OPL", "fairsharing": "FAIRsharing.ez2nhb", - "obofoundry": "OPL", + "obofoundry": "opl", "ols": "opl", "ontobee": "OPL" }, @@ -19895,7 +19899,7 @@ "mappings": { "aberowl": "OPMI", "bioportal": "OPMI", - "obofoundry": "OPMI", + "obofoundry": "opmi", "ols": "opmi", "ontobee": "OPMI" }, @@ -19994,7 +19998,7 @@ "mappings": { "aberowl": "ORNASEQ", "bioportal": "ORNASEQ", - "obofoundry": "ORNASEQ", + "obofoundry": "ornaseq", "ols": "ornaseq", "ontobee": "ORNASEQ" }, @@ -20231,7 +20235,7 @@ "biocontext": "OVAE", "bioportal": "OVAE", "fairsharing": "FAIRsharing.w4x6n4", - "obofoundry": "OVAE", + "obofoundry": "ovae", "ols": "ovae", "ontobee": "OVAE" }, @@ -20382,7 +20386,7 @@ "homepage": "http://www.plantontology.org", "mappings": { "biocontext": "PAO", - "obofoundry": "PAO" + "obofoundry": "pao" }, "name": "Plant Anatomy Ontology", "preferred_prefix": "PAO", @@ -20483,7 +20487,7 @@ "go": "PATO", "miriam": "pato", "n2t": "pato", - "obofoundry": "PATO", + "obofoundry": "pato", "ols": "pato", "ontobee": "PATO", "prefixcommons": "pato" @@ -20615,7 +20619,7 @@ "mappings": { "aberowl": "PCL", "bioportal": "PCL", - "obofoundry": "PCL", + "obofoundry": "pcl", "ols": "pcl", "ontobee": "PCL" }, @@ -20659,7 +20663,7 @@ "bioportal": "PCO", "ecoportal": "PCO", "fairsharing": "FAIRsharing.vq28qp", - "obofoundry": "PCO", + "obofoundry": "pco", "ols": "pco", "ontobee": "PCO" }, @@ -20681,7 +20685,7 @@ "homepage": "http://4dx.embl.de/platy", "mappings": { "biocontext": "PD_ST", - "obofoundry": "PD_ST" + "obofoundry": "pd_st" }, "name": "Platynereis stage ontology", "preferred_prefix": "PD_ST", @@ -20840,7 +20844,7 @@ "biocontext": "PDRO", "bioportal": "PDRO", "fairsharing": "FAIRsharing.9te3ev", - "obofoundry": "PDRO", + "obofoundry": "pdro", "ols": "pdro", "ontobee": "PDRO" }, @@ -20869,7 +20873,7 @@ "biocontext": "PDUMDV", "bioportal": "PDUMDV", "fairsharing": "FAIRsharing.493qns", - "obofoundry": "PdumDv", + "obofoundry": "pdumdv", "ols": "pdumdv", "ontobee": "PDUMDV" }, @@ -20906,7 +20910,7 @@ "biocontext": "PECO", "bioportal": "PECO", "fairsharing": "FAIRsharing.6yNXYK", - "obofoundry": "PECO", + "obofoundry": "peco", "ols": "peco", "ontobee": "PECO" }, @@ -21105,7 +21109,7 @@ "homepage": "http://www.plantontology.org", "mappings": { "biocontext": "PGDSO", - "obofoundry": "PGDSO" + "obofoundry": "pgdso" }, "name": "Plant Growth and Development Stage", "preferred_prefix": "PGDSO", @@ -21300,7 +21304,7 @@ "mappings": { "aberowl": "PHIPO", "bioportal": "PHIPO", - "obofoundry": "PHIPO", + "obofoundry": "phipo", "ols": "phipo", "ontobee": "PHIPO" }, @@ -21562,7 +21566,7 @@ "biocontext": "PLANA", "bioportal": "PLANA", "fairsharing": "FAIRsharing.g1qrqs", - "obofoundry": "PLANA", + "obofoundry": "plana", "ols": "plana", "ontobee": "PLANA" }, @@ -21595,7 +21599,7 @@ "mappings": { "aberowl": "PLANP", "bioportal": "PLANP", - "obofoundry": "PLANP", + "obofoundry": "planp", "ols": "planp", "ontobee": "PLANP" }, @@ -21654,7 +21658,7 @@ "homepage": "http://www.sanger.ac.uk/Users/mb4/PLO/", "mappings": { "biocontext": "PLO", - "obofoundry": "PLO" + "obofoundry": "plo" }, "name": "Plasmodium Life Cycle", "preferred_prefix": "PLO", @@ -21799,7 +21803,7 @@ "go": "PO", "miriam": "po", "n2t": "po", - "obofoundry": "PO", + "obofoundry": "po", "ols": "po", "ontobee": "PO", "prefixcommons": "po" @@ -21888,7 +21892,7 @@ "biocontext": "PORO", "bioportal": "PORO", "fairsharing": "FAIRsharing.93g1th", - "obofoundry": "PORO", + "obofoundry": "poro", "ols": "poro", "ontobee": "PORO" }, @@ -21935,7 +21939,7 @@ "biocontext": "PPO", "bioportal": "PPO", "fairsharing": "FAIRsharing.hakg7c", - "obofoundry": "PPO", + "obofoundry": "ppo", "ols": "ppo", "ontobee": "PPO" }, @@ -21990,7 +21994,7 @@ "go": "PR", "miriam": "pr", "n2t": "pr", - "obofoundry": "PR", + "obofoundry": "pr", "ols": "pr", "ontobee": "PR", "prefixcommons": "pr", @@ -22118,20 +22122,22 @@ "ro", "sbo" ], - "description": "PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes.", + "description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.", "download_owl": "http://purl.obolibrary.org/obo/proco.owl", "example": "0000001", "homepage": "https://github.com/proco-ontology/PROCO", "license": "CC BY 4.0", "mappings": { "aberowl": "PROCO", - "obofoundry": "PROCO", + "obofoundry": "proco", + "ols": "proco", "ontobee": "PROCO" }, "name": "Process Chemistry Ontology", "preferred_prefix": "PROCO", "repository": "https://github.com/proco-ontology/PROCO", - "uri_format": "http://purl.obolibrary.org/obo/PROCO_$1" + "uri_format": "http://purl.obolibrary.org/obo/PROCO_$1", + "version": "PROCO release 20220414" }, "prodom": { "description": "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences.", @@ -22177,7 +22183,7 @@ "aberowl": "PROPREO", "biocontext": "PROPREO", "bioportal": "PROPREO", - "obofoundry": "PROPREO", + "obofoundry": "propreo", "prefixcommons": "propreo" }, "name": "Proteomics data and process provenance", @@ -22330,7 +22336,7 @@ "mappings": { "aberowl": "PSDO", "bioportal": "PSDO", - "obofoundry": "PSDO", + "obofoundry": "psdo", "ols": "psdo", "ontobee": "PSDO" }, @@ -22404,7 +22410,7 @@ "aberowl": "PSO", "bioportal": "PSO", "fairsharing": "FAIRsharing.dyj433", - "obofoundry": "PSO", + "obofoundry": "pso", "ols": "pso", "ontobee": "PSO" }, @@ -22676,7 +22682,7 @@ "fairsharing": "FAIRsharing.f73xhd", "miriam": "pw", "n2t": "pw", - "obofoundry": "PW", + "obofoundry": "pw", "ols": "pw", "ontobee": "PW", "prefixcommons": "pw", @@ -22839,7 +22845,7 @@ "mappings": { "aberowl": "RBO", "bioportal": "RBO", - "obofoundry": "RBO", + "obofoundry": "rbo", "ols": "rbo", "ontobee": "RBO" }, @@ -23113,7 +23119,7 @@ "go": "RESID", "miriam": "resid", "n2t": "resid", - "obofoundry": "RESID", + "obofoundry": "resid", "prefixcommons": "resid" }, "name": "Protein covalent bond", @@ -23148,7 +23154,7 @@ "biocontext": "REX", "bioportal": "REX", "fairsharing": "FAIRsharing.g0a7s0", - "obofoundry": "REX", + "obofoundry": "rex", "ols": "rex", "ontobee": "REX", "prefixcommons": "rex" @@ -23434,7 +23440,7 @@ "biocontext": "RNAO", "bioportal": "RNAO", "fairsharing": "FAIRsharing.kqt2h2", - "obofoundry": "RNAO", + "obofoundry": "rnao", "ols": "rnao", "ontobee": "RNAO", "prefixcommons": "rnao" @@ -23478,7 +23484,6 @@ "psdo", "pso", "rbo", - "upa", "xpo", "zp" ], @@ -23507,7 +23512,7 @@ "go": "RO", "miriam": "ro", "n2t": "ro", - "obofoundry": "RO", + "obofoundry": "ro", "ols": "ro", "ontobee": "RO", "prefixcommons": "ro", @@ -23578,7 +23583,7 @@ "biocontext": "RS", "bioportal": "RS", "fairsharing": "FAIRsharing.vajn3f", - "obofoundry": "RS", + "obofoundry": "rs", "ols": "rs", "ontobee": "RS", "prefixcommons": "rs" @@ -23620,7 +23625,7 @@ "biocontext": "RXNO", "bioportal": "RXNO", "fairsharing": "FAIRsharing.w4tncg", - "obofoundry": "RXNO", + "obofoundry": "rxno", "ols": "rxno", "ontobee": "RXNO", "wikidata": "P2106" @@ -23765,7 +23770,7 @@ "aberowl": "SAO", "biocontext": "SAO", "bioportal": "SAO", - "obofoundry": "SAO", + "obofoundry": "sao", "prefixcommons": "sao" }, "name": "Subcellular Anatomy Ontology", @@ -23816,7 +23821,7 @@ "fairsharing": "FAIRsharing.s19src", "miriam": "sbo", "n2t": "sbo", - "obofoundry": "SBO", + "obofoundry": "sbo", "ols": "sbo", "ontobee": "SBO", "prefixcommons": "sbo" @@ -23848,13 +23853,11 @@ "envo", "eupath", "exo", - "gaz", "gsso", "hp", "hsapdv", "ico", "ido", - "idomal", "mp", "nbo", "ncit", @@ -23879,7 +23882,7 @@ "aberowl": "SCDO", "bioportal": "SCDO", "fairsharing": "FAIRsharing.kkq6pw", - "obofoundry": "SCDO", + "obofoundry": "scdo", "ols": "scdo", "ontobee": "SCDO" }, @@ -24172,7 +24175,7 @@ "aberowl": "SEP", "biocontext": "SEP", "bioportal": "SEP", - "obofoundry": "SEP", + "obofoundry": "sep", "ontobee": "SEP", "prefixcommons": "sep" }, @@ -24197,7 +24200,7 @@ "aberowl": "SEPIO", "biocontext": "SEPIO", "bioportal": "SEPIO", - "obofoundry": "SEPIO", + "obofoundry": "sepio", "ols": "sepio", "ontobee": "SEPIO" }, @@ -24335,7 +24338,7 @@ "biocontext": "SIBO", "bioportal": "SIBO", "fairsharing": "FAIRsharing.q09hck", - "obofoundry": "SIBO", + "obofoundry": "sibo", "ols": "sibo", "ontobee": "SIBO" }, @@ -24725,7 +24728,7 @@ "go": "SO", "miriam": "so", "n2t": "so", - "obofoundry": "SO", + "obofoundry": "so", "ols": "so", "ontobee": "SO", "prefixcommons": "so" @@ -24752,7 +24755,7 @@ "aberowl": "SOPHARM", "biocontext": "SOPHARM", "bioportal": "SOPHARM", - "obofoundry": "SOPHARM" + "obofoundry": "sopharm" }, "name": "Suggested Ontology for Pharmacogenomics", "preferred_prefix": "SOPHARM", @@ -24804,7 +24807,7 @@ "biocontext": "SPD", "bioportal": "SPD", "fairsharing": "FAIRsharing.yecp83", - "obofoundry": "SPD", + "obofoundry": "spd", "ols": "spd", "ontobee": "SPD", "prefixcommons": "spd", @@ -24968,7 +24971,7 @@ "biocontext": "STATO", "bioportal": "STATO", "fairsharing": "FAIRsharing.na5xp", - "obofoundry": "STATO", + "obofoundry": "stato", "ols": "stato", "ontobee": "STATO" }, @@ -25277,7 +25280,7 @@ "biocontext": "SWO", "bioportal": "SWO", "fairsharing": "FAIRsharing.sp3szt", - "obofoundry": "SWO", + "obofoundry": "swo", "ols": "swo", "ontobee": "SWO", "prefixcommons": "swo" @@ -25310,7 +25313,7 @@ "biocontext": "SYMP", "bioportal": "SYMP", "fairsharing": "FAIRsharing.ay74mj", - "obofoundry": "SYMP", + "obofoundry": "symp", "ols": "symp", "ontobee": "SYMP", "wikidata": "P8656" @@ -25375,7 +25378,7 @@ "biocontext": "TADS", "bioportal": "TADS", "fairsharing": "FAIRsharing.8wm364", - "obofoundry": "TADS", + "obofoundry": "tads", "ols": "tads", "ontobee": "TADS" }, @@ -25396,7 +25399,7 @@ "deprecated": true, "mappings": { "biocontext": "TAHE", - "obofoundry": "TAHE" + "obofoundry": "tahe" }, "name": "Terminology of Anatomy of Human Embryology", "preferred_prefix": "TAHE", @@ -25412,7 +25415,7 @@ "deprecated": true, "mappings": { "biocontext": "TAHH", - "obofoundry": "TAHH" + "obofoundry": "tahh" }, "name": "Terminology of Anatomy of Human Histology", "preferred_prefix": "TAHH", @@ -25487,7 +25490,7 @@ "aberowl": "TAO", "biocontext": "TAO", "bioportal": "TAO", - "obofoundry": "TAO", + "obofoundry": "tao", "prefixcommons": "tao" }, "name": "Teleost Anatomy Ontology", @@ -25531,7 +25534,7 @@ "biocontext": "TAXRANK", "bioportal": "TAXRANK", "fairsharing": "FAIRsharing.p1sejz", - "obofoundry": "TAXRANK", + "obofoundry": "taxrank", "ols": "taxrank", "ontobee": "TAXRANK", "prefixcommons": "taxrank" @@ -25638,7 +25641,7 @@ "biocontext": "TGMA", "bioportal": "TGMA", "fairsharing": "FAIRsharing.dqnfkg", - "obofoundry": "TGMA", + "obofoundry": "tgma", "ols": "tgma", "ontobee": "TGMA", "prefixcommons": "tgma" @@ -25770,7 +25773,7 @@ "biocontext": "TO", "bioportal": "PTO", "fairsharing": "FAIRsharing.w69t6r", - "obofoundry": "TO", + "obofoundry": "to", "ols": "to", "ontobee": "TO" }, @@ -25874,7 +25877,7 @@ "biocontext": "TRANS", "bioportal": "TRANS", "fairsharing": "FAIRsharing.nygmp7", - "obofoundry": "TRANS", + "obofoundry": "trans", "ols": "trans", "ontobee": "TRANS" }, @@ -26008,7 +26011,7 @@ "biocontext": "TTO", "bioportal": "TTO", "fairsharing": "FAIRsharing.1rj558", - "obofoundry": "TTO", + "obofoundry": "tto", "ols": "tto", "ontobee": "TTO", "prefixcommons": "tto" @@ -26035,7 +26038,7 @@ "mappings": { "aberowl": "TXPO", "bioportal": "TXPO", - "obofoundry": "TXPO", + "obofoundry": "txpo", "ols": "txpo", "ontobee": "TXPO" }, @@ -26103,7 +26106,7 @@ "go": "UBERON", "miriam": "uberon", "n2t": "uberon", - "obofoundry": "UBERON", + "obofoundry": "uberon", "ols": "uberon", "ontobee": "UBERON", "wikidata": "P1554" @@ -26785,7 +26788,7 @@ "fairsharing": "FAIRsharing.mjnypw", "miriam": "uo", "n2t": "uo", - "obofoundry": "UO", + "obofoundry": "uo", "ols": "uo", "ontobee": "UO", "prefixcommons": "uo" @@ -26820,7 +26823,7 @@ "bioportal": "UPA", "edam": "2645", "go": "UniPathway", - "obofoundry": "UPA", + "obofoundry": "upa", "ols": "upa", "ontobee": "UPA", "prefixcommons": "unipathway", @@ -26854,7 +26857,7 @@ "biocontext": "UPHENO", "bioportal": "UPHENO", "fairsharing": "FAIRsharing.r41qhx", - "obofoundry": "UPHENO", + "obofoundry": "upheno", "ols": "upheno", "ontobee": "UPHENO" }, @@ -26934,7 +26937,7 @@ "fairsharing": "FAIRsharing.65xkbs", "miriam": "vario", "n2t": "vario", - "obofoundry": "VariO", + "obofoundry": "vario", "ols": "vario", "ontobee": "VariO" }, @@ -27115,7 +27118,7 @@ "aberowl": "VHOG", "biocontext": "VHOG", "bioportal": "VHOG", - "obofoundry": "VHOG", + "obofoundry": "vhog", "prefixcommons": "vhog" }, "name": "Vertebrate Homologous Organ Group Ontology", @@ -27288,7 +27291,7 @@ "biocontext": "VO", "bioportal": "VO", "fairsharing": "FAIRsharing.zwtww5", - "obofoundry": "VO", + "obofoundry": "vo", "ols": "vo", "ontobee": "VO", "prefixcommons": "vo" @@ -27327,7 +27330,7 @@ "aberowl": "VSAO", "biocontext": "VSAO", "bioportal": "VSAO", - "obofoundry": "VSAO" + "obofoundry": "vsao" }, "name": "Vertebrate Skeletal Anatomy Ontology", "preferred_prefix": "VSAO", @@ -27389,7 +27392,7 @@ "biocontext": "VT", "bioportal": "VT", "fairsharing": "FAIRsharing.10gr18", - "obofoundry": "VT", + "obofoundry": "vt", "ols": "vt", "ontobee": "VT", "prefixcommons": "vt" @@ -27418,7 +27421,7 @@ "biocontext": "VTO", "bioportal": "VTO", "fairsharing": "FAIRsharing.akmeb9", - "obofoundry": "VTO", + "obofoundry": "vto", "ols": "vto", "ontobee": "VTO" }, @@ -27494,7 +27497,7 @@ "bioportal": "WB-BT", "fairsharing": "FAIRsharing.phk7dd", "go": "WBbt", - "obofoundry": "WBbt", + "obofoundry": "wbbt", "ols": "wbbt", "ontobee": "WBbt", "prefixcommons": "wbbt" @@ -27529,7 +27532,7 @@ "bioportal": "WB-LS", "fairsharing": "FAIRsharing.sm90nh", "go": "WBls", - "obofoundry": "WBls", + "obofoundry": "wbls", "ols": "wbls", "ontobee": "WBLS", "prefixcommons": "wbls" @@ -27564,7 +27567,7 @@ "bioportal": "WB-PHENOTYPE", "fairsharing": "FAIRsharing.agvc7y", "go": "WBPhenotype", - "obofoundry": "WBPhenotype", + "obofoundry": "wbphenotype", "ols": "wbphenotype", "ontobee": "WBPhenotype", "prefixcommons": "wbphenotype" @@ -27882,7 +27885,7 @@ "biocontext": "XAO", "bioportal": "XAO", "fairsharing": "FAIRsharing.17zapb", - "obofoundry": "XAO", + "obofoundry": "xao", "ols": "xao", "ontobee": "XAO", "wikidata": "P4495" @@ -27916,7 +27919,7 @@ "biocontext": "XCO", "bioportal": "XCO", "fairsharing": "FAIRsharing.x39h5y", - "obofoundry": "XCO", + "obofoundry": "xco", "ols": "xco", "ontobee": "XCO", "prefixcommons": "xco" @@ -28007,7 +28010,7 @@ "mappings": { "aberowl": "XLMOD", "bioportal": "XLMOD", - "obofoundry": "XLMOD", + "obofoundry": "xlmod", "ols": "xlmod", "ontobee": "XLMOD" }, @@ -28079,7 +28082,7 @@ "aberowl": "XPO", "biolink": "XPO", "bioportal": "XPO", - "obofoundry": "XPO", + "obofoundry": "xpo", "ols": "xpo", "ontobee": "XPO" }, @@ -28200,12 +28203,11 @@ "deprecated": true, "homepage": "http://www.yeastgenome.org/", "mappings": { - "obofoundry": "YPO", + "obofoundry": "ypo", "ols": "ypo" }, "name": "Yeast phenotypes", - "preferred_prefix": "YPO", - "uri_format": "http://purl.obolibrary.org/obo/YPO_$1" + "preferred_prefix": "YPO" }, "yrcpdr": { "description": "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions.", @@ -28236,7 +28238,7 @@ "aberowl": "ZEA", "biocontext": "ZEA", "bioportal": "ZEA", - "obofoundry": "ZEA", + "obofoundry": "zea", "prefixcommons": "zea" }, "name": "Maize gross anatomy", @@ -28265,7 +28267,7 @@ "biocontext": "ZECO", "bioportal": "ZECO", "fairsharing": "FAIRsharing.np2wfz", - "obofoundry": "ZECO", + "obofoundry": "zeco", "ols": "zeco", "ontobee": "ZECO" }, @@ -28324,7 +28326,7 @@ "biocontext": "ZFA", "bioportal": "ZFA", "fairsharing": "FAIRsharing.s3r6sk", - "obofoundry": "ZFA", + "obofoundry": "zfa", "ols": "zfa", "ontobee": "ZFA", "prefixcommons": "zfa" @@ -28396,7 +28398,7 @@ "biocontext": "ZFS", "bioportal": "ZFS", "fairsharing": "FAIRsharing.bc8ayj", - "obofoundry": "ZFS", + "obofoundry": "zfs", "ols": "zfs", "ontobee": "ZFS" }, @@ -28448,7 +28450,7 @@ "aberowl": "ZP", "biocontext": "ZP", "bioportal": "ZP", - "obofoundry": "ZP", + "obofoundry": "zp", "ols": "zp", "ontobee": "ZP" }, diff --git a/exports/registry/registry.tsv b/exports/registry/registry.tsv index 4e72d75e8..99e9b0f95 100644 --- a/exports/registry/registry.tsv +++ b/exports/registry/registry.tsv @@ -2,7 +2,7 @@ identifier name homepage description pattern example email uri_format download.o 3dmet 3D Metabolites http://www.3dmet.dna.affrc.go.jp/ 3DMET is a database collecting three-dimensional structures of natural metabolites. ^B\d{5}$ B00162 http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1 False 3DMET 2635 3dmet 3dmet 3dmet P2796 4dn.biosource 4D Nucleome Data Portal Biosource https://data.4dnucleome.org/biosources The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. ^4DN[A-Z]{2}[A-Z0-9]{7}$ 4DNSR73BT2A2 https://data.4dnucleome.org/biosources/$1 4DN False 4DN 4dn 4dn 4dn.replicate 4D Nucleome Data Portal Experiment Replicate https://data.4dnucleome.org/experiment-set-replicates/ Database portal containing replicate experiments of different assays and samples 4DNESWX1J3QU https://data.4dnucleome.org/experiment-set-replicates/$1 False -aao Amphibian gross anatomy http://github.com/seger/aao A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/AAO_$1 True AAO AAO aao +aao Amphibian gross anatomy http://github.com/seger/aao A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/AAO_$1 True AAO aao aao abcd AntiBodies Chemically Defined database https://web.expasy.org/abcd/ The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies AD834 https://web.expasy.org/abcd/ABCD_$1 False ABCD ABCD abm Applied Biological Materials cell line products https://www.abmgood.com/Cell-Biology.html Cell line collections T0599 https://www.abmgood.com/catalogsearch/result/?cat=&q=$1 False ABM abs Annotated Regulatory Binding Sites http://genome.crg.es/datasets/abs2005/ The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. ^A\d+$ A0014 http://genome.crg.es/datasets/abs2005/entries/$1.html False ABS 2741 abs abs abs @@ -10,10 +10,10 @@ ac Activity Streams http://www.w3.org/ns/activitystreams Activity Streams is an aceview.worm Aceview Worm https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression. ^[a-z0-9-]+$ aap-1 https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1 False ACEVIEW.WORM aceview.worm aceview.worm aceview.worm addexbio AddexBio cell line products https://www.addexbio.com/productshow?id=4 Cell line collections C0020004/4992 https://www.addexbio.com/productdetail?pid=$1 False AddexBio addgene Addgene Plasmid Repository http://addgene.org/ Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world. ^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$ 50943 http://addgene.org/$1 False addgene addgene addgene -ado Alzheimer's Disease Ontology https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining. 0000001 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/ADO_$1 False ADO ADO ADO -adw Animal natural history and life history http://www.animaldiversity.org Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. ^[A-Z_a-z]+$ Lycalopex_vetulus adw_geeks@umich.edu https://animaldiversity.org/accounts/$1 True ADW ADW ADW adw adw ADW -aeo Anatomical Entity Ontology https://github.com/obophenotype/human-developmental-anatomy-ontology/ AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology ^\d{7}$ 0001017 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/AEO_$1 https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo AEO_RETIRED True AEO AEO AEO AEO aeo AEO -aero Adverse Event Reporting Ontology http://purl.obolibrary.org/obo/aero The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events ^\d{7}$ 0000125 mcourtot@gmail.com http://purl.obolibrary.org/obo/AERO_$1 True AERO AERO AERO AERO +ado Alzheimer's Disease Ontology https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining. 0000001 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/ADO_$1 False ADO ADO ado ado +adw Animal natural history and life history http://www.animaldiversity.org Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology. ^[A-Z_a-z]+$ Lycalopex_vetulus adw_geeks@umich.edu https://animaldiversity.org/accounts/$1 True ADW ADW ADW adw adw adw +aeo Anatomical Entity Ontology https://github.com/obophenotype/human-developmental-anatomy-ontology/ AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology ^\d{7}$ 0001017 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/AEO_$1 https://raw.githubusercontent.com/obophenotype/human-developmental-anatomy-ontology/master/src/ontology/aeo.obo AEO_RETIRED True AEO AEO AEO aeo aeo AEO +aero Adverse Event Reporting Ontology http://purl.obolibrary.org/obo/aero The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events ^\d{7}$ 0000125 mcourtot@gmail.com http://purl.obolibrary.org/obo/AERO_$1 True AERO AERO AERO aero affy.probeset Affymetrix Probeset http://www.affymetrix.com/ An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration. ^\d{4,}((_[asx])?_at)$ 243002_at https://www.affymetrix.com/LinkServlet?probeset=$1 False AFFY.PROBESET affy.probeset affy.probeset afo Allotrope Merged Ontology Suite https://www.allotrope.org/ Allotrope Merged Ontology Suite False AFO AFO afo aftol.taxonomy Assembling the Fungal Tree of Life - Taxonomy https://aftol.umn.edu The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species. ^\d+$ 959 http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1 False AFTOL.TAXONOMY aftol.taxonomy aftol.taxonomy @@ -30,13 +30,13 @@ The Alliance of Genome Resources was founded by the following Model Organism dat - [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database - [FlyBase](https://flybase.org) - [Xenbase](https://www.xenbase.org)" ^[1-9][0-9]{14}$ 100000000000001 cjmungall@lbl.gov https://www.alliancegenome.org/accession/$1 False -agro Agronomy Ontology https://github.com/AgriculturalSemantics/agro AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities ^\d{8}$ 00020007 m.a.laporte@cgiar.org http://purl.obolibrary.org/obo/AGRO_$1 https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo False AGRO AGRO AGRO AGRO AGRO agro AGRO +agro Agronomy Ontology https://github.com/AgriculturalSemantics/agro AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities ^\d{8}$ 00020007 m.a.laporte@cgiar.org http://purl.obolibrary.org/obo/AGRO_$1 https://raw.githubusercontent.com/KrishnaTO/agro/master/agro.obo False AGRO AGRO AGRO AGRO agro agro AGRO agrovoc Agronomy Vocabulary https://data.apps.fao.org/catalog/organization/agrovoc AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages. ^[a-z0-9]+$ 2842 http://aims.fao.org/aos/agrovoc/c_$1 False AGROVOC AGROVOC -aism Ontology for the Anatomy of the Insect SkeletoMuscular system https://github.com/insect-morphology/aism The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. ^\d{7}$ 0000027 entiminae@gmail.com http://purl.obolibrary.org/obo/AISM_$1 False AISM AISM AISM aism AISM +aism Ontology for the Anatomy of the Insect SkeletoMuscular system https://github.com/insect-morphology/aism The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research. ^\d{7}$ 0000027 entiminae@gmail.com http://purl.obolibrary.org/obo/AISM_$1 False AISM AISM aism aism AISM allergome Allergome http://www.allergome.org/ Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources. ^\d+$ 1948 http://www.allergome.org/script/dettaglio.php?id_molecule=$1 False ALLERGOME allergome allergome allergome Allergome alzforum.mutation Alzforum Mutations https://www.alzforum.org/mutations Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease. app-d678n-tottori https://www.alzforum.org/mutations/$1 Alzforum_mut False amoebadb AmoebaDB http://amoebadb.org/amoeba/ AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^EDI_\d+$ EDI_244000 https://amoebadb.org/amoeba/app/record/gene/$1 False AMOEBADB amoebadb amoebadb amoebadb -amphx The Amphioxus Development and Anatomy Ontology https://github.com/EBISPOT/amphx_ontology An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). ^\d+$ 1000160 hescriva@obs-banyuls.fr http://purl.obolibrary.org/obo/AMPHX_$1 False AMPHX AMPHX AMPHX amphx AMPHX +amphx The Amphioxus Development and Anatomy Ontology https://github.com/EBISPOT/amphx_ontology An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum). ^\d+$ 1000160 hescriva@obs-banyuls.fr http://purl.obolibrary.org/obo/AMPHX_$1 False AMPHX AMPHX amphx amphx AMPHX antibodyregistry Antibody Registry http://antibodyregistry.org/ The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information. ^\d{6}$ 493771 http://antibodyregistry.org/AB_$1 False ANTIBODYREGISTRY antibodyregistry antibodyregistry antweb AntWeb ID http://www.antweb.org/ AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures. ^casent\d+(\-D\d+)?$ casent0106247 http://www.antweb.org/specimen.do?name=$1 False ANTWEB antweb antweb antweb P5299 aop AOPWiki https://aopwiki.org/ International repository of Adverse Outcome Pathways. ^\d+$ 98 https://aopwiki.org/aops/$1 False AOP aop aop @@ -47,13 +47,13 @@ apaonto Psychology Ontology https://bioportal.bioontology.org/ontologies/APAONTO apd Antimicrobial Peptide Database http://aps.unmc.edu/AP/ The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides. ^\d{5}$ 01001 http://aps.unmc.edu/AP/database/query_output.php?ID=$1 False APD apd apd apd aphidbase.transcript AphidBase Transcript http://www.aphidbase.com/aphidbase AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information. ^ACYPI\d{6}(-RA)?$ ACYPI000159 http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1 False APHIDBASE.TRANSCRIPT aphidbase.transcript aphidbase.transcript apid.interactions APID Interactomes http://cicblade.dep.usal.es:8080/APID/ APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier. ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$ P01116 http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1 False APID.INTERACTIONS apid.interactions apid.interactions uniprot -apo Ascomycete phenotype ontology http://www.yeastgenome.org/ A structured controlled vocabulary for the phenotypes of Ascomycete fungi. ^\d{7}$ 0000184 stacia@stanford.edu https://www.yeastgenome.org/observable/APO:$1 False APO YPO APO APO apo APO -apollosv Apollo Structured Vocabulary https://github.com/ApolloDev/apollo-sv Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models ^\d{8}$ 00000443 hoganwr@ufl.edu http://purl.obolibrary.org/obo/APOLLO_SV_$1 False APOLLO_SV APOLLO-SV APOLLO_SV apollo_sv APOLLO_SV +apo Ascomycete phenotype ontology http://www.yeastgenome.org/ A structured controlled vocabulary for the phenotypes of Ascomycete fungi. ^\d{7}$ 0000184 stacia@stanford.edu https://www.yeastgenome.org/observable/APO:$1 False APO YPO APO apo apo APO +apollosv Apollo Structured Vocabulary https://github.com/ApolloDev/apollo-sv Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models ^\d{8}$ 00000443 hoganwr@ufl.edu http://purl.obolibrary.org/obo/APOLLO_SV_$1 False APOLLO_SV APOLLO-SV apollo_sv apollo_sv APOLLO_SV arachnoserver ArachnoServer http://www.arachnoserver.org/ ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information. ^AS\d{6}$ AS000060 http://www.arachnoserver.org/toxincard.html?id=$1 False ARACHNOSERVER 2578 arachnoserver arachnoserver arachnoserver ArachnoServer araport Arabidopsis Information Portal https://www.araport.org/ Website with general information about Arabidopsis and functionalities such as a genomic viewer AT1G01010 https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1 False Araport ardb Antibiotic Resistance Genes Database http://ardb.cbcb.umd.edu/ The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes. ^[A-Z_]{3}[0-9]{4,}$ CAE46076 http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1 False ARDB ardb ardb ark Archival Resource Key http://n2t.net/ An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type. ^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ /12345/fk1234 http://n2t.net/ark:$1 False ARK ark ark -aro Antibiotic Resistance Ontology https://github.com/arpcard/aro Antibiotic resistance genes and mutations ^\d{7}$ 1000001 mcarthua@mcmaster.ca http://purl.obolibrary.org/obo/ARO_$1 False ARO ARO ARO ARO aro ARO +aro Antibiotic Resistance Ontology https://github.com/arpcard/aro Antibiotic resistance genes and mutations ^\d{7}$ 1000001 mcarthua@mcmaster.ca http://purl.obolibrary.org/obo/ARO_$1 False ARO ARO ARO aro aro ARO arrayexpress ArrayExpress https://www.ebi.ac.uk/arrayexpress/ ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations. ^[AEP]-\w{4}-\d+$ E-MEXP-1712 https://www.ebi.ac.uk/arrayexpress/experiments/$1 False ARRAYEXPRESS ArrayExpress arrayexpress arrayexpress arrayexpress arrayexpress.platform ArrayExpress Platform https://www.ebi.ac.uk/arrayexpress/ ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results. ^[AEP]-\w{4}-\d+$ A-GEOD-50 https://www.ebi.ac.uk/arrayexpress/arrays/$1 False ARRAYEXPRESS.PLATFORM arrayexpress.platform arrayexpress.platform arraymap ArrayMap https://www.arraymap.org arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome. ^[\w\-:,]{3,64}$ icdom:8500_3 https://www.arraymap.org/pgx:$1 False ARRAYMAP arraymap arraymap @@ -68,7 +68,7 @@ atc Anatomical Therapeutic Chemical Classification System http://www.whocc.no/at atcc American Type Culture Collection https://www.lgcstandards-atcc.org The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences. ^([A-Z]+-)?\d+$ 11303 https://www.atcc.org/products/$1 ATCC|ATCC number|ATCC(dna)|ATCC(in host) False ATCC ATCC atcc atcc atcvet Anatomical Therapeutic Chemical Vetinary http://www.whocc.no/atcvet/atcvet_index/ The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use. ^Q[A-Z0-9]+$ QJ51RV02 http://www.whocc.no/atcvet/atcvet_index/?code=$1 False ATCVET atcvet atcvet atfdb.family Animal TFDB Family http://www.bioguo.org/AnimalTFDB/family_index.php The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found. ^\w+$ CUT http://www.bioguo.org/AnimalTFDB/family.php?fam=$1 False ATFDB.FAMILY atfdb.family atfdb.family -ato Amphibian taxonomy http://www.amphibanat.org Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource ^\d{7}$ 0000000 david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/ATO_$1 True ATO ATO ATO ATO +ato Amphibian taxonomy http://www.amphibanat.org Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource ^\d{7}$ 0000000 david.c.blackburn@gmail.com http://purl.obolibrary.org/obo/ATO_$1 True ATO ATO ATO ato atol Animal Trait Ontology for Livestock http://www.atol-ontology.com ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production. ^\d{7}$ 0002233 pylebail@rennes.inra.fr https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=atol.owl False ATOL ATOL ATOL atol autdb AutDB http://autism.mindspec.org/autdb/ AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. ^[A-Z]+[A-Z-0-9]{2,}$ ADA http://autism.mindspec.org/GeneDetail/$1 False AUTDB autdb autdb bacdive Bacterial Diversity Metadatabase https://bacdive.dsmz.de/ BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. ^[0-9]+$ 131392 https://bacdive.dsmz.de/strain/$1 False bacdive bacdive @@ -79,9 +79,9 @@ bams Brain Architecture Knowledge Management System Neuroanatomical Ontology htt bao BioAssay Ontology http://bioassayontology.org The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. ^\d{7}$ 0002989 http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1 BAO False BAO BAO BAO bao bao bao BAO bbkg Blue Brain Project Knowledge Graph https://portal.bluebrain.epfl.ch Blue Brain Project's published data as knowledge graphs and Web Studios. ^[-\w]+(?:\/[-\w]+)(?:\/\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)$ topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a https://bbp.epfl.ch/nexus/web/studios/public/$1 False bbkg bbtp Blue Brain Project Topological sampling Knowledge Graph https://portal.bluebrain.epfl.ch "Input data and analysis results for the paper ""Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )." ^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1 False bbtp -bcgo Beta Cell Genomics Ontology https://github.com/obi-bcgo/bcgo An application ontology built for beta cell genomics studies. ^\d{7}$ 0000015 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/BCGO_$1 https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl True BCGO BCGO BCGO BCGO BCGO BCGO +bcgo Beta Cell Genomics Ontology https://github.com/obi-bcgo/bcgo An application ontology built for beta cell genomics studies. ^\d{7}$ 0000015 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/BCGO_$1 https://github.com/obi-bcgo/bcgo/raw/master/ontology/bcgo.owl True BCGO BCGO BCGO BCGO bcgo BCGO bcio The Behaviour Change Intervention Ontology https://www.humanbehaviourchange.org/ The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation. ^\d{6}$ 040000 http://humanbehaviourchange.org/ontology/bcio.owl False BCI-O BCI-O bcio -bco Biological Collections Ontology https://github.com/BiodiversityOntologies/bco An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. ^\d{7}$ 0000081 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/BCO_$1 False BCO BCO BCO BCO BCO BCO bco BCO +bco Biological Collections Ontology https://github.com/BiodiversityOntologies/bco An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys. ^\d{7}$ 0000081 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/BCO_$1 False BCO BCO BCO BCO BCO bco bco BCO bcrc BCRC Strain Collection Catalog https://catalog.bcrc.firdi.org.tw Cell line collections ^\d+$ 60316 https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1 False BCRC bcrj Banco de Celulas do Rio de Janeiro http://bcrj.org.br/celula/bcrj Cell line collections ^\d{4}$ 0278 http://bcrj.org.br/celula/$1 False BCRJ bdgp.est Berkeley Drosophila Genome Project EST database https://www.ncbi.nlm.nih.gov/dbEST/index.html The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI). ^\w+(\.)?(\d+)?$ EY223054.1 https://www.ncbi.nlm.nih.gov/nucest/$1 False BDGP.EST bdgp.est bdgp.est dbest @@ -91,7 +91,7 @@ beetlebase Tribolium Genome Database -- Insertion http://beetlebase.org/ BeetleB begdb Benchmark Energy & Geometry Database http://www.begdb.com The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods. ^[0-9]+$ 4214 http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1 False BEGDB begdb begdb beiresources BEI Resources https://www.beiresources.org Cell line collections MRA-253 https://www.beiresources.org/Catalog/cellBanks/$1.aspx BEI_Resources False BEI_Resources bel Biological Expression Language https://biological-expression-language.github.io/ The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents. 9-1-1 Complex False -bfo Basic Formal Ontology http://ifomis.org/bfo/ The upper level ontology upon which OBO Foundry ontologies are built. ^\d{7}$ 0000001 phismith@buffalo.edu http://purl.obolibrary.org/obo/BFO_$1 False BFO BFO BFO BFO BFO bfo BFO +bfo Basic Formal Ontology http://ifomis.org/bfo/ The upper level ontology upon which OBO Foundry ontologies are built. ^\d{7}$ 0000001 phismith@buffalo.edu http://purl.obolibrary.org/obo/BFO_$1 False BFO BFO BFO BFO bfo bfo BFO bgee.family Bgee family http://bgee.unil.ch/bgee/bgee Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species. ^(ENSFM|ENSGTV:)\d+$ ENSFM00500000270089 http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1 False BGEE.FAMILY bgee.family bgee.family bgee.gene Bgee gene https://bgee.org/ Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee. ^[A-Za-z]+\d+$ FBgn0000015 https://bgee.org/?page=gene&gene_id=$1 False BGEE.GENE bgee.gene bgee.gene bgee.organ Bgee organ http://bgee.unil.ch/bgee/bgee Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures. ^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\:\d+$ EHDAA:2185 http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1 False BGEE.ORGAN bgee.organ bgee.organ @@ -101,7 +101,7 @@ bigg.compartment BiGG Compartment http://bigg.ucsd.edu/compartments/ BiGG is a k bigg.metabolite BiGG Metabolite http://bigg.ucsd.edu/universal/metabolites BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes. ^[a-z_A-Z0-9]+$ 12dgr161 http://bigg.ucsd.edu/models/universal/metabolites/$1 False BIGG.METABOLITE bigg.metabolite bigg.metabolite bigg.model BiGG Model http://bigg.ucsd.edu/models BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models. ^[a-z_A-Z0-9]+$ iECABU_c1320 http://bigg.ucsd.edu/models/$1 False BIGG.MODEL bigg.model bigg.model bigg.reaction BiGG Reaction http://bigg.ucsd.edu/universal/reactions BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions. ^[a-z_A-Z0-9]+$ 13GS http://bigg.ucsd.edu/models/universal/reactions/$1 False BIGG.REACTION bigg.reaction bigg.reaction -bila Bilateria anatomy This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. http://purl.obolibrary.org/obo/BILA_$1 True BILA BILA +bila Bilateria anatomy http://4dx.embl.de/4DXpress This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. 0000000 henrich@embl.de http://purl.obolibrary.org/obo/BILA_$1 True BILA bila bindingdb BindingDB https://www.bindingdb.org BindingDB is the first public database of protein-small molecule affinity data. ^\w\d+$ e999 http://www.bindingdb.org/compact/$1 False BINDINGDB bindingdb bindingdb bindingdb BindingDB biocarta.pathway BioCarta Pathway https://www.biocarta.com/ BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps. ^([hm]\_)?\w+Pathway$ h_aktPathway https://cgap.nci.nih.gov/Pathways/BioCarta/$1 False BIOCARTA.PATHWAY biocarta.pathway biocarta.pathway biocatalogue.service BioCatalogue Service https://www.biocatalogue.org/ The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all. ^\d+$ 614 https://www.biocatalogue.org/services/$1 False BIOCATALOGUE.SERVICE biocatalogue.service biocatalogue.service @@ -112,7 +112,7 @@ biolegend BioLegend https://www.biolegend.com BioLegend is a life sciences suppl biolink Biolink Model https://biolink.github.io/biolink-model/ A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. ^\S+$ Gene https://w3id.org/biolink/vocab/$1 False BIOLINK BIOLINK biolink biominder Bio-MINDER Tissue Database https://datalab.rwth-aachen.de/MINDER Database of the dielectric properties of biological tissues. ^[a-z0-9\-]+$ aef4c195-9cf9-46db-a12a-7cfd1ff3eec3 https://datalab.rwth-aachen.de/MINDER/resource/$1 False BIOMINDER biominder biominder biomodels.db BioModels Database https://www.ebi.ac.uk/biomodels/ BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. ^((BIOMD|MODEL)\d{10})|(BMID\d{12})$ BIOMD0000000048 https://www.ebi.ac.uk/biomodels/$1 BIOMD False BIOMODELS.DB biomodels.db biomodels.db -biomodels.kisao Kinetic Simulation Algorithm Ontology https://github.com/SED-ML/KiSAO The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. ^\d+$ 0000057 jonrkarr@gmail.com https://www.biomodels.net/kisao/KISAO#KISAO_$1 kisao False KISAO KISAO KISAO biomodels.kisao biomodels.kisao KISAO kisao KISAO kisao +biomodels.kisao Kinetic Simulation Algorithm Ontology https://github.com/SED-ML/KiSAO The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment. ^\d+$ 0000057 jonrkarr@gmail.com https://www.biomodels.net/kisao/KISAO#KISAO_$1 kisao False KISAO KISAO KISAO biomodels.kisao biomodels.kisao kisao kisao KISAO kisao biomodels.teddy Terminology for Description of Dynamics http://teddyontology.sourceforge.net/ The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology. ^\d+$ 0000066 https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1 http://svn.code.sf.net/p/teddyontology/code/teddy/tags/current/teddy-inferred.owl teddy False TEDDY BIOMODELS.TEDDY TEDDY biomodels.teddy biomodels.teddy teddy teddy biomodels.vocabulary SBML RDF Vocabulary http://biomodels.net/rdf/vocabulary.rdf Vocabulary used in the RDF representation of SBML models. ^[A-Za-z]+$ rateRule http://biomodels.net/rdf/vocabulary.rdf#$1 False BIOMODELS.VOCABULARY biomodels.vocabulary biomodels.vocabulary bionumbers BioNumbers https://bionumbers.hms.harvard.edu BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data. ^\d+$ 104674 https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1 False BIONUMBERS 2660 bionumbers bionumbers bionumbers @@ -139,15 +139,15 @@ bko SBGN Bricks data and ontology http://www.sbgnbricks.org/ SBGN bricks represe bmrb Biological Magnetic Resonance Data Bank http://www.bmrb.wisc.edu/ BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy. ^(bmr|bmse|bmst)?[0-9]{1,6}$ 15000 http://rest.bmrb.wisc.edu/bmrb/$1/html False bmrb BMRB bmrb.restraint NMR Restraints Grid https://restraintsgrid.bmrb.io/NRG/MRGridServlet The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively. ^\d+$ 28789 https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1 False bold.taxonomy Barcode of Life database http://www.boldsystems.org/ The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information. ^\d+$ 27267 http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1 False BOLD.TAXONOMY bold.taxonomy bold.taxonomy -bootstrep Gene Regulation Ontology http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html vlee@ebi.ac.uk http://purl.obolibrary.org/obo/BOOTSTREP_$1 True BOOTSTREP BOOTSTREP +bootstrep Gene Regulation Ontology http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html vlee@ebi.ac.uk http://purl.obolibrary.org/obo/BOOTSTREP_$1 True BOOTSTREP bootstrep bpdb Bio-Pesticides DataBase https://sitem.herts.ac.uk/aeru/bpdb/index.htm Database of biopesticides maintained by the University of Hertfordshire ^\d+$ 2404 https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm False brenda BRENDA, The Comprehensive Enzyme Information System https://www.brenda-enzymes.org/ BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. ^((\d+\.-\.-\.-)|(\d+\.\d+\.-\.-)|(\d+\.\d+\.\d+\.-)|(\d+\.\d+\.\d+\.\d+))$ 1.1.1.1 https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1 False BRENDA brenda brenda brenda BRENDA brenda.ligand BRENDA Ligand https://www.brenda-enzymes.de/ligand.php Information for ligands in the BRENDA database. ^\d+$ 278 https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1 False brenda.ligandgroup BRENDA Ligand Group https://www.brenda-enzymes.de/ligand.php Information for ligand groups (chemical classes). ^\d+$ 18030 https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1 False broad Broad Fungal Genome Initiative https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/ Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. ^S\d+$ S7000002168151102 https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1 False BROAD broad broad bs Biosapiens Protein Feature Ontology https://github.com/The-Sequence-Ontology/SO-Ontologies SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library. ^\d+$ 00042 https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/subsets/biosapiens.obo False -bspo Biological Spatial Ontology https://github.com/obophenotype/biological-spatial-ontology An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. ^\d{7}$ 0000029 cjmungall@lbl.gov http://purl.obolibrary.org/obo/BSPO_$1 https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo False BSPO BSPO BSPO BSPO bspo BSPO -bto BRENDA tissue / enzyme source http://www.brenda-enzymes.org The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. ^\d{7}$ 0000590 c.dudek@tu-braunschweig.de https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1 BTO False BTO BTO BTO BTO bto bto BTO bto BTO bto P5501 +bspo Biological Spatial Ontology https://github.com/obophenotype/biological-spatial-ontology An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. ^\d{7}$ 0000029 cjmungall@lbl.gov http://purl.obolibrary.org/obo/BSPO_$1 https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.obo False BSPO BSPO BSPO bspo bspo BSPO +bto BRENDA tissue / enzyme source http://www.brenda-enzymes.org The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. ^\d{7}$ 0000590 c.dudek@tu-braunschweig.de https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1 BTO False BTO BTO BTO BTO bto bto bto bto BTO bto P5501 bugbase.expt BugBase Expt http://bugs.sgul.ac.uk/E-BUGS BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments. ^\d+$ 288 http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view False BUGBASE.EXPT bugbase.expt bugbase.expt bugbase.protocol BugBase Protocol http://bugs.sgul.ac.uk/E-BUGS BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols. ^\d+$ 67 http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view False BUGBASE.PROTOCOL bugbase.protocol bugbase.protocol bykdb Bacterial Tyrosine Kinase Database https://bykdb.ibcp.fr/BYKdb/ The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information. ^[A-Z0-9]+$ A0A009E7X8 https://bykdb.ibcp.fr/data/html/annotated/$1.html False BYKDB bykdb bykdb bykdb uniprot @@ -157,7 +157,7 @@ cadsr Cancer Data Standards Registry and Repository https://wiki.nci.nih.gov/dis caloha CALIPHO Group Ontology of Human Anatomy https://github.com/calipho-sib/controlled-vocabulary This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins. ^TS-\d+$ TS-0001 https://download.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo False cameo Continuous Automated Model Evaluation https://cameo3d.org The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB. ^[0-9\-_]+$ 2019-08-03_00000089_1 https://www.cameo3d.org/sp/targets/target/$1 False CAMEO cameo cameo caps CAPS-DB http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. ^\d+$ 434 http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1 False CAPS caps caps -caro Common Anatomy Reference Ontology https://github.com/obophenotype/caro/ None ^\d{7}$ 0000000 haendel@ohsu.edu http://purl.obolibrary.org/obo/CARO_$1 False CARO CARO CARO CARO caro CARO +caro Common Anatomy Reference Ontology https://github.com/obophenotype/caro/ None ^\d{7}$ 0000000 haendel@ohsu.edu http://purl.obolibrary.org/obo/CARO_$1 False CARO CARO CARO caro caro CARO cas CAS Chemical Registry https://commonchemistry.cas.org/ CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. ^\d{1,7}\-\d{2}\-\d$ 50-00-0 https://commonchemistry.cas.org/detail?ref=$1 CASID|CAS_RN|SECONDARY_CAS_RN|cas_id False CAS 000446 1002 cas cas cas P231 casspc Eschmeyer's Catalog of Fishes https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp ^\d+$ 5359 https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1 True cath CATH Protein Structural Domain Superfamily http://www.cathdb.info CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence. ^[1-6]\.[0-9]+\.[0-9]+\.[0-9]+$ 1.10.8.10 http://www.cathdb.info/cathnode/$1 False CATH 2700 cath cath cath @@ -172,9 +172,9 @@ ccds Consensus CDS http://www.ncbi.nlm.nih.gov/CCDS/ The Consensus CDS (CCDS) pr ccle Cancer Cell Line Encyclopedia Cells https://www.cbioportal.org/study/summary?id=ccle_broad_2019 Datasets around different cancer cell lines generated by the Broad Institute and Novartis BT20_BREAST https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1 ccle.cell False CCLE cco Cell Cycle Ontology http://www.semantic-systems-biology.org/apo The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. ^\w+$ 0000003 vladimir.n.mironov@gmail.com https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1 https://www.bio.ntnu.no/ontology/CCO/cco.owl https://www.bio.ntnu.no/ontology/CCO/cco.obo False CCO CCO CCO cco cco cco cco ccrid National Experimental Cell Resource Sharing Platform http://www.cellresource.cn Cell line databases/resources 4201PAT-CCTCC00348 http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1 False CCRID -cdao Comparative Data Analysis Ontology https://github.com/evoinfo/cdao The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. ^\d{7}$ 0000072 balhoff@renci.org http://purl.obolibrary.org/obo/CDAO_$1 False CDAO CDAO CDAO CDAO CDAO cdao CDAO +cdao Comparative Data Analysis Ontology https://github.com/evoinfo/cdao The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character. ^\d{7}$ 0000072 balhoff@renci.org http://purl.obolibrary.org/obo/CDAO_$1 False CDAO CDAO CDAO CDAO cdao cdao CDAO cdd Conserved Domain Database at NCBI https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. ^(cd)?\d{5}$ cd00400 https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1 False CDD 2666 cdd cdd cdd CDD -cdno Compositional Dietary Nutrition Ontology https://cdno.info/ None ^\d{7}$ 0000013 l.andres.hernandez.18@student.scu.edu.au http://purl.obolibrary.org/obo/CDNO_$1 False CDNO CDNO CDNO cdno CDNO +cdno Compositional Dietary Nutrition Ontology https://cdno.info/ None ^\d{7}$ 0000013 l.andres.hernandez.18@student.scu.edu.au http://purl.obolibrary.org/obo/CDNO_$1 False CDNO CDNO cdno cdno CDNO cdpd Canadian Drug Product Database http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN). ^\d+$ 63250 http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1 False CDPD cdpd cdpd cdt Current Dental Terminology https://www.ada.org/publications/CDT The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment. ^\d{7}$ 1000001 https://github.com/oral-health-and-disease-ontologies/ohd-ontology/blob/master/src/ontology/older/CDTCodes%20as%20Classes_pruned.owl False cell_biolabs Cell Biolabs cell line products https://www.cellbiolabs.com Cell line collections AKR-270 https://www.cellbiolabs.com/search?keywords=$1 False Cell_Biolabs @@ -185,32 +185,32 @@ cellopub Cellosaurus Publication https://web.expasy.org/cellosaurus/ Cellosaurus cellosaurus Cellosaurus https://web.expasy.org/cellosaurus/ The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines. ^[A-Z0-9]{4}$ 0440 https://web.expasy.org/cellosaurus/CVCL_$1 https://ftp.expasy.org/databases/cellosaurus/cellosaurus.obo CVCL False CELLOSAURUS Cellosaurus cellosaurus cellosaurus P3289 cellosaurus.resource Cellosaurus Registry https://web.expasy.org/cellosaurus/ The set of prefixes used in the Cellosaurus resource 4DN https://bioregistry.io/metaregistry/cellosaurus/$1 False cellrepo Cell Version Control Repository https://cellrepo.ico2s.org/ The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines ^[0-9]+$ 82 https://cellrepo.ico2s.org/repositories/$1 False cellrepo -ceph Cephalopod Ontology https://github.com/obophenotype/cephalopod-ontology An anatomical and developmental ontology for cephalopods ^\d{7}$ 0000109 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CEPH_$1 https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo True CEPH CEPH CEPH CEPH ceph CEPH +ceph Cephalopod Ontology https://github.com/obophenotype/cephalopod-ontology An anatomical and developmental ontology for cephalopods ^\d{7}$ 0000109 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CEPH_$1 https://raw.githubusercontent.com/obophenotype/cephalopod-ontology/master/ceph.obo True CEPH CEPH CEPH ceph ceph CEPH cgd Candida Genome Database http://www.candidagenome.org/ The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products. ^CAL\d{7}$ CAL0003079 http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1 False CGD cgd cgd cgd CGD cghdb CGH Data Base http://www.cghtmd.jp/CGHDatabase/index_e.jsp Cell line databases/resources 300165/p13898_2106T http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en False CGH-DB cgnc Chicken Gene Nomenclature Consortium http://birdgenenames.org/cgnc/ Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans) ^\d+$ 10087 http://birdgenenames.org/cgnc/GeneReport?id=$1 BirdBase|CGNC False cgnc cgsc Coli Genetic Stock Center http://cgsc.biology.yale.edu/index.php The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. ^\d+$ 74 http://cgsc.biology.yale.edu/Site.php?ID=$1 False CGSC cgsc cgsc cgsc charprot CharProt http://www.jcvi.org/charprotdb CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession. ^CH_\d+$ CH_001923 http://www.jcvi.org/charprotdb/index.cgi/view/$1 False CHARPROT charprot charprot -chebi Chemical Entities of Biological Interest http://www.ebi.ac.uk/chebi Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. ^\d+$ 24867 amalik@ebi.ac.uk https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 CHEBI|CHEBIID|ChEBI False CHEBI CHEBI CHEBI ChEBI 000407 1174 chebi chebi CHEBI chebi CHEBI chebi P683 +chebi Chemical Entities of Biological Interest http://www.ebi.ac.uk/chebi Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. ^\d+$ 24867 amalik@ebi.ac.uk https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1 CHEBI|CHEBIID|ChEBI False CHEBI CHEBI CHEBI ChEBI 000407 1174 chebi chebi chebi chebi CHEBI chebi P683 chembl ChEMBL https://www.ebi.ac.uk/chembl ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL4303805 https://www.ebi.ac.uk/chembl/entity/$1 ChEMBL|ChEMBL_ID|chembl False 000412 chembl chembl ChEMBL chembl.cell ChEMBL database of bioactive drug-like small molecules - Cell lines section https://www.ebi.ac.uk/chembldb Chemistry resources CHEMBL3307800 https://www.ebi.ac.uk/chembl/cell_line_report_card/$1 ChEMBL-Cells False ChEMBL-Cells chembl chembl.compound ChEMBL https://www.ebi.ac.uk/chembldb/ ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL465070 https://www.ebi.ac.uk/chembl/compound/inspect/$1 False CHEMBL.COMPOUND 2646 chembl.compound chembl.compound P592 chembl chembl.target ChEMBL target https://www.ebi.ac.uk/chembldb/ ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature. ^CHEMBL\d+$ CHEMBL3467 https://www.ebi.ac.uk/chembl/target/inspect/$1 ChEMBL-Targets False CHEMBL.TARGET ChEMBL-Targets chembl.target chembl.target chembl chemdb ChemDB http://cdb.ics.uci.edu/ ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. ^\d+$ 3966782 http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1 False CHEMDB chemdb chemdb chemdb chemidplus ChemIDplus https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. ^\d+\-\d+\-\d+$ 57-27-2 https://chem.nlm.nih.gov/chemidplus/rn/$1 ChemIDplus False CHEMIDPLUS 2658 chemidplus chemidplus chemidplus -cheminf Chemical Information Ontology https://github.com/semanticchemistry/semanticchemistry Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. ^\d{6}$ 000410 egon.willighagen@gmail.com http://purl.obolibrary.org/obo/CHEMINF_$1 https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl False CHEMINF CHEMINF CHEMINF CHEMINF cheminf CHEMINF +cheminf Chemical Information Ontology https://github.com/semanticchemistry/semanticchemistry Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them. ^\d{6}$ 000410 egon.willighagen@gmail.com http://purl.obolibrary.org/obo/CHEMINF_$1 https://github.com/semanticchemistry/semanticchemistry/raw/master/ontology/cheminf.owl False CHEMINF CHEMINF CHEMINF cheminf cheminf CHEMINF chemspider ChemSpider http://www.chemspider.com/ ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources. ^\d+$ 56586 http://www.chemspider.com/Chemical-Structure.$1.html ChemSpiderID|Chemspider False CHEMSPIDER 000405 1173 chemspider chemspider chemspider P661 chickenqtldb Animal Genome Chicken QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs. ^\d+$ 14362 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False CHICKENQTLDB chickenqtldb chickenqtldb chickenqtldb qtldb -chiro ChEBI Integrated Role Ontology https://github.com/obophenotype/chiro CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/CHIRO_$1 False CHIRO CHIRO CHIRO chiro CHIRO -chmo Chemical Methods Ontology https://github.com/rsc-ontologies/rsc-cmo CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). ^\d{7}$ 0002902 batchelorc@rsc.org http://purl.obolibrary.org/obo/CHMO_$1 False CHMO CHMO CHMO CHMO chmo CHMO -cido Coronavirus Infectious Disease Ontology https://github.com/cido-ontology/cido The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. ^\d{7}$ 0000005 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/CIDO_$1 False CIDO CIDO CIDO cido CIDO -cio Confidence Information Ontology https://github.com/BgeeDB/confidence-information-ontology An ontology to capture confidence information about annotations. ^\d{7}$ 0000040 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/CIO_$1 False CIO CIO CIO CIO cio CIO +chiro ChEBI Integrated Role Ontology https://github.com/obophenotype/chiro CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/CHIRO_$1 False CHIRO CHIRO chiro chiro CHIRO +chmo Chemical Methods Ontology https://github.com/rsc-ontologies/rsc-cmo CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI). ^\d{7}$ 0002902 batchelorc@rsc.org http://purl.obolibrary.org/obo/CHMO_$1 False CHMO CHMO CHMO chmo chmo CHMO +cido Coronavirus Infectious Disease Ontology https://github.com/cido-ontology/cido The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment. ^\d{7}$ 0000005 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/CIDO_$1 False CIDO CIDO cido cido CIDO +cio Confidence Information Ontology https://github.com/BgeeDB/confidence-information-ontology An ontology to capture confidence information about annotations. ^\d{7}$ 0000040 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/CIO_$1 False CIO CIO CIO cio cio CIO citexplore CiteXplore https://www.ebi.ac.uk/citexplore/ One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes. C6155 https://europepmc.org/article/CTX/$1 CTX False citexplore cito Citation Typing Ontology http://www.sparontologies.net/ontologies/cito An ontology that enables characterization of the nature or type of citations, both factually and rhetorically. sharesAuthorInstitutionWith http://purl.org/spar/cito/$1 False civic.aid CIViC Assertion https://civicdb.org/ A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC. ^[0-9]+$ 3 https://civicdb.org/links/assertions/$1 False civic.aid civic.eid CIViC Evidence https://civicdb.org/ Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract). ^[0-9]+$ 1199 https://civicdb.org/links/evidence/$1 False civic.eid -cl Cell Ontology https://obophenotype.github.io/cell-ontology/ The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. ^\d{7}$ 0000062 addiehl@buffalo.edu https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo False CL CL CL CL CL cl cl CL cl CL cl P7963 -clao Collembola Anatomy Ontology https://github.com/luis-gonzalez-m/Collembola CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda). ^\d{7}$ 0000088 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/CLAO_$1 False CLAO CLAO CLAO clao CLAO +cl Cell Ontology https://obophenotype.github.io/cell-ontology/ The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. ^\d{7}$ 0000062 addiehl@buffalo.edu https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1 https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-full.obo False CL CL CL CL CL cl cl cl cl CL cl P7963 +clao Collembola Anatomy Ontology https://github.com/luis-gonzalez-m/Collembola CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda). ^\d{7}$ 0000088 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/CLAO_$1 False CLAO CLAO clao clao CLAO classyfire ClassyFire http://classyfire.wishartlab.com/ ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API. ^\d{7}$ 0004828 http://classyfire.wishartlab.com/tax_nodes/C$1 http://classyfire.wishartlab.com/system/downloads/1_0/chemont/ChemOnt_2_1.obo.zip CHEMONTID False classyfire cldb Cell Line Database http://bioinformatics.hsanmartino.it/hypercldb/indexes.html The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories. ^(cl|tum)\d+$ cl3603 http://bioinformatics.hsanmartino.it/hypercldb/$1.html False CLDB CLDB cldb cldb clingene ClinGen Allele Registry https://reg.clinicalgenome.org The allele registry provides and maintains identifiers for genetic variants CA981206459 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1 False @@ -219,12 +219,12 @@ clinvar ClinVar Variation http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives clinvar.record ClinVar Record http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession. ^RCV\d+(\.\d+)?$ RCV000033555.3 http://www.ncbi.nlm.nih.gov/clinvar/$1 False CLINVAR.RECORD clinvar.record clinvar.record clinvar.submission ClinVar Submission http://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession. ^SCV\d+(\.\d+)?$ SCV000151292 http://www.ncbi.nlm.nih.gov/clinvar?term=$1 False CLINVAR.SUBMISSION clinvar.submission clinvar.submission clinvar.submitter ClinVar Submitter https://www.ncbi.nlm.nih.gov/clinvar/ ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs). ^\d+$ 26957 https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1 False clinvar.submitter -clo Cell Line Ontology http://www.clo-ontology.org The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. ^\d{7}$ 0000091 siiraa@umich.edu http://purl.obolibrary.org/obo/CLO_$1 CLO False CLO CLO CLO CLO CLO clo CLO clo P2158 +clo Cell Line Ontology http://www.clo-ontology.org The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. ^\d{7}$ 0000091 siiraa@umich.edu http://purl.obolibrary.org/obo/CLO_$1 CLO False CLO CLO CLO CLO clo clo CLO clo P2158 cls Cell Lines Service https://cls.shop/ Cell line collections 300108/p3934_A-172 https://cls.shop/$1 False CLS -clyh Clytia hemisphaerica Development and Anatomy Ontology https://github.com/EBISPOT/clyh_ontology Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. ^\d+$ 1000100 lucas.leclere@obs-vlfr.fr http://purl.obolibrary.org/obo/CLYH_$1 False CLYH CLYH CLYH clyh CLYH +clyh Clytia hemisphaerica Development and Anatomy Ontology https://github.com/EBISPOT/clyh_ontology Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica. ^\d+$ 1000100 lucas.leclere@obs-vlfr.fr http://purl.obolibrary.org/obo/CLYH_$1 False CLYH CLYH clyh clyh CLYH cmecs Costal and Marine Ecological Classification Standard https://cmecscatalog.org/cmecs Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard. ^\d+$ 595 https://cmecscatalog.org/cmecs/classification/unit/$1.html False -cmf CranioMaxilloFacial ontology https://code.google.com/p/craniomaxillofacial-ontology/ This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain engelsta@ohsu.edu http://purl.obolibrary.org/obo/CMF_$1 True CMF CMF CMF CMF -cmo Clinical measurement ontology http://rgd.mcw.edu/rgdweb/ontology/search.html Morphological and physiological measurement records generated from clinical and model organism research and health programs. ^\d{7}$ 0001350 jrsmith@mcw.edu http://purl.obolibrary.org/obo/CMO_$1 False CMO CMO CMO CMO cmo CMO +cmf CranioMaxilloFacial ontology https://code.google.com/p/craniomaxillofacial-ontology/ This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain engelsta@ohsu.edu http://purl.obolibrary.org/obo/CMF_$1 True CMF CMF cmf CMF +cmo Clinical measurement ontology http://rgd.mcw.edu/rgdweb/ontology/search.html Morphological and physiological measurement records generated from clinical and model organism research and health programs. ^\d{7}$ 0001350 jrsmith@mcw.edu http://purl.obolibrary.org/obo/CMO_$1 False CMO CMO CMO cmo cmo CMO cmpo Cellular Microscopy Phenotype Ontology http://www.ebi.ac.uk/cmpo CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. ^\d{7}$ 0000435 jupp@ebi.ac.uk False CMPO CMPO cmpo co_320 Rice ontology https://cropontology.org/ontology/CO_320/Rice Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables ^\d{7}$ 0000618 helpdesk@cropontology-curationtool.org https://www.cropontology.org/rdf/CO_320:$1 False CO_320 CO_320 co_320 co_321 Wheat ontology https://cropontology.org/ontology/CO_321/Wheat July 2018 ^\d{7}$ 0000449 helpdesk@cropontology-curationtool.org https://www.cropontology.org/rdf/CO_321:$1 False CO_321 CO_321 co_321 @@ -258,7 +258,7 @@ co_359 Sunflower ontology https://cropontology.org/ontology/CO_359/Sunflower Dec co_360 Sugar Kelp trait ontology http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait Sugar Kelp trait ontology ^\d{7}$ 0000071 helpdesk@cropontology-curationtool.org https://www.cropontology.org/rdf/CO_360:$1 False CO_360 CO_360 co_360 co_365 Fababean ontology https://cropontology.org/ontology/CO_365/Fababean developed by ICARDA - Dec 2018 ^\d{7}$ 0000205 helpdesk@cropontology-curationtool.org https://www.cropontology.org/rdf/CO_365:$1 False CO_365 CO_365 co_365 co_366 Bambara groundnut ontology http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut version Dec 2019 ^\d{7}$ 0000072 helpdesk@cropontology-curationtool.org https://www.cropontology.org/rdf/CO_366:$1 False CO_366 CO_366 co_366 -cob Core Ontology for Biology and Biomedicine https://github.com/OBOFoundry/COB COB brings together key terms from a wide range of OBO projects to improve interoperability. ^\d{7}$ 0000080 bpeters@lji.org http://purl.obolibrary.org/obo/COB_$1 False COB COB COB cob COB +cob Core Ontology for Biology and Biomedicine https://github.com/OBOFoundry/COB COB brings together key terms from a wide range of OBO projects to improve interoperability. ^\d{7}$ 0000080 bpeters@lji.org http://purl.obolibrary.org/obo/COB_$1 False COB COB cob cob COB coconut COlleCtion of Open Natural ProdUcTs https://coconut.naturalproducts.net "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a ""flat"" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties." ^CNP\d{7}$ CNP0171505 https://coconut.naturalproducts.net/compound/coconut_id/$1 False codelink GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). ^GE\d+$ GE86325 False cog Cluster of orthologous genes https://www.ncbi.nlm.nih.gov/research/cog/ COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems. ^COG\d+$ COG0001 cogs@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/research/cog/cog/$1 COG_Cluster False cog @@ -266,7 +266,7 @@ cog.category COG Categories https://www.ncbi.nlm.nih.gov/research/cog/ Higher-le cog.pathway COG Pathways https://www.ncbi.nlm.nih.gov/research/cog/pathways Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. NAD%20biosynthesis cogs@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1 False cog cohd MIMIC III Database https://github.com/MIT-LCP/mimic-omop MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012 False col.taiwan Catalogue of Life in Taiwan http://taibnet.sinica.edu.tw/home.php Identifier (name code) for a taxon in the catalogue of life in taiwan ^[1-9]\d{5}$ 431472 https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1 False P3088 -colao Coleoptera Anatomy Ontology https://github.com/insect-morphology/colao The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. ^\d{7}$ 0000000 entiminae@gmail.com http://purl.obolibrary.org/obo/COLAO_$1 False COLAO COLAO COLAO colao COLAO +colao Coleoptera Anatomy Ontology https://github.com/insect-morphology/colao The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research. ^\d{7}$ 0000000 entiminae@gmail.com http://purl.obolibrary.org/obo/COLAO_$1 False COLAO COLAO colao colao COLAO colonatlas Colorectal Cancer Atlas http://www.coloncanceratlas.org Cell line databases/resources ALA http://www.coloncanceratlas.org/search_cell_line?cell_line=$1 False ColonAtlas combine.specifications COMBINE specifications https://co.mbine.org/standards/ The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network. ^\w+(\-|\.|\w)*$ sbgn.er.level-1.version-1.2 https://co.mbine.org/specifications/$1 False COMBINE.SPECIFICATIONS combine.specifications combine.specifications come The Bioinorganic Motif Database https://www.flymine.org/come COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif. MOL000160 https://www.flymine.org/come/entry?gn=$1 False come @@ -286,11 +286,11 @@ covid19 COVID-19 Surveillance Ontology https://covid19.sfb.uit.no Curated contex covoc CoVoc Coronavirus Vocabulary https://github.com/EBISPOT/covoc The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. ^\d{7}$ 0010034 zmp@ebi.ac.uk False covoc cp Cellular Phenotypes True cpc Cooperative Patent Classification https://worldwide.espacenet.com/classification The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013. ^([A-H,Y]|[A-H, Y]\d{2}|[A-H, Y]\d{2}[A-Z]|[A-H, Y]\d{2}[A-Z]\d{1,3}|[A-H, Y]\d{2}[A-Z]\d{1,3}(\/)?\d{2,})$ A01M1/026 https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1 False CPC cpc cpc -cpga Cereal Plant Gross Anatomy http://www.gramene.org/plant_ontology/ po-discuss@plantontology.org http://purl.obolibrary.org/obo/GRO_$1 True gro.cpga GRO-CPGA GRO +cpga Cereal Plant Gross Anatomy http://www.gramene.org/plant_ontology/ A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology. po-discuss@plantontology.org True gro.cpga GRO-CPGA gro cpt Current Procedural Terminology https://www.aapc.com Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)] ^\d+$ 00103 https://www.aapc.com/codes/cpt-codes/$1 False CPT CPT credit CASRAI Contributor Roles Taxonomy https://casrai.org/credit/ CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. Software False crisprdb CRISPRdb http://crispr.i2bc.paris-saclay.fr/ "Repeated CRISPR (""clustered regularly interspaced short palindromic repeats"") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data." ^[0-9]+$ 551115 http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1 False CRISPRDB crisprdb crisprdb -cro Contributor Role Ontology https://github.com/data2health/contributor-role-ontology A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. ^\d{7}$ 0000038 whimar@ohsu.edu http://purl.obolibrary.org/obo/CRO_$1 https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo False CRO CRO CRO CRO cro CRO +cro Contributor Role Ontology https://github.com/data2health/contributor-role-ontology A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability. ^\d{7}$ 0000038 whimar@ohsu.edu http://purl.obolibrary.org/obo/CRO_$1 https://raw.githubusercontent.com/data2health/contributor-role-ontology/master/cro.obo False CRO CRO CRO cro cro CRO cryoem Cryo Electron Microscopy ontology http://scipion.i2pc.es/ontology/cryoem Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles ^\d{7}$ 0000052 isanchez@cnb.csic.es False CRYOEM CRYOEM cryoem cryptodb CryptoDB https://cryptodb.org/cryptodb/ CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ cgd7_230 https://cryptodb.org/cryptodb/app/record/gene/$1 False CRYPTODB cryptodb cryptodb cryptodb csa Catalytic Site Atlas https://www.ebi.ac.uk/thornton-srv/databases/CSA/ The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme. ^[0-9][A-Za-z0-9]{3}$ 1a05 https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1 False CSA csa csa csa @@ -301,10 +301,10 @@ cst.ab Cell Signaling Technology Antibody http://www.cellsignal.com/catalog/inde ctd.chemical CTD Chemical http://ctdbase.org/ The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. ^[CD]\d+$ D001151 http://ctdbase.org/detail.go?type=chem&acc=$1 False CTD.CHEMICAL ctd.chemical ctd.chemical ctd mesh ctd.disease CTD Disease http://ctdbase.org/ The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. ^D\d+$ D053716 http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1 False CTD.DISEASE ctd.disease ctd.disease ctd mesh ctd.gene CTD Gene http://ctdbase.org/ The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences. ^\d+$ 101 http://ctdbase.org/detail.go?type=gene&acc=$1 False CTD.GENE ctd.gene ctd.gene ctd ncbigene -cteno Ctenophore Ontology https://github.com/obophenotype/ctenophore-ontology An anatomical and developmental ontology for ctenophores (Comb Jellies) ^\d{7}$ 0000047 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CTENO_$1 https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo False CTENO CTENO CTENO CTENO cteno CTENO -cto Clinical Trials Ontology https://github.com/ClinicalTrialOntology/CTO/ The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. ^\d{7}$ 0000022 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/CTO_$1 False CTO CTO CTO cto CTO +cteno Ctenophore Ontology https://github.com/obophenotype/ctenophore-ontology An anatomical and developmental ontology for ctenophores (Comb Jellies) ^\d{7}$ 0000047 cjmungall@lbl.gov http://purl.obolibrary.org/obo/CTENO_$1 https://raw.githubusercontent.com/obophenotype/ctenophore-ontology/master/cteno.obo False CTENO CTENO CTENO cteno cteno CTENO +cto Clinical Trials Ontology https://github.com/ClinicalTrialOntology/CTO/ The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials. ^\d{7}$ 0000022 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/CTO_$1 False CTO CTO cto cto CTO cubedb Cube db http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available. ^[A-Za-z_0-9]+$ AKR http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/ True CUBEDB cubedb cubedb -cvdo Cardiovascular Disease Ontology https://github.com/OpenLHS/CVDO An ontology to describe entities related to cardiovascular diseases ^\d{7}$ 0000546 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/CVDO_$1 False CVDO CVDO CVDO CVDO cvdo CVDO +cvdo Cardiovascular Disease Ontology https://github.com/OpenLHS/CVDO An ontology to describe entities related to cardiovascular diseases ^\d{7}$ 0000546 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/CVDO_$1 False CVDO CVDO CVDO cvdo cvdo CVDO d1id DataONE https://www.dataone.org DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences. ^\S+$ 00030692-0FE1-4A1B-955E-A2E55D659267 https://cn.dataone.org/cn/v2/resolve/{$1} False D1ID d1id d1id dailymed DailyMed https://dailymed.nlm.nih.gov/dailymed/ DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read. ^[A-Za-z0-9-]+$ 973a9333-fec7-46dd-8eb5-25738f06ee54 https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1 False DAILYMED dailymed dailymed dailymed dandi Distributed Archives for Neurophysiology Data Integration https://dandiarchive.org/ "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable). @@ -328,12 +328,12 @@ dbsnp NCBI dbSNP https://www.ncbi.nlm.nih.gov/snp/ The dbSNP database is a repos dbvar.study Database of Genomic Structural Variation - Study https://www.ncbi.nlm.nih.gov/dbvar Studies in dbVar. nstd102 https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 dbvar.studies False dbvar.variant Database of Genomic Structural Variation - Variant https://www.ncbi.nlm.nih.gov/dbvar Variants in dbVar. nsv3875336 https://www.ncbi.nlm.nih.gov/dbvar/variants/$1 dbvar.variants False dc Dublin Core https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. contributor http://purl.org/dc/terms/$1 False DC dc DC dcterms -dc_cl Dendritic cell http://www.dukeontologygroup.org/Projects.html ^\d{7}$ 0000003 Lindsay.Cowell@utsouthwestern.edu http://purl.obolibrary.org/obo/DC_CL_$1 True DC_CL DC_CL +dc_cl Dendritic cell http://www.dukeontologygroup.org/Projects.html ^\d{7}$ 0000003 Lindsay.Cowell@utsouthwestern.edu http://purl.obolibrary.org/obo/DC_CL_$1 True DC_CL dc_cl dcat Data Catalog https://www.w3.org/ns/dcat DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web Dataset http://www.w3.org/ns/dcat#$1 False DCAT dcat DCAT dcterms Dublin Core Metadata Vocabulary https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. title http://purl.org/dc/terms/$1 dc.terms False dcterms dcterms DCTERMS dctypes Dublin Core Types https://dublincore.org/specifications/dublin-core/dcmi-terms/ This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Collection http://purl.org/dc/dcmitype/$1 False dctypes -ddanat Dictyostelium discoideum anatomy http://dictybase.org/ A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum ^\d{7}$ 0000006 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDANAT_$1 False DDANAT DDANAT DDANAT DDANAT ddanat DDANAT ddanat -ddpheno Dictyostelium discoideum phenotype ontology http://dictybase.org/ A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. ^\d{7}$ 0001417 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDPHENO_$1 https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo False DDPHENO DDPHENO DDPHENO DDPHENO ddpheno DDPHENO +ddanat Dictyostelium discoideum anatomy http://dictybase.org/ A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum ^\d{7}$ 0000006 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDANAT_$1 False DDANAT DDANAT DDANAT ddanat ddanat DDANAT ddanat +ddpheno Dictyostelium discoideum phenotype ontology http://dictybase.org/ A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum. ^\d{7}$ 0001417 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDPHENO_$1 https://raw.githubusercontent.com/obophenotype/dicty-phenotype-ontology/master/ddpheno.obo False DDPHENO DDPHENO DDPHENO ddpheno ddpheno DDPHENO debio Decentralized Biomedical Ontology https://biopragmatics.github.io/debio A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON. ^\d{7}$ 0000001 cthoyt@gmail.com https://biopragmatics.github.io/debio/$1 False decipher DECIPHER CNV Syndromes https://www.deciphergenomics.org/ CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms ^\d+$ 1 https://www.deciphergenomics.org/syndrome/$1 False DECIPHER degradome Degradome Database http://degradome.uniovi.es/ The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced. ^[AMCST][0-9x][0-9]$ Ax1 http://degradome.uniovi.es/cgi-bin/protease/$1 False DEGRADOME degradome degradome @@ -355,11 +355,11 @@ dictybase dictyBase http://dictybase.org A resource for Dictyostelid discoideum dictybase.est dictyBase Expressed Sequence Tag http://dictybase.org/ The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information. ^DDB\d+$ DDB0016567 http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1 False DICTYBASE.EST dictybase.est dictybase.est dictybase dictybase.gene Dictybase Gene http://dictybase.org/ The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information. ^DDB_G\d+$ DDB_G0267522 http://dictybase.org/gene/$1 False DICTYBASE.GENE dictybase.gene dictybase.gene dictybase did Decentralized Identifier https://w3c-ccg.github.io/did-spec/ DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary. ^[a-z0-9]+:[A-Za-z0-9.\-:]+$ sov:WRfXPg8dantKVubE3HX8pw https://uniresolver.io/#did:$1 False did did -dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology https://github.com/DIDEO/DIDEO The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology ^\d{8}$ 00000180 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/DIDEO_$1 False DIDEO DIDEO DIDEO DIDEO dideo DIDEO -dinto The Drug-Drug Interactions Ontology http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto A formal represention for drug-drug interactions knowledge. maria.herrero@kcl.ac.uk http://purl.obolibrary.org/obo/DINTO_$1 True DINTO DINTO DINTO DINTO DINTO +dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology https://github.com/DIDEO/DIDEO The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology ^\d{8}$ 00000180 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/DIDEO_$1 False DIDEO DIDEO DIDEO dideo dideo DIDEO +dinto The Drug-Drug Interactions Ontology http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto A formal represention for drug-drug interactions knowledge. maria.herrero@kcl.ac.uk http://purl.obolibrary.org/obo/DINTO_$1 True DINTO DINTO DINTO dinto DINTO dip Database of Interacting Proteins https://dip.doe-mbi.ucla.edu/ The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions ^DIP(\:)?\-\d{1,}[ENXS]$ DIP-743N https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1 False DIP 2616 dip dip dip DIP discoverx DiscoverX cell line products https://www.discoverx.com/products-applications/cell-lines Cell line collections 95-0166C6 https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact False DiscoverX -disdriv Disease Drivers Ontology http://www.disease-ontology.org Drivers of human diseases including environmental, maternal and social exposures. ^\d+$ 0000000 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/DISDRIV_$1 False DISDRIV DISDRIV DISDRIV disdriv +disdriv Disease Drivers Ontology http://www.disease-ontology.org Drivers of human diseases including environmental, maternal and social exposures. ^\d+$ 0000000 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/DISDRIV_$1 False DISDRIV DISDRIV disdriv disdriv diseaseclass Disease Class Legacy disease classes that later became MONDO ^\d{7}$ 0000598 https://github.com/obophenotype/human-disease-ontology/raw/master/src/experimental/missing-omc.obo True diseasesdb Diseases Database http://www.diseasesdatabase.com/ The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities. ^\d+$ 1784 False P557 disprot DisProt https://disprot.org/ DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature. ^DP\d{5}$ DP00003 https://disprot.org/$1 False DISPROT 2723 disprot disprot disprot DisProt @@ -369,18 +369,18 @@ dlxc Circular double stranded DNA sequences composed https://doulix.com DOULIX l dmba Developing Mouse Brain Atlas https://developingmouse.brain-map.org/ A controlled vocabulary to support the study of transcription in the developing mouse brain ^\d+$ 688 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-dmba.obo False doco Document Components Ontology http://www.sparontologies.net/ontologies/doco An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix). Paragraph http://purl.org/spar/doco/$1 False doi Digital Object Identifier https://www.doi.org/ The Digital Object Identifier System is for identifying content objects in the digital environment. ^(doi\:)?\d{2}\.\d{4}.*$ 10.1101/2022.07.08.499378 https://doi.org/$1 False DOI DOI 1188 doi doi doi -doid Human Disease Ontology http://www.disease-ontology.org The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. ^\d+$ 0110974 lynn.schriml@gmail.com https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo do False DOID DOID DOID doid doid DOID doid DOID do P699 +doid Human Disease Ontology http://www.disease-ontology.org The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. ^\d+$ 0110974 lynn.schriml@gmail.com https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1 https://github.com/DiseaseOntology/HumanDiseaseOntology/raw/main/src/ontology/doid.obo do False DOID DOID DOID doid doid doid doid DOID do P699 dommino Database of Macromolecular Interactions http://korkinlab.org/dommino DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. ^[0-9][A-Za-z0-9]{3}$ 2GC4 http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1 False DOMMINO dommino dommino door Database for Prokaryotic Operons http://csbl.bmb.uga.edu/DOOR/operon.php DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes. ^\d+$ 1398574 http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1 False DOOR door door door doqcs.model Database of Quantitative Cellular Signaling: Model http://doqcs.ncbs.res.in/ The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models. ^\d+$ 57 http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1 False DOQCS.MODEL doqcs.model doqcs.model doqcs.model doqcs doqcs.pathway Database of Quantitative Cellular Signaling: Pathway http://doqcs.ncbs.res.in/ The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways. ^\d+$ 131 http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1 False DOQCS.PATHWAY doqcs.pathway doqcs.pathway doqcs.pathway doqcs -dpo Drosophila Phenotype Ontology http://purl.obolibrary.org/obo/fbcv An ontology for the description of Drosophila melanogaster phenotypes. cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 False DPO DPO FBcv dpo DPO fbcv +dpo Drosophila Phenotype Ontology http://purl.obolibrary.org/obo/fbcv An ontology for the description of Drosophila melanogaster phenotypes. cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 False DPO DPO dpo dpo DPO fbcv dpv Description of Plant Viruses http://www.dpvweb.net/ Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. ^\d+$ 100 http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1 False DPV dpv dpv dragondb.allele DragonDB Allele http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information. ^\w+$ cho http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele True DRAGONDB.ALLELE dragondb.allele dragondb.allele dragondb dragondb.dna DragonDB DNA http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information. ^\d\w+$ 3hB06 http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA True DRAGONDB.DNA dragondb.dna dragondb.dna dragondb dragondb.locus DragonDB Locus http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information. ^\w+$ DEF http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus True DRAGONDB.LOCUS dragondb.locus dragondb.locus dragondb dragondb.protein DragonDB Protein http://www.antirrhinum.net/ DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information. ^\w+$ AMDEFA http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide True DRAGONDB.PROTEIN dragondb.protein dragondb.protein dragondb -dron The Drug Ontology https://github.com/ufbmi/dron We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). ^\d{8}$ 00023232 hoganwr@gmail.com http://purl.obolibrary.org/obo/DRON_$1 False DRON DRON DRON DRON dron DRON +dron The Drug Ontology https://github.com/ufbmi/dron We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive). ^\d{8}$ 00023232 hoganwr@gmail.com http://purl.obolibrary.org/obo/DRON_$1 False DRON DRON DRON dron dron DRON drsc Drosophila RNAi Screening Center http://flyrnai.org/ The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene. ^DRSC\d+$ DRSC05221 http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1 False DRSC drsc drsc drugbank DrugBank http://www.drugbank.ca The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information. ^DB\d{5}$ DB14938 http://www.drugbank.ca/drugs/$1 DRUGBANK_ID|DrugBank False DrugBank DrugBank 000406 2326 drugbank drugbank drugbank DrugBank P715 drugbank.category DrugBank Drug Category https://go.drugbank.com/categories Close to 5K Categorizations for drugs, similar to ATCC. ^DBCAT\d+$ DBCAT000600 https://www.drugbank.ca/categories/$1 False drugbank @@ -389,24 +389,24 @@ drugbankv4.target DrugBank Target v4 http://www.drugbank.ca/targets The DrugBank drugcentral Drug Central http://drugcentral.org DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. ^\d+$ 307 http://drugcentral.org/drugcard/$1 Drug_Central False DrugCentral dsmz Deutsche Sammlung von Mikroorganismen und Zellkulturen https://www.dsmz.de The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). ACC-1 https://www.dsmz.de/collection/catalogue/details/culture/$1 False DSMZ dto Drug Target Ontology https://github.com/DrugTargetOntology/DTO DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors. ^\d+$ 90000018 False DTO DTO -duo Data Use Ontology https://github.com/EBISPOT/DUO DUO is an ontology which represent data use conditions. ^\d{7}$ 0000046 mcourtot@gmail.com http://purl.obolibrary.org/obo/DUO_$1 False DUO DUO DUO DUO duo DUO +duo Data Use Ontology https://github.com/EBISPOT/DUO DUO is an ontology which represent data use conditions. ^\d{7}$ 0000046 mcourtot@gmail.com http://purl.obolibrary.org/obo/DUO_$1 False DUO DUO DUO duo duo DUO eaglei eagle-i https://hawaii.eagle-i.net Discovery tool for biomedical research resources available at institutions throughout the U.S. 0000012b-5661-2f63-2f73-b43980000000 http://hawaii.eagle-i.net/i/$1 False eagle-i easychair.cfp EasyChair Call for Paper https://easychair.org/cfp/ Conferences in EasyChair SysBioCancer2022 https://easychair.org/cfp/$1 False easychair.topic EasyChair Topic https://easychair.org/cfp/ Call for paper topics in EasyChair ^\d+$ 27106865 https://easychair.org/cfp/topic.cgi?tid=$1 False ebisc European Bank for induced pluripotent Stem Cells https://www.ebisc.org Cell line collections ESi007-A https://cells.ebisc.org/$1 False EBiSC ecacc European Collection of Authenticated Cell Culture https://www.phe-culturecollections.org.uk/collections/ecacc.aspx The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). ^\d+$ 90062901 https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1 False ECACC -ecao The Echinoderm Anatomy and Development Ontology https://github.com/echinoderm-ontology/ecao_ontology None ^\d{7}$ 0107180 ettensohn@cmu.edu http://purl.obolibrary.org/obo/ECAO_$1 False ECAO ECAO ECAO ecao ECAO +ecao The Echinoderm Anatomy and Development Ontology https://github.com/echinoderm-ontology/ecao_ontology None ^\d{7}$ 0107180 ettensohn@cmu.edu http://purl.obolibrary.org/obo/ECAO_$1 False ECAO ECAO ecao ecao ECAO eccode Enzyme Commission Code https://www.ebi.ac.uk/intenz/ The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions. ^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.n\d{1,3})?$ 1.1.1.1 https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1 EC|EC number|EC-CODE|ECCODE|EC_CODE|ec-code|intenz False EC-CODE 1011 ec-code ec-code intenz P591 ecg Electrocardiogram Ontology https://bioportal.bioontology.org/ontologies/ECG The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms. ^\d+$ 000000159 ECGOntology False ECG ECG echobase EchoBASE post-genomic database for Escherichia coli http://www.york.ac.uk/ EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. ^EB\d+$ EB0170 http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1 False ECHOBASE echobase echobase echobase EchoBASE ecmdb E. coli Metabolite Database https://ecmdb.ca The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes. ^ECMDB\d+$ ECMDB00005 http://ecmdb.ca/compounds/$1 ECMDB False -eco Evidence ontology https://github.com/evidenceontology/evidenceontology/ Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. ^\d{7}$ 0007807 mgiglio@som.umaryland.edu https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 False ECO ECO ECO eco eco ECO eco ECO eco -ecocore An ontology of core ecological entities https://github.com/EcologicalSemantics/ecocore Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. ^\d+$ 00000001 p.buttigieg@gmail.com http://purl.obolibrary.org/obo/ECOCORE_$1 False ECOCORE ECOCORE ECOCORE ECOCORE ecocore ECOCORE +eco Evidence ontology https://github.com/evidenceontology/evidenceontology/ Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity. ^\d{7}$ 0007807 mgiglio@som.umaryland.edu https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1 False ECO ECO ECO eco eco eco eco ECO eco +ecocore An ontology of core ecological entities https://github.com/EcologicalSemantics/ecocore Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms. ^\d+$ 00000001 p.buttigieg@gmail.com http://purl.obolibrary.org/obo/ECOCORE_$1 False ECOCORE ECOCORE ECOCORE ecocore ecocore ECOCORE ecocyc EcoCyc http://ecocyc.org/ EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways. AICARTRANSIMPCYCLO-CPLX https://biocyc.org/gene?id=$1 False ecogene Database of Escherichia coli Sequence and Function http://ecogene.org/ The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites. ^EG\d+$ EG10173 http://www.ecogene.org/gene/$1 False EcoGene ecogene ecogene ecogene ecolexicon EcoLexicon http://ecolexicon.ugr.es/en/index.htm EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology. canal False ecoliwiki EcoliWiki from EcoliHub http://ecoliwiki.net/colipedia/ EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes. ^[A-Za-z0-9-]+$ aaeA http://ecoliwiki.net/colipedia/index.php/$1:Gene False ECOLIWIKI ecoliwiki ecoliwiki -ecto Environmental conditions, treatments and exposures ontology https://github.com/EnvironmentOntology/environmental-exposure-ontology ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). ^\d{7}$ 0000001 annethessen@gmail.com http://purl.obolibrary.org/obo/ECTO_$1 False ECTO ECTO ECTO ecto ECTO +ecto Environmental conditions, treatments and exposures ontology https://github.com/EnvironmentOntology/environmental-exposure-ontology ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology). ^\d{7}$ 0000001 annethessen@gmail.com http://purl.obolibrary.org/obo/ECTO_$1 False ECTO ECTO ecto ecto ECTO ecyano.entity E-cyanobacterium entity http://www.e-cyanobacterium.org/bcs/entity/ E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities. ^\d+$ 23 https://www.e-cyanobacterium.org/bcs/entity/$1 False ECYANO.ENTITY ecyano.entity ecyano.entity ecyano ecyano.experiment E-cyanobacterium Experimental Data https://www.e-cyanobacterium.org/experiments-repository/ E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments. ^\d+$ 18 https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1 False ecyano.experiment ecyano ecyano.model E-cyanobacterium model http://e-cyanobacterium.org/models/ E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models. ^\d+$ 26 https://e-cyanobacterium.org/models/model/$1 False ECYANO.MODEL ecyano.model ecyano.model @@ -421,12 +421,12 @@ efo Experimental Factor Ontology http://www.ebi.ac.uk/efo The Experimental Facto ega.dataset European Genome-phenome Archive Dataset https://ega-archive.org/ The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'. ^EGAD\d{11}$ EGAD00000000001 https://www.ebi.ac.uk/ega/datasets/$1 False EGA.DATASET ega.dataset ega.dataset ega.study European Genome-phenome Archive Study https://www.ebi.ac.uk/ega/studies The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets. ^EGAS\d{11}$ EGAS00000000001 https://www.ebi.ac.uk/ega/studies/$1 False EGA.STUDY ega.study ega.study eggnog eggNOG http://eggnog.embl.de/version_3.0/ eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). ^\w+$ veNOG12876 http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1 False EGGNOG eggnog eggnog eggnog eggNOG -ehda Human developmental anatomy, timed version http://genex.hgu.mrc.ac.uk/ ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDA_$1 True EHDA EHDA EHDA EHDA ehda -ehdaa Human developmental anatomy, abstract version ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA_$1 True EHDAA EHDAA EHDAA EHDAA ehdaa -ehdaa2 Human developmental anatomy, abstract https://github.com/obophenotype/human-developmental-anatomy-ontology A structured controlled vocabulary of stage-specific anatomical structures of the developing human. ^\d{7}$ 0000000 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA2_$1 EHDAA2_RETIRED|HDAA2|RETIRED_EHDAA2 True EHDAA2 EHDAA2 EHDAA2 EHDAA2 ehdaa2 EHDAA2 +ehda Human developmental anatomy, timed version http://genex.hgu.mrc.ac.uk/ ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDA_$1 True EHDA EHDA EHDA ehda ehda +ehdaa Human developmental anatomy, abstract version ^\d+$ 1 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA_$1 True EHDAA EHDAA EHDAA ehdaa ehdaa +ehdaa2 Human developmental anatomy, abstract https://github.com/obophenotype/human-developmental-anatomy-ontology A structured controlled vocabulary of stage-specific anatomical structures of the developing human. ^\d{7}$ 0000000 J.Bard@ed.ac.uk http://purl.obolibrary.org/obo/EHDAA2_$1 EHDAA2_RETIRED|HDAA2|RETIRED_EHDAA2 True EHDAA2 EHDAA2 EHDAA2 ehdaa2 ehdaa2 EHDAA2 elm Eukaryotic Linear Motif Resource http://elm.eu.org/ Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances. ^[A-Za-z_0-9]+$ CLV_MEL_PAP_1 http://elm.eu.org/elms/elmPages/$1.html False ELM elm elm ELM -emap Mouse gross anatomy and development, timed http://emouseatlas.org A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). ^\d+$ 1 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/EMAP_$1 True EMAP EMAP EMAP -emapa Mouse Developmental Anatomy Ontology http://www.informatics.jax.org/expression.shtml An ontology for mouse anatomy covering embryonic development and postnatal stages. ^\d+$ 26753 Terry.Hayamizu@jax.org http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1 EMAPA_RETIRED False EMAPA EMAPA EMAPA EMAPA emapa EMAPA +emap Mouse gross anatomy and development, timed http://emouseatlas.org A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus). ^\d+$ 1 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/EMAP_$1 True EMAP EMAP emap +emapa Mouse Developmental Anatomy Ontology http://www.informatics.jax.org/expression.shtml An ontology for mouse anatomy covering embryonic development and postnatal stages. ^\d+$ 26753 Terry.Hayamizu@jax.org http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1 EMAPA_RETIRED False EMAPA EMAPA EMAPA emapa emapa EMAPA emdb Electron Microscopy Data Bank https://www.ebi.ac.uk/pdbe/emdb/ The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. ^EMD-\d{4}$ EMD-1001 https://www.ebi.ac.uk/pdbe/entry/emdb/$1 False EMDB 1146 emdb emdb emolecules Reaxys eMolecules https://reaxys.emolecules.com Catalog of purchasable reagents and building blocks ^\d+$ 491187 https://reaxys.emolecules.com/cgi-bin/more?vid=$1 False empiar Electron Microscopy Public Image Archive https://www.ebi.ac.uk/pdbe/emdb EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure ^\d+$ 10595 https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1 False @@ -441,67 +441,67 @@ ensembl.plant Ensembl Plants https://plants.ensembl.org/ Ensembl Genomes consist ensembl.protist Ensembl Protists https://protists.ensembl.org Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes. ^\w+$ PF3D7_1328700 https://protists.ensembl.org/id/$1 False ENSEMBL.PROTIST ensembl.protist ensembl.protist ensembl.protist ensemblglossary Ensembl Glossary http://ensembl.org/glossary The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used. ^\d{7}$ 0000198 False ensemblglossary envipath enviPath https://envipath.org/ enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products. ^[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}\/[\w-]+\/[\w^_]{8}-[\w^_]{4}-[\w^_]{4}-[\w^_]{4}-[\w^_]{12}$ 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea https://envipath.org/package/$1 False envipath -envo Environment Ontology http://environmentontology.org/ The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. ^\d{7,8}$ 09200010 p.buttigieg@gmail.com https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1 False ENVO ENVO ENVO ENVO envo envo ENVO envo ENVO +envo Environment Ontology http://environmentontology.org/ The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. ^\d{7,8}$ 09200010 p.buttigieg@gmail.com https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1 False ENVO ENVO ENVO ENVO envo envo envo envo ENVO enzo Enzo Life Sciences https://www.enzolifesciences.com Enzo Life Sciences is an antibody vendor. ALX-210-175 https://www.enzolifesciences.com/$1 Enzo Life Sciences False -eo Plant Environment Ontology http://planteome.org/ The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. ^\d{7}$ 0007404 jaiswalp@science.oregonstate.edu http://archive.gramene.org/db/ontology/search?query=EO:$1 True EO EO EO eo eo EO eo +eo Plant Environment Ontology http://planteome.org/ The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies. ^\d{7}$ 0007404 jaiswalp@science.oregonstate.edu http://archive.gramene.org/db/ontology/search?query=EO:$1 True EO EO EO eo eo eo eo eol Environment Ontology for Livestock http://www.atol-ontology.com The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems. ^\d{7}$ 0001927 pylebail@rennes.inra.fr https://sicpa-web.cati.inrae.fr/ontologies/visualisation/ontologie/atol/creation_fichier_owl.php?filename=eol.owl False EOL EOL EOL eol eolife Encyclopedia of Life https://eol.org A collaborative project intended to create an encyclopedia documenting all living species known to science ^\d+$ 1044544 https://eol.org/pages/$1 False P830 epcc European Paediatric Cardiac Codes https://www.aepc.org/european-paediatric-cardiac-coding Collection of European paediatric cardiac coding files False epd Eukaryotic Promoter Database http://epd.vital-it.ch/ The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. ^[A-Z-_0-9]+$ TA_H3 http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1 False EPD 2386 epd epd EPD -epio Epilepsy Ontology https://github.com/SCAI-BIO/EpilepsyOntology A application driven Epilepsy Ontology with official terms from the ILAE. ^\d{7}$ 0000011 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/EPIO_$1 False EPIO EPIO EPIO EPIO -epo Epidemiology Ontology https://code.google.com/p/epidemiology-ontology/ An ontology designed to support the semantic annotation of epidemiology resources http://purl.obolibrary.org/obo/EPO_$1 https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl True EPO EPO EPO EPO EPO +epio Epilepsy Ontology https://github.com/SCAI-BIO/EpilepsyOntology A application driven Epilepsy Ontology with official terms from the ILAE. ^\d{7}$ 0000011 alpha.tom.kodamullil@scai.fraunhofer.de http://purl.obolibrary.org/obo/EPIO_$1 False EPIO EPIO epio EPIO +epo Epidemiology Ontology https://code.google.com/p/epidemiology-ontology/ An ontology designed to support the semantic annotation of epidemiology resources http://purl.obolibrary.org/obo/EPO_$1 https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/epidemiology-ontology/epo.owl True EPO EPO EPO epo EPO epso Epilepsy and Seizure Ontology http://prism.case.edu/prism/index.php/EpilepsyOntology The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. ^\d{7}$ 0000400 False EPSO EPSO EPSO erm European Registry of Materials https://nanocommons.github.io/identifiers/ The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project. ^ERM[0-9]{8}$ ERM00000044 https://nanocommons.github.io/identifiers/registry#$1 False erm erm -ero eagle-i resource ontology https://open.med.harvard.edu/wiki/display/eaglei/Ontology An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. ^\d{7}$ 0001655 Marc_Ciriello@hms.harvard.edu http://purl.obolibrary.org/obo/ERO_$1 True ERO ERO ERO ERO ero ERO +ero eagle-i resource ontology https://open.med.harvard.edu/wiki/display/eaglei/Ontology An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens. ^\d{7}$ 0001655 Marc_Ciriello@hms.harvard.edu http://purl.obolibrary.org/obo/ERO_$1 True ERO ERO ERO ero ero ERO erv Human Endogenous Retrovirus Database https://herv.img.cas.cz/ Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features. ^[A-Za-z0-9\-\_]+$ THE1B https://herv.img.cas.cz/s/$1 False ERV erv erv estdab European Searchable Tumour Line Database https://www.ebi.ac.uk/ipd/estdab/ Cell line databases/resources ^\d{3}$ 046 https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1 True ESTDAB eu89h JRC Data Catalogue http://data.jrc.ec.europa.eu/ The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union. ^[a-z0-9\-_]+$ jrc-eurl-ecvam-chemagora http://data.europa.eu/89h/$1 False EU89H eu89h eu89h euclinicaltrials EU Clinical Trials https://www.clinicaltrialsregister.eu/ "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004. It also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population." ^\d{4}\-\d{6}\-\d{2}$ 2008-005144-16 https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1 False EUCLINICALTRIALS euclinicaltrials euclinicaltrials -eupath VEuPathDB ontology https://github.com/VEuPathDB-ontology/VEuPathDB-ontology The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. ^\d{7}$ 0010316 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/EUPATH_$1 False EUPATH EUPATH EUPATH EUPATH eupath EUPATH +eupath VEuPathDB ontology https://github.com/VEuPathDB-ontology/VEuPathDB-ontology The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available. ^\d{7}$ 0010316 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/EUPATH_$1 False EUPATH EUPATH EUPATH eupath eupath EUPATH eurofir European Food Information Resource Network https://www.eurofir.org EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries. False -ev eVOC (Expressed Sequence Annotation for Humans) http://www.evocontology.org/ evoc@sanbi.ac.za http://purl.obolibrary.org/obo/EV_$1 True EV EV +ev eVOC (Expressed Sequence Annotation for Humans) http://www.evocontology.org/ evoc@sanbi.ac.za http://purl.obolibrary.org/obo/EV_$1 True EV ev evm eVOC mouse development stage True exac.gene ExAC Gene http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information. ^ENSG\d{11}$ ENSG00000169174 http://exac.broadinstitute.org/gene/$1 False EXAC.GENE exac.gene exac.gene exac.transcript ExAC Transcript http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information. ^ENST\d{11}$ ENST00000407236 http://exac.broadinstitute.org/transcript/$1 False EXAC.TRANSCRIPT exac.transcript exac.transcript exac.variant ExAC Variant http://exac.broadinstitute.org/ The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information. ^\d{1,2}\-\d+\-[GATC]\-[GATC]$ 22-46615880-T-C http://exac.broadinstitute.org/variant/$1 False EXAC.VARIANT exac.variant exac.variant -exo Exposure ontology https://github.com/CTDbase/exposure-ontology ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. ^\d{7}$ 0000078 annethessen@gmail.com http://purl.obolibrary.org/obo/EXO_$1 ExO False EXO EXO EXO ExO exo ExO +exo Exposure ontology https://github.com/CTDbase/exposure-ontology ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics. ^\d{7}$ 0000078 annethessen@gmail.com http://purl.obolibrary.org/obo/EXO_$1 ExO False EXO EXO EXO exo exo ExO fabio FaBiO, the FRBR-aligned Bibliographic Ontology https://github.com/sparontologies/fabio The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references. d4e2515 https://sparontologies.github.io/fabio/current/fabio.html#$1 False FaBiO facebase FaceBase Data Repository https://www.facebase.org FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects. ^FB\d{8}$ FB00000917 https://www.facebase.org/data/record/#1/isa:dataset/accession=$1 False FACEBASE facebase facebase fairsharing FAIRsharing https://fairsharing.org/ The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies. ^bsg-[dscp]?\d{6}$ bsg-000052 https://fairsharing.org/$1 False FAIRSHARING fairsharing fairsharing faldo Feature Annotation Location Description Ontology http://biohackathon.org/resource/faldo It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources ForwardStrandPosition http://biohackathon.org/resource/faldo#$1 False FALDO FALDO faldo FALDO -fao Fungal gross anatomy https://github.com/obophenotype/fungal-anatomy-ontology/ A structured controlled vocabulary for the anatomy of fungi. ^\d{7}$ 0000001 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FAO_$1 False FAO FAO FAO FAO fao FAO fao -fbbi Biological Imaging Methods Ontology http://cellimagelibrary.org/ A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. ^\d+$ 00000268 wawong@gmail.com http://purl.obolibrary.org/obo/FBbi_$1 FBbi False FBbi FBbi FBbi FBbi fbbi FBBI fbbi -fbbt Drosophila gross anatomy http://purl.obolibrary.org/obo/fbbt An ontology of Drosophila melanogaster anatomy. ^\d{8}$ 00007294 cp390@cam.ac.uk https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 FBbt|FBbt_root False FBBT FBbt FB-BT FBbt fbbt FBBT fbbt flybase -fbcv FlyBase Controlled Vocabulary http://purl.obolibrary.org/obo/fbcv A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. ^\d{7}$ 0000586 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo FBcv False FBCV FBcv FB-CV FBcv fbcv FBCV fbcv flybase -fbdv Drosophila development http://purl.obolibrary.org/obo/fbdv An ontology of Drosophila melanogaster developmental stages. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBdv_$1 FBdv False FBDV FBdv FB-DV FBdv fbdv FBdv fbdv +fao Fungal gross anatomy https://github.com/obophenotype/fungal-anatomy-ontology/ A structured controlled vocabulary for the anatomy of fungi. ^\d{7}$ 0000001 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FAO_$1 False FAO FAO FAO fao fao FAO fao +fbbi Biological Imaging Methods Ontology http://cellimagelibrary.org/ A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research. ^\d+$ 00000268 wawong@gmail.com http://purl.obolibrary.org/obo/FBbi_$1 FBbi False FBbi FBbi FBbi fbbi fbbi FBBI fbbi +fbbt Drosophila gross anatomy http://purl.obolibrary.org/obo/fbbt An ontology of Drosophila melanogaster anatomy. ^\d{8}$ 00007294 cp390@cam.ac.uk https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1 FBbt|FBbt_root False FBBT FBbt FB-BT fbbt fbbt FBBT fbbt flybase +fbcv FlyBase Controlled Vocabulary http://purl.obolibrary.org/obo/fbcv A miscellaneous ontology of terms used for curation in FlyBase, including the DPO. ^\d{7}$ 0000586 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBcv_$1 https://raw.githubusercontent.com/FlyBase/flybase-controlled-vocabulary/master/fbcv.obo FBcv False FBCV FBcv FB-CV fbcv fbcv FBCV fbcv flybase +fbdv Drosophila development http://purl.obolibrary.org/obo/fbdv An ontology of Drosophila melanogaster developmental stages. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBdv_$1 FBdv False FBDV FBdv FB-DV fbdv fbdv FBdv fbdv fbol International Fungal Working Group Fungal Barcoding. http://www.fungalbarcoding.org/ DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms. ^\d+$ 2224 http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T True FBOL fbol fbol fbql FlyBase Qualifiers ^\d+$ 00005254 True fbrf FlyBase Reference Report https://flybase.org FlyBase internal citation identifiers ^\d{7}$ 0187632 https://flybase.org/reports/FBrf$1 False flybase -fbsp Fly taxonomy http://www.flybase.org/ The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBSP_$1 True FB-SP FBSP FB-SP FBSP flybase +fbsp Fly taxonomy http://www.flybase.org/ The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase. ^\d{8}$ 00000000 cp390@cam.ac.uk http://purl.obolibrary.org/obo/FBSP_$1 True FB-SP FBSP FB-SP fbsp flybase fbtc Flybase Cell Line https://flybase.org The cell line vocabulary inside FlyBase ^\d{7}$ 0000190 https://flybase.org/reports/FBtc$1 False flybase fcb the FAIR Cookbook https://w3id.org "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR). " ^FCB\d{3}$ FCB005 https://w3id.org/faircookbook/$1 False fcb fcsfree Fetal Calf Serum-Free Database https://fcs-free.org Cell line databases/resources 240-17-488-3-4-12 https://fcs-free.org/fcs-database?$1 False FCS-free -fideo Food Interactions with Drugs Evidence Ontology https://gitub.u-bordeaux.fr/erias/fideo The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there. ^\d{8}$ 00000021 georgeta.bordea@u-bordeaux.fr http://purl.obolibrary.org/obo/FIDEO_$1 False FIDEO FIDEO FIDEO fideo FIDEO +fideo Food Interactions with Drugs Evidence Ontology https://gitub.u-bordeaux.fr/erias/fideo The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there. ^\d{8}$ 00000021 georgeta.bordea@u-bordeaux.fr http://purl.obolibrary.org/obo/FIDEO_$1 False FIDEO FIDEO fideo fideo FIDEO fishbase.species FishBase http://fishbase.org Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years. ^\d+$ 6472 fishbase False P938 fivestars Five Stars of Online Research Articles Ontology http://www.sparontologies.net/ontologies/fivestars An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata. hasOpenAccessRating False -fix Physico-chemical methods and properties https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical methods and properties. ^\d{7}$ 0000390 http://purl.obolibrary.org/obo/FIX_$1 True FIX FIX FIX FIX fix FIX fix chebi -flopo Flora Phenotype Ontology https://github.com/flora-phenotype-ontology/flopoontology Traits and phenotypes of flowering plants occurring in digitized Floras ^\d{7}$ 0005250 robert.hoehndorf@kaust.edu.sa http://purl.obolibrary.org/obo/FLOPO_$1 False FLOPO FLOPO FLOPO FLOPO FLOPO flopo FLOPO +fix Physico-chemical methods and properties https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical methods and properties. ^\d{7}$ 0000390 http://purl.obolibrary.org/obo/FIX_$1 True FIX FIX FIX fix fix FIX fix chebi +flopo Flora Phenotype Ontology https://github.com/flora-phenotype-ontology/flopoontology Traits and phenotypes of flowering plants occurring in digitized Floras ^\d{7}$ 0005250 robert.hoehndorf@kaust.edu.sa http://purl.obolibrary.org/obo/FLOPO_$1 False FLOPO FLOPO FLOPO FLOPO flopo flopo FLOPO flowrepository FlowRepository https://flowrepository.org/ FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field. ^FR\-FCM\-\w{4}$ FR-FCM-ZYGW https://flowrepository.org/id/$1 False flowrepository flowrepository -flu Influenza Ontology http://purl.obolibrary.org/obo/flu/ ^\d{7}$ 0000404 burkesquires@gmail.com http://purl.obolibrary.org/obo/FLU_$1 True FLU FLU FLU FLU +flu Influenza Ontology http://purl.obolibrary.org/obo/flu/ ^\d{7}$ 0000404 burkesquires@gmail.com http://purl.obolibrary.org/obo/FLU_$1 True FLU FLU FLU flu flybase FlyBase Gene http://flybase.org/ FlyBase is the database of the Drosophila Genome Projects and of associated literature. ^FB\w{2}\d{7}$ FBgn0011293 https://flybase.org/reports/$1 FB|FlyBase False FlyBase FlyBase 1089 fb fb flybase FlyBase P3852 flybrain.ndb FlyBrain Neuron Database https://flybrain-ndb.virtualflybrain.org A database of fly neurons and pathways with an associated 3D viewer. ^\d+$ 10531 https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html False -fma Foundational Model of Anatomy http://si.washington.edu/projects/fma The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. ^\d+$ 63189 mejino@u.washington.edu https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 FMAID|FMA_RETIRED True FMA FMA FMA 1182 fma fma FMA fma FMA fma +fma Foundational Model of Anatomy http://si.washington.edu/projects/fma The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. ^\d+$ 63189 mejino@u.washington.edu https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1 FMAID|FMA_RETIRED True FMA FMA FMA 1182 fma fma fma fma FMA fma foaf Friend of a Friend http://xmlns.com/foaf/spec/ FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world. familyName http://xmlns.com/foaf/0.1/$1 False foaf foaf FOAF -fobi Food-Biomarker Ontology https://github.com/pcastellanoescuder/FoodBiomarkerOntology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data ^\d{6}$ 030719 polcaes@gmail.com http://purl.obolibrary.org/obo/FOBI_$1 False FOBI FOBI FOBI FOBI fobi FOBI +fobi Food-Biomarker Ontology https://github.com/pcastellanoescuder/FoodBiomarkerOntology FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data ^\d{6}$ 030719 polcaes@gmail.com http://purl.obolibrary.org/obo/FOBI_$1 False FOBI FOBI FOBI fobi fobi FOBI foodb.compound FooDB Compound https://foodb.ca/ FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds. ^FDB\d+$ FDB002100 http://foodb.ca/compounds/$1 foodb False FOODB.COMPOUND foodb.compound foodb.compound foodb.food FooDB Food https://foodb.ca/foods Foods in FooDB ^FOOD\d+$ FOOD00020 https://foodb.ca/foods/$1 False -foodon The Food Ontology https://foodon.org/ FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. ^[0-9]{8}$ 03307879 damion_dooley@sfu.ca https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 False FOODON FOODON FOODON FOODON foodon foodon FOODON foodon FOODON +foodon The Food Ontology https://foodon.org/ FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies. ^[0-9]{8}$ 03307879 damion_dooley@sfu.ca https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1 False FOODON FOODON FOODON FOODON foodon foodon foodon foodon FOODON fossilworks.journal Fossilworks Journal http://fossilworks.org Identifier for a journal article in the fossilworks website ^\d+$ 61467 http://fossilworks.org/?a=referenceInfo&reference_no=$1 False P7720 fossilworks fossilworks.taxon Fossilworks Taxon http://www.fossilworks.org Identifier for an animal, plant, or microorganism from the fossilworks website ^[1-9]\d{0,5}$ 40565 http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1 False P842 fossilworks -fovt FuTRES Ontology of Vertebrate Traits https://github.com/futres/fovt None ^\d{7}$ 0000009 meghan.balk@gmail.com http://purl.obolibrary.org/obo/FOVT_$1 False FOVT FOVT FOVT fovt FOVT +fovt FuTRES Ontology of Vertebrate Traits https://github.com/futres/fovt None ^\d{7}$ 0000009 meghan.balk@gmail.com http://purl.obolibrary.org/obo/FOVT_$1 False FOVT FOVT fovt fovt FOVT fplx FamPlex https://sorgerlab.github.io/famplex/ FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships. ^[a-zA-Z0-9][A-Za-z0-9_]+$ GPIb_IX_V https://sorgerlab.github.io/famplex/$1 famplex False FPLX FPLX FPLX fplx fplx fr FAIR* Reviews Ontology http://www.sparontologies.net/ontologies/fr An ontology that enables the description of reviews of scientific articles and other scholarly resources. ReviewVersion False frapo Funding, Research Administration and Projects Ontology http://www.sparontologies.net/ontologies/frapo An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc. Grant http://purl.org/cerif/frapo/$1 False FRAPO @@ -517,36 +517,36 @@ fungidb FungiDB https://fungidb.org/fungidb FungiDB is a genomic resource for fu fungorum Index Fungorum http://www.indexfungorum.org identifier for a fungus taxon in Index Fungorum ^[1-9]\d{0,5}$ 154022 http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1 False P1391 fyeco Fission Yeast Experimental Conditions Ontology https://github.com/pombase/fypo PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase. ^\d{7}$ 0000003 vw253@cam.ac.uk False fyler Fyler https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906 A hierarchical classification of congenital heart disease ^\d+$ 4447 False -fypo Fission Yeast Phenotype Ontology https://github.com/pombase/fypo A formal ontology of phenotypes observed in fission yeast. ^\d{7}$ 0001707 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FYPO_$1 http://purl.obolibrary.org/obo/fypo.obo False FYPO FYPO FYPO FYPO fypo FYPO +fypo Fission Yeast Phenotype Ontology https://github.com/pombase/fypo A formal ontology of phenotypes observed in fission yeast. ^\d{7}$ 0001707 vw253@cam.ac.uk http://purl.obolibrary.org/obo/FYPO_$1 http://purl.obolibrary.org/obo/fypo.obo False FYPO FYPO FYPO fypo fypo FYPO ga4ghdos Data Object Service http://github.com/ga4gh/data-object-service-schemas Assists in resolving data across cloud resources. ^[a-zA-Z0-9\-:#/\.]+$ dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d https://dataguids.org/ga4gh/dos/v1/dataobjects/$1 False GA4GHDOS ga4ghdos ga4ghdos gabi Network of Different Plant Genomic Research Projects http://www.gabipd.org/ GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'. ^\w+$ 2679240 http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject False GABI gabi gabi gabi galen GALEN https://www.opengalen.org MagnitudeValueType True GALEN GALEN gard Genetic and Rare Diseases Information Center https://rarediseases.info.nih.gov/diseases Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease. ^\d+$ 6038 GARD|Genetic and Rare Diseases Information Center False P4317 gateway Health Data Research Innovation Gateway https://www.hdruk.ac.uk The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access. ^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$ fd8d0743-344a-4758-bb97-f8ad84a37357 https://web.www.healthdatagateway.org/dataset/$1 False gateway -gaz Gazetteer http://environmentontology.github.io/gaz/ A gazetteer constructed on ontological principles ^\d{8}$ 00620027 lschriml@som.umaryland.edu http://purl.obolibrary.org/obo/GAZ_$1 http://purl.obolibrary.org/obo/gaz.obo True GAZ GAZ GAZ GAZ gaz GAZ P6778 +gaz Gazetteer http://environmentontology.github.io/gaz/ A gazetteer constructed on ontological principles ^\d{8}$ 00620027 lschriml@som.umaryland.edu http://purl.obolibrary.org/obo/GAZ_$1 http://purl.obolibrary.org/obo/gaz.obo True GAZ GAZ GAZ gaz gaz GAZ P6778 gbif Global Biodiversity Information Facility https://www.gbif.org/species "Database of living organisms, taxonomic. The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth." ^\d+$ 4238 https://www.gbif.org/species/$1 False P846 gc Genetic Code https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries. ^\d+$ 11 https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1 gc_id False gcst GWAS Catalog https://www.ebi.ac.uk The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide. ^GCST\d{6}\d*$ GCST000035 https://www.ebi.ac.uk/gwas/studies/$1 False gcst gcst gdc Genomic Data Commons Data Portal https://gdc.cancer.gov The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. ^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$ ae8c77fe-e6c8-44d5-8265-4a38c637bbef https://portal.gdc.cancer.gov/cases/$1 False GDC gdc gdc gdsc Genomics of Drug Sensitivity in Cancer https://www.cancerrxgene.org The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies. ^[0-9]+$ 1242 https://www.cancerrxgene.org/translation/Drug/$1 False GDSC gdsc gdsc -gecko Genomics Cohorts Knowledge Ontology https://github.com/IHCC-cohorts/GECKO An ontology to represent genomics cohort attributes. ^\d{7}$ 0000044 rbca.jackson@gmail.com http://purl.obolibrary.org/obo/GECKO_$1 False GECKO GECKO GECKO gecko GECKO +gecko Genomics Cohorts Knowledge Ontology https://github.com/IHCC-cohorts/GECKO An ontology to represent genomics cohort attributes. ^\d{7}$ 0000044 rbca.jackson@gmail.com http://purl.obolibrary.org/obo/GECKO_$1 False GECKO GECKO gecko gecko GECKO gemet General Multilingual Environmental Thesaurus https://www.eionet.europa.eu/gemet/en/themes/ The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts. ^\d+$ 627 https://www.eionet.europa.eu/gemet/en/concept/$1 False GEMET genatlas Genatlas http://genatlas.medecine.univ-paris5.fr/ GenAtlas is a database containing information on human genes, markers and phenotypes. ^\w+$ HBB http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1 False GENATLAS genatlas genatlas genatlas GenAtlas genbank GenBank https://www.ncbi.nlm.nih.gov/genbank/ GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). U49845 https://www.ncbi.nlm.nih.gov/nucleotide/$1 False GenBank 000304 2292 genbank GenBank genecards GeneCards http://www.genecards.org/ The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene. ^[A-Za-z-0-9_]+(\@)?$ ABL1 https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1 False GENECARDS genecards genecards genecards GeneCards genedb GeneDB https://www.genedb.org/ "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the ""Pathogen Genomics"" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed." ^[\w\d\.-]*$ LinJ.20.0070 https://www.genedb.org/gene/$1 True GENEDB 1035 genedb genedb genedb GeneDB P3382 genefarm GeneFarm http://urgi.versailles.inra.fr/Genefarm/ GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products. ^\d+$ 4892 https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1 False GENEFARM genefarm genefarm genefarm -genepio Genomic Epidemiology Ontology http://genepio.org/ The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. ^\d{7}$ 0001885 damion_dooley@sfu.ca http://purl.obolibrary.org/obo/GENEPIO_$1 False GENEPIO GENEPIO GENEPIO genepio GENEPIO +genepio Genomic Epidemiology Ontology http://genepio.org/ The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks. ^\d{7}$ 0001885 damion_dooley@sfu.ca http://purl.obolibrary.org/obo/GENEPIO_$1 False GENEPIO GENEPIO genepio genepio GENEPIO genetree GeneTree http://www.ensembl.org/ Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl. ^ENSGT\d+$ ENSGT00550000074763 http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1 False GENETREE genetree genetree genetree GeneTree genewiki Gene Wiki http://en.wikipedia.org/wiki/Gene_Wiki The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI. ^\d+$ 1017 http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1 False GENEWIKI genewiki genewiki GeneWiki geno Genotype Ontology https://github.com/monarch-initiative/GENO-ontology/ "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. -Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" ^\d{7}$ 0000632 mhb120@gmail.com http://purl.obolibrary.org/obo/GENO_$1 https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo False GENO GENO GENO GENO geno GENO +Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013" ^\d{7}$ 0000632 mhb120@gmail.com http://purl.obolibrary.org/obo/GENO_$1 https://raw.githubusercontent.com/monarch-initiative/GENO-ontology/develop/geno-full.obo False GENO GENO GENO geno geno GENO genpept GenPept https://www.ncbi.nlm.nih.gov/protein The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank. ^\w{3}\d{5}(\.\d+)?$ CAA71118.1 https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept False GENPEPT genpept genpept genprop Genome Properties https://www.ebi.ac.uk/interpro/genomeproperties/ Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome. ^GenProp\d+$ GenProp0699 https://www.ebi.ac.uk/interpro/genomeproperties/#$1 False GENPROP genprop genprop geo NCBI Gene Expression Omnibus https://www.ncbi.nlm.nih.gov/geo/ The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval. ^G(PL|SM|SE|DS)\d+$ GDS1234 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1 False GEO GEO GEO 1147 geo geo geo -geogeo Geographical Entity Ontology https://github.com/ufbmi/geographical-entity-ontology/wiki "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in ""The US declared war on Germany"" vs. the US in ""The plane entered US airspace""." ^\d{9}$ 000000021 hoganwr@gmail.com http://purl.obolibrary.org/obo/GEO_$1 False GEO GEO geogeo GEO geo GEO +geogeo Geographical Entity Ontology https://github.com/ufbmi/geographical-entity-ontology/wiki "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in ""The US declared war on Germany"" vs. the US in ""The plane entered US airspace""." ^\d{9}$ 000000021 hoganwr@gmail.com http://purl.obolibrary.org/obo/GEO_$1 False GEO GEO geogeo geo geo GEO geonames GeoNames https://www.geonames.org The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. ^\d+$ 3532759 https://www.geonames.org/$1 Geomames|Geonamaes False geonames.feature GeoNames Feature Code https://www.geonames.org/export/codes.html All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. ADM1 https://www.geonames.org/recent-changes/featurecode/$1/ False gexo Gene Expression Ontology http://www.semantic-systems-biology.org/apo Gene Expression Ontology vladimir.n.mironov@gmail.com https://www.bio.ntnu.no/ontology/GeXO/gexo.owl https://www.bio.ntnu.no/ontology/GeXO/gexo.obo False GEXO GEXO gexo @@ -570,9 +570,9 @@ gmd.gcms Golm Metabolome Database GC-MS spectra http://gmd.mpimp-golm.mpg.de/ Go gmd.profile Golm Metabolome Database Profile http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 10b38aaf-b977-4950-85b8-f4775f66658d http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 False GMD.PROFILE gmd.profile gmd.profile gmd.ref Golm Metabolome Database Reference Substance http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 8cf84adb-b4db-4807-ac98-0004247c35df http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 False GMD.REF gmd.ref gmd.ref gmelin Gmelins Handbuch der anorganischen Chemie https://link.springer.com/bookseries/562 The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. ^[1-9][0-9]{3,6}$ 1466 False 1004 P1578 -gno Glycan Naming and Subsumption Ontology https://gnome.glyomics.org/ An ontology for glycans based on GlyTouCan, but organized by subsumption. ^\d{8}$ 10004892 nje5@georgetown.edu http://purl.obolibrary.org/obo/GNO_$1 False GNO GNO GNO gno GNO +gno Glycan Naming and Subsumption Ontology https://gnome.glyomics.org/ An ontology for glycans based on GlyTouCan, but organized by subsumption. ^\d{8}$ 10004892 nje5@georgetown.edu http://purl.obolibrary.org/obo/GNO_$1 False GNO GNO gno gno GNO gnpis GnpIS https://urgi.versailles.inra.fr/gnpis/ GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. ^[A-Za-z0-9]+$ AY109603 https://urgi.versailles.inra.fr/gnpis/#result/term=$1 False GNPIS gnpis gnpis -go Gene Ontology http://geneontology.org/ The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. ^\d{7}$ 0032571 suzia@stanford.edu http://amigo.geneontology.org/amigo/term/GO:$1 gobp|gobpid|gocc|goccid|gomf|gomfid False GO GO GO GO 1176 go go GO go GO go GO P686 +go Gene Ontology http://geneontology.org/ The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. ^\d{7}$ 0032571 suzia@stanford.edu http://amigo.geneontology.org/amigo/term/GO:$1 gobp|gobpid|gocc|goccid|gomf|gomfid False GO GO GO GO 1176 go go go go GO go GO P686 go.model Gene Ontology Causal Assembly Model http://www.geneontology.org/gocam GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform. 5fce9b7300001250 http://noctua.geneontology.org/editor/graph/gomodel:$1 False go.ref Gene Ontology Database references http://www.geneontology.org/cgi-bin/references.cgi "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of ""GO content"" meetings at which substantial changes in the ontologies are discussed and made." ^\d{7}$ 0000041 https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md False GO_REF go_ref go.ref go.resource Gene Ontology Registry http://geneontology.org/ A database-specific registry supporting curation in the Gene Ontology CHEBI https://bioregistry.io/metaregistry/go/$1 False @@ -608,7 +608,7 @@ grin.taxonomy Germplasm Resources Information Network http://www.ars-grin.gov/cg gro Gene Regulation Ontology True GRO GRO grsdb G-Rich Sequences Database http://bioinformatics.ramapo.edu/GRSDB2/ GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank. ^\d+$ 10142 http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1 False GRSDB grsdb grsdb grsdb gsfa General Standard for Food Additives Online Database http://www.fao.org/gsfaonline "The ""Codex General Standard for Food Additives"" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database." ^\d+$ 174 http://www.fao.org/gsfaonline/additives/details.html?id=$1 FAO/WHO_standards False -gsso Gender, Sex, and Sexual Orientation Ontology https://gsso.research.cchmc.org/ The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. ^\d{6}$ 002368 kronkcj@mail.uc.edu http://purl.obolibrary.org/obo/GSSO_$1 False GSSO GSSO gsso GSSO gsso GSSO +gsso Gender, Sex, and Sexual Orientation Ontology https://gsso.research.cchmc.org/ The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology. ^\d{6}$ 002368 kronkcj@mail.uc.edu http://purl.obolibrary.org/obo/GSSO_$1 False GSSO GSSO gsso gsso gsso GSSO gtex Genotype-Tissue Expression https://www.gtexportal.org The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. ^\w.+$ BRIP1 https://www.gtexportal.org/home/gene/$1 False GTEX gtex gtex gtr Genetic Testing Registry https://www.ncbi.nlm.nih.gov/gtr/ The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease AN0097748 https://www.ncbi.nlm.nih.gov/gtr/conditions/$1 medgen.gtr False gudmap Genitourinary Development Molecular Anatomy Project http://www.gudmap.org/ The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract. ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ Q-2958 https://gudmap.org/id/$1 False GUDMAP gudmap gudmap @@ -617,10 +617,10 @@ gwascentral.phenotype GWAS Central Phenotype https://www.gwascentral.org/phenoty gwascentral.study GWAS Central Study https://www.gwascentral.org/studies GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study. ^HGVST\d+$ HGVST1828 https://www.gwascentral.org/study/$1 False GWASCENTRAL.STUDY gwascentral.study gwascentral.study gxa.expt GXA Expt https://www.ebi.ac.uk/gxa/ The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments. ^[AEP]-\w{4}-\d+$ E-MTAB-2037 https://www.ebi.ac.uk/gxa/experiments/$1 False GXA.EXPT gxa.expt gxa.expt gxa.gene GXA Gene https://www.ebi.ac.uk/gxa/ The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes. ^\w+$ AT4G01080 https://www.ebi.ac.uk/gxa/genes/$1 False GXA.GENE gxa.gene gxa.gene -habronattus Habronattus courtship http://www.mesquiteproject.org/ontology/Habronattus/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/HABRONATTUS_$1 True HABRONATTUS HABRONATTUS +habronattus Habronattus courtship http://www.mesquiteproject.org/ontology/Habronattus/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/HABRONATTUS_$1 True HABRONATTUS habronattus hamap High-quality Automated and Manual Annotation of microbial Proteomes https://hamap.expasy.org/ HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. ^MF_\d+$ MF_01400 https://hamap.expasy.org/unirule/$1 False HAMAP 2766 hamap hamap hamap HAMAP -hancestro Human Ancestry Ontology https://github.com/EBISPOT/ancestro Human ancestry ontology for the NHGRI GWAS Catalog ^\d{4}$ 0290 danielle.welter@uni.lu http://purl.obolibrary.org/obo/HANCESTRO_$1 False HANCESTRO HANCESTRO HANCESTRO hancestro HANCESTRO -hao Hymenoptera Anatomy Ontology http://hymao.org A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) ^\d{7}$ 0000187 diapriid@gmail.com http://purl.obolibrary.org/obo/HAO_$1 False HAO HAO HAO HAO hao HAO +hancestro Human Ancestry Ontology https://github.com/EBISPOT/ancestro Human ancestry ontology for the NHGRI GWAS Catalog ^\d{4}$ 0290 danielle.welter@uni.lu http://purl.obolibrary.org/obo/HANCESTRO_$1 False HANCESTRO HANCESTRO hancestro hancestro HANCESTRO +hao Hymenoptera Anatomy Ontology http://hymao.org A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) ^\d{7}$ 0000187 diapriid@gmail.com http://purl.obolibrary.org/obo/HAO_$1 False HAO HAO HAO hao hao HAO hba Human Brain Atlas https://human.brain-map.org A controlled vocabulary to support the study of transcription in the human brain ^\d+$ 4005 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo False hcao Human Cell Atlas Ontology https://www.humancellatlas.org Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. False hcao hcpcs Healthcare Common Procedure Coding System https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. G8944 False HCPCS HCPCS @@ -640,26 +640,26 @@ hmdb Human Metabolome Database http://www.hmdb.ca/ The Human Metabolome Database hms.lincs.compound HMS LINCS Compound https://lincs.hms.harvard.edu/db/sm/ Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols. 10001-101 https://lincs.hms.harvard.edu/db/sm/$1 HMS-LINCS|hmsl_id False hog Homologous Organ Groups https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc. ^\d{7}$ 0000255 ftp://ftp.bgee.org/general/ontologies/HOG.obo False hogenom Database of Complete Genome Homologous Genes Families http://pbil.univ-lyon1.fr/databases/hogenom/ HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier. ^\w+$ HBG284870 http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1 False HOGENOM hogenom hogenom hogenom HOGENOM -hom Homology Ontology https://github.com/BgeeDB/homology-ontology This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. ^\d{7}$ 0000049 bgee@sib.swiss http://purl.obolibrary.org/obo/HOM_$1 False HOM HOM HOM HOM hom HOM +hom Homology Ontology https://github.com/BgeeDB/homology-ontology This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology. ^\d{7}$ 0000049 bgee@sib.swiss http://purl.obolibrary.org/obo/HOM_$1 False HOM HOM HOM hom hom HOM homd.seq HOMD Sequence Metainformation http://www.homd.org/index.php The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information. ^SEQF\d+$ SEQF1003 http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1 False HOMD.SEQ homd.seq homd.seq homd.seq homd.taxon HOMD Taxonomy http://www.homd.org/index.php The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information. ^\d+$ 811 www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1 False HOMD.TAXON homd.taxon homd.taxon homd.taxon homologene HomoloGene https://www.ncbi.nlm.nih.gov/homologene/ HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. ^\d+$ 1000 https://www.ncbi.nlm.nih.gov/homologene/$1 False HOMOLOGENE homologene homologene homologene P593 horizon_discovery Horizon Discovery cell line collection https://horizondiscovery.com/ Cell line collections HD+118-001 https://horizondiscovery.com/en/search?searchterm=$1 False Horizon_Discovery hovergen Homologous Vertebrate Genes Database https://pbil.univ-lyon1.fr/databases/hovergen.php HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. ^HBG\d+$ HBG004341 http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN False HOVERGEN hovergen hovergen hovergen -hp Human Phenotype Ontology http://www.human-phenotype-ontology.org/ The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. ^\d{7}$ 0011140 dr.sebastian.koehler@gmail.com https://hpo.jax.org/app/browse/term/HP:$1 http://purl.obolibrary.org/obo/hp.obo hpo False HP_O HPO HP_O hp hp HP hp HP P3841 +hp Human Phenotype Ontology http://www.human-phenotype-ontology.org/ The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. ^\d{7}$ 0011140 dr.sebastian.koehler@gmail.com https://hpo.jax.org/app/browse/term/HP:$1 http://purl.obolibrary.org/obo/hp.obo hpo False HP_O HPO HP_O hp hp hp hp HP P3841 hpa Human Protein Atlas tissue profile information http://www.proteinatlas.org/ The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers. ^ENSG\d{11}$ ENSG00000026508 http://www.proteinatlas.org/$1 False HPA hpa hpa hpa HPA hpath Histopathology Ontology https://github.com/Novartis/hpath An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. ^\d+$ 2000191 MC False hpath hpm.peptide Human Proteome Map Peptide http://www.humanproteomemap.org/index.php The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra. ^\d+$ 9606117 http://www.humanproteomemap.org/spectrum.php?pep_id=$1 False HPM.PEPTIDE hpm.peptide hpm.peptide hpm.protein Human Proteome Map Protein http://www.humanproteomemap.org/index.php The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins. ^\d+$ 1968 http://www.humanproteomemap.org/protein.php?hpm_id=$1 False HPM.PROTEIN hpm.protein hpm.protein hprd Human Protein Reference Database http://www.hprd.org/ The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. ^\d+$ 00001 http://www.hprd.org/protein/$1 False HPRD hprd hprd hprd hpscreg Human Pluripotent Stem Cell Registry https://hpscreg.eu/ hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines). ^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$ BCRTi001-A https://hpscreg.eu/cell-line/$1 False hPSCreg hpscreg hpscreg -hsapdv Human Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv Life cycle stages for Human ^\d{7}$ 0000194 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/HSAPDV_$1 HsapDv False HSAPDV HSAPDV HSAPDV HsapDv hsapdv HSAPDV +hsapdv Human Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv Life cycle stages for Human ^\d{7}$ 0000194 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/HSAPDV_$1 HsapDv False HSAPDV HSAPDV HSAPDV hsapdv hsapdv HSAPDV hsdb Hazardous Substances Data Bank https://pubchem.ncbi.nlm.nih.gov/source/hsdb The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. ^\d+$ 5621 https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1 False P2062 -hso Health Surveillance Ontology https://w3id.org/hso "The health Surveillance Ontology (HSO) focuses on ""surveillance system level data"", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance." ^\d{7}$ 0000062 fernanda.dorea@sva.se http://purl.obolibrary.org/obo/HSO_$1 False HSO HSO HSO hso HSO +hso Health Surveillance Ontology https://w3id.org/hso "The health Surveillance Ontology (HSO) focuses on ""surveillance system level data"", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance." ^\d{7}$ 0000062 fernanda.dorea@sva.se http://purl.obolibrary.org/obo/HSO_$1 False HSO HSO hso hso HSO hssp Database of homology-derived secondary structure of proteins http://swift.cmbi.kun.nl/swift/hssp/ HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. ^\w{4}$ 102l ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2 False HSSP hssp hssp hssp -htn Hypertension Ontology https://github.com/aellenhicks/htn_owl An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines ^\d{8}$ 00000014 aellenhicks@gmail.com http://purl.obolibrary.org/obo/HTN_$1 False HTN HTN HTN htn HTN +htn Hypertension Ontology https://github.com/aellenhicks/htn_owl An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines ^\d{8}$ 00000014 aellenhicks@gmail.com http://purl.obolibrary.org/obo/HTN_$1 False HTN HTN htn htn HTN huge Human Unidentified Gene-Encoded http://www.kazusa.or.jp/huge/ The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. ^KIAA\d{4}$ KIAA0001 https://www.kazusa.or.jp/huge/gfpage/$1 False HUGE huge huge huge HUGE -iao Information Artifact Ontology https://github.com/information-artifact-ontology/IAO/ An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. ^\d{7}$ 0000030 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/IAO_$1 False IAO IAO IAO iao iao IAO iao IAO +iao Information Artifact Ontology https://github.com/information-artifact-ontology/IAO/ An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch. ^\d{7}$ 0000030 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/IAO_$1 False IAO IAO IAO iao iao iao iao IAO icd10 International Classification of Diseases, 10th Revision https://icd.who.int/browse10 The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes. ^[A-Z]\d+(\.[-\d+])?$ C34 http://apps.who.int/classifications/icd10/browse/2010/en#/$1 ICD|ICD-10|ICD10 False ICD10 ICD ICD10 2611 icd icd icd P494 icd10cm International Classification of Diseases, 10th Revision, Clinical Modification https://www.icd10data.com/ICD10CM ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States. F4521 https://icd.codes/icd10cm/$1 ICD10CM False ICD10CM ICD10CM P4229 icd10pcs International Classification of Diseases, 10th Revision, Procedure Coding System https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis. @@ -672,21 +672,21 @@ icdc Integrated Canine Data Commons https://caninecommons.cancer.gov/#/ The Inte icdo International Classification of Diseases for Oncology https://www.who.int/classifications/icd/adaptations/oncology/en/ The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases ^[8-9]\d{3}(/[0-3])?$ 9861/3 http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1 ICD-O|ICDO False ICDO icdo P563 iceberg.element ICEberg element http://db-mml.sjtu.edu.cn/ICEberg/ ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements. ^\d+$ 100 http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1 False ICEBERG.ELEMENT iceberg.element iceberg.element iceberg.family ICEberg family http://db-mml.sjtu.edu.cn/ICEberg/ ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families. ^\d+$ 1 http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1 False ICEBERG.FAMILY iceberg.family iceberg.family -iceo Integrative and Conjugative Element Ontology https://github.com/ontoice/ICEO A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. ^\d{7}(_\d)?$ 0000712_1 liumeng94@sjtu.edu.cn http://purl.obolibrary.org/obo/ICEO_$1 False ICEO ICEO ICEO iceo ICEO +iceo Integrative and Conjugative Element Ontology https://github.com/ontoice/ICEO A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. ^\d{7}(_\d)?$ 0000712_1 liumeng94@sjtu.edu.cn http://purl.obolibrary.org/obo/ICEO_$1 False ICEO ICEO iceo iceo ICEO icepo Ion Channel Electrophysiology Ontology https://download.nextprot.org/pub/current_release/controlled_vocabularies/ The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. ^\d{7}$ 0000002 https://download.nextprot.org/pub/current_release/controlled_vocabularies/icepo.obo False iclc Interlab Cell Line Collection http://www.iclc.it Cell line collections ATL98012 http://www.iclc.it/details/det_list.php?line_id=$1 False ICLC -ico Informed Consent Ontology https://github.com/ICO-ontology/ICO The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. ^\d{7}$ 0000066 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/ICO_$1 False ICO ICO ICO ICO ico ICO +ico Informed Consent Ontology https://github.com/ICO-ontology/ICO The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. ^\d{7}$ 0000066 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/ICO_$1 False ICO ICO ICO ico ico ICO ideal Intrinsically Disordered proteins with Extensive Annotations and Literature https://www.ideal-db.org IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. ^IID\d+$ IID00001 http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1 False IDEAL ideal ideal IDEAL -ido Infectious Disease Ontology http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. ^[0-9]+$ 0000504 Lindsay.Cowell@utsouthwestern.edu https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 False IDO IDO IDO ido ido IDO ido IDO +ido Infectious Disease Ontology http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases. ^[0-9]+$ 0000504 Lindsay.Cowell@utsouthwestern.edu https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1 False IDO IDO IDO ido ido ido ido IDO idocovid19 The COVID-19 Infectious Disease Ontology https://github.com/infectious-disease-ontology-extensions/ido-covid-19 The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease. ^\d{7}$ 0001191 johnbeverley2021@u.northwestern.edu False IDO-COVID-19 IDO-COVID-19 idocovid19 idoden Dengue Fever Ontology https://bioportal.bioontology.org/ontologies/IDODEN An ontology for dengue fever. ^\d{7}$ 0003463 False IDODEN IDODEN -idomal Malaria Ontology https://www.vectorbase.org/ontology-browser An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. ^\d{7}$ 0002350 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/IDOMAL_$1 http://purl.obolibrary.org/obo/idomal.obo True IDOMAL IDOMAL IDOMAL IDOMAL idomal IDOMAL +idomal Malaria Ontology https://www.vectorbase.org/ontology-browser An application ontology to cover all aspects of malaria as well as the intervention attempts to control it. ^\d{7}$ 0002350 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/IDOMAL_$1 http://purl.obolibrary.org/obo/idomal.obo True IDOMAL IDOMAL IDOMAL idomal idomal IDOMAL idoo Identifiers.org Ontology http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology Identifiers.org Ontology ^[0-9a-zA-Z]+$ DataCollection http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1 False idoo idoo idot Identifiers.org Terms http://biomodels.net/vocab/idot.rdf Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets. ^[A-Za-z]+$ identifierPattern https://biomodels.net/vocab/idot.rdf#$1 False idot idot idot idpo Intrinsically Disordered Proteins Ontology https://www.disprot.org/ontology IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR. ^\d{5}$ 00056 f.quaglia@ibiom.cnr.it https://www.disprot.org/idpo/IDPO:$1 False idr Image Data Resource https://idr.openmicroscopy.org "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image"" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools." ^[0-9]{4}$ 0001 https://idr.openmicroscopy.org/search/?query=Name:idr$1 False idr iedb Immune Epitope Database https://www.lji.org/ The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes. ^[0-9]+$ 1038233 https://www.iedb.org/reference/$1 False iedb -iev Event (INOH pathway ontology) http://www.inoh.org ^\d{7}$ 0000000 http://purl.obolibrary.org/obo/IEV_$1 True IEV IEV iev +iev Event (INOH pathway ontology) http://www.inoh.org ^\d{7}$ 0000000 http://purl.obolibrary.org/obo/IEV_$1 True IEV iev iev igrhcellid Integrated Genomic Resources of human Cell Lines for Identification http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi Cell line databases/resources ACHN http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1 False IGRhCellID igsn International Geo Sample Number http://www.geosamples.org/ IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents. ^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$ AU124 http://igsn.org/$1 False igsn igsn igsr International Genome Sample Resource https://www.internationalgenome.org/ The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project. NA06985 https://www.internationalgenome.org/data-portal/sample/$1 False IGSR @@ -699,13 +699,13 @@ img.gene Integrated Microbial Genomes Gene http://img.jgi.doe.gov/ The integrate img.taxon Integrated Microbial Genomes Taxon http://img.jgi.doe.gov/ The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information. ^\d+$ 648028003 http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1 False IMG.TAXON img.taxon img.taxon img.taxon imgt.hla IMGT/HLA human major histocompatibility complex sequence database https://www.ebi.ac.uk/imgt/hla/allele.html IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature. ^[A-Z0-9*:]+$ A*01:01:01:01 https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1 IPD-IMGT/HLA False IMGT.HLA IPD-IMGT/HLA 2773 imgt.hla imgt.hla imgthla imgt.ligm ImMunoGeneTics database covering immunoglobulins and T-cell receptors http://www.imgt.org/ IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates. ^M\d+$ M94112 http://www.imgt.org/ligmdb/view?id=$1 False IMGT.LIGM imgt.ligm imgt.ligm imgt.ligm -imr Molecule role (INOH Protein name/family name ontology) http://www.inoh.org ^\d{7}$ 0000001 curator@inoh.org http://purl.obolibrary.org/obo/IMR_$1 True IMR IMR imr +imr Molecule role (INOH Protein name/family name ontology) http://www.inoh.org ^\d{7}$ 0000001 curator@inoh.org http://purl.obolibrary.org/obo/IMR_$1 True IMR imr imr inaturalist.taxon iNaturalist Taxonomy https://www.inaturalist.org/taxa Identifier for a species in iNaturalist ^[1-9]\d{0,6}$ 21723 https://www.inaturalist.org/taxa/$1 False P3151 inchi InChI http://www.chemspider.com/ The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier. ^InChI\=1S?\/[A-Za-z0-9\.]+(\+[0-9]+)?(\/[cnpqbtmsih][A-Za-z0-9\-\+\(\)\,\/\?\;\.]+)*$ InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 http://www.chemspider.com/$1 False INCHI inchi inchi P234 inchikey InChIKey http://www.chemspider.com/ The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI. ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])$ RYYVLZVUVIJVGH-UHFFFAOYSA-N http://www.chemspider.com/inchikey=$1 False INCHIKEY inchikey inchikey P235 inhand The International Harmonization of Nomenclature and Diagnostic criteria https://www.goreni.org/gr3_nomenclature.php The standard reference for nomenclature and diagnostic criteria in toxicologic pathology. False inn International Nonproprietary Names https://www.who.int/teams/health-product-and-policy-standards/inn Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. fluticasone https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1 INN_ID False P2275 -ino Interaction Network Ontology https://github.com/INO-ontology/ino he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. ^\d{7}$ 0000003 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/INO_$1 False INO INO INO ino INO +ino Interaction Network Ontology https://github.com/INO-ontology/ino he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles. ^\d{7}$ 0000003 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/INO_$1 False INO INO ino ino INO insdc Nucleotide Sequence Database https://www.ncbi.nlm.nih.gov/Genbank/ The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ X58356 https://www.ncbi.nlm.nih.gov/nuccore/$1 False INSDC insdc insdc insdc insdc.cds INSDC CDS http://getentry.ddbj.nig.ac.jp The coding sequence or protein identifiers as maintained in INSDC. ^([A-Z]\d{5}|[A-Z]{2}\d{6}|[A-Z]{4}\d{8}|[A-J][A-Z]{2}\d{5})(\.\d+)?$ AAA35559 http://getentry.ddbj.nig.ac.jp/getentry/dad/$1 False INSDC.CDS insdc.cds insdc.cds ncbiprotein insdc.gca Genome assembly database https://www.ebi.ac.uk/ena/browse/genome-assembly-database The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage. ^GC[AF]_[0-9]{9}\.[0-9]+$ GCA_000155495.1 https://www.ebi.ac.uk/ena/data/view/$1 False INSDC.GCA insdc.gca insdc.gca @@ -714,7 +714,7 @@ insdc.sra Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra The Sequence Re intact IntAct protein interaction database https://www.ebi.ac.uk/intact/ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. ^EBI\-[0-9]+$ EBI-2307691 https://www.ebi.ac.uk/intact/interaction/$1 False INTACT intact intact intact IntAct intact.molecule IntAct Molecule https://www.ebi.ac.uk/intact/ IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules. ^EBI\-[0-9]+$ EBI-366083 https://www.ebi.ac.uk/intact/molecule/$1 False INTACT.MOLECULE intact.molecule intact.molecule interlex InterLex https://www.fdilab.org InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. ^[0-9]+$ 0101963 https://scicrunch.org/scicrunch/interlex/view/ilx_$1 ILX False ilx -interpro InterPro http://www.ebi.ac.uk/interpro/index.html InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. ^IPR\d{6}$ IPR016380 interhelp@ebi.ac.uk https://www.ebi.ac.uk/interpro/entry/$1 IP|IPR|InterPro False IPR 1133 interpro interpro IPR interpro InterPro P2926 +interpro InterPro http://www.ebi.ac.uk/interpro/index.html InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. ^IPR\d{6}$ IPR016380 interhelp@ebi.ac.uk https://www.ebi.ac.uk/interpro/entry/$1 IP|IPR|InterPro False IPR 1133 interpro interpro ipr interpro InterPro P2926 ird.segment IRD Segment Sequence http://www.fludb.org/ Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s). ^\w+(\_)?\d+(\.\d+)?$ CY077097 http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1 False IRD.SEGMENT ird.segment ird.segment ird.segment irefweb iRefWeb http://wodaklab.org/iRefWeb/ iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived. ^\d+$ 617102 http://wodaklab.org/iRefWeb/interaction/show/$1 False IREFWEB irefweb irefweb irefweb iro Insect Resistance Ontology ^\d{7}$ 0000008 https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1 True @@ -769,10 +769,10 @@ knapsack KNApSAcK http://www.knapsackfamily.com/KNApSAcK/ "KNApSAcK provides inf taxonomic class with which they are associated." ^C\d{8}$ C00000001 http://www.knapsackfamily.com/knapsack_core/information.php?word=$1 False KNAPSACK knapsack knapsack P2064 kupo Kidney and Urinary Pathway Ontology http://www.kupkb.org/ ^\d{7}$ 0001009 True kyinno KYinno cell lines https://www.kyinno.com/ Cell line collections KC-0979 https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf False KYinno -labo clinical LABoratory Ontology https://github.com/OpenLHS/LABO LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. ^\d{7}$ 0000124 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/LABO_$1 False LABO LABO LABO labo LABO +labo clinical LABoratory Ontology https://github.com/OpenLHS/LABO LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. ^\d{7}$ 0000124 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/LABO_$1 False LABO LABO labo labo LABO lbo Livestock Breed Ontology http://bioportal.bioontology.org/ontologies/LBO A vocabulary for cattle, chicken, horse, pig, and sheep breeds. ^\d{7}$ 0000487 caripark@iastate.edu https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo False LBO LBO LBO lbo lei Global LEI Index https://www.gleif.org/ Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ HWUPKR0MPOU8FGXBT394 https://www.gleif.org/lei/$1 False lei lei -lepao Lepidoptera Anatomy Ontology https://github.com/insect-morphology/lepao The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. ^\d{7}$ 0000005 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/LEPAO_$1 False LEPAO LEPAO LEPAO lepao +lepao Lepidoptera Anatomy Ontology https://github.com/insect-morphology/lepao The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. ^\d{7}$ 0000005 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/LEPAO_$1 False LEPAO LEPAO lepao lepao lgai.cede LG Chemical Entity Detection Dataset (LGCEDe) https://www.lgresearch.ai LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR). ^LGCEDe-S-\d{9}$ LGCEDe-S-000002244 https://s3.us-east-2.amazonaws.com/lg.cede/$1 False lgai.cede lgic Ligand-Gated Ion Channel database https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available. ^\w+$ 5HT3Arano https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php True LGIC lgic lgic licebase LiceBase https://licebase.org Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects. ^[A-Za-z0-9\-\/]+$ EMLSAT00000003403 https://licebase.org/?q=$1 False LICEBASE licebase licebase @@ -788,9 +788,9 @@ lincs.smallmolecule LINCS Small Molecule http://lincsportal.ccs.miami.edu/SmallM linguist Linguist https://github.com/github/linguist Registry of programming languages for the Linguist program for detecting and highlighting programming languages. ^[a-zA-Z0-9 +#'*]+$ Python https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 False linguist lipidbank LipidBank http://lipidbank.jp/index.html LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. ^\w+\d+$ BBA0001 http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 False LIPIDBANK 2665 lipidbank lipidbank lipidbank lipidmaps LIPID MAPS http://www.lipidmaps.org The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ LMPR0102010012 http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 LIPID MAPS|LIPID_MAPS_class|LIPID_MAPS_instance False LIPIDMAPS 000564 2625 lipidmaps lipidmaps lipidmaps P2063 -lipro Lipid Ontology An ontology representation of the LIPIDMAPS nomenclature classification. bakerc@unb.ca http://purl.obolibrary.org/obo/LIPRO_$1 True LIPRO LIPRO LIPRO LIPRO +lipro Lipid Ontology An ontology representation of the LIPIDMAPS nomenclature classification. bakerc@unb.ca http://purl.obolibrary.org/obo/LIPRO_$1 True LIPRO LIPRO LIPRO lipro lncipedia LNCipedia https://lncipedia.org A comprehensive compendium of human long non-coding RNAs SNHG3 False -loggerhead Loggerhead nesting http://www.mesquiteproject.org/ontology/Loggerhead/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/LOGGERHEAD_$1 True LOGGERHEAD LOGGERHEAD +loggerhead Loggerhead nesting http://www.mesquiteproject.org/ontology/Loggerhead/index.html peteremidford@yahoo.com http://purl.obolibrary.org/obo/LOGGERHEAD_$1 True LOGGERHEAD loggerhead loinc Logical Observation Identifiers Names and Codes https://loinc.org/ The international standard for identifying health measurements, observations, and documents. LL379-9 https://loinc.org/$1 LNC False LOINC LOINC lonza Lonza https://knowledge.lonza.com Contains information about cells and data sheets related to transfection. ^\d+$ 968 https://knowledge.lonza.com/cell?id=$1 False Lonza lotus LOTUS Initiative for Open Natural Products Research https://lotus.naturalproducts.net LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry. ^LTS\d{7}$ LTS0004651 adriano.rutz@ik.me https://lotus.naturalproducts.net/compound/lotus_id/$1 False @@ -798,20 +798,20 @@ lpt Livestock Product Trait Ontology https://github.com/AnimalGenome/livestock-p lrg Locus Reference Genomic http://www.lrg-sequence.org/ A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI. ^LRG_\d+$ LRG_1 ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml False LRG lrg lrg lspci Laboratory of Systems Pharmacology Compound https://labsyspharm.github.io/lspci/ Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions) ^\d+$ 1 https://labsyspharm.github.io/lspci/$1 False lter Long Term Ecological Research Controlled Vocabulary https://vocab.lternet.edu/vocab/vocab/index.php Ecological terms ^\d+$ 182 https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1 False -ma Mouse adult gross anatomy https://github.com/obophenotype/mouse-anatomy-ontology A structured controlled vocabulary of the adult anatomy of the mouse (Mus) ^\d+$ 0002502 Terry.Hayamizu@jax.org http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 False MA MA MA ma ma MA ma MA ma +ma Mouse adult gross anatomy https://github.com/obophenotype/mouse-anatomy-ontology A structured controlled vocabulary of the adult anatomy of the mouse (Mus) ^\d+$ 0002502 Terry.Hayamizu@jax.org http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1 False MA MA MA ma ma ma ma MA ma macie Mechanism, Annotation and Classification in Enzymes https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved. ^M\d{4}$ M0001 https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1 False MACIE 2641 macie macie macie maizegdb.locus MaizeGDB Locus http://www.maizegdb.org/ MaizeGDB is the maize research community's central repository for genetics and genomics information. ^\d+$ 25011 http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1 MaizeGDB False MAIZEGDB.LOCUS maizegdb.locus maizegdb.locus maizegdb MaizeGDB -mamo Mathematical modeling ontology http://sourceforge.net/p/mamo-ontology/wiki/Home/ The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. ^\d{7}$ 0000026 http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 True MAMO MAMO MAMO mamo mamo MAMO mamo MAMO -mao Multiple alignment http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html julie@igbmc.u-strasbg.fr http://purl.obolibrary.org/obo/MAO_$1 True MAO MAO mao +mamo Mathematical modeling ontology http://sourceforge.net/p/mamo-ontology/wiki/Home/ The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. ^\d{7}$ 0000026 http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1 True MAMO MAMO MAMO mamo mamo mamo mamo MAMO +mao Multiple alignment http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html julie@igbmc.u-strasbg.fr http://purl.obolibrary.org/obo/MAO_$1 True MAO mao mao massbank MassBank http://www.massbank.jp MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da). ^[A-Z]{2}[A-Z0-9][0-9]{5}$ PB000166 http://www.massbank.jp/RecordDisplay?id=$1 False MASSBANK massbank massbank P6689 massive MassIVE https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. ^MSV\d+$ MSV000082131 https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1 False MASSIVE massive massive MassIVE -mat Minimal Anatomical Terminology ^\d{7}$ 0000000 j.bard@ed.ac.uk http://purl.obolibrary.org/obo/MAT_$1 True MAT MAT MAT MAT +mat Minimal Anatomical Terminology ^\d{7}$ 0000000 j.bard@ed.ac.uk http://purl.obolibrary.org/obo/MAT_$1 True MAT MAT MAT mat matrixdb MatrixDB http://matrixdb.univ-lyon1.fr/ MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides MULT_4_VAR1_bovine http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1 False matrixdb matrixdb.association MatrixDB Association http://matrixdb.univ-lyon1.fr/ MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$ P00747__P07355 http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association False MATRIXDB.ASSOCIATION matrixdb.association matrixdb.association -maxo Medical Action Ontology https://github.com/monarch-initiative/MAxO An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. ^\d{7}$ 0000008 Leigh.Carmody@jax.org http://purl.obolibrary.org/obo/MAXO_$1 False MAXO MAXO MAXO maxo MAXO +maxo Medical Action Ontology https://github.com/monarch-initiative/MAxO An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. ^\d{7}$ 0000008 Leigh.Carmody@jax.org http://purl.obolibrary.org/obo/MAXO_$1 False MAXO MAXO maxo maxo MAXO mba Mouse Brain Atlas https://mouse.brain-map.org A controlled vocabulary to support the study of transcription in the mouse brain ^\d+$ 688 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-mba.obo False mcc Cell Line Ontology [derivative] True MCCL -mco Microbial Conditions Ontology https://github.com/microbial-conditions-ontology/microbial-conditions-ontology Microbial Conditions Ontology is an ontology... ^\d+$ 0000858 citlalli.mejiaalmonte@gmail.com http://purl.obolibrary.org/obo/MCO_$1 False MCO MCO MCO mco MCO +mco Microbial Conditions Ontology https://github.com/microbial-conditions-ontology/microbial-conditions-ontology Microbial Conditions Ontology is an ontology... ^\d+$ 0000858 citlalli.mejiaalmonte@gmail.com http://purl.obolibrary.org/obo/MCO_$1 False MCO MCO mco mco MCO mdm Medical Data Models https://medical-data-models.org/ The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems. ^\d+$ 4776 https://medical-data-models.org/forms/$1 False MDM MDM MDM mdm mdm meddra Medical Dictionary for Regulatory Activities Terminology http://bioportal.bioontology.org/ontologies/MEDDRA The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT). ^\d+$ 10015919 http://purl.bioontology.org/ontology/MEDDRA/$1 MEDRA|MeDRA|MedDRA|Medical Dictionary for Regulatory Activities False MEDDRA MEDDRA MEDDRA meddra meddra P3201 medgen Human Medical Genetics https://www.ncbi.nlm.nih.gov/medgen/ MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder. ^[CN]*\d{4,7}$ 760050 https://www.ncbi.nlm.nih.gov/medgen/$1 False MedGen medgen medgen @@ -830,22 +830,22 @@ metanetx.compartment MetaNetX compartment https://www.metanetx.org/ MetaNetX/MNX metanetx.reaction MetaNetX reaction https://www.metanetx.org/ MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions. ^(MNXR\d+|EMPTY)$ MNXR101574 https://www.metanetx.org/equa_info/$1 False METANETX.REACTION metanetx.reaction metanetx.reaction metlin Metabolite and Tandem Mass Spectrometry Database http://masspec.scripps.edu/ The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry. ^\d{4}$ 1455 http://metlin.scripps.edu/metabo_info.php?molid=$1 False METLIN metlin metlin mex Metabolome Express https://www.metabolome-express.org/ A public place to process, interpret and share GC/MS metabolomics datasets. ^\d+$ 36 https://www.metabolome-express.org/datasetview.php?datasetid=$1 False MEX mex mex -mf Mental Functioning Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. ^\d{7}$ 0000091 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MF_$1 False MF MF MF MF mf MF -mfmo Mammalian Feeding Muscle Ontology https://github.com/rdruzinsky/feedontology The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. ^\d{7}$ 0000208 druzinsk@uic.edu http://purl.obolibrary.org/obo/MFMO_$1 False MFMO MFMO MFMO MFMO mfmo MFMO -mfo Medaka fish anatomy and development A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. Thorsten.Henrich@embl-heidelberg.de http://purl.obolibrary.org/obo/MFO_$1 True MFO MFO MFO MFO mfo -mfoem Emotion Ontology https://github.com/jannahastings/emotion-ontology An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. ^\d{6}$ 000204 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOEM_$1 False MFOEM MFOEM MFOEM MFOEM mfoem MFOEM -mfomd Mental Disease Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). ^\d{7}$ 0000046 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOMD_$1 False MFOMD MFOMD MFOMD MFOMD mfomd MFOMD +mf Mental Functioning Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning. ^\d{7}$ 0000091 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MF_$1 False MF MF MF mf mf MF +mfmo Mammalian Feeding Muscle Ontology https://github.com/rdruzinsky/feedontology The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors. ^\d{7}$ 0000208 druzinsk@uic.edu http://purl.obolibrary.org/obo/MFMO_$1 False MFMO MFMO MFMO mfmo mfmo MFMO +mfo Medaka fish anatomy and development A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes. Thorsten.Henrich@embl-heidelberg.de http://purl.obolibrary.org/obo/MFO_$1 True MFO MFO MFO mfo mfo +mfoem Emotion Ontology https://github.com/jannahastings/emotion-ontology An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings. ^\d{6}$ 000204 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOEM_$1 False MFOEM MFOEM MFOEM mfoem mfoem MFOEM +mfomd Mental Disease Ontology https://github.com/jannahastings/mental-functioning-ontology The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). ^\d{7}$ 0000046 janna.hastings@gmail.com http://purl.obolibrary.org/obo/MFOMD_$1 False MFOMD MFOMD MFOMD mfomd mfomd MFOMD mge Aclame http://aclame.ulb.ac.be/ ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. ^\d+$ 2 http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1 False mge mge mgi Mouse Genome Informatics http://www.informatics.jax.org/ The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. ^\d+$ 6017782 http://www.informatics.jax.org/accession/MGI:$1 MGD|MGI False MGI MGI 3274 mgi mgi mgi MGI P671 mgnify.analysis MGnify Analysis https://www.ebi.ac.uk/metagenomics/ Analyses of microbiome data within MGnify ^MGYA\d+$ MGYA00002270 https://www.ebi.ac.uk/metagenomics/analyses/$1 False mgnify.proj MGnify Project https://www.ebi.ac.uk/metagenomics MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis. ^[A-Z]+[0-9]+$ ERP004492 https://www.ebi.ac.uk/metagenomics/projects/$1 False mgnify.proj mgnify.proj mgnify.samp MGnify Sample https://www.ebi.ac.uk/metagenomics The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples. ^[A-Z]+[0-9]+$ SRS086444 https://www.ebi.ac.uk/metagenomics/samples/$1 False mgnify.samp mgnify.samp -mi Molecular Interactions Controlled Vocabulary https://github.com/HUPO-PSI/psi-mi-CV The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. ^\d{4}$ 0058 pporras@ebi.ac.uk https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 PSI-MI False MI PSIMI MI mi psimi MI mi MI psi.mi +mi Molecular Interactions Controlled Vocabulary https://github.com/HUPO-PSI/psi-mi-CV The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative. ^\d{4}$ 0058 pporras@ebi.ac.uk https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1 PSI-MI False MI PSIMI MI mi psimi mi mi MI psi.mi miaa Minimal Information About Anatomy ontology True miapa Minimum Anformation About a Phylogenetic Analysis Ontology http://www.evoio.org/wiki/MIAPA "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. -This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA." ^\d{7}$ 0000010 hilmar.lapp@duke.edu http://purl.obolibrary.org/obo/MIAPA_$1 False MIAPA MIAPA MIAPA MIAPA miapa MIAPA -micro Ontology of Prokaryotic Phenotypic and Metabolic Characters https://github.com/carrineblank/MicrO An ontology of prokaryotic phenotypic and metabolic characters ^\d{7}$ 0002999 carrine.blank@umontana.edu http://purl.obolibrary.org/obo/MICRO_$1 False MICRO MICRO MICRO micro MicrO +This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA." ^\d{7}$ 0000010 hilmar.lapp@duke.edu http://purl.obolibrary.org/obo/MIAPA_$1 False MIAPA MIAPA MIAPA miapa miapa MIAPA +micro Ontology of Prokaryotic Phenotypic and Metabolic Characters https://github.com/carrineblank/MicrO An ontology of prokaryotic phenotypic and metabolic characters ^\d{7}$ 0002999 carrine.blank@umontana.edu http://purl.obolibrary.org/obo/MICRO_$1 False MICRO MICRO micro micro MicrO microscope MicroScope http://www.genoscope.cns.fr/agc/microscope MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. ^\d+$ 5601141 http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1 False MICROSCOPE microscope microscope microsporidia MicrosporidiaDB http://microsporidiadb.org/micro/ MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ ECU03_0820i http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False MICROSPORIDIA microsporidia microsporidia microsporidia millipore Merck Millipore (EMD Millipore) https://www.merckmillipore.com/ Cell line collections SCC111 https://www.merckmillipore.com/catalogue/item/$1 False Millipore @@ -862,39 +862,39 @@ mirex mirEX http://comgen.pl/mirex/?page=home mirEX is a comprehensive platform miriam Identifiers.org namespace https://www.ebi.ac.uk Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. ^[a-z_\.]+$ pubmed https://registry.identifiers.org/registry/$1 identifiers.namespace False 1162 identifiers.namespace miriam.collection MIRIAM Registry collection https://www.ebi.ac.uk/miriam/ MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections. ^MIR:000\d{5}$ MIR:00000008 https://www.ebi.ac.uk/miriam/main/$1 True MIRIAM.COLLECTION miriam.collection miriam.collection miriam.resource MIRIAM Registry resource https://www.ebi.ac.uk/miriam/ MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases. ^MIR:001\d{5}$ MIR:00100005 https://www.ebi.ac.uk/miriam/main/resources/$1 False MIRIAM.RESOURCE miriam.resource miriam.resource miriam.resource -mirnao microRNA Ontology http://code.google.com/p/mirna-ontology/ An application ontology for use with miRNA databases. topalis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRNAO_$1 True MIRNAO MIRNAO MIRNAO MIRNAO miRNAO +mirnao microRNA Ontology http://code.google.com/p/mirna-ontology/ An application ontology for use with miRNA databases. topalis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRNAO_$1 True MIRNAO MIRNAO MIRNAO mirnao miRNAO mirnest miRNEST http://rhesus.amu.edu.pl/mirnest/copy/ miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species. ^MNEST\d+$ MNEST029358 http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1 False MIRNEST mirnest mirnest mirnest -miro Mosquito insecticide resistance https://github.com/VEuPathDB-ontology/MIRO Application ontology for entities related to insecticide resistance in mosquitos ^\d{8}$ 40000617 louis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRO_$1 http://purl.obolibrary.org/obo/miro.obo True MIRO MIRO MIRO MIRO miro MIRO +miro Mosquito insecticide resistance https://github.com/VEuPathDB-ontology/MIRO Application ontology for entities related to insecticide resistance in mosquitos ^\d{8}$ 40000617 louis@imbb.forth.gr http://purl.obolibrary.org/obo/MIRO_$1 http://purl.obolibrary.org/obo/miro.obo True MIRO MIRO MIRO miro miro MIRO mirtarbase miRTarBase http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. ^MIRT\d{6}$ MIRT000002 http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1 False MIRTARBASE mirtarbase mirtarbase mirte miRNA Target Prediction at EMBL http://www.russelllab.org/miRNAs/ This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs miR-1 False mlc MLCommons Association https://mlcommons.org/en/ MLCommons Association artifacts, including benchmark results, datasets, and saved models. ^[0-9a-zA-Z\.\-\_]+$ 0.7-123 https://www.mlcommons.org/mlc-id/$1 False mlc mmdb Molecular Modeling Database http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites. ^\d{1,5}$ 50885 http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1 False MMDB 2667 mmdb mmdb mmdb mmmp.biomaps Melanoma Molecular Map Project Biomaps http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma. ^\d+$ 37 http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1 mmmp:biomaps False MMMP:BIOMAPS mmmp:biomaps biomaps -mmo Measurement method ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 A representation of the variety of methods used to make clinical and phenotype measurements. ^\d{7}$ 0000574 jrsmith@mcw.edu http://purl.obolibrary.org/obo/MMO_$1 False MMO MMO MMO MMO mmo MMO +mmo Measurement method ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000 A representation of the variety of methods used to make clinical and phenotype measurements. ^\d{7}$ 0000574 jrsmith@mcw.edu http://purl.obolibrary.org/obo/MMO_$1 False MMO MMO MMO mmo mmo MMO mmp.cat MarCat https://mmp.sfb.uit.no/databases/marcat/ MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples. ^MMP\d+.\d+$ MMP743597.11 https://mmp.sfb.uit.no/databases/marcat/#/records/$1 False MMP.CAT mmp.cat mmp.cat mmp.db MarDB https://mmp.sfb.uit.no/databases/mardb/ MarDB includes all sequenced marine microbial genomes regardless of level of completeness. ^MMP\d+.\d+$ MMP02954345.1 https://mmp.sfb.uit.no/databases/mardb/#/records/$1 False MMP.DB mmp.db mmp.db mmp.fun MarFun https://mmp.sfb.uit.no/databases/marfun MarFun is manually curated database for marine fungi which is a part of the MAR databases. ^MMP\d+.\d+$ MMP3888430 https://mmp.sfb.uit.no/databases/marfun/#/records/$1 False mmp.fun mmp.ref MarRef https://mmp.sfb.uit.no/databases/marref/ MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. ^MMP\d+.\d+$ MMP3312982.2 https://mmp.sfb.uit.no/databases/marref/#/records/$1 False MMP.REF mmp.ref mmp.ref mmrrc Mutant Mouse Resource and Research Centers https://www.mmrrc.org The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections. ^\d+$ 70 http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1 False MMRRC MMRRC mmrrc mmrrc mmsl Multum MediSource Lexicon https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included. ^\d+$ 3355 MMSL_CODE False -mmusdv Mouse Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv Life cycle stages for Mus Musculus ^\d{7}$ 0000066 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/MMUSDV_$1 MmusDv False MMUSDV MMUSDV MMUSDV MmusDv mmusdv MMUSDV -mo Microarray experimental conditions http://mged.sourceforge.net/ontologies/MGEDontology.php The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. ^\w+$ ArrayGroup stoeckrt@pcbi.upenn.edu http://purl.obolibrary.org/obo/MO_$1 True MO MO MO mo mo MO +mmusdv Mouse Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv Life cycle stages for Mus Musculus ^\d{7}$ 0000066 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/MMUSDV_$1 MmusDv False MMUSDV MMUSDV MMUSDV mmusdv mmusdv MMUSDV +mo Microarray experimental conditions http://mged.sourceforge.net/ontologies/MGEDontology.php The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. ^\w+$ ArrayGroup stoeckrt@pcbi.upenn.edu http://purl.obolibrary.org/obo/MO_$1 True MO MO MO mo mo mo mobidb MobiDB http://mobidb.bio.unipd.it MobiDB is a database of protein disorder and mobility annotations. ^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$ P10636 https://mobidb.org/$1 False MOBIDB mobidb mobidb MobiDB uniprot -mod Protein modification http://www.psidev.info/MOD The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. ^\d{5}$ 01467 pierre-alain.binz@chuv.ch https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1 PSI-MOD False PSIMOD MOD PSIMOD mod mod MOD mod MOD psi.mod +mod Protein modification http://www.psidev.info/MOD The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications. ^\d{5}$ 01467 pierre-alain.binz@chuv.ch https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1 PSI-MOD False PSIMOD MOD PSIMOD mod mod mod mod MOD psi.mod modeldb ModelDB http://senselab.med.yale.edu/ModelDB/ ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment. ^\d+$ 45539 http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1 False MODELDB 2669 modeldb modeldb modeldb molbase Molbase http://www.molbase.com/ Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier. ^(\d{1,7}\-\d{2}\-\d)|([A-Za-z0-9\+\-\_]+)$ 128796-39-4 http://www.molbase.com/en/index.php?app=search&search_keyword=$1 False MOLBASE molbase molbase molbase.sheffield MolBase https://winter.group.shef.ac.uk/molbase/ An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students. ^\d+$ 1868 True molmedb MolMeDB http://www.upol.cz/en/ MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. ^[m,M]{2}[0-9]{5}[0-9]*$ MM00040 https://molmedb.upol.cz/mol/$1 False molmedb -mondo Monarch Disease Ontology https://monarch-initiative.github.io/mondo A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. ^\d{7}$ 0000001 nicole@tislab.org http://purl.obolibrary.org/obo/MONDO_$1 http://purl.obolibrary.org/obo/mondo.obo False MONDO MONDO MONDO MONDO mondo MONDO P5270 -mop Molecular Process Ontology https://github.com/rsc-ontologies/rxno MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. ^\d{7}$ 0000079 batchelorc@rsc.org http://purl.obolibrary.org/obo/MOP_$1 https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo False MOP MOP MOP MOP mop MOP +mondo Monarch Disease Ontology https://monarch-initiative.github.io/mondo A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. ^\d{7}$ 0000001 nicole@tislab.org http://purl.obolibrary.org/obo/MONDO_$1 http://purl.obolibrary.org/obo/mondo.obo False MONDO MONDO MONDO mondo mondo MONDO P5270 +mop Molecular Process Ontology https://github.com/rsc-ontologies/rxno MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation. ^\d{7}$ 0000079 batchelorc@rsc.org http://purl.obolibrary.org/obo/MOP_$1 https://raw.githubusercontent.com/rsc-ontologies/rxno/master/mop.obo False MOP MOP MOP mop mop MOP morpheus Morpheus model repository https://morpheus.gitlab.io/ "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software. " ^M[0-9]{4,}$ M0001 https://morpheus.gitlab.io/models/$1 False morpheus -mp Mammalian Phenotype Ontology http://www.informatics.jax.org/searches/MP_form.shtml The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. ^\d{7}$ 0005452 drsbello@gmail.com http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 False MP MP MP mp mp MP mp MP mp -mpath Mouse pathology ontology http://www.pathbase.net A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes ^\d+$ 728 pns12@hermes.cam.ac.uk http://purl.obolibrary.org/obo/MPATH_$1 https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo MPATH False MPATH MPATH MPATH MPATH mpath MPATH mpath +mp Mammalian Phenotype Ontology http://www.informatics.jax.org/searches/MP_form.shtml The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways. ^\d{7}$ 0005452 drsbello@gmail.com http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1 False MP MP MP mp mp mp mp MP mp +mpath Mouse pathology ontology http://www.pathbase.net A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes ^\d+$ 728 pns12@hermes.cam.ac.uk http://purl.obolibrary.org/obo/MPATH_$1 https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo MPATH False MPATH MPATH MPATH mpath mpath MPATH mpath mpid Microbial Protein Interaction Database http://www.jcvi.org/mpidb/about.php The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts. ^\d+$ 172 http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1 mpidb False MPID mpid mpid -mpio Minimum PDDI Information Ontology https://github.com/MPIO-Developers/MPIO An ontology of minimum information regarding potential drug-drug interaction information. ^\d{7}$ 0000004 mbrochhausen@uams.edu http://purl.obolibrary.org/obo/MPIO_$1 False MPIO MPIO MPIO MPIO mpio MPIO -mro MHC Restriction Ontology https://github.com/IEDB/MRO The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. ^\d{7}$ 0000634 bpeters@lji.org http://purl.obolibrary.org/obo/MRO_$1 False MRO MRO MRO MRO mro MRO -ms Mass spectrometry ontology http://www.psidev.info/groups/controlled-vocabularies The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. ^\d{7}$ 1000560 gerhard.mayer@rub.de https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 False MS MS MS ms ms MS ms MS +mpio Minimum PDDI Information Ontology https://github.com/MPIO-Developers/MPIO An ontology of minimum information regarding potential drug-drug interaction information. ^\d{7}$ 0000004 mbrochhausen@uams.edu http://purl.obolibrary.org/obo/MPIO_$1 False MPIO MPIO MPIO mpio mpio MPIO +mro MHC Restriction Ontology https://github.com/IEDB/MRO The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions. ^\d{7}$ 0000634 bpeters@lji.org http://purl.obolibrary.org/obo/MRO_$1 False MRO MRO MRO mro mro MRO +ms Mass spectrometry ontology http://www.psidev.info/groups/controlled-vocabularies The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. ^\d{7}$ 1000560 gerhard.mayer@rub.de https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1 False MS MS MS ms ms ms ms MS msigdb Molecular Signatures Database https://www.gsea-msigdb.org The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can ^M\d+$ M1 https://biopragmatics.github.io/providers/msigdb/$1 msig False msio Metabolomics Standards Initiative Ontology https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies. ^\d{7}$ 0000111 False msio multicellds MultiCellDS http://multicellds.org/MultiCellDB.php MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata. MCDS_S_0000000001 http://multicellds.org/MultiCellDB/$1 False @@ -916,7 +916,7 @@ napp Nucleic Acids Phylogenetic Profiling http://napp.u-psud.fr/ NAPP (Nucleic A narcis National Academic Research and Collaborations Information System http://www.narcis.nl NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. ^oai\:cwi\.nl\:\d+$ oai:cwi.nl:4725 http://www.narcis.nl/publication/RecordID/$1 False NARCIS narcis narcis nasc NASC code http://arabidopsis.info/ The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. ^(\w+)?\d+$ N1899 http://arabidopsis.info/StockInfo?NASC_id=$1 False NASC nasc nasc nasc nbn National Bibliography Number http://nbn-resolving.org/resolve_urn.htm The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier. ^urn\:nbn\:[A-Za-z_0-9]+\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$ urn:nbn:fi:tkk-004781 http://nbn-resolving.org/resolver?identifier=$1&verb=redirect False NBN nbn nbn -nbo Neuro Behavior Ontology https://github.com/obo-behavior/behavior-ontology/ An ontology of human and animal behaviours and behavioural phenotypes ^\d{7}$ 0000564 g.gkoutos@bham.ac.uk http://purl.obolibrary.org/obo/NBO_$1 https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo False NBO NBO NBO NBO nbo NBO +nbo Neuro Behavior Ontology https://github.com/obo-behavior/behavior-ontology/ An ontology of human and animal behaviours and behavioural phenotypes ^\d{7}$ 0000564 g.gkoutos@bham.ac.uk http://purl.obolibrary.org/obo/NBO_$1 https://github.com/obo-behavior/behavior-ontology/raw/master/nbo.obo False NBO NBO NBO nbo nbo NBO nbrc NITE Biological Resource Center http://www.nbrc.nite.go.jp/e/index.html NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information. ^\d+$ 00001234 http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1 False NBRC nbrc nbrc nbrc ncats.bioplanet National Center for Advancing Translation Sciences BioPlanet https://tripod.nih.gov/bioplanet/ The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays. ^\d+$ 3 ruili.huang@nih.gov https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1 False ncats.drug NCATS Drugs https://drugs.ncats.io/ "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including: @@ -931,10 +931,10 @@ ncbi.resource NCBI Registry https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ ncbibook NCBI Bookshelf https://www.ncbi.nlm.nih.gov/books The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. ^NBK\d+$ NBK331 https://www.ncbi.nlm.nih.gov/books/$1 False ncbigene Entrez Gene https://www.ncbi.nlm.nih.gov/gene Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. ^\d+$ 100010 https://www.ncbi.nlm.nih.gov/gene/$1 EGID|EntrezGene|NCBIGene|entrez|entrez gene/locuslink False NCBIGene 1027 ncbigene ncbigene ncbigene P351 ncbiprotein NCBI Protein https://www.ncbi.nlm.nih.gov/protein The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. ^(\w+\d+(\.\d+)?)|(NP_\d+)$ CAA71118.1 https://www.ncbi.nlm.nih.gov/protein/$1 False NCBIProtein ncbiprotein ncbiprotein ncbi.protein -ncbitaxon NCBI Taxonomy https://github.com/obophenotype/ncbitaxon The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. ^\d+$ 2170610 frederic.bastian@unil.ch https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 http://purl.obolibrary.org/obo/ncbitaxon.obo NCBITaxon|NCBI_Taxon_ID|NCBI_taxid|TAX|TaxonomyID|taxid|taxon|taxonomy|uniprot.taxonomy False NCBITAXON NCBITAXON TAXONOMY NCBITAXON NCBI_TaxID 1179 taxonomy taxonomy NCBITaxon ncbitaxon NCBITaxon uniprot.taxonomy P685 +ncbitaxon NCBI Taxonomy https://github.com/obophenotype/ncbitaxon The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. ^\d+$ 2170610 frederic.bastian@unil.ch https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1 http://purl.obolibrary.org/obo/ncbitaxon.obo NCBITaxon|NCBI_Taxon_ID|NCBI_taxid|TAX|TaxonomyID|taxid|taxon|taxonomy|uniprot.taxonomy False NCBITAXON NCBITAXON TAXONOMY NCBITAXON NCBI_TaxID 1179 taxonomy taxonomy ncbitaxon ncbitaxon NCBITaxon uniprot.taxonomy P685 ncim NCI Metathesaurus http://ncim.nci.nih.gov/ NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical. ^C\d+$ C0026339 http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1 False NCIM ncim ncim -ncit NCI Thesaurus https://github.com/NCI-Thesaurus/thesaurus-obo-edition NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. ^C\d+$ C138986 haendel@ohsu.edu http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 http://purl.obolibrary.org/obo/ncit.obo NCI|NCI2004_11_17|NCIT|NCIT_Thesaurus|NCITm|NCITt|NCI_Thesaurus|NCIt|ncithesaurus False NCIT NCIT NCIT NCIt ncit ncit NCIT ncit NCIT ncit P1748 -ncro Non-Coding RNA Ontology http://omnisearch.soc.southalabama.edu/w/index.php/Ontology An ontology for non-coding RNA, both of biological origin, and engineered. ^\d{7}$ 0002927 huang@southalabama.edu http://purl.obolibrary.org/obo/NCRO_$1 http://purl.obolibrary.org/obo/ncro.owl https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo False NCRO NCRO NCRO NCRO ncro NCRO +ncit NCI Thesaurus https://github.com/NCI-Thesaurus/thesaurus-obo-edition NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code. ^C\d+$ C138986 haendel@ohsu.edu http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1 http://purl.obolibrary.org/obo/ncit.obo NCI|NCI2004_11_17|NCIT|NCIT_Thesaurus|NCITm|NCITt|NCI_Thesaurus|NCIt|ncithesaurus False NCIT NCIT NCIT NCIt ncit ncit ncit ncit NCIT ncit P1748 +ncro Non-Coding RNA Ontology http://omnisearch.soc.southalabama.edu/w/index.php/Ontology An ontology for non-coding RNA, both of biological origin, and engineered. ^\d{7}$ 0002927 huang@southalabama.edu http://purl.obolibrary.org/obo/NCRO_$1 http://purl.obolibrary.org/obo/ncro.owl https://raw.githubusercontent.com/OmniSearch/ncro/master/src/ontology/ncro.obo False NCRO NCRO NCRO ncro ncro NCRO ndc National Drug Code http://www.accessdata.fda.gov/scripts/cder/ndc/ The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily. ^\d+\-\d+\-\d+$ 0002-1975-61 http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1 False NDC ndc ndc nddf National Drug Data File https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements. ^\d{6}$ 002678 False NDDF NDDF ndex Network Data Exchange https://www.ndexbio.org The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge. aa78a43f-9c4d-11eb-9e72-0ac135e8bacf https://www.ndexbio.org/viewer/networks/$1 False @@ -953,10 +953,10 @@ nextprot.family neXtProt family https://www.nextprot.org/ "NeXtProt is a compreh ngl NASA GeneLab https://genelab-data.ndc.nasa.gov/genelab/ NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA. ^GLDS-\d+$ GLDS-141 https://genelab-data.ndc.nasa.gov/genelab/accession/$1 False NGL ngl ngl nhcdr NINDS Human Cell and Data Repository https://stemcells.nindsgenetics.org Cell line collections ND50028 https://stemcells.nindsgenetics.org?line=$1 False NHCDR niaest NIA Mouse cDNA Project http://lgsun.grc.nia.nih.gov/cDNA/ A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones. ^\w\d{4}\w\d{2}(\-[35])?$ J0705A10 http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1 False NIAEST niaest niaest niaest -nif.cell NIF Cell http://neuinfo.org/ Neuronal cell types smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_CELL_$1 True NIFCELL NIF_CELL NIFCELL NIF_CELL nif -nif.dysfunction NIF Dysfunction http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 True NIF_DYSFUNCTION NIF_DYSFUNCTION nif +nif.cell NIF Cell http://neuinfo.org/ Neuronal cell types smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_CELL_$1 True NIFCELL NIF_CELL NIFCELL nif_cell nif +nif.dysfunction NIF Dysfunction http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1 True NIF_DYSFUNCTION nif_dysfunction nif nif.ext NIF Standard Ontology: External https://github.com/SciCrunch/NIF-Ontology "NIFEXT covers IRIs that were ""external"" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed." ^\d+$ 7123 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nifext_$1 NIFEXT False nif -nif.grossanatomy NIF Gross Anatomy http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 True NIF_GROSSANATOMY NIF_GROSSANATOMY nif +nif.grossanatomy NIF Gross Anatomy http://neuinfo.org/ smtifahim@gmail.com http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1 True NIF_GROSSANATOMY nif_grossanatomy nif nif.std NIF Standard Ontology https://github.com/SciCrunch/NIF-Ontology NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing. ^BAMSC\d+$ BAMSC981 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/$1 NIFSTD False NIFSTD NIFSTD nif nihreporter.project NIH RePORTER https://reporter.nih.gov/ RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding. ^\d+$ 10343835 https://reporter.nih.gov/project-details/$1 False nist NIST Chemistry WebBook https://webbook.nist.gov/chemistry/ The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species. NIST|NIST Chemistry WebBook False @@ -975,10 +975,10 @@ nlx.qual NIF Standard Ontology: Qualities https://github.com/SciCrunch/NIF-Ontol nlx.res NIF Standard Ontology: Digital Resources https://github.com/SciCrunch/NIF-Ontology NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites ^\d+$ 090924 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_res_$1 NLXRES False nif nlx.sub NIF Standard Ontology: Subcellular Entities https://github.com/SciCrunch/NIF-Ontology NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO). ^\d+$ 090803 tgbugs@gmail.com http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1 NLXSUB|nif_subcellular False nif nmdc National Microbiome Data Collaborative https://microbiomedata.org/ An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem. ^[\w\-.]{3,}$ y3ax-8bq3-60 donny@polyneme.xyz https://drs.microbiomedata.org/objects/$1 False nmdc -nmr NMR-instrument specific component of metabolomics investigations http://msi-ontology.sourceforge.net/ nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. ^\d+$ 1000003 schober@imbi.uni-freiburg.de https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1 https://nmrml.org/cv/stable/nmrCV.owl nmrcv True NMR NMR NMR nmr nmr NMR nmrcv nmr +nmr NMR-instrument specific component of metabolomics investigations http://msi-ontology.sourceforge.net/ nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi. ^\d+$ 1000003 schober@imbi.uni-freiburg.de https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1 https://nmrml.org/cv/stable/nmrCV.owl nmrcv True NMR NMR NMR nmr nmr nmr nmrcv nmr nmrshiftdb2 NMR Shift Database https://nmrshiftdb.nmr.uni-koeln.de NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. ^[0-9]+$ 234 https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1 False nmrshiftdb2 noaa NOAA Fisheries Species Directory https://www.fisheries.noaa.gov/species-directory Identifier for a species on the noaa fisheries website ^[a-z]+(\-[a-z]+)*$ long-finned-pilot-whale https://www.fisheries.noaa.gov/species/$1 False P6049 -nomen A nomenclatural ontology for biological names https://github.com/SpeciesFileGroup/nomen NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. ^\d{7}$ 0000295 diapriid@gmail.com http://purl.obolibrary.org/obo/NOMEN_$1 False NOMEN NOMEN NOMEN nomen NOMEN +nomen A nomenclatural ontology for biological names https://github.com/SpeciesFileGroup/nomen NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature. ^\d{7}$ 0000295 diapriid@gmail.com http://purl.obolibrary.org/obo/NOMEN_$1 False NOMEN NOMEN nomen nomen NOMEN noncodev3 NONCODE v3 http://www.noncode.org/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4. ^\d+$ 377550 http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1 False NONCODEV3 noncodev3 noncodev3 noncodev4.gene NONCODE v4 Gene http://www.bioinfo.org/NONCODEv4/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions. ^NONHSAG\d{5}$ NONHSAG00001 http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1 False NONCODEV4.GENE noncodev4.gene noncodev4.gene noncodev4.rna NONCODE v4 Transcript http://www.bioinfo.org/NONCODEv4/ NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts. ^NONHSAT\d{6}$ NONHSAT000001 http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1 False NONCODEV4.RNA noncodev4.rna noncodev4.rna @@ -990,12 +990,12 @@ npo NanoParticle Ontology https://bioportal.bioontology.org/ontologies/NPO An on nuclearbd NucleaRDB http://www.receptors.org/nucleardb/ NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. ^\w+\_\w+$ prgr_human http://www.receptors.org/nucleardb/proteins/$1 False NUCLEARBD nuclearbd nuclearbd nucleotide Nucleotide https://www.ncbi.nlm.nih.gov/ The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. ^[a-zA-Z0-9_\.]+$ 880798137 https://www.ncbi.nlm.nih.gov/nuccore/$1 False nucleotide insdc oa Web Annotation Ontology http://www.w3.org/ns/oa The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. sourceDateStart http://www.w3.org/ns/oa#$1 False OA oa OA -oae Ontology of Adverse Events https://github.com/OAE-ontology/OAE/ The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. ^\d{7}$ 0002959 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OAE_$1 False OAE OAE OAE OAE oae OAE -oarcs Ontology of Arthropod Circulatory Systems https://github.com/aszool/oarcs OArCS is an ontology describing the Arthropod ciruclatory system. ^\d{7}$ 0000029 mjyoder@illinois.edu http://purl.obolibrary.org/obo/OARCS_$1 False OARCS OARCS OARCS OARCS oarcs OARCS -oba Ontology of Biological Attributes https://github.com/obophenotype/bio-attribute-ontology A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. ^\d{7}$ 0000001 cjmungall@lbl.gov http://purl.obolibrary.org/obo/OBA_$1 False OBA OBA OBA OBA oba OBA -obcs Ontology of Biological and Clinical Statistics https://github.com/obcs/obcs OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ^\d{7}$ 0000121 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OBCS_$1 False OBCS OBCS OBCS OBCS obcs OBCS -obi Ontology for Biomedical Investigations http://obi-ontology.org The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). ^\d{7}$ 0400109 bpeters@lji.org http://purl.obolibrary.org/obo/OBI_$1 https://github.com/obi-ontology/obi/raw/master/views/obi.obo False OBI OBI OBI obi obi OBI obi OBI obi -obib Ontology for Biobanking https://github.com/biobanking/biobanking The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. ^\d{7}$ 0000389 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OBIB_$1 False OBIB OBIB OBIB OBIB obib OBIB +oae Ontology of Adverse Events https://github.com/OAE-ontology/OAE/ The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc. ^\d{7}$ 0002959 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OAE_$1 False OAE OAE OAE oae oae OAE +oarcs Ontology of Arthropod Circulatory Systems https://github.com/aszool/oarcs OArCS is an ontology describing the Arthropod ciruclatory system. ^\d{7}$ 0000029 mjyoder@illinois.edu http://purl.obolibrary.org/obo/OARCS_$1 False OARCS OARCS OARCS oarcs oarcs OARCS +oba Ontology of Biological Attributes https://github.com/obophenotype/bio-attribute-ontology A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO. ^\d{7}$ 0000001 cjmungall@lbl.gov http://purl.obolibrary.org/obo/OBA_$1 False OBA OBA OBA oba oba OBA +obcs Ontology of Biological and Clinical Statistics https://github.com/obcs/obcs OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. ^\d{7}$ 0000121 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OBCS_$1 False OBCS OBCS OBCS obcs obcs OBCS +obi Ontology for Biomedical Investigations http://obi-ontology.org The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO). ^\d{7}$ 0400109 bpeters@lji.org http://purl.obolibrary.org/obo/OBI_$1 https://github.com/obi-ontology/obi/raw/master/views/obi.obo False OBI OBI OBI obi obi obi obi OBI obi +obib Ontology for Biobanking https://github.com/biobanking/biobanking The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology. ^\d{7}$ 0000389 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OBIB_$1 False OBIB OBIB OBIB obib obib OBIB obo Internal OBO and PyOBO Relations http://www.obofoundry.org/ Community development of interoperable ontologies for the biological sciences http://purl.obolibrary.org/obo/$1 False OBO oboinowl OBO in OWL https://github.com/geneontology/go-ontology/tree/master/contrib This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties hasDbXref http://www.geneontology.org/formats/oboInOwl#$1 https://github.com/geneontology/go-ontology/raw/master/contrib/oboInOwl.obo oboformat|oio False oboInOwl occ OpenCitations Corpus https://w3id.org/oc/corpus The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law. ^[a-z][a-z]/[0-9]+$ br/1 https://w3id.org/oc/corpus/$1 False occ occ @@ -1012,7 +1012,7 @@ odam Open Data for Access and Mining https://metabolome.cgfb.u-bordeaux.fr/ Expe odc.sci Open Data Commons for Spinal Cord Injury https://odc-sci.org The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data. ^[0-9]*$ 602 https://odc-sci.org/data/$1 False odc.sci odc.tbi Open Data Commons for Traumatic Brain Injury https://odc-tbi.org The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data. ^[0-9]*$ 408 https://odc-tbi.org/data/$1 False odc.tbi odor Odor Molecules DataBase http://senselab.med.yale.edu/OdorDB OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors ^\d+$ 74 http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5 False ODOR odor odor -ogg The Ontology of Genes and Genomes https://bitbucket.org/hegroup/ogg OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ^\d+$ 3000887619 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OGG_$1 False OGG OGG OGG OGG ogg OGG +ogg The Ontology of Genes and Genomes https://bitbucket.org/hegroup/ogg OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. ^\d+$ 3000887619 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OGG_$1 False OGG OGG OGG ogg ogg OGG ogi Ontology for genetic interval https://code.google.com/archive/p/ontology-for-genetic-interval/ "OGI formalized the genomic element by defining an upper class 'genetic interval'. The definition of 'genetic interval' is ""the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture."" @@ -1024,51 +1024,51 @@ Yu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval Yu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF) -" ^\d{7}$ 0000019 linikujp@gmail.com http://purl.obolibrary.org/obo/OGI_$1 OGI.owl True OGI OGI OGI OGI ogi OGI +" ^\d{7}$ 0000019 linikujp@gmail.com http://purl.obolibrary.org/obo/OGI_$1 OGI.owl True OGI OGI OGI ogi ogi OGI ogms Ontology for General Medical Science https://github.com/OGMS/ogms "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. -OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology." ^\d{7}$ 0000031 baeverma@jcvi.org http://purl.obolibrary.org/obo/OGMS_$1 ogms/OMRE False OGMS OGMS OGMS OGMS ogms OGMS -ogsf Ontology of Genetic Susceptibility Factor https://github.com/linikujp/OGSF An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. ^\d{7}$ 0000025 linikujp@gmail.com http://purl.obolibrary.org/obo/OGSF_$1 False OGSF OGSF OGSF OGSF ogsf OGSF -ohd Oral Health and Disease Ontology https://purl.obolibrary.org/obo/ohd/home The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. ^\d{7}$ 0000006 wdduncan@gmail.com http://purl.obolibrary.org/obo/OHD_$1 False OHD OHD OHD OHD ohd OHD -ohmi Ontology of Host-Microbiome Interactions https://github.com/ohmi-ontology/ohmi OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. ^\d{7}$ 0000460 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OHMI_$1 False OHMI OHMI OHMI OHMI ohmi OHMI -ohpi Ontology of Host Pathogen Interactions https://github.com/OHPI/ohpi OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). ^\d+$ 9001411 edong@umich.edu http://purl.obolibrary.org/obo/OHPI_$1 False OHPI OHPI OHPI ohpi OHPI +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology." ^\d{7}$ 0000031 baeverma@jcvi.org http://purl.obolibrary.org/obo/OGMS_$1 ogms/OMRE False OGMS OGMS OGMS ogms ogms OGMS +ogsf Ontology of Genetic Susceptibility Factor https://github.com/linikujp/OGSF An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process. ^\d{7}$ 0000025 linikujp@gmail.com http://purl.obolibrary.org/obo/OGSF_$1 False OGSF OGSF OGSF ogsf ogsf OGSF +ohd Oral Health and Disease Ontology https://purl.obolibrary.org/obo/ohd/home The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records. ^\d{7}$ 0000006 wdduncan@gmail.com http://purl.obolibrary.org/obo/OHD_$1 False OHD OHD OHD ohd ohd OHD +ohmi Ontology of Host-Microbiome Interactions https://github.com/ohmi-ontology/ohmi OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. ^\d{7}$ 0000460 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OHMI_$1 False OHMI OHMI OHMI ohmi ohmi OHMI +ohpi Ontology of Host Pathogen Interactions https://github.com/OHPI/ohpi OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration). ^\d+$ 9001411 edong@umich.edu http://purl.obolibrary.org/obo/OHPI_$1 False OHPI OHPI ohpi ohpi OHPI oid OID Repository http://www.oid-info.com/introduction.htm OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes. ^[\d.]+$ 2.16.840 http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display False oid oid -olatdv Medaka Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv Life cycle stages for Medaka ^\d{7}$ 0000210 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/OLATDV_$1 False OLATDV OLATDV OLATDV OlatDv olatdv OLATDV +olatdv Medaka Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv Life cycle stages for Medaka ^\d{7}$ 0000210 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/OLATDV_$1 False OLATDV OLATDV OLATDV olatdv olatdv OLATDV om Ontology of units of Measure https://github.com/HajoRijgersberg/OM The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging Dimension hajo.rijgersberg@wur.nl http://www.ontology-of-units-of-measure.org/resource/om-2/$1 False OM OM OM om oma.grp OMA Group https://omabrowser.org/cgi-bin/gateway.pl OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs. ^[A-Z]+$ LCSCCPN https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1 False OMA.GRP oma.grp oma.grp oma.hog OMA HOGs https://omabrowser.org Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. ^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ 0459895 https://omabrowser.org/oma/hog/HOG:$1 False oma.hog oma.protein OMA Protein https://omabrowser.org/cgi-bin/gateway.pl OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records. ^[A-Z0-9]{5}\d+$ HUMAN16963 https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1 False OMA.PROTEIN oma.protein oma.protein omia Online Mendelian Inheritance in Animals http://omia.angis.org.au/ Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse). ^\d+$ 1000 http://omia.angis.org.au/$1/ True OMIA omia omia omia -omiabis Ontologized MIABIS https://github.com/OMIABIS/omiabis-dev An ontological version of MIABIS (Minimum Information About BIobank data Sharing) ^\d{7}$ 0001079 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OMIABIS_$1 True OMIABIS OMIABIS OMIABIS OMIABIS omiabis OMIABIS +omiabis Ontologized MIABIS https://github.com/OMIABIS/omiabis-dev An ontological version of MIABIS (Minimum Information About BIobank data Sharing) ^\d{7}$ 0001079 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OMIABIS_$1 True OMIABIS OMIABIS OMIABIS omiabis omiabis OMIABIS omim Online Mendelian Inheritance in Man https://omim.org/ Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders. ^\d+$ 603903 ahamosh@jhmi.edu https://omim.org/entry/$1 OMIM|mim False OMIM OMIM OMIM 1153 mim mim omim MIM P492 omim.ps OMIM Phenotypic Series https://www.omim.org/phenotypicSeriesTitles/all A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome. ^PS\d+$ PS214100 ahamosh@jhmi.edu https://omim.org/phenotypicSeries/$1 MIMPS|OMIMPS|PS|mim.ps False omim -omit Ontology for MicroRNA Target http://omit.cis.usouthal.edu/ The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). ^\d{7}$ 0000069 huang@southalabama.edu https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1 https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo OMIT False OMIT OMIT OMIT omit omit OMIT omit OMIT -omo OBO Metadata Ontology https://github.com/information-artifact-ontology/ontology-metadata An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). cjmungall@lbl.gov http://purl.obolibrary.org/obo/OMO_$1 False OMO OMO OMO omo OMO +omit Ontology for MicroRNA Target http://omit.cis.usouthal.edu/ The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes). ^\d{7}$ 0000069 huang@southalabama.edu https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1 https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo OMIT False OMIT OMIT OMIT omit omit omit omit OMIT +omo OBO Metadata Ontology https://github.com/information-artifact-ontology/ontology-metadata An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO). cjmungall@lbl.gov http://purl.obolibrary.org/obo/OMO_$1 False OMO OMO omo omo OMO omop Observational Medical Outcomes Partnership https://www.ohdsi.org/data-standardization/the-common-data-model/ The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format. False -omp Ontology of Microbial Phenotypes http://microbialphenotypes.org An ontology of phenotypes covering microbes ^\d{7}$ 0005067 jimhu@tamu.edu http://purl.obolibrary.org/obo/OMP_$1 False OMP OMP OMP OMP omp OMP -omrse Ontology of Medically Related Social Entities https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. ^\d{8}$ 00000022 hoganwr@gmail.com http://purl.obolibrary.org/obo/OMRSE_$1 https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo False OMRSE OMRSE OMRSE OMRSE omrse OMRSE +omp Ontology of Microbial Phenotypes http://microbialphenotypes.org An ontology of phenotypes covering microbes ^\d{7}$ 0005067 jimhu@tamu.edu http://purl.obolibrary.org/obo/OMP_$1 False OMP OMP OMP omp omp OMP +omrse Ontology of Medically Related Social Entities https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations. ^\d{8}$ 00000022 hoganwr@gmail.com http://purl.obolibrary.org/obo/OMRSE_$1 https://github.com/ufbmi/OMRSE/raw/master/omrse-full.obo False OMRSE OMRSE OMRSE omrse omrse OMRSE oncotree OncoTree http://oncotree.mskcc.org OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. BLL http://oncotree.mskcc.org/api/tumorTypes/search/code/$1 False -one Ontology for Nutritional Epidemiology https://github.com/cyang0128/Nutritional-epidemiologic-ontologies An ontology to standardize research output of nutritional epidemiologic studies. ^\d{7}$ 0001021 chenyangnutrition@gmail.com http://purl.obolibrary.org/obo/ONE_$1 False ONE ONE ONE one ONE -ons Ontology for Nutritional Studies https://github.com/enpadasi/Ontology-for-Nutritional-Studies The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. ^\d{7}$ 0000060 francesco.vitali@ibba.cnr.it http://purl.obolibrary.org/obo/ONS_$1 False ONS ONS ONS ons ONS +one Ontology for Nutritional Epidemiology https://github.com/cyang0128/Nutritional-epidemiologic-ontologies An ontology to standardize research output of nutritional epidemiologic studies. ^\d{7}$ 0001021 chenyangnutrition@gmail.com http://purl.obolibrary.org/obo/ONE_$1 False ONE ONE one one ONE +ons Ontology for Nutritional Studies https://github.com/enpadasi/Ontology-for-Nutritional-Studies The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies. ^\d{7}$ 0000060 francesco.vitali@ibba.cnr.it http://purl.obolibrary.org/obo/ONS_$1 False ONS ONS ons ons ONS ontoavida Ontology for Avida digital evolution platform https://gitlab.com/fortunalab/ontoavida "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment). The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. OntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA). -More information can be found at https://obofoundry.org/ontology/ontoavida.html" ^\d{8}$ 00000001 fortuna@ebd.csic.es http://purl.obolibrary.org/obo/ONTOAVIDA_$1 False ONTOAVIDA ONTOAVIDA ONTOAVIDA ontoavida ONTOAVIDA -ontoneo Obstetric and Neonatal Ontology http://ontoneo.com The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. ^\d{8}$ 00000098 fernanda.farinelli@gmail.com http://purl.obolibrary.org/obo/ONTONEO_$1 False ONTONEO ONTONEO ONTONEO ONTONEO ontoneo ONTONEO -oostt Ontology of Organizational Structures of Trauma centers and Trauma systems https://github.com/OOSTT/OOSTT An ontology built for representating the organizational components of trauma centers and trauma systems. ^\d{8}$ 00000099 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OOSTT_$1 False OOSTT OOSTT OOSTT OOSTT oostt OOSTT +More information can be found at https://obofoundry.org/ontology/ontoavida.html" ^\d{8}$ 00000001 fortuna@ebd.csic.es http://purl.obolibrary.org/obo/ONTOAVIDA_$1 False ONTOAVIDA ONTOAVIDA ontoavida ontoavida ONTOAVIDA +ontoneo Obstetric and Neonatal Ontology http://ontoneo.com The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby. ^\d{8}$ 00000098 fernanda.farinelli@gmail.com http://purl.obolibrary.org/obo/ONTONEO_$1 False ONTONEO ONTONEO ONTONEO ontoneo ontoneo ONTONEO +oostt Ontology of Organizational Structures of Trauma centers and Trauma systems https://github.com/OOSTT/OOSTT An ontology built for representating the organizational components of trauma centers and trauma systems. ^\d{8}$ 00000099 mbrochhausen@gmail.com http://purl.obolibrary.org/obo/OOSTT_$1 False OOSTT OOSTT OOSTT oostt oostt OOSTT opb Ontology of Physics for Biology http://bioportal.bioontology.org/ontologies/OPB The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. ^\d+$ 00573 http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1 False OPB OPB OPB opb opb opb openalex OpenAlex https://openalex.org/ OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other. ^[WAICV]\d{2,}$ W2741809807 hpiwowar@gmail.com https://openalex.org/$1 False -opl Ontology for Parasite LifeCycle https://github.com/OPL-ontology/OPL The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. ^\d{7}$ 0000319 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OPL_$1 False OPL OPL OPL OPL opl OPL +opl Ontology for Parasite LifeCycle https://github.com/OPL-ontology/OPL The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. ^\d{7}$ 0000319 jiezheng@pennmedicine.upenn.edu http://purl.obolibrary.org/obo/OPL_$1 False OPL OPL OPL opl opl OPL opm Orientations of Proteins in Membranes Database http://opm.phar.umich.edu/ The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization. ^[0-9][A-Za-z0-9]{3}$ 1h68 http://opm.phar.umich.edu/protein.php?pdbid=$1 False OPM opm opm -opmi Ontology of Precision Medicine and Investigation https://github.com/OPMI/opmi OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. ^\d{7}$ 0000101 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OPMI_$1 False OPMI OPMI OPMI opmi OPMI +opmi Ontology of Precision Medicine and Investigation https://github.com/OPMI/opmi OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles. ^\d{7}$ 0000101 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OPMI_$1 False OPMI OPMI opmi opmi OPMI orcid Open Researcher and Contributor https://orcid.org ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities. ^\d{4}-\d{4}-\d{4}-\d{3}(\d|X)$ 0000-0002-5355-2576 https://orcid.org/$1 ORCID|ORCiD False ORCID orcid orcid P496 ordb Olfactory Receptor Database http://senselab.med.yale.edu/OrDB/ The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs). ^\d+$ 8497 http://senselab.med.yale.edu/ORDB/Data/$1 False ORDB ordb ordb ordb oridb.sacch OriDB Saccharomyces http://cerevisiae.oridb.org/index.php OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae. ^\d+$ 1 http://cerevisiae.oridb.org/details.php?id=$1 False ORIDB.SACCH oridb.sacch oridb.sacch oridb.schizo OriDB Schizosaccharomyces http://pombe.oridb.org/index.php OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe. ^\d+$ 1 http://pombe.oridb.org/details.php?id=$1 False ORIDB.SCHIZO oridb.schizo oridb.schizo -ornaseq Ontology of RNA Sequencing http://kim.bio.upenn.edu/software/ornaseq.shtml An application ontology designed to annotate next-generation sequencing experiments performed on RNA. ^\d{7}$ 0000010 safisher@upenn.edu http://purl.obolibrary.org/obo/ORNASEQ_$1 False ORNASEQ ORNASEQ ORNASEQ ornaseq ORNASEQ +ornaseq Ontology of RNA Sequencing http://kim.bio.upenn.edu/software/ornaseq.shtml An application ontology designed to annotate next-generation sequencing experiments performed on RNA. ^\d{7}$ 0000010 safisher@upenn.edu http://purl.obolibrary.org/obo/ORNASEQ_$1 False ORNASEQ ORNASEQ ornaseq ornaseq ORNASEQ orphanet Orphanet http://www.orpha.net/consor/ Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases. ^\d+$ 85163 http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1 ORPHA False Orphanet orphanet orphanet orphanet Orphanet P1550 orphanet.ordo Orphanet Rare Disease Ontology https://www.ebi.ac.uk/ols/ontologies/ordo "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)." ^C?\d+$ C023 http://www.orpha.net/ORDO/Orphanet_$1 http://www.orphadata.org/data/ORDO/ordo_orphanet.owl ordo False ordo ORPHANET.ORDO ORDO ORDO orphanet.ordo orphanet.ordo ordo @@ -1081,7 +1081,7 @@ oryzabase.stage Oryzabase Stage http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Or oryzabase.strain Oryzabase Strain http://www.shigen.nig.ac.jp/rice/oryzabaseV4/ Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information. ^\d+$ 1 http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1 False ORYZABASE.STRAIN oryzabase.strain oryzabase.strain otl Oryza Tag Line http://oryzatagline.cirad.fr/ Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information. ^A[A-Z]+\d+$ AADB12 http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 False OTL otl otl otl otol Open Tree of Life https://tree.opentreeoflife.org Identifier for an entity in open tree of life ^[1-9]\d*$ 3905431 https://tree.opentreeoflife.org/taxonomy/browse?id=$1 False P9157 -ovae Ontology of Vaccine Adverse Events http://www.violinet.org/ovae/ OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ^\d{7}$ 0000609 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OVAE_$1 False OVAE OVAE OVAE OVAE ovae OVAE +ovae Ontology of Vaccine Adverse Events http://www.violinet.org/ovae/ OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). ^\d{7}$ 0000609 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/OVAE_$1 False OVAE OVAE OVAE ovae ovae OVAE owl Web Ontology Language https://www.w3.org/TR/owl-features/ Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. Ontology http://www.w3.org/2002/07/owl#$1 False owl p3db.protein P3DB Protein http://www.p3db.org/ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites. ^\d+$ 70 http://www.p3db.org/protein.php?id=$1&ref=0 False P3DB.PROTEIN p3db.protein p3db.protein p3db.site P3DB Site http://www.p3db.org/ Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins. ^\d+$ 65 http://www.p3db.org/phosphosite.php?id=$1&ref=0 False P3DB.SITE p3db.site p3db.site @@ -1092,26 +1092,26 @@ panther.node PANTHER Node http://pantree.org/ The PANTHER (Protein ANalysis THro panther.pathway PANTHER Pathway http://www.pantherdb.org/ The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components. ^P\d{5}$ P00024 http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1 False PANTHER.PATHWAY 1161 panther.pathway panther.pathway panther panther.pthcmp PANTHER Pathway Component http://www.pantherdb.org/ "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway components may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation." ^(G|P|U|C|S)\d{5}$ P00266 http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1 False PANTHER.PTHCMP panther.pthcmp panther.pthcmp panther -pao Plant Anatomy Ontology http://www.plantontology.org jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PAO_$1 True PAO PAO +pao Plant Anatomy Ontology http://www.plantontology.org jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PAO_$1 True PAO pao pass2 Protein Alignment organised as Structural Superfamily http://caps.ncbs.res.in/pass2 The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. ^\d+$ 46977 http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1 True PASS2 pass2 pass2 pass2 pathbank PathBank https://pathbank.org PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. ^(SMP|PW)\d+$ SMP0000219 https://pathbank.org/view/$1 False pathwaycommons Pathway Commons http://www.pathwaycommons.org/pc/ Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language. ^\d+$ 485991 http://www.pathwaycommons.org/pc/record2.do?id=$1 False PATHWAYCOMMONS pathwaycommons pathwaycommons pathwaycommons PathwayCommons -pato Phenotype And Trait Ontology https://github.com/pato-ontology/pato/ PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. ^\d{7}$ 0001998 g.gkoutos@gmail.com https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 False PATO PATO PATO PATO pato pato PATO pato PATO pato +pato Phenotype And Trait Ontology https://github.com/pato-ontology/pato/ PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. ^\d{7}$ 0001998 g.gkoutos@gmail.com https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1 False PATO PATO PATO PATO pato pato pato pato PATO pato pav Provenance, Authoring, and Versioning Vocabulary https://pav-ontology.github.io/pav/ PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources. ^[a-z][a-zA-Z]+$ authoredBy http://purl.org/pav/$1 False PAV pav PAV paxdb.organism PaxDb Organism http://pax-db.org/ PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species. ^\d+$ 9606 http://pax-db.org/#!species/$1 False PAXDB.ORGANISM paxdb.organism paxdb.organism paxdb.protein PaxDb Protein http://pax-db.org/ PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels. ^\d+$ 977869 http://pax-db.org/#!protein/$1 False PAXDB.PROTEIN paxdb.protein paxdb.protein pazar Pazar Transcription Factor http://www.pazar.info/ The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors. ^TF\w+$ TF0001053 http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1 False PAZAR pazar pazar pazar pba Primate Brain Atlas https://www.blueprintnhpatlas.org/ A controlled vocabulary to support the study of transcription in the primate brain ^\d+$ 128011350 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-pba.obo False -pcl Provisional Cell Ontology https://github.com/obophenotype/provisional_cell_ontology Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. ^\d{7}$ 0011124 davidos@ebi.ac.uk http://purl.obolibrary.org/obo/PCL_$1 False PCL PCL PCL pcl PCL -pco Population and Community Ontology https://github.com/PopulationAndCommunityOntology/pco The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. ^\d{7}$ 0000021 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PCO_$1 False PCO PCO PCO PCO PCO PCO pco PCO -pd_st Platynereis stage ontology http://4dx.embl.de/platy henrich@embl.de http://purl.obolibrary.org/obo/PD_ST_$1 True PD_ST PD_ST +pcl Provisional Cell Ontology https://github.com/obophenotype/provisional_cell_ontology Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties. ^\d{7}$ 0011124 davidos@ebi.ac.uk http://purl.obolibrary.org/obo/PCL_$1 False PCL PCL pcl pcl PCL +pco Population and Community Ontology https://github.com/PopulationAndCommunityOntology/pco The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. ^\d{7}$ 0000021 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PCO_$1 False PCO PCO PCO PCO PCO pco pco PCO +pd_st Platynereis stage ontology http://4dx.embl.de/platy henrich@embl.de http://purl.obolibrary.org/obo/PD_ST_$1 True PD_ST pd_st pdb PDB Structure https://www.wwpdb.org/ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. ^[0-9][A-Za-z0-9]{3}$ 2gc4 https://www.wwpdb.org/pdb?id=$1 RCSB_PDB|pdbe|pdbj|wwpdb False PDB 1127 pdb pdb pdbj RCSB-PDB P638 pdb-ccd Chemical Component Dictionary https://www.ebi.ac.uk/pdbe-srv/pdbechem/ The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. ^\w{1,3}$ AB0 https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1 pdbechem False PDB-CCD pdb-ccd pdb-ccd pdb.ligand pdb.ligand Protein Data Bank Ligand http://www.pdb.org/ The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands. ^[A-Za-z0-9]+$ TRQ http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1 PDB_CHEM_ID False PDB.LIGAND pdb.ligand pdb.ligand pdbligand P3636 pdc.study Proteomic Data Commons https://pdc.cancer.gov/pdc The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public. ^PDC\d+$ PDC000351 https://pdc.cancer.gov/pdc/study/$1 False -pdro The Prescription of Drugs Ontology https://github.com/OpenLHS/PDRO An ontology to describe entities related to prescription of drugs ^\d{7}$ 0010039 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/PDRO_$1 False PDRO PDRO PDRO PDRO pdro PDRO -pdumdv Platynereis Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv Life cycle stages for Platynereis dumerilii ^\d{7}$ 0001410 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/PDUMDV_$1 PdumDv False PDUMDV PDUMDV PDUMDV PdumDv pdumdv PDUMDV -peco Plant Experimental Conditions Ontology http://planteome.org/ A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. ^\d{7}$ 0007114 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PECO_$1 https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo False PECO PECO PECO PECO PECO peco PECO +pdro The Prescription of Drugs Ontology https://github.com/OpenLHS/PDRO An ontology to describe entities related to prescription of drugs ^\d{7}$ 0010039 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/PDRO_$1 False PDRO PDRO PDRO pdro pdro PDRO +pdumdv Platynereis Developmental Stages https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv Life cycle stages for Platynereis dumerilii ^\d{7}$ 0001410 frederic.bastian@unil.ch http://purl.obolibrary.org/obo/PDUMDV_$1 PdumDv False PDUMDV PDUMDV PDUMDV pdumdv pdumdv PDUMDV +peco Plant Experimental Conditions Ontology http://planteome.org/ A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments. ^\d{7}$ 0007114 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/PECO_$1 https://raw.githubusercontent.com/Planteome/plant-experimental-conditions-ontology/master/peco.obo False PECO PECO PECO PECO peco peco PECO ped Protein Ensemble Database https://proteinensemble.org/ The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. ^PED\d{5}$ PED00037 https://proteinensemble.org/$1 False ped ped.ensemble Protein Ensemble Database ensemble https://proteinensemble.org/ The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins. ^PED\d{5}e\d{3}$ PED00017e001 https://proteinensemble.org/$1 False ped.ensemble ped peff PSI Extended File Format https://www.psidev.info/peff ^\d{7}$ 0001011 https://github.com/HUPO-PSI/PEFF/raw/master/CV/psi-peff-OBSOLETE-DO_NOT_USE.obo True @@ -1123,7 +1123,7 @@ pesticides Alan Wood's Pesticides http://www.alanwood.net/pesticides The Alan Wo pfam Pfam https://pfam.xfam.org/ The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored. ^PF\d{5}$ PF11779 https://pfam.xfam.org/family/$1 PF False PFAM 1138 pfam pfam pfam Pfam P3519 pfam.clan Pfam Clans https://pfam.xfam.org Higher order grouping of Pfam families ^CL\d+$ CL0192 https://pfam.xfam.org/clan/$1 False 2758 pfr Proteoform Atlas http://repository.topdownproteomics.org/proteoforms Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets. ^\d+$ 1001 http://repository.topdownproteomics.org/proteoforms/$1 TDR False -pgdso Plant Growth and Development Stage http://www.plantontology.org po-discuss@plantontology.org http://purl.obolibrary.org/obo/PGDSO_$1 True PGDSO PGDSO +pgdso Plant Growth and Development Stage http://www.plantontology.org po-discuss@plantontology.org http://purl.obolibrary.org/obo/PGDSO_$1 True PGDSO pgdso pgs Polygenic Score Catalog http://pgscatalog.org The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation. ^PGS[0-9]{6}$ PGS000018 https://www.pgscatalog.org/pgs/$1 False pgs pgx Progenetix https://progenetix.org/ "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt ""neoplasm"" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs." ^\w{3,15}[-_]\w[\w.-]{3,128}$ pgxbs-kftva5zv https://progenetix.org/services/ids/$1 Progenetix False PGX Progenetix pgx pgx pharmacodb.cell PharmacoDB Cells https://pharmacodb.ca/cell_lines Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line. 22RV1_12_2019 https://pharmacodb.ca/cell_lines/$1 False PharmacoDB @@ -1136,7 +1136,7 @@ pharmgkb.pathways PharmGKB Pathways http://www.pharmgkb.org/ "The PharmGKB datab PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies." ^PA\d+$ PA146123006 http://www.pharmgkb.org/pathway/$1 False PHARMGKB.PATHWAYS 2650 pharmgkb.pathways pharmgkb.pathways pharmgkb.pathways P7001 phenolexplorer Phenol-Explorer http://www.phenol-explorer.eu/foods/ Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. ^\d+$ 75 http://phenol-explorer.eu/foods/$1 False PHENOLEXPLORER phenolexplorer phenolexplorer phenx PhenX Toolkit https://www.phenxtoolkit.org/ A Web-based catalog of recommended measurement protocols ^\d+$ 130502 https://www.phenxtoolkit.org/protocols/view/$1 False PHENX PHENX -phipo Pathogen Host Interaction Phenotype Ontology https://github.com/PHI-base/phipo Ontology of species-neutral phenotypes observed in pathogen-host interactions. ^\d{7}$ 0000001 alayne.cuzick@rothamsted.ac.uk http://purl.obolibrary.org/obo/PHIPO_$1 False PHIPO PHIPO PHIPO phipo PHIPO +phipo Pathogen Host Interaction Phenotype Ontology https://github.com/PHI-base/phipo Ontology of species-neutral phenotypes observed in pathogen-host interactions. ^\d{7}$ 0000001 alayne.cuzick@rothamsted.ac.uk http://purl.obolibrary.org/obo/PHIPO_$1 False PHIPO PHIPO phipo phipo PHIPO phosphopoint.kinase PhosphoPoint Kinase http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 False PHOSPHOPOINT.KINASE phosphopoint.kinase phosphopoint.kinase phosphopoint.protein PhosphoPoint Phosphoprotein http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 False PHOSPHOPOINT.PROTEIN phosphopoint.protein phosphopoint.protein phosphosite.protein PhosphoSite Protein http://www.phosphosite.org/homeAction.do PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database. ^\d{5}$ 12300 http://www.phosphosite.org/proteinAction.do?id=$1 False PHOSPHOSITE.PROTEIN phosphosite.protein phosphosite.protein @@ -1151,35 +1151,35 @@ pina Protein Interaction Network Analysis http://cbg.garvan.unsw.edu.au/pina/ Pr piroplasma PiroplasmaDB http://piroplasmadb.org/ PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^TA\d+$ TA14985 http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False PIROPLASMA piroplasma piroplasma pirsf PIR Superfamily Classification System https://pir.georgetown.edu/ The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. ^PIRSF\d{6}$ PIRSF000100 https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1 False PIRSF 1136 pirsf pirsf pirsf PIRSF pkdb PK-DB https://www.hu-berlin.de/?set_language=en&cl=en PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. ^PKDB[0-9]{5}$ PKDB00198 https://pk-db.com/data/$1 False pkdb -plana Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology https://github.com/obophenotype/planaria-ontology PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. ^\d{7}$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANA_$1 False PLANA PLANA PLANA PLANA plana PLANA -planp Planarian Phenotype Ontology https://github.com/obophenotype/planarian-phenotype-ontology Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. ^\d+$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANP_$1 False PLANP PLANP PLANP planp PLANP +plana Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology https://github.com/obophenotype/planaria-ontology PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea. ^\d{7}$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANA_$1 False PLANA PLANA PLANA plana plana PLANA +planp Planarian Phenotype Ontology https://github.com/obophenotype/planarian-phenotype-ontology Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea. ^\d+$ 0000001 smr@stowers.org http://purl.obolibrary.org/obo/PLANP_$1 False PLANP PLANP planp planp PLANP planttfdb Plant Transcription Factor Database http://planttfdb.cbi.pku.edu.cn The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors. ^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\._\-#]*)$ Ath_AT1G01030.1 http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1 False PLANTTFDB planttfdb planttfdb planttfdb plasmodb PlasmoDB http://plasmodb.org/plasmo/ AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ PF11_0344 http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 ApiDB_PlasmoDB False PLASMODB plasmodb plasmodb plasmodb -plo Plasmodium Life Cycle http://www.sanger.ac.uk/Users/mb4/PLO/ mb4@sanger.ac.uk http://purl.obolibrary.org/obo/PLO_$1 True PLO PLO +plo Plasmodium Life Cycle http://www.sanger.ac.uk/Users/mb4/PLO/ mb4@sanger.ac.uk http://purl.obolibrary.org/obo/PLO_$1 True PLO plo pmap.cutdb CutDB http://cutdb.burnham.org The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). ^\d+$ 25782 http://cutdb.burnham.org/relation/show/$1 False PMAP.CUTDB pmap.cutdb pmap.cutdb pmap.cutdb pmap.substratedb SubstrateDB http://substrate.burnham.org/ The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates. ^\d+$ 1915 http://substrate.burnham.org/protein/annotation/$1/html False PMAP.SUBSTRATEDB pmap.substratedb pmap.substratedb pmap.substratedb pmc Pubmed Central http://europepmc.org/ PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature. ^PMC\d+$ PMC3084216 http://europepmc.org/articles/$1 PMC|PMCID False PMCID pmc pmc pmc P932 pmdb Protein Model Database https://bioinformatics.cineca.it/PMDB/ The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques. ^PM\d{7}$ PM0012345 https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1 False PMDB pmdb pmdb pmdb pmp Protein Model Portal http://www.proteinmodelportal.org/ The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Q0VCA6 http://www.proteinmodelportal.org/query/uniprot/$1 False PMP pmp pmp pmp uniprot pmr Physical Medicine and Rehabilitation https://www.auckland.ac.nz/en.html Resource for the community to store, retrieve, search, reference, and reuse CellML models. ^[a-z0-9]{32,32}$ ebf69ca24298b28b2361e7d43eb52d6c https://models.physiomeproject.org/exposure/$1 False PMR PMR pmr -po Plant Ontology http://browser.planteome.org/amigo The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. ^\d+$ 0009089 jaiswalp@science.oregonstate.edu http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1 False PO PO PO PO 1180 po po PO po PO po +po Plant Ontology http://browser.planteome.org/amigo The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. ^\d+$ 0009089 jaiswalp@science.oregonstate.edu http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1 False PO PO PO PO 1180 po po po po PO po pocketome Pocketome http://www.pocketome.org/sfSearch.cgi?act=browseall Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries. ^[A-Za-z_0-9]+$ 1433C_TOBAC_1_252 http://www.pocketome.org/files/$1.html False POCKETOME pocketome pocketome polbase PolBase http://polbase.neb.com/ Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity. ^[A-Za-z-0-9]+$ 19-T4 https://polbase.neb.com/polymerases/$1#sequences False POLBASE polbase polbase pombase PomBase http://www.pombase.org/ PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets. ^S\w+(\.)?\w+(\.)?$ SPCC13B11.01 http://www.pombase.org/spombe/result/$1 PomBase False PomBase pombase pombase pombase PomBase P6245 -poro Porifera Ontology https://github.com/obophenotype/porifera-ontology An ontology describing the anatomical structures and characteristics of Porifera (sponges) ^\d{7}$ 0000550 robert.thacker@stonybrook.edu http://purl.obolibrary.org/obo/PORO_$1 False PORO PORO PORO PORO poro PORO +poro Porifera Ontology https://github.com/obophenotype/porifera-ontology An ontology describing the anatomical structures and characteristics of Porifera (sponges) ^\d{7}$ 0000550 robert.thacker@stonybrook.edu http://purl.obolibrary.org/obo/PORO_$1 False PORO PORO PORO poro poro PORO ppdb Pesticide Properties DataBase https://sitem.herts.ac.uk/aeru/ppdb/ PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. ^\d+$ 1484 https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm False -ppo Plant Phenology Ontology https://github.com/PlantPhenoOntology/PPO An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. ^\d{7}$ 0002058 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PPO_$1 False PPO PPO PPO PPO PPO ppo PPO +ppo Plant Phenology Ontology https://github.com/PlantPhenoOntology/PPO An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales. ^\d{7}$ 0002058 rlwalls2008@gmail.com http://purl.obolibrary.org/obo/PPO_$1 False PPO PPO PPO PPO ppo ppo PPO ppr Europe PMC Preprints https://europepmc.org Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000. ppr103739 https://europepmc.org/article/ppr/$1 False -pr Protein Ontology http://proconsortium.org The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. ^\d+$ 000000024 dan5@georgetown.edu https://proconsortium.org/app/entry/PR:$1 PR|PRO False PR PR PR PR pr pr PR pr PR pr PRO P4926 +pr Protein Ontology http://proconsortium.org The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies. ^\d+$ 000000024 dan5@georgetown.edu https://proconsortium.org/app/entry/PR:$1 PR|PRO False PR PR PR PR pr pr pr pr PR pr PRO P4926 prefixcommons Prefix Commons https://prefixcommons.org A registry of life science prefxes ChEBI https://bioregistry.io/metaregistry/prefixcommons/$1 False pride PRIDE Controlled Vocabulary https://github.com/PRIDE-Utilities/pride-ontology The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays. ^\d+$ 1 https://www.ebi.ac.uk/pride/archive/assays/$1 False PRIDE PRIDE PRIDE pride pride pride pride PRIDE pride.project PRIDE Project https://www.ebi.ac.uk/pride/ The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects. ^P(X|R)D\d{6}$ PXD000440 https://www.ebi.ac.uk/pride/archive/projects/$1 False PRIDE.PROJECT pride.project pride.project prints PRINTS compendium of protein fingerprints http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/ PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. ^PR\d{5}$ PR00001 http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off False PRINTS prints prints PRINTS probonto Probability Distribution Ontology http://probonto.org ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities. ^PROB_c\d+$ PROB_c0000005 probonto.dev@gmail.com https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1 False PROBONTO probonto probonto probonto -proco Process Chemistry Ontology https://github.com/proco-ontology/PROCO PROCO covers process chemistry, the chemical field concerned with scaling up laboratory syntheses to commercially viable processes. 0000001 wes_schafer@merck.com http://purl.obolibrary.org/obo/PROCO_$1 False PROCO PROCO PROCO +proco Process Chemistry Ontology https://github.com/proco-ontology/PROCO PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry. 0000001 wes_schafer@merck.com http://purl.obolibrary.org/obo/PROCO_$1 False PROCO proco proco PROCO prodom ProDom http://prodom.prabi.fr/prodom/current/html/home.php ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. ^PD\d+$ PD10000 http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1 False PRODOM prodom prodom prodom proglyc ProGlycProt http://www.proglycprot.org/ ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. ^[A-Z]C\d{1,3}$ AC119 http://www.proglycprot.org/detail.aspx?ProId=$1 False PROGLYC proglyc proglyc -propreo Proteomics data and process provenance http://lsdis.cs.uga.edu/projects/glycomics/propreo/ satya30@uga.edu http://purl.obolibrary.org/obo/PROPREO_$1 True PROPREO PROPREO PROPREO PROPREO propreo +propreo Proteomics data and process provenance http://lsdis.cs.uga.edu/projects/glycomics/propreo/ satya30@uga.edu http://purl.obolibrary.org/obo/PROPREO_$1 True PROPREO PROPREO PROPREO propreo propreo prosite PROSITE https://www.expasy.org/prosite/ PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. ^PS\d{5}$ PS00001 https://prosite.expasy.org/$1 False PROSITE prosite prosite prosite PROSITE P4355 protclustdb ProtClustDB https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. ^\w+$ O80725 https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1 False PROTCLUSTDB protclustdb protclustdb protclustdb proteomicsdb.peptide ProteomicsDB Peptide https://www.proteomicsdb.org/#peptideSearch ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein. ^\d+$ 53504 https://www.proteomicsdb.org/#human/proteinDetails/$1 False PROTEOMICSDB.PEPTIDE proteomicsdb.peptide proteomicsdb.peptide @@ -1188,11 +1188,11 @@ protonet.cluster ProtoNet Cluster http://www.protonet.cs.huji.ac.il/ ProtoNet pr protonet.proteincard ProtoNet ProteinCard http://www.protonet.cs.huji.ac.il/ ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. ^\d+$ 16941567 http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1 False PROTONET.PROTEINCARD protonet.proteincard protonet.proteincard protonet.proteincard prov PROV Namespace https://www.w3.org/ns/prov The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web. Activity http://www.w3.org/ns/prov#$1 False PROV prov prov pscdb Protein Structural Change Database http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion. ^\d+$ 051 http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html False PSCDB pscdb pscdb -psdo Performance Summary Display Ontology https://github.com/Display-Lab/psdo "Performance Summary Display Ontology (PSDO) (pronounced ""pseudo"" or ""sudo"") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed." ^\d{7}$ 0000055 zachll@umich.edu http://purl.obolibrary.org/obo/PSDO_$1 False PSDO PSDO PSDO psdo PSDO +psdo Performance Summary Display Ontology https://github.com/Display-Lab/psdo "Performance Summary Display Ontology (PSDO) (pronounced ""pseudo"" or ""sudo"") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed." ^\d{7}$ 0000055 zachll@umich.edu http://purl.obolibrary.org/obo/PSDO_$1 False PSDO PSDO psdo psdo PSDO pseudogene PseudoGene http://www.pseudogene.org This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. PGOHUM00000289843 http://tables.pseudogene.org/[?species_name]/$1 pseudogene.org False pseudo pseudogene pseudomonas Pseudomonas Genome Database http://www.pseudomonas.com/ The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation. ^P\w+$ PSEEN0001 http://www.pseudomonas.com/feature/show/?locus_tag=$1 False PSEUDOMONAS pseudomonas pseudomonas psipar Protein Affinity Reagents https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms. ^PAR:\d+$ PAR:0116 https://www.ebi.ac.uk/ontology-lookup/?termId=$1 False PSIPAR psipar psipar -pso Plant Stress Ontology https://github.com/Planteome/plant-stress-ontology The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. ^\d{7}$ 0000013 cooperl@oregonstate.edu http://purl.obolibrary.org/obo/PSO_$1 False PSO PSO PSO pso PSO +pso Plant Stress Ontology https://github.com/Planteome/plant-stress-ontology The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter. ^\d{7}$ 0000013 cooperl@oregonstate.edu http://purl.obolibrary.org/obo/PSO_$1 False PSO PSO pso pso PSO pspub Phenoscape Publication https://wiki.phenoscape.org/wiki/Curation_workflow Documentation of the Phenoscape Curation Workflow False pubchem.bioassay NCBI PubChem database of bioassay records https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results. ^\d+$ 1018 https://pubchem.ncbi.nlm.nih.gov/bioassay/$1 False PUBCHEM.BIOASSAY 2638 pubchem.bioassay pubchem.bioassay pubchem.bioassay pubchem pubchem.cell PubChem Cell Line https://pubchem.ncbi.nlm.nih.gov Cell Lines in PubChem ^\d+$ 31 https://pubchem.ncbi.nlm.nih.gov/cell/$1 False pubchem @@ -1203,7 +1203,7 @@ pubchem.substance PubChem Substance ID (SID) https://pubchem.ncbi.nlm.nih.gov/ P publons.researcher Publons Researcher https://publons.com/researcher Database of researchers to track publications, citation metrics, peer reviews, and journal editing work. ^\d+$ 1981638 https://publons.com/researcher/$1 False pubmed PubMed https://www.ncbi.nlm.nih.gov/PubMed/ PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. ^\d+$ 16333295 https://www.ncbi.nlm.nih.gov/pubmed/$1 MEDLINE|PMID|pmid False PUBMED PubMed 000302 1187 pubmed pubmed pubmed P698 puro Publishing Roles Ontology http://www.sparontologies.net/ontologies/pro An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians. RoleInTime http://purl.org/spar/pro/$1 False -pw Pathway ontology http://rgd.mcw.edu/rgdweb/ontology/search.html The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions. ^\d{7}$ 0000423 gthayman@mcw.edu http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo False PW PW PW pw pw PW pw PW pw P7333 +pw Pathway ontology http://rgd.mcw.edu/rgdweb/ontology/search.html The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions. ^\d{7}$ 0000423 gthayman@mcw.edu http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/pathway/pathway.obo False PW PW PW pw pw pw pw PW pw P7333 pwo Publishing Workflow Ontology http://www.sparontologies.net/ontologies/pwo An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity. Workflow http://purl.org/spar/pwo/$1 False px ProteomeXchange http://www.proteomexchange.org/ The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination. ^(R)?PXD\d{6}$ PXD000500 http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1 False PX px px pypi PyPI https://www.python.org/psf/ The Python Package Index (PyPI) is a repository for Python packages. ^[a-zA-Z_][a-zA-Z0-9\-_]+$ numpy https://pypi.org/project/$1 False pypi @@ -1213,7 +1213,7 @@ radiomics Radiomics Ontology http://www.radiomics.org/RO The Radiomics Ontology rapdb.locus RAP-DB Locus https://rapdb.dna.affrc.go.jp/ Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB. ^Os\S+g\d{7}$ Os01g0883800 https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1 irgsp False rapdb.locus rapdb.transcript RAP-DB Transcript https://rapdb.dna.affrc.go.jp/ Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB. ^Os\S+t\d{7}-\d{2}$ Os01t0883800-02 https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1 False rapdb.transcript rbk Rebuilding a Kidney https://www.rebuildingakidney.org/ (Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. ^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$ Q-2958 https://www.rebuildingakidney.org/id/$1 False RBK rbk rbk -rbo Radiation Biology Ontology https://github.com/Radiobiology-Informatics-Consortium/RBO RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. ^\d{8}$ 00000105 daniel.c.berrios@nasa.gov http://purl.obolibrary.org/obo/RBO_$1 False RBO RBO RBO rbo RBO +rbo Radiation Biology Ontology https://github.com/Radiobiology-Informatics-Consortium/RBO RBO is an ontology for the effects of radiation on biota in terrestrial and space environments. ^\d{8}$ 00000105 daniel.c.berrios@nasa.gov http://purl.obolibrary.org/obo/RBO_$1 False RBO RBO rbo rbo RBO rcb RIKEN Bioresource Center Cell Bank https://cell.brc.riken.jp/en/rcb Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center. ^RCB\d+$ RCB0002 https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1 False RCB rdf Resource Description Framework http://www.w3.org/1999/02/22-rdf-syntax-ns This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts RDF http://www.w3.org/1999/02/22-rdf-syntax-ns#$1 False rdf rdfs RDF Schema https://www.w3.org/TR/rdf-schema/ RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary. label http://www.w3.org/2000/01/rdf-schema#$1 False RDFS rdfs RDFS @@ -1228,9 +1228,9 @@ reo Reagent Ontology https://github.com/tis-lab/reagent-ontology The Reagent Ont repeatsdb.protein RepeatsDB Protein https://repeatsdb.org/ RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database. ^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$ P29894 https://repeatsdb.org/protein/$1 False repeatsdb.protein uniprot repeatsdb.structure RepeatsDB Structure https://repeatsdb.org/ RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database. ^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$ 2gc4E https://repeatsdb.org/structure/$1 False repeatsdb.structure reproduceme REPRODUCE-ME Ontology https://w3id.org/reproduceme/research The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility. MicrobeamManipulation sheeba.samuel@uni-jena.de False REPRODUCE-ME REPRODUCE-ME reproduceme -resid Protein covalent bond https://proteininformationresource.org/resid/ The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. ^AA\d{4}$ AA0001 john.garavelli@ebi.ac.uk https://proteininformationresource.org/cgi-bin/resid?id=$1 True RESID 2619 resid resid RESID resid +resid Protein covalent bond https://proteininformationresource.org/resid/ The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. ^AA\d{4}$ AA0001 john.garavelli@ebi.ac.uk https://proteininformationresource.org/cgi-bin/resid?id=$1 True RESID 2619 resid resid resid resid reto Regulation of Transcription Ontology http://www.semantic-systems-biology.org/apo Regulation of Transcription vladimir.n.mironov@gmail.com https://www.bio.ntnu.no/ontology/ReTO/reto.owl https://www.bio.ntnu.no/ontology/ReTO/reto.obo False RETO RETO reto -rex Physico-chemical process https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. ^\d{7}$ 0000512 http://purl.obolibrary.org/obo/REX_$1 http://purl.obolibrary.org/obo/rex.owl True REX REX REX REX rex REX rex chebi +rex Physico-chemical process https://www.ebi.ac.uk/chebi/ An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. ^\d{7}$ 0000512 http://purl.obolibrary.org/obo/REX_$1 http://purl.obolibrary.org/obo/rex.owl True REX REX REX rex rex REX rex chebi rexo Regulation of Gene Expression Ontology http://www.semantic-systems-biology.org/apo Regulation of Gene Expression vladimir.n.mironov@gmail.com https://www.bio.ntnu.no/ontology/ReXO/rexo.owl https://www.bio.ntnu.no/ontology/ReXO/rexo.obo False REXO REXO rexo rfam Rfam database of RNA families https://rfam.xfam.org/ The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. ^RF\d{5}$ RF00230 https://rfam.xfam.org/family/$1 False RFAM 2356 rfam rfam rgd Rat Genome Database http://rgd.mcw.edu/ Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes. ^\d{4,}$ 7499841 http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1 RGD False RGD RGD RGD RGD 2620 rgd rgd rgd RGD P3853 @@ -1248,14 +1248,14 @@ ricenetdb.reaction RiceNetDB Reaction http://bis.zju.edu.cn/ricenetdb RiceNetDB rnacentral RNAcentral https://rnacentral.org/ RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. ^URS[0-9A-F]{10}(\_\d+)?$ URS0000759CF4 https://rnacentral.org/rna/$1 LNCRNADB False RNACENTRAL 3856 rnacentral rnacentral rnamod The RNA Modification Database http://rna.rega.kuleuven.be/rnamods/ A comprehensive listing of post-transcriptionally modified nucleosides from RNA - ^\d{3}$ 051 http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1 False rnamods RNA Modification Database http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. ^\d{3}$ 101 http://mods.rna.albany.edu/mods/modifications/view/$1 False RNAMODS rnamods rnamods rnamods -rnao RNA ontology https://github.com/bgsu-rna/rnao Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. ^\d{7}$ 0000128 BatchelorC@rsc.org http://purl.obolibrary.org/obo/RNAO_$1 True RNAO RNAO RNAO RNAO rnao RNAO rnao -ro Relation Ontology https://oborel.github.io/ The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. ^\d{7}$ 0002533 cjmungall@lbl.gov http://purl.obolibrary.org/obo/RO_$1 RO_proposed_relation|obo_rel|oborel False RO RO RO OBOREL ro ro RO ro RO ro P3590 +rnao RNA ontology https://github.com/bgsu-rna/rnao Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures. ^\d{7}$ 0000128 BatchelorC@rsc.org http://purl.obolibrary.org/obo/RNAO_$1 True RNAO RNAO RNAO rnao rnao RNAO rnao +ro Relation Ontology https://oborel.github.io/ The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies. ^\d{7}$ 0002533 cjmungall@lbl.gov http://purl.obolibrary.org/obo/RO_$1 RO_proposed_relation|obo_rel|oborel False RO RO RO OBOREL ro ro ro ro RO ro P3590 rouge Rodent Unidentified Gene-Encoded Large Proteins http://www.kazusa.or.jp/rouge/ The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. ^m\w+$ mKIAA4200 https://www.kazusa.or.jp/rouge/gfpage/$1 False ROUGE rouge rouge rouge Rouge rrid Research Resource Identification https://scicrunch.org/resolver "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools. The initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch." ^[a-zA-Z]+.+$ AB_262044 https://scicrunch.org/resolver/RRID:$1 False RRID rrid rrid -rs Rat Strain Ontology http://rgd.mcw.edu/rgdweb/search/strains.html Ontology of rat strains ^\d{7}$ 0001807 sjwang@mcw.edu http://purl.obolibrary.org/obo/RS_$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo False RS RS RS RS rs RS rs +rs Rat Strain Ontology http://rgd.mcw.edu/rgdweb/search/strains.html Ontology of rat strains ^\d{7}$ 0001807 sjwang@mcw.edu http://purl.obolibrary.org/obo/RS_$1 https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.owl https://download.rgd.mcw.edu/pub/data_release/ontology_obo_files/rat_strain/rat_strain.obo False RS RS RS rs rs RS rs runbiosimulations runBioSimulations https://icahn.mssm.edu/ runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive. ^[0-9a-z]{24,24}$ 5fde96bdc5f1aa9ff0cce18a https://run.biosimulations.org/simulations/$1 False runbiosimulations -rxno Name Reaction Ontology https://github.com/rsc-ontologies/rxno RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. ^\d{7}$ 0000253 batchelorc@rsc.org http://purl.obolibrary.org/obo/RXNO_$1 https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo False RXNO RXNO RXNO RXNO rxno RXNO P2106 +rxno Name Reaction Ontology https://github.com/rsc-ontologies/rxno RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization. ^\d{7}$ 0000253 batchelorc@rsc.org http://purl.obolibrary.org/obo/RXNO_$1 https://github.com/rsc-ontologies/rxno/raw/master/rxno.obo False RXNO RXNO RXNO rxno rxno RXNO P2106 rxnorm RxNorm https://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary. ^[0-9]{1,7}$ 221058 https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1 RXCUI False RXNORM RXCUI RXNORM P3345 sabiork.compound SABIO-RK Compound http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information. ^\d+$ 75 http://sabiork.h-its.org/newSearch?q=$1 False sabiork.compound sabiork.compound sabiork.ec SABIO-RK EC Record http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data. ^((\d+)|(\d+\.\d+)|(\d+\.\d+\.\d+)|(\d+\.\d+\.\d+\.\d+))$ 2.7.1.1 http://sabiork.h-its.org/newSearch?q=ecnumber:$1 False SABIORK.EC sabiork.ec sabiork.ec sabiork.ec eccode @@ -1263,10 +1263,10 @@ sabiork.kineticrecord SABIO Reaction Kinetics http://sabiork.h-its.org/ SABIO-RK sabiork.reaction SABIO-RK Reaction http://sabiork.h-its.org/ SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information. ^\d+$ 75 http://sabiork.h-its.org/reacdetails.jsp?reactid=$1 SABIO-RK False SABIORK.REACTION 2309 sabiork.reaction sabiork.reaction sabiork.reaction SABIO-RK sael Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List True salk Salk Institute for Biological Studies https://www.salk.edu/ Scientific research institute for neuroscience, genetics, immunology, plant biology and more. ^\d{6}$ 037727 https://abrc.osu.edu/stocks/number/SALK_$1 False -sao Subcellular Anatomy Ontology http://ccdb.ucsd.edu/CCDBWebSite/sao.html ^\d+$ 5277619 slarson@ncmir.ucsd.edu http://uri.neuinfo.org/nif/nifstd/sao$1 True SAO SAO SAO SAO sao +sao Subcellular Anatomy Ontology http://ccdb.ucsd.edu/CCDBWebSite/sao.html ^\d+$ 5277619 slarson@ncmir.ucsd.edu http://uri.neuinfo.org/nif/nifstd/sao$1 True SAO SAO SAO sao sao sasbdb Small Angle Scattering Biological Data Bank http://www.sasbdb.org/ Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data. ^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$ SASDAX8 http://www.sasbdb.org/data/$1 False SASBDB sasbdb sasbdb SASBDB -sbo Systems Biology Ontology http://www.ebi.ac.uk/sbo/ The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. ^\d{7}$ 0000485 sheriff@ebi.ac.uk https://www.ebi.ac.uk/sbo/main/SBO:$1 False SBO SBO SBO sbo sbo SBO sbo SBO sbo -scdo Sickle Cell Disease Ontology https://scdontology.h3abionet.org/ An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. ^\d{7}$ 0000728 giant.plankton@gmail.com http://purl.obolibrary.org/obo/SCDO_$1 False SCDO SCDO SCDO scdo SCDO +sbo Systems Biology Ontology http://www.ebi.ac.uk/sbo/ The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort. ^\d{7}$ 0000485 sheriff@ebi.ac.uk https://www.ebi.ac.uk/sbo/main/SBO:$1 False SBO SBO SBO sbo sbo sbo sbo SBO sbo +scdo Sickle Cell Disease Ontology https://scdontology.h3abionet.org/ An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease. ^\d{7}$ 0000728 giant.plankton@gmail.com http://purl.obolibrary.org/obo/SCDO_$1 False SCDO SCDO scdo scdo SCDO schem Selventa Chemicals https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt Selventa legacy chemical namespace used with the Biological Expression Language ^A\d{4}$ A0001 https://biopragmatics.github.io/providers/schem/$1 False schema Schema.org https://schema.org Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. Person https://schema.org/$1 False SCHEMA SCHEMA scholia.resource Scholia Registry https://scholia.toolforge.org/ A frontend to Wikidata doi https://bioregistry.io/metaregistry/scholia/$1 False @@ -1286,14 +1286,14 @@ sedml.language SED-ML model format http://sed-ml.org/ Model format that can be u seed The SEED; http://seed-viewer.theseed.org/seedviewer.cgi This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. ^\w+$ Biotin_biosynthesis http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1 False SEED seed seed seed.compound SEED Compound http://modelseed.org/ This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems. ^cpd\d+$ cpd15380 http://modelseed.org/biochem/compounds/$1 False SEED.COMPOUND seed.compound seed.compound seed.reaction SEED Reactions http://modelseed.org/biochem/reactions/ ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions. ^rxn\d+$ rxn00001 http://modelseed.org/biochem/reactions/$1 False seed.reaction seed.reaction -sep Sample processing and separation techniques https://psidev.info/sepcv A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. ^\d{5}$ 00073 psidev-gps-dev@lists.sourceforge.net http://purl.obolibrary.org/obo/SEP_$1 https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo True SEP SEP SEP SEP SEP sep -sepio Scientific Evidence and Provenance Information Ontology https://github.com/monarch-initiative/SEPIO-ontology An ontology for representing the provenance of scientific claims and the evidence that supports them. ^\d{7}$ 0000048 mhb120@gmail.com http://purl.obolibrary.org/obo/SEPIO_$1 False SEPIO SEPIO SEPIO SEPIO sepio SEPIO +sep Sample processing and separation techniques https://psidev.info/sepcv A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments. ^\d{5}$ 00073 psidev-gps-dev@lists.sourceforge.net http://purl.obolibrary.org/obo/SEP_$1 https://raw.githubusercontent.com/HUPO-PSI/gelml/master/CV/sep.obo True SEP SEP SEP sep SEP sep +sepio Scientific Evidence and Provenance Information Ontology https://github.com/monarch-initiative/SEPIO-ontology An ontology for representing the provenance of scientific claims and the evidence that supports them. ^\d{7}$ 0000048 mhb120@gmail.com http://purl.obolibrary.org/obo/SEPIO_$1 False SEPIO SEPIO SEPIO sepio sepio SEPIO sfam Selventa Families https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt Selventa legacy protein family namespace used with the Biological Expression Language ^F\d{4}$ F0001 https://biopragmatics.github.io/providers/sfam/$1 False sgd Saccharomyces Genome Database https://www.yeastgenome.org/ The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae. ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$ S000002493 https://www.yeastgenome.org/locus/$1 False SGD 2632 sgd sgd sgd SGD P3406 sgd.pathways Saccharomyces genome database pathways http://pathway.yeastgenome.org/ Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). ^PWY\w{2}\-\d{3}$ PWY3O-214 http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1 False SGD.PATHWAYS sgd.pathways sgd.pathways sgd.pathways sgn Sol Genomics Network http://solgenomics.net/ The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant. ^\d+$ 0001 http://solgenomics.net/phenome/locus_display.pl?locus_id=$1 False SGN sgn sgn sgn sheepqtldb Animal Genome Sheep QTL https://www.animalgenome.org/QTLdb The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs. ^\d+$ 19803 https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1 False SHEEPQTLDB sheepqtldb sheepqtldb sheepqtldb qtldb -sibo Social Insect Behavior Ontology https://github.com/obophenotype/sibo Social Behavior in insects ^\d{7}$ 0000509 cjmungall@lbl.gov http://purl.obolibrary.org/obo/SIBO_$1 True SIBO SIBO SIBO SIBO sibo SIBO +sibo Social Insect Behavior Ontology https://github.com/obophenotype/sibo Social Behavior in insects ^\d{7}$ 0000509 cjmungall@lbl.gov http://purl.obolibrary.org/obo/SIBO_$1 True SIBO SIBO SIBO sibo sibo SIBO sider.drug SIDER Drug http://sideeffects.embl.de/ SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER. ^\d+$ 2244 http://sideeffects.embl.de/drugs/$1 False SIDER.DRUG sider.drug sider.drug sider.effect SIDER Side Effect http://sideeffects.embl.de/ SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER. ^C\d+$ C0017565 http://sideeffects.embl.de/se/$1 False SIDER.EFFECT sider.effect sider.effect umls sigmaaldrich Sigma Aldrich https://www.sigmaaldrich.com Sigma Aldrich is a life sciences supply vendor. HPA000698 https://www.sigmaaldrich.com/US/en/product/sigma/$1 False @@ -1316,11 +1316,11 @@ snornabase snoRNABase https://www-snorna.biotoul.fr/ "A comprehensive database o human H/ACA and C/D box snoRNAs." SR0000178 False snp2tfbs SNP to Transcription Factor Binding Sites https://ccg.epfl.ch/snp2tfbs/ SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome. ^rs[0-9]+$ rs11603840 https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1 False snp2tfbs dbsnp -so Sequence types and features ontology http://www.sequenceontology.org/ The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. ^\d{7}$ 0001157 keilbeck@genetics.utah.edu http://www.sequenceontology.org/miso/current_release/term/SO:$1 https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo False SO SO SO SO so so SO so SO so -sopharm Suggested Ontology for Pharmacogenomics http://www.loria.fr/~coulet/sopharm2.0_description.php Adrien.Coulet@loria.fr http://purl.obolibrary.org/obo/SOPHARM_$1 True SOPHARM SOPHARM SOPHARM SOPHARM +so Sequence types and features ontology http://www.sequenceontology.org/ The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data. ^\d{7}$ 0001157 keilbeck@genetics.utah.edu http://www.sequenceontology.org/miso/current_release/term/SO:$1 https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/Ontology_Files/so.obo False SO SO SO SO so so so so SO so +sopharm Suggested Ontology for Pharmacogenomics http://www.loria.fr/~coulet/sopharm2.0_description.php Adrien.Coulet@loria.fr http://purl.obolibrary.org/obo/SOPHARM_$1 True SOPHARM SOPHARM SOPHARM sopharm soybase Glycine max Genome Database http://soybase.org/ SoyBase is a repository for curated genetics, genomics and related data resources for soybean. ^\w+(\-)?\w+(\-)?\w+$ BARC-013845-01256 http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1 False SOYBASE soybase soybase span Span http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality. False -spd Spider Ontology http://research.amnh.org/atol/files/ An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). ^\d{7}$ 0000001 ramirez@macn.gov.ar http://purl.obolibrary.org/obo/SPD_$1 False SPD SPD SPD SPD spd SPD spd P4537 +spd Spider Ontology http://research.amnh.org/atol/files/ An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow). ^\d{7}$ 0000001 ramirez@macn.gov.ar http://purl.obolibrary.org/obo/SPD_$1 False SPD SPD SPD spd spd SPD spd P4537 spdx Software Package Data Exchange License https://spdx.org/licenses The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception. ^[0-9A-Za-z\-.]+$ CC-BY-1.0 https://spdx.org/licenses/$1 False spdx spdx spike.map SPIKE Map http://www.cs.tau.ac.il/~spike/ SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps. ^spike\d{5}$ spike00001 http://www.cs.tau.ac.il/~spike/maps/$1.html False SPIKE.MAP spike.map spike.map splash Spectra Hash Code http://mona.fiehnlab.ucdavis.edu/ The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance. ^splash\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$ splash10-0zq2000000-77302b0326a418630a84 http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1 False SPLASH splash splash @@ -1330,7 +1330,7 @@ srao FAIRsharing Subject Ontology https://github.com/FAIRsharing/subject-ontolog ssbd.dataset System Science of Biological Dynamics dataset https://ssbd.riken.jp Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. ^\d+$ 1 https://ssbd.riken.jp/database/dataset/$1 False ssbd.project System Science of Biological Dynamics project https://ssbd.riken.jp Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations. ^\d+$ 1 https://ssbd.riken.jp/database/project/$1 False stap Statistical Torsional Angles Potentials http://psb.kobic.re.kr/STAP/refinement/ STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). ^[0-9][A-Za-z0-9]{3}$ 1a24 http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 False STAP stap stap -stato The Statistical Methods Ontology http://stato-ontology.org/ STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. ^\d{7}$ 0000288 alejandra.gonzalez.beltran@gmail.com http://purl.obolibrary.org/obo/STATO_$1 False STATO STATO STATO STATO stato STATO +stato The Statistical Methods Ontology http://stato-ontology.org/ STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. ^\d{7}$ 0000288 alejandra.gonzalez.beltran@gmail.com http://purl.obolibrary.org/obo/STATO_$1 False STATO STATO STATO stato stato STATO stitch Search Tool for Interactions of Chemicals http://stitch.embl.de/ STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. ^\w{14}$ BQJCRHHNABKAKU http://stitch.embl.de/interactions/$1 False STITCH stitch stitch stitch storedb Store DB https://www.storedb.org/ STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. ^(STUDY|FILE|DATASET)\d+$ STUDY1040 https://www.storedb.org/?$1 False STOREDB storedb storedb storedb.dataset STOREDB at University of Cambridge https://www.storedb.org/ Datasets inside StoreDB ^\d+$ 1251 https://www.storedb.org/?STOREDB:DATASET$1 True storedb @@ -1350,32 +1350,32 @@ swh Software Heritage https://archive.softwareheritage.org Software Heritage is swiss-model SWISS-MODEL Repository https://swissmodel.expasy.org The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences. ^\w+$ P23298 https://swissmodel.expasy.org/repository/uniprot/$1 False SWISS-MODEL swiss-model swiss-model swissmodel uniprot swisslipid SwissLipid http://www.swisslipids.org/#/ SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions. ^\d+$ 000000341 https://www.swisslipids.org/#/entity/SLM:$1 slm|swisslipids False SWISSLIPID slm swisslipid SwissLipids P8691 swissregulon SwissRegulon http://swissregulon.unibas.ch A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. ^[A-Za-z0-9]+$ AHR http://swissregulon.unibas.ch/query/$1 False SWISSREGULON swissregulon swissregulon -swo Software ontology https://github.com/allysonlister/swo The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. ^\d{7}$ 0000144 allyson.lister@oerc.ox.ac.uk http://purl.obolibrary.org/obo/SWO_$1 https://github.com/allysonlister/swo/raw/master/release/swo.owl False SWO SWO SWO SWO swo SWO swo -symp Symptom Ontology http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. ^\d{7}$ 0019171 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/SYMP_$1 SYMP False SYMP SYMP SYMP SYMP symp SYMP P8656 +swo Software ontology https://github.com/allysonlister/swo The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. ^\d{7}$ 0000144 allyson.lister@oerc.ox.ac.uk http://purl.obolibrary.org/obo/SWO_$1 https://github.com/allysonlister/swo/raw/master/release/swo.owl False SWO SWO SWO swo swo SWO swo +symp Symptom Ontology http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases. ^\d{7}$ 0019171 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/SYMP_$1 SYMP False SYMP SYMP SYMP symp symp SYMP P8656 syoid Gemina Symptom Ontology True t3db Toxin and Toxin Target Database http://www.t3db.org/ Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. ^T3D\d+$ T3D0001 http://www.t3db.org/toxins/$1 False T3DB 2662 t3db t3db t3db -tads Tick Anatomy Ontology https://www.vectorbase.org/ontology-browser The anatomy of the Tick, Families: Ixodidae, Argassidae ^\d{7}$ 0000547 dsonensh@odu.edu http://purl.obolibrary.org/obo/TADS_$1 http://purl.obolibrary.org/obo/tads.obo True TADS TADS TADS TADS tads TADS -tahe Terminology of Anatomy of Human Embryology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHE_$1 True TAHE TAHE -tahh Terminology of Anatomy of Human Histology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHH_$1 True TAHH TAHH +tads Tick Anatomy Ontology https://www.vectorbase.org/ontology-browser The anatomy of the Tick, Families: Ixodidae, Argassidae ^\d{7}$ 0000547 dsonensh@odu.edu http://purl.obolibrary.org/obo/TADS_$1 http://purl.obolibrary.org/obo/tads.obo True TADS TADS TADS tads tads TADS +tahe Terminology of Anatomy of Human Embryology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHE_$1 True TAHE tahe +tahh Terminology of Anatomy of Human Histology pierre.sprumont@unifr.ch http://purl.obolibrary.org/obo/TAHH_$1 True TAHH tahh tair.gene TAIR Gene http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus. ^\d{7}$ 2200934 http://arabidopsis.org/servlets/TairObject?accession=Gene:$1 False TAIR.GENE tair.gene tair.gene tair.gene tair.locus The Arabidopsis Information Resource http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS. ^\d+$ 2200950 http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 False TAIR.LOCUS tair.locus tair.locus tair.locus tair.protein TAIR Protein http://arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept ^\d{10}$ 1009107926 http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1 False TAIR.PROTEIN tair.protein tair.protein tair.protein -tao Teleost Anatomy Ontology http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa ^\d{7}$ 0000086 wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/TAO_$1 TAO_RETIRED True TAO TAO TAO TAO tao +tao Teleost Anatomy Ontology http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa ^\d{7}$ 0000086 wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/TAO_$1 TAO_RETIRED True TAO TAO TAO tao tao tarbase TarBase http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used. ^[a-z]{3}\-(mir|let|lin)\-\w+(\-\w+\-\w+)$ hsa-let-7a-2-3p http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1 False TARBASE tarbase tarbase -taxrank Taxonomic rank vocabulary https://github.com/phenoscape/taxrank A vocabulary of taxonomic ranks (species, family, phylum, etc) ^\d{7}$ 0000001 balhoff@renci.org http://purl.obolibrary.org/obo/TAXRANK_$1 False TAXRANK TAXRANK TAXRANK TAXRANK taxrank TAXRANK taxrank +taxrank Taxonomic rank vocabulary https://github.com/phenoscape/taxrank A vocabulary of taxonomic ranks (species, family, phylum, etc) ^\d{7}$ 0000001 balhoff@renci.org http://purl.obolibrary.org/obo/TAXRANK_$1 False TAXRANK TAXRANK TAXRANK taxrank taxrank TAXRANK taxrank tcb Tick Cell Biobank https://www.pirbright.ac.uk/tick-cell-lines-views-page Cell line collections ^\d+$ 2966 https://www.pirbright.ac.uk/node/$1 False TCB tcdb Transporter Classification Database https://www.tcdb.org The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally. ^\d+(\.[A-Z])?(\.\d+)?(\.\d+)?(\.\d+)?$ 5.A.1.1.1 http://www.tcdb.org/search/result.php?tc=$1 TC False TCDB 2756 tcdb tcdb tcdb TCDB P7260 te Terminologia Embryologica https://ifaa.unifr.ch/ The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia] E5.11.2.0.0.0.4 False P1693 tfclass Classification of Transcription Factors in Mammalia http://tfclass.bioinf.med.uni-goettingen.de TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.. 2.1.1 http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1 False tgd Tetrahymena Genome Database http://ciliate.org/index.php/ The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature. ^TTHERM\_\d+$ TTHERM_00648910 http://ciliate.org/index.php/feature/details/$1 False TGD tgd tgd tgd -tgma Mosquito gross anatomy ontology https://www.vectorbase.org/ontology-browser A structured controlled vocabulary of the anatomy of mosquitoes. ^\d{7}$ 0000984 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/TGMA_$1 http://purl.obolibrary.org/obo/tgma.obo True TGMA TGMA TGMA TGMA tgma TGMA tgma +tgma Mosquito gross anatomy ontology https://www.vectorbase.org/ontology-browser A structured controlled vocabulary of the anatomy of mosquitoes. ^\d{7}$ 0000984 topalis@imbb.forth.gr http://purl.obolibrary.org/obo/TGMA_$1 http://purl.obolibrary.org/obo/tgma.obo True TGMA TGMA TGMA tgma tgma TGMA tgma tgn Getty Thesaurus of Geographic Names https://www.getty.edu/research/tools/vocabularies/tgn/ ^\d+$ 1023371 http://vocab.getty.edu/page/tgn/$1 True th Terminologia Histologica https://ifaa.unifr.ch/ The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] H3.03.00.0.00007 False thermofisher Thermo Fisher Scientific https://www.thermofisher.com ThermoFisher is a life sciences supply vendor. OSR00185W https://www.thermofisher.com/antibody/product/$1 False tigrfam TIGR protein families http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. ^TIGR\d+$ TIGR00010 https://www.ncbi.nlm.nih.gov/cdd?term=$1 False TIGRFAM 1141 tigrfam tigrfam tkg Tohoku University cell line catalog http://www2.idac.tohoku.ac.jp/dep/ccr/ Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. ^\d+$ 0221 http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html False TKG tngb Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections ^\d+$ 67035 http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 False TNGB -to Plant Trait Ontology http://browser.planteome.org/amigo A controlled vocabulary to describe phenotypic traits in plants. ^\d{7}$ 0000630 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/TO_$1 False TO TO TO PTO TO to TO +to Plant Trait Ontology http://browser.planteome.org/amigo A controlled vocabulary to describe phenotypic traits in plants. ^\d{7}$ 0000630 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/TO_$1 False TO TO TO PTO to to TO tokue TOKU-E Cell-culture Database http://cell-lines.toku-e.com Cell line databases/resources http://cell-lines.toku-e.com/Cell-Lines_$1.html True TOKU-E tol Tree of Life Web Project ID http://tolweb.org/tree/ "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). @@ -1383,7 +1383,7 @@ Each page contains information about a particular group, with pages linked one t topdb Topology Data Bank of Transmembrane Proteins http://topdb.enzim.hu/ The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. ^[A-Z0-9]+$ AP00378 http://topdb.enzim.hu/?m=show&id=$1 False TOPDB 2789 topdb topdb topdb topfind TopFind https://topfind.clip.msl.ubc.ca TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$ Q9UKQ2 http://clipserve.clip.ubc.ca/topfind/proteins/$1 False TOPFIND topfind topfind uniprot toxoplasma ToxoDB http://toxodb.org/toxo/ ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+$ TGME49_053730 http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False TOXOPLASMA toxoplasma toxoplasma -trans Pathogen Transmission Ontology https://github.com/DiseaseOntology/PathogenTransmissionOntology The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. ^\d{7}$ 0000024 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/TRANS_$1 False TRANS TRANS TRANS TRANS trans TRANS +trans Pathogen Transmission Ontology https://github.com/DiseaseOntology/PathogenTransmissionOntology The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles. ^\d{7}$ 0000024 lynn.schriml@gmail.com http://purl.obolibrary.org/obo/TRANS_$1 False TRANS TRANS TRANS trans trans TRANS transyt Transport Systems Tracker https://www.bio.di.uminho.pt/ The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. ^T[A-Z]\d{7}$ TR0000001 https://transyt.bio.di.uminho.pt/reactions/$1 False transyt treebase TreeBASE http://treebase.org/ TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc. ^TB[1,2]?:[A-Z][a-z]?\d+$ TB2:S1000 http://purl.org/phylo/treebase/phylows/study/$1?format=html False TREEBASE treebase treebase treebase treefam TreeFam http://www.treefam.org/ TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. ^\w{1,2}\d+$ TF101014 http://www.treefam.org/family/$1 False TREEFAM treefam treefam treefam TreeFam @@ -1391,13 +1391,13 @@ trichdb TrichDB http://trichdb.org/trichdb/ TrichDB is one of the databases that tritrypdb TriTrypDB http://tritrypdb.org/tritrypdb/ TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. ^\w+(\.)?\w+(\.)?\w+$ Tb927.8.620 http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1 False TRITRYPDB tritrypdb tritrypdb ttd.drug TTD Drug http://bidd.nus.edu.sg/group/ttd/ttd.asp The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. ^DAP\d+$ DAP000773 http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1 False TTD.DRUG 2653 ttd.drug ttd.drug ttd.target TTD Target http://bidd.nus.edu.sg/group/ttd/ttd.asp The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. ^TTDS\d+$ TTDS00056 http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1 False TTD.TARGET 2654 ttd.target ttd.target -tto Teleost taxonomy ontology https://github.com/phenoscape/teleost-taxonomy-ontology An ontology covering the taxonomy of teleosts (bony fish) ^\d+$ 1058367 balhoff@renci.org http://purl.obolibrary.org/obo/TTO_$1 False TTO TTO TTO TTO tto TTO tto +tto Teleost taxonomy ontology https://github.com/phenoscape/teleost-taxonomy-ontology An ontology covering the taxonomy of teleosts (bony fish) ^\d+$ 1058367 balhoff@renci.org http://purl.obolibrary.org/obo/TTO_$1 False TTO TTO TTO tto tto TTO tto txpo Toxic Process Ontology https://toxpilot.nibiohn.go.jp/ "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms. -In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp" ^\d{7}$ 0002066 yuki.yamagata@riken.jp http://purl.obolibrary.org/obo/TXPO_$1 False TXPO TXPO TXPO txpo TXPO -uberon Uber Anatomy Ontology http://uberon.org Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. ^\d+$ 2005080 cjmungall@lbl.gov http://purl.obolibrary.org/obo/UBERON_$1 http://purl.obolibrary.org/obo/uberon/basic.obo UBERON|Uber-anatomy ontology|Uberon False UBERON UBERON UBERON UBERON uberon uberon UBERON uberon UBERON P1554 +In applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp" ^\d{7}$ 0002066 yuki.yamagata@riken.jp http://purl.obolibrary.org/obo/TXPO_$1 False TXPO TXPO txpo txpo TXPO +uberon Uber Anatomy Ontology http://uberon.org Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. ^\d+$ 2005080 cjmungall@lbl.gov http://purl.obolibrary.org/obo/UBERON_$1 http://purl.obolibrary.org/obo/uberon/basic.obo UBERON|Uber-anatomy ontology|Uberon False UBERON UBERON UBERON UBERON uberon uberon uberon uberon UBERON P1554 ubio.namebank uBio NameBank http://www.ubio.org "NameBank is a ""biological name server"" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context." ^\d+$ 2555646 http://www.ubio.org/browser/details.php?namebankID=$1 False UBIO.NAMEBANK ubio.namebank ubio.namebank ubprop Uberon Property True ucsc UCSC Genome Browser https://genome.ucsc.edu/ The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. uc001rvw.5 ftp://hgdownload.cse.ucsc.edu/goldenPath/$1 False UCSC UCSC P2576 @@ -1430,13 +1430,13 @@ unirule UniRule https://www.uniprot.org/unirule/ Rules are devised and tested by unists Database of Sequence Tagged Sites https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. ^\d+$ 456789 https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1 False UNISTS 2389 unists unists unists unite Molecular database for the identification of fungi http://unite.ut.ee/ UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa. ^UDB\d{6}$ UDB000691 http://unite.ut.ee/bl_forw.php?nimi=$1 False UNITE 2390 unite unite unite unpd Universal Natural Products Database http://pkuxxj.pku.edu.cn/UNPD/ True -uo Units of measurement ontology https://github.com/bio-ontology-research-group/unit-ontology Ontology of standardized units ^\d{7}$ 0000080 g.gkoutos@gmail.com https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1 False UO UO UO uo uo UO uo UO uo -upa Unipathway https://github.com/geneontology/unipathway A manually curated resource for the representation and annotation of metabolic pathways ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ UCR00513 Anne.Morgat@sib.swiss http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo UPa|unipathway|unipathway.pathway True UPA UNIPATHWAY UPA 2645 UPA upa UPA unipathway UniPathway -upheno Unified Phenotype Ontology https://github.com/obophenotype/upheno The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/UPHENO_$1 https://github.com/obophenotype/upheno/blob/master/upheno.owl False UPHENO UPHENO UPHENO UPHENO upheno UPHENO +uo Units of measurement ontology https://github.com/bio-ontology-research-group/unit-ontology Ontology of standardized units ^\d{7}$ 0000080 g.gkoutos@gmail.com https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1 False UO UO UO uo uo uo uo UO uo +upa Unipathway https://github.com/geneontology/unipathway A manually curated resource for the representation and annotation of metabolic pathways ^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\d{5}$ UCR00513 Anne.Morgat@sib.swiss http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1 https://raw.githubusercontent.com/geneontology/unipathway/master/upa.obo UPa|unipathway|unipathway.pathway True UPA UNIPATHWAY UPA 2645 upa upa UPA unipathway UniPathway +upheno Unified Phenotype Ontology https://github.com/obophenotype/upheno The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology. vasilevs@ohsu.edu http://purl.obolibrary.org/obo/UPHENO_$1 https://github.com/obophenotype/upheno/blob/master/upheno.owl False UPHENO UPHENO UPHENO upheno upheno UPHENO uspto United States Patent and Trademark Office http://patft.uspto.gov/netahtml/PTO/index.html The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement. ^(D|PP|R|T|H|X|AI)?\d+$ 4145692 http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1 False USPTO uspto uspto validatordb ValidatorDB https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ Database of validation results for ligands and non-standard residues in the Protein Data Bank. ^[A-Za-z0-9\/]+$ 2h6o https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1 False VALIDATORDB validatordb validatordb pdb vandf Veterans Administration National Drug File https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. ^\d+$ 4019477 False VANDF VANDF -vario Variation Ontology http://variationontology.org The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. ^\d+$ 0376 mauno.vihinen@med.lu.se http://purl.obolibrary.org/obo/VARIO_$1 True VARIO VARIO VARIO VARIO vario vario VariO vario VariO +vario Variation Ontology http://variationontology.org The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level. ^\d+$ 0376 mauno.vihinen@med.lu.se http://purl.obolibrary.org/obo/VARIO_$1 True VARIO VARIO VARIO VARIO vario vario vario vario VariO vbase2 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse http://www.vbase2.org/vbase2.php The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. ^\w+$ humIGHV025 http://www.vbase2.org/vgene.php?id=$1 False VBASE2 vbase2 vbase2 vbase2 vbrc Viral Bioinformatics Resource Center http://vbrc.org/ The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. ^\d+$ 35742 http://vbrc.org/gene_detail.asp?gene_id=$1 False VBRC vbrc vbrc vbrc vcell VCell Published Models https://health.uconn.edu/ Models developed with the Virtual Cell (VCell) software prorgam. ^\d{5,}$ 201022999 https://vcell.org/biomodel-$1 False vcell @@ -1447,7 +1447,7 @@ vfb Virtual Fly Brain https://VirtualFlyBrain.org An interactive tool for neurob vfdb.gene VFDB Gene http://www.mgc.ac.cn/VFs/ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes. ^\w+$ VFG2154 http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1 False VFDB.GENE vfdb.gene vfdb.gene vfdb.genus VFDB Genus http://www.mgc.ac.cn/VFs/ VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus. ^\w+$ Chlamydia http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1 False VFDB.GENUS vfdb.genus vfdb.genus vgnc Vertebrate Gene Nomenclature Committee https://vertebrate.genenames.org The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. ^((VGNC|vgnc):)?\d{1,9}$ VGNC:3792 https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1 False VGNC vgnc VGNC -vhog Vertebrate Homologous Organ Group Ontology ^\d{7}$ 0000411 http://purl.obolibrary.org/obo/VHOG_$1 ftp://ftp.bgee.org/general/ontologies/vHOG.obo VHOG_RETIRED True VHOG VHOG VHOG VHOG vhog +vhog Vertebrate Homologous Organ Group Ontology ^\d{7}$ 0000411 http://purl.obolibrary.org/obo/VHOG_$1 ftp://ftp.bgee.org/general/ontologies/vHOG.obo VHOG_RETIRED True VHOG VHOG VHOG vhog vhog viaf Virtual International Authority File http://viaf.org The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web. ^\d+$ 75121530 http://viaf.org/viaf/$1 False viaf viaf vido The Virus Infectious Disease Ontology https://github.com/infectious-disease-ontology-extensions/ido-virus The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc. ^\d{7}$ 0001114 johnbeverley2021@u.northwestern.edu False VIDO VIDO vido VIDO vipr Virus Pathogen Resource http://www.viprbrc.org/brc/home.do?decorator=vipr The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information. ^[A-Za-z 0-9]+$ BeAn 70563 http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena False VIPR vipr vipr @@ -1457,19 +1457,19 @@ vmc Variation Modelling Collaboration True vmhgene VMH Gene https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[0-9]+\.[0-9]+$ 8639.1 https://www.vmh.life/#gene/$1 False vmhgene vmhmetabolite VMH metabolite https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[a-zA-Z0-9_\(\_\)\[\]]+$ h2o https://www.vmh.life/#metabolite/$1 False VMHMETABOLITE vmhmetabolite vmhmetabolite vmhreaction VMH reaction https://www.vmh.life/ The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease. ^[a-zA-Z0-9_\(\_\)\[\]]+$ HEX1 https://www.vmh.life/#reaction/$1 False VMHREACTION vmhreaction vmhreaction -vo Vaccine Ontology http://www.violinet.org/vaccineontology The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. ^\d{7}$ 0000093 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/VO_$1 False VO VO VO VO vo VO vo +vo Vaccine Ontology http://www.violinet.org/vaccineontology The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities. ^\d{7}$ 0000093 yongqunh@med.umich.edu http://purl.obolibrary.org/obo/VO_$1 False VO VO VO vo vo VO vo void Vocabulary of Interlinked Datasets http://vocab.deri.ie/void The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary. feature http://rdfs.org/ns/void#$1 False void -vsao Vertebrate Skeletal Anatomy Ontology https://www.nescent.org/phenoscape/Main_Page Vertebrate skeletal anatomy ontology. wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/VSAO_$1 VSAO_RETIRED True VSAO VSAO VSAO VSAO +vsao Vertebrate Skeletal Anatomy Ontology https://www.nescent.org/phenoscape/Main_Page Vertebrate skeletal anatomy ontology. wasila.dahdul@usd.edu http://purl.obolibrary.org/obo/VSAO_$1 VSAO_RETIRED True VSAO VSAO VSAO vsao vsdb Veterinary Substances DataBase https://sitem.herts.ac.uk/aeru/vsdb Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source. ^\d+$ 1868 https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm False vso Vital Sign Ontology https://bioportal.bioontology.org/ontologies/VSO The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. ^\d{7}$ 0000041 https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1 False VSO VSO vso -vt Vertebrate trait ontology https://github.com/AnimalGenome/vertebrate-trait-ontology An ontology of traits covering vertebrates ^\d{7}$ 0000685 caripark@iastate.edu http://purl.obolibrary.org/obo/VT_$1 https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo False VT VT VT VT VT vt VT vt -vto Vertebrate Taxonomy Ontology https://github.com/phenoscape/vertebrate-taxonomy-ontology Comprehensive hierarchy of extinct and extant vertebrate taxa. ^\d{7}$ 9008500 balhoff@renci.org http://purl.obolibrary.org/obo/VTO_$1 False VTO VTO VTO VTO vto VTO +vt Vertebrate trait ontology https://github.com/AnimalGenome/vertebrate-trait-ontology An ontology of traits covering vertebrates ^\d{7}$ 0000685 caripark@iastate.edu http://purl.obolibrary.org/obo/VT_$1 https://github.com/AnimalGenome/vertebrate-trait-ontology/raw/master/current_release/vt.obo False VT VT VT VT vt vt VT vt +vto Vertebrate Taxonomy Ontology https://github.com/phenoscape/vertebrate-taxonomy-ontology Comprehensive hierarchy of extinct and extant vertebrate taxa. ^\d{7}$ 9008500 balhoff@renci.org http://purl.obolibrary.org/obo/VTO_$1 False VTO VTO VTO vto vto VTO vuid Veterans Health Administration (VHA) unique identifier https://www.va.gov/health The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year. ^\d+$ 4007166 False vz ViralZone http://viralzone.expasy.org/ ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ^\d+$ 886 https://viralzone.expasy.org/$1 False vz wb.rnai WormBase RNAi https://www.wormbase.org/ WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes. ^WBRNAi\d{8}$ WBRNAi00086878 https://www.wormbase.org/species/c_elegans/rnai/$1 False WB.RNAI wb.rnai wb.rnai -wbbt C. elegans Gross Anatomy Ontology https://github.com/obophenotype/c-elegans-gross-anatomy-ontology Ontology about the gross anatomy of the C. elegans ^\d{7}$ 0001290 raymond@caltech.edu http://purl.obolibrary.org/obo/WBbt_$1 WBbt False WBBT WBbt WB-BT WBbt wbbt WBbt wbbt -wbls C. elegans development ontology https://github.com/obophenotype/c-elegans-development-ontology Ontology about the development and life stages of the C. elegans ^\d{7}$ 0000690 cgrove@caltech.edu http://www.wormbase.org/get?name=$1 WBls False WBLS WBLS WB-LS WBls wbls WBLS wbls wormbase -wbphenotype C. elegans phenotype https://github.com/obophenotype/c-elegans-phenotype-ontology Ontology about C. elegans and other nematode phenotypes ^\d{7}$ 0000983 cgrove@caltech.edu http://www.wormbase.org/get?name=$1 WBPhenotype False WBPHENOTYPE WBPhenotype WB-PHENOTYPE WBPhenotype wbphenotype WBPhenotype wbphenotype wormbase +wbbt C. elegans Gross Anatomy Ontology https://github.com/obophenotype/c-elegans-gross-anatomy-ontology Ontology about the gross anatomy of the C. elegans ^\d{7}$ 0001290 raymond@caltech.edu http://purl.obolibrary.org/obo/WBbt_$1 WBbt False WBBT WBbt WB-BT wbbt wbbt WBbt wbbt +wbls C. elegans development ontology https://github.com/obophenotype/c-elegans-development-ontology Ontology about the development and life stages of the C. elegans ^\d{7}$ 0000690 cgrove@caltech.edu http://www.wormbase.org/get?name=$1 WBls False WBLS WBLS WB-LS wbls wbls WBLS wbls wormbase +wbphenotype C. elegans phenotype https://github.com/obophenotype/c-elegans-phenotype-ontology Ontology about C. elegans and other nematode phenotypes ^\d{7}$ 0000983 cgrove@caltech.edu http://www.wormbase.org/get?name=$1 WBPhenotype False WBPHENOTYPE WBPhenotype WB-PHENOTYPE wbphenotype wbphenotype WBPhenotype wbphenotype wormbase webelements Web Elements https://www.webelements.com/ Browser for the periodic table of the elements ^\w+$ chromium https://www.webelements.com/$1 False wgs84 WGS84 Geo Positioning https://www.w3.org/2003/01/geo/wgs84_pos A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum latitude http://www.w3.org/2003/01/geo/wgs84_pos#$1 False wicell WiCell Research Institute Cell Collection https://www.wicell.org Cell line collections ai10e-kctd13b https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true False WiCell @@ -1485,15 +1485,15 @@ wormbase WormBase database of nematode biology https://www.wormbase.org/ WormBas wormpep Wormpep https://www.wormbase.org/db/seq/protein Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project. ^CE\d{5}$ CE28239 https://www.wormbase.org/db/seq/protein?name=$1 False WORMPEP wormpep wormpep wormpep worms World Register of Marine Species http://www.marinespecies.org/ The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts. ^\d+$ 146421 http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1 False WORMS worms worms P850 wwf.ecoregion World Wildlife Fund Ecoregion https://www.worldwildlife.org/biomes WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions. ^AT\d+$ AT1402 https://www.worldwildlife.org/ecoregions/$1 WWF False P1294 -xao Xenopus Anatomy Ontology http://www.xenbase.org/anatomy/xao.do?method=display XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. ^\d{7}$ 0004486 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XAO_$1 False XAO XAO XAO XAO xao XAO P4495 -xco Experimental condition ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. ^\d{7}$ 0000780 jrsmith@mcw.edu https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1 False XCO XCO XCO XCO xco XCO xco +xao Xenopus Anatomy Ontology http://www.xenbase.org/anatomy/xao.do?method=display XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis. ^\d{7}$ 0004486 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XAO_$1 False XAO XAO XAO xao xao XAO P4495 +xco Experimental condition ontology https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000 Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms. ^\d{7}$ 0000780 jrsmith@mcw.edu https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1 False XCO XCO XCO xco xco XCO xco xenbase Xenbase https://www.xenbase.org/ Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions. ^XB\-\w+\-\d+$ XB-GENE-922462 troy_pells@yahoo.ca https://www.xenbase.org/entry/$1 Xenbase False Xenbase 2738 xenbase xenbase xenbase Xenbase ximbio Ximbio https://ximbio.com Cell line collections ^\d+$ 151022 https://ximbio.com/reagent/$1 False Ximbio xl Cross-linker reagents ontology http://www.psidev.info/groups/controlled-vocabularies A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. psidev-ms-vocab@lists.sourceforge.net http://purl.obolibrary.org/obo/XL_$1 True XL XL xl XL -xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary http://www.psidev.info/groups/controlled-vocabularies A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. ^\d{5}$ 00050 lutz.fischer@tu-berlin.de http://purl.obolibrary.org/obo/XLMOD_$1 https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo False XLMOD XLMOD XLMOD xlmod XLMOD +xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary http://www.psidev.info/groups/controlled-vocabularies A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry. ^\d{5}$ 00050 lutz.fischer@tu-berlin.de http://purl.obolibrary.org/obo/XLMOD_$1 https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo False XLMOD XLMOD xlmod xlmod XLMOD xmetdb Xenobiotics Metabolism Database https://xmetdb.org Metabolites in the Xenobiotics Metabolism Database. ^\d+$ 171 http://www.xmetdb.org/xmetdb/protocol/$1 True xml Extensible Markup Language https://www.w3.org/TR/xml/ The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML. lang http://www.w3.org/XML/1998/namespace#$1 False xml -xpo Xenopus Phenotype Ontology https://github.com/obophenotype/xenopus-phenotype-ontology XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. ^\d+$ 0100002 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XPO_$1 False XPO XPO XPO xpo XPO +xpo Xenopus Phenotype Ontology https://github.com/obophenotype/xenopus-phenotype-ontology XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis. ^\d+$ 0100002 Erik.Segerdell@cchmc.org http://purl.obolibrary.org/obo/XPO_$1 False XPO XPO xpo xpo XPO xsd XML Schema Definition http://www.w3.org/2001/XMLSchema This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language. decimal http://www.w3.org/2001/XMLSchema#$1 False xsd xuo XUO True ydpm Yeast Deletion and the Mitochondrial Proteomics Project http://www-deletion.stanford.edu/YDPM/ The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. ^Y[A-Z]{2}\d+[CW]$ YAL001C http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1 False YDPM ydpm ydpm ydpm @@ -1501,13 +1501,13 @@ yeastintron Yeast Intron Database v4.3 http://intron.ucsc.edu/yeast4.3/ The YEas yetfasco YeTFasCo http://yetfasco.ccbr.utoronto.ca/ The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. ^\w+\_\d+(\.\d+)?$ YOR172W_571.0 http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1 False YETFASCO yetfasco yetfasco yid Yeast Intron Database v3 http://compbio.soe.ucsc.edu/yeast_introns.html The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]. ^[A-Z0-9]+$ SNR17A http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1 False YID yid yid ymdb Yeast Metabolome Database http://www.ymdb.ca The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). ^YMDB\d+$ YMDB00001 http://www.ymdb.ca/compounds/$1 False -ypo Yeast phenotypes http://www.yeastgenome.org/ cherry@genome.stanford.edu http://purl.obolibrary.org/obo/YPO_$1 True YPO ypo +ypo Yeast phenotypes http://www.yeastgenome.org/ cherry@genome.stanford.edu True ypo ypo yrcpdr YRC PDR http://www.yeastrc.org/pdr/ The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. ^\d+$ 2673500 http://yeastrc.org/pdr/viewProtein.do?id=$1 False YRCPDR yrcpdr yrcpdr -zea Maize gross anatomy http://www.maizemap.org/ Leszek@missouri.edu http://purl.obolibrary.org/obo/ZEA_$1 True ZEA ZEA ZEA ZEA zea -zeco Zebrafish Experimental Conditions Ontology https://github.com/ybradford/zebrafish-experimental-conditions-ontology Ontology of Zebrafish Experimental Conditions ^\d{7}$ 0000171 ybradford@zfin.org http://purl.obolibrary.org/obo/ZECO_$1 False ZECO ZECO ZECO ZECO zeco ZECO +zea Maize gross anatomy http://www.maizemap.org/ Leszek@missouri.edu http://purl.obolibrary.org/obo/ZEA_$1 True ZEA ZEA ZEA zea zea +zeco Zebrafish Experimental Conditions Ontology https://github.com/ybradford/zebrafish-experimental-conditions-ontology Ontology of Zebrafish Experimental Conditions ^\d{7}$ 0000171 ybradford@zfin.org http://purl.obolibrary.org/obo/ZECO_$1 False ZECO ZECO ZECO zeco zeco ZECO zenodo.record Zenodo https://zenodo.org Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts. ^\d+$ 4390079 https://zenodo.org/record/$1 zenodo False P4901 -zfa Zebrafish anatomy and development ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources ZFA description. ^\d{7}$ 0005926 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFA_$1 ZFA_RETIRED False ZFA ZFA ZFA ZFA zfa ZFA zfa +zfa Zebrafish anatomy and development ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources ZFA description. ^\d{7}$ 0005926 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFA_$1 ZFA_RETIRED False ZFA ZFA ZFA zfa zfa ZFA zfa zfin Zebrafish Information Network Gene http://zfin.org ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN. ^ZDB\-\w+\-\d+\-\d+$ ZDB-GENE-041118-11 http://zfin.org/$1 ZFIN False ZFIN zfin zfin zfin ZFIN P3870 -zfs Zebrafish developmental stages ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources Developmental stages of the Zebrafish ^\d{7}$ 0000050 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFS_$1 False ZFS ZFS ZFS ZFS zfs ZFS +zfs Zebrafish developmental stages ontology https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources Developmental stages of the Zebrafish ^\d{7}$ 0000050 van_slyke@zfin.org http://purl.obolibrary.org/obo/ZFS_$1 False ZFS ZFS ZFS zfs zfs ZFS zinc ZINC is not Commercial http://zinc15.docking.org/ ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. ^(ZINC)?\d+$ ZINC1084 http://zinc15.docking.org/substances/$1 False ZINC zinc zinc P2084 -zp Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phenotype-ontology The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. ^\d+$ 0019030 ybradford@zfin.org http://purl.obolibrary.org/obo/ZP_$1 False ZP ZP ZP ZP zp ZP +zp Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phenotype-ontology The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism. ^\d+$ 0019030 ybradford@zfin.org http://purl.obolibrary.org/obo/ZP_$1 False ZP ZP ZP zp zp ZP diff --git a/exports/registry/registry.yml b/exports/registry/registry.yml index 2c1dc059d..780486fe8 100644 --- a/exports/registry/registry.yml +++ b/exports/registry/registry.yml @@ -60,7 +60,7 @@ aao: mappings: biocontext: AAO fairsharing: FAIRsharing.mxx5rp - obofoundry: AAO + obofoundry: aao prefixcommons: aao name: Amphibian gross anatomy no_own_terms: true @@ -170,10 +170,10 @@ ado: depends_on: - bfo description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses - varieties of concepts related to Alzheimer'S Disease, structured by upper level - Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities - that demonstrate the network of the understanding on Alzheimer's disease and can - be readily applied for text mining. + varieties of concepts related to Alzheimer'S Disease, foundamentally structured + by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational + entities that demonstrate the nextwork of the understanding on Alzheimer's disease + and can be readily applied for text mining. download_owl: http://purl.obolibrary.org/obo/ado.owl example: '0000001' homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO @@ -182,11 +182,13 @@ ado: aberowl: ADO bioportal: ADO fairsharing: FAIRsharing.ckd4rf - obofoundry: ADO + obofoundry: ado + ols: ado name: Alzheimer's Disease Ontology preferred_prefix: ADO repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO uri_format: http://purl.obolibrary.org/obo/ADO_$1 + version: 2.0.0 adw: contact: email: adw_geeks@umich.edu @@ -206,14 +208,12 @@ adw: fairsharing: FAIRsharing.t9fvdn miriam: adw n2t: adw - obofoundry: ADW + obofoundry: adw name: Animal natural history and life history pattern: ^[A-Z_a-z]+$ preferred_prefix: ADW uri_format: https://animaldiversity.org/accounts/$1 aeo: - appears_in: - - ehdaa2 contact: email: J.Bard@ed.ac.uk github: null @@ -232,7 +232,7 @@ aeo: biocontext: AEO bioportal: AEO fairsharing: FAIRsharing.93ee19 - obofoundry: AEO + obofoundry: aeo ols: aeo ontobee: AEO name: Anatomical Entity Ontology @@ -262,7 +262,7 @@ aero: biocontext: AERO bioportal: AERO fairsharing: FAIRsharing.rycy2x - obofoundry: AERO + obofoundry: aero name: Adverse Event Reporting Ontology pattern: ^\d{7}$ preferred_prefix: AERO @@ -442,7 +442,7 @@ agro: biocontext: AGRO bioportal: AGRO fairsharing: FAIRsharing.m40bhw - obofoundry: AGRO + obofoundry: agro ols: agro ontobee: AGRO name: Agronomy Ontology @@ -498,7 +498,7 @@ aism: mappings: aberowl: AISM bioportal: AISM - obofoundry: AISM + obofoundry: aism ols: aism ontobee: AISM name: Ontology for the Anatomy of the Insect SkeletoMuscular system @@ -577,7 +577,7 @@ amphx: mappings: aberowl: AMPHX bioportal: AMPHX - obofoundry: AMPHX + obofoundry: amphx ols: amphx ontobee: AMPHX name: The Amphioxus Development and Anatomy Ontology @@ -750,7 +750,7 @@ apo: biocontext: YPO bioportal: APO fairsharing: FAIRsharing.dyqz3y - obofoundry: APO + obofoundry: apo ols: apo ontobee: APO name: Ascomycete phenotype ontology @@ -777,7 +777,7 @@ apollosv: aberowl: APOLLO_SV bioportal: APOLLO-SV fairsharing: FAIRsharing.ngv2xx - obofoundry: APOLLO_SV + obofoundry: apollo_sv ols: apollo_sv ontobee: APOLLO_SV name: Apollo Structured Vocabulary @@ -864,7 +864,7 @@ aro: aberowl: ARO biocontext: ARO bioportal: ARO - obofoundry: ARO + obofoundry: aro ols: aro ontobee: ARO name: Antibiotic Resistance Ontology @@ -1156,7 +1156,7 @@ ato: biocontext: ATO bioportal: ATO fairsharing: FAIRsharing.ayjdsm - obofoundry: ATO + obofoundry: ato name: Amphibian taxonomy pattern: ^\d{7}$ preferred_prefix: ATO @@ -1350,7 +1350,7 @@ bcgo: biocontext: BCGO bioportal: BCGO cellosaurus: BCGO - obofoundry: BCGO + obofoundry: bcgo ontobee: BCGO name: Beta Cell Genomics Ontology pattern: ^\d{7}$ @@ -1392,7 +1392,7 @@ bco: bioportal: BCO ecoportal: BCO fairsharing: FAIRsharing.8ktkqy - obofoundry: BCO + obofoundry: bco ols: bco ontobee: BCO name: Biological Collections Ontology @@ -1572,7 +1572,7 @@ bfo: bioportal: BFO fairsharing: FAIRsharing.wcpd6f go: BFO - obofoundry: BFO + obofoundry: bfo ols: bfo ontobee: BFO name: Basic Formal Ontology @@ -1723,13 +1723,21 @@ bigg.reaction: preferred_prefix: bigg.reaction uri_format: http://bigg.ucsd.edu/models/universal/reactions/$1 bila: + contact: + email: henrich@embl.de + github: null + name: Thorsten Heinrich + orcid: null deprecated: true description: This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource. + download_owl: http://purl.obolibrary.org/obo/bila.owl + example: '0000000' + homepage: http://4dx.embl.de/4DXpress mappings: biocontext: BILA fairsharing: FAIRsharing.eqgjeq - obofoundry: BILA + obofoundry: bila name: Bilateria anatomy preferred_prefix: BILA uri_format: http://purl.obolibrary.org/obo/BILA_$1 @@ -1930,7 +1938,7 @@ biomodels.kisao: fairsharing: FAIRsharing.jcg19w miriam: biomodels.kisao n2t: biomodels.kisao - obofoundry: KISAO + obofoundry: kisao ols: kisao ontobee: KISAO prefixcommons: kisao @@ -2428,7 +2436,7 @@ bootstrep: homepage: http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html mappings: biocontext: BOOTSTREP - obofoundry: BOOTSTREP + obofoundry: bootstrep name: Gene Regulation Ontology preferred_prefix: BOOTSTREP uri_format: http://purl.obolibrary.org/obo/BOOTSTREP_$1 @@ -2556,7 +2564,7 @@ bspo: biocontext: BSPO bioportal: BSPO fairsharing: FAIRsharing.newa3z - obofoundry: BSPO + obofoundry: bspo ols: bspo ontobee: BSPO name: Biological Spatial Ontology @@ -2591,7 +2599,7 @@ bto: go: BTO miriam: bto n2t: bto - obofoundry: BTO + obofoundry: bto ols: bto ontobee: BTO prefixcommons: bto @@ -2766,7 +2774,6 @@ caro: appears_in: - aism - colao - - ehdaa2 - lepao - pco contact: @@ -2785,7 +2792,7 @@ caro: bioportal: CARO fairsharing: FAIRsharing.3kcgmr go: CARO - obofoundry: CARO + obofoundry: caro ols: caro ontobee: CARO name: Common Anatomy Reference Ontology @@ -3077,7 +3084,7 @@ cdao: biocontext: CDAO bioportal: CDAO fairsharing: FAIRsharing.kay31r - obofoundry: CDAO + obofoundry: cdao ols: cdao ontobee: CDAO name: Comparative Data Analysis Ontology @@ -3127,7 +3134,7 @@ cdno: mappings: aberowl: CDNO bioportal: CDNO - obofoundry: CDNO + obofoundry: cdno ols: cdno ontobee: CDNO name: Compositional Dietary Nutrition Ontology @@ -3295,7 +3302,7 @@ ceph: biocontext: CEPH bioportal: CEPH fairsharing: FAIRsharing.p58bm4 - obofoundry: CEPH + obofoundry: ceph ols: ceph ontobee: CEPH name: Cephalopod Ontology @@ -3429,7 +3436,7 @@ chebi: go: CHEBI miriam: chebi n2t: chebi - obofoundry: CHEBI + obofoundry: chebi ols: chebi ontobee: CHEBI prefixcommons: chebi @@ -3601,7 +3608,7 @@ cheminf: biocontext: CHEMINF bioportal: CHEMINF fairsharing: FAIRsharing.sjhvyy - obofoundry: CHEMINF + obofoundry: cheminf ols: cheminf ontobee: CHEMINF name: Chemical Information Ontology @@ -3677,7 +3684,7 @@ chiro: mappings: aberowl: CHIRO bioportal: CHIRO - obofoundry: CHIRO + obofoundry: chiro ols: chiro ontobee: CHIRO name: ChEBI Integrated Role Ontology @@ -3711,7 +3718,7 @@ chmo: biocontext: CHMO bioportal: CHMO fairsharing: FAIRsharing.9j4wh2 - obofoundry: CHMO + obofoundry: chmo ols: chmo ontobee: CHMO name: Chemical Methods Ontology @@ -3739,7 +3746,7 @@ cido: aberowl: CIDO bioportal: CIDO fairsharing: FAIRsharing.aVmpKl - obofoundry: CIDO + obofoundry: cido ols: cido ontobee: CIDO name: Coronavirus Infectious Disease Ontology @@ -3765,7 +3772,7 @@ cio: biocontext: CIO bioportal: CIO fairsharing: FAIRsharing.e3t0yw - obofoundry: CIO + obofoundry: cio ols: cio ontobee: CIO name: Confidence Information Ontology @@ -3854,7 +3861,6 @@ cl: appears_in: - clo - ecao - - ehdaa2 - go - mco - pcl @@ -3893,7 +3899,7 @@ cl: go: CL miriam: cl n2t: cl - obofoundry: CL + obofoundry: cl ols: cl ontobee: CL prefixcommons: cl @@ -3923,7 +3929,7 @@ clao: mappings: aberowl: CLAO bioportal: CLAO - obofoundry: CLAO + obofoundry: clao ols: clao ontobee: CLAO name: Collembola Anatomy Ontology @@ -4101,7 +4107,7 @@ clo: bioportal: CLO cellosaurus: CLO fairsharing: FAIRsharing.4dvtcz - obofoundry: CLO + obofoundry: clo ols: clo ontobee: CLO prefixcommons: clo @@ -4143,7 +4149,7 @@ clyh: mappings: aberowl: CLYH bioportal: CLYH - obofoundry: CLYH + obofoundry: clyh ols: clyh ontobee: CLYH name: Clytia hemisphaerica Development and Anatomy Ontology @@ -4182,7 +4188,7 @@ cmf: mappings: aberowl: CMF biocontext: CMF - obofoundry: CMF + obofoundry: cmf ontobee: CMF name: CranioMaxilloFacial ontology preferred_prefix: CMF @@ -4207,7 +4213,7 @@ cmo: biocontext: CMO bioportal: CMO fairsharing: FAIRsharing.dq78pn - obofoundry: CMO + obofoundry: cmo ols: cmo ontobee: CMO name: Clinical measurement ontology @@ -4727,7 +4733,7 @@ cob: mappings: aberowl: COB bioportal: COB - obofoundry: COB + obofoundry: cob ols: cob ontobee: COB name: Core Ontology for Biology and Biomedicine @@ -4906,7 +4912,7 @@ colao: mappings: aberowl: COLAO bioportal: COLAO - obofoundry: COLAO + obofoundry: colao ols: colao ontobee: COLAO name: Coleoptera Anatomy Ontology @@ -5236,14 +5242,15 @@ cpga: name: Plant Ontology Administrators orcid: null deprecated: true + description: A structured controlled vocabulary for the anatomy of Graminae. Please + note that this ontology has now been superseded by the Plant Ontology. homepage: http://www.gramene.org/plant_ontology/ mappings: biocontext: gro.cpga bioportal: GRO-CPGA - obofoundry: GRO + obofoundry: gro name: Cereal Plant Gross Anatomy preferred_prefix: GRO - uri_format: http://purl.obolibrary.org/obo/GRO_$1 cpt: contributor: email: null @@ -5325,7 +5332,7 @@ cro: aberowl: CRO biocontext: CRO bioportal: CRO - obofoundry: CRO + obofoundry: cro ols: cro ontobee: CRO name: Contributor Role Ontology @@ -5524,7 +5531,7 @@ cteno: biocontext: CTENO bioportal: CTENO fairsharing: FAIRsharing.mgxgza - obofoundry: CTENO + obofoundry: cteno ols: cteno ontobee: CTENO name: Ctenophore Ontology @@ -5552,7 +5559,7 @@ cto: aberowl: CTO bioportal: CTO fairsharing: FAIRsharing.qp211a - obofoundry: CTO + obofoundry: cto ols: cto ontobee: CTO name: Clinical Trials Ontology @@ -5595,7 +5602,7 @@ cvdo: biocontext: CVDO bioportal: CVDO fairsharing: FAIRsharing.2basyz - obofoundry: CVDO + obofoundry: cvdo ols: cvdo ontobee: CVDO name: Cardiovascular Disease Ontology @@ -5995,7 +6002,7 @@ dc_cl: homepage: http://www.dukeontologygroup.org/Projects.html mappings: biocontext: DC_CL - obofoundry: DC_CL + obofoundry: dc_cl name: Dendritic cell pattern: ^\d{7}$ preferred_prefix: DC_CL @@ -6063,7 +6070,7 @@ ddanat: bioportal: DDANAT fairsharing: FAIRsharing.z656ab go: DDANAT - obofoundry: DDANAT + obofoundry: ddanat ols: ddanat ontobee: DDANAT prefixcommons: ddanat @@ -6091,7 +6098,7 @@ ddpheno: biocontext: DDPHENO bioportal: DDPHENO fairsharing: FAIRsharing.9c1p18 - obofoundry: DDPHENO + obofoundry: ddpheno ols: ddpheno ontobee: DDPHENO name: Dictyostelium discoideum phenotype ontology @@ -6435,7 +6442,7 @@ dideo: biocontext: DIDEO bioportal: DIDEO fairsharing: FAIRsharing.9y8f0n - obofoundry: DIDEO + obofoundry: dideo ols: dideo ontobee: DIDEO name: Drug-drug Interaction and Drug-drug Interaction Evidence Ontology @@ -6459,7 +6466,7 @@ dinto: aberowl: DINTO biocontext: DINTO bioportal: DINTO - obofoundry: DINTO + obofoundry: dinto ontobee: DINTO name: The Drug-Drug Interactions Ontology preferred_prefix: DINTO @@ -6507,7 +6514,7 @@ disdriv: mappings: aberowl: DISDRIV bioportal: DISDRIV - obofoundry: DISDRIV + obofoundry: disdriv ols: disdriv name: Disease Drivers Ontology pattern: ^\d+$ @@ -6710,7 +6717,7 @@ doid: fairsharing: FAIRsharing.8b6wfq miriam: doid n2t: doid - obofoundry: DOID + obofoundry: doid ols: doid ontobee: DOID prefixcommons: do @@ -6811,7 +6818,7 @@ dpo: mappings: aberowl: DPO bioportal: DPO - obofoundry: FBcv + obofoundry: dpo ols: dpo ontobee: DPO name: Drosophila Phenotype Ontology @@ -6923,7 +6930,7 @@ dron: biocontext: DRON bioportal: DRON fairsharing: FAIRsharing.w5ntfd - obofoundry: DRON + obofoundry: dron ols: dron ontobee: DRON name: The Drug Ontology @@ -7086,7 +7093,7 @@ duo: biocontext: DUO bioportal: DUO fairsharing: FAIRsharing.5dnjs2 - obofoundry: DUO + obofoundry: duo ols: duo ontobee: DUO name: Data Use Ontology @@ -7176,7 +7183,7 @@ ecao: mappings: aberowl: ECAO bioportal: ECAO - obofoundry: ECAO + obofoundry: ecao ols: ecao ontobee: ECAO name: The Echinoderm Anatomy and Development Ontology @@ -7319,7 +7326,7 @@ eco: go: ECO miriam: eco n2t: eco - obofoundry: ECO + obofoundry: eco ols: eco ontobee: ECO prefixcommons: eco @@ -7358,7 +7365,7 @@ ecocore: aberowl: ECOCORE biocontext: ECOCORE bioportal: ECOCORE - obofoundry: ECOCORE + obofoundry: ecocore ols: ecocore ontobee: ECOCORE name: An ontology of core ecological entities @@ -7466,7 +7473,7 @@ ecto: aberowl: ECTO biolink: ECTO bioportal: ECTO - obofoundry: ECTO + obofoundry: ecto ols: ecto ontobee: ECTO name: Environmental conditions, treatments and exposures ontology @@ -7826,7 +7833,7 @@ ehda: aberowl: EHDA biocontext: EHDA bioportal: EHDA - obofoundry: EHDA + obofoundry: ehda prefixcommons: ehda name: Human developmental anatomy, timed version pattern: ^\d+$ @@ -7845,7 +7852,7 @@ ehdaa: aberowl: EHDAA biocontext: EHDAA bioportal: EHDAA - obofoundry: EHDAA + obofoundry: ehdaa prefixcommons: ehdaa name: Human developmental anatomy, abstract version pattern: ^\d+$ @@ -7874,7 +7881,7 @@ ehdaa2: biocontext: EHDAA2 bioportal: EHDAA2 fairsharing: FAIRsharing.7zxrs6 - obofoundry: EHDAA2 + obofoundry: ehdaa2 ols: ehdaa2 ontobee: EHDAA2 name: Human developmental anatomy, abstract @@ -7918,7 +7925,7 @@ emap: mappings: biocontext: EMAP bioportal: EMAP - obofoundry: EMAP + obofoundry: emap name: Mouse gross anatomy and development, timed pattern: ^\d+$ preferred_prefix: EMAP @@ -7942,7 +7949,7 @@ emapa: bioportal: EMAPA fairsharing: FAIRsharing.j0fa1d go: EMAPA - obofoundry: EMAPA + obofoundry: emapa ols: emapa ontobee: EMAPA name: Mouse Developmental Anatomy Ontology @@ -8281,7 +8288,7 @@ envo: fairsharing: FAIRsharing.azqskx miriam: envo n2t: envo - obofoundry: ENVO + obofoundry: envo ols: envo ontobee: ENVO name: Environment Ontology @@ -8334,7 +8341,7 @@ eo: biocontext: EO miriam: eo n2t: eo - obofoundry: EO + obofoundry: eo prefixcommons: eo name: Plant Environment Ontology namespace_in_lui: true @@ -8434,7 +8441,7 @@ epio: mappings: aberowl: EPIO bioportal: EPIO - obofoundry: EPIO + obofoundry: epio ontobee: EPIO name: Epilepsy Ontology pattern: ^\d{7}$ @@ -8451,7 +8458,7 @@ epo: aberowl: EPO biocontext: EPO bioportal: EPO - obofoundry: EPO + obofoundry: epo ontobee: EPO name: Epidemiology Ontology preferred_prefix: EPO @@ -8502,7 +8509,7 @@ ero: biocontext: ERO bioportal: ERO fairsharing: FAIRsharing.nwgynk - obofoundry: ERO + obofoundry: ero ols: ero ontobee: ERO name: eagle-i resource ontology @@ -8602,7 +8609,7 @@ eupath: biocontext: EUPATH bioportal: EUPATH fairsharing: FAIRsharing.9rhr9j - obofoundry: EUPATH + obofoundry: eupath ols: eupath ontobee: EUPATH name: VEuPathDB ontology @@ -8637,7 +8644,7 @@ ev: homepage: http://www.evocontology.org/ mappings: biocontext: EV - obofoundry: EV + obofoundry: ev name: eVOC (Expressed Sequence Annotation for Humans) preferred_prefix: EV references: @@ -8731,7 +8738,7 @@ exo: biolink: ExO bioportal: EXO fairsharing: FAIRsharing.6hna78 - obofoundry: ExO + obofoundry: exo ols: exo ontobee: ExO name: Exposure ontology @@ -8839,7 +8846,7 @@ fao: biocontext: FAO bioportal: FAO fairsharing: FAIRsharing.xs6t67 - obofoundry: FAO + obofoundry: fao ols: fao ontobee: FAO prefixcommons: fao @@ -8867,7 +8874,7 @@ fbbi: biocontext: FBbi bioportal: FBbi fairsharing: FAIRsharing.ny3z9j - obofoundry: FBbi + obofoundry: fbbi ols: fbbi ontobee: FBBI prefixcommons: fbbi @@ -8898,7 +8905,7 @@ fbbt: bioportal: FB-BT fairsharing: FAIRsharing.y2qkst go: FBbt - obofoundry: FBbt + obofoundry: fbbt ols: fbbt ontobee: FBBT prefixcommons: fbbt @@ -8933,7 +8940,7 @@ fbcv: biocontext: FBcv bioportal: FB-CV fairsharing: FAIRsharing.6tgyxf - obofoundry: FBcv + obofoundry: fbcv ols: fbcv ontobee: FBCV prefixcommons: fbcv @@ -8964,7 +8971,7 @@ fbdv: biocontext: FBdv bioportal: FB-DV fairsharing: FAIRsharing.p52pzj - obofoundry: FBdv + obofoundry: fbdv ols: fbdv ontobee: FBdv prefixcommons: fbdv @@ -9036,7 +9043,7 @@ fbsp: aberowl: FB-SP biocontext: FBSP bioportal: FB-SP - obofoundry: FBSP + obofoundry: fbsp name: Fly taxonomy part_of: flybase pattern: ^\d{8}$ @@ -9104,7 +9111,7 @@ fideo: mappings: aberowl: FIDEO bioportal: FIDEO - obofoundry: FIDEO + obofoundry: fideo ols: fideo ontobee: FIDEO name: Food Interactions with Drugs Evidence Ontology @@ -9159,7 +9166,7 @@ fix: biocontext: FIX bioportal: FIX fairsharing: FAIRsharing.wwy1ns - obofoundry: FIX + obofoundry: fix ols: fix ontobee: FIX prefixcommons: fix @@ -9186,7 +9193,7 @@ flopo: biocontext: FLOPO bioportal: FLOPO fairsharing: FAIRsharing.ny9vnm - obofoundry: FLOPO + obofoundry: flopo ols: flopo ontobee: FLOPO name: Flora Phenotype Ontology @@ -9224,7 +9231,7 @@ flu: aberowl: FLU biocontext: FLU bioportal: FLU - obofoundry: FLU + obofoundry: flu name: Influenza Ontology pattern: ^\d{7}$ preferred_prefix: FLU @@ -9303,7 +9310,7 @@ fma: go: FMA miriam: fma n2t: fma - obofoundry: FMA + obofoundry: fma ols: fma ontobee: FMA prefixcommons: fma @@ -9355,7 +9362,7 @@ fobi: aberowl: FOBI agroportal: FOBI bioportal: FOBI - obofoundry: FOBI + obofoundry: fobi ols: fobi ontobee: FOBI name: Food-Biomarker Ontology @@ -9415,7 +9422,6 @@ foodon: - bfo - chebi - envo - - eo - ncbitaxon - obi - ro @@ -9437,7 +9443,7 @@ foodon: fairsharing: FAIRsharing.dzxae miriam: foodon n2t: foodon - obofoundry: FOODON + obofoundry: foodon ols: foodon ontobee: FOODON name: The Food Ontology @@ -9514,7 +9520,7 @@ fovt: mappings: aberowl: FOVT bioportal: FOVT - obofoundry: FOVT + obofoundry: fovt ols: fovt ontobee: FOVT name: FuTRES Ontology of Vertebrate Traits @@ -9814,7 +9820,7 @@ fypo: bioportal: FYPO fairsharing: FAIRsharing.4vr0ys go: FYPO - obofoundry: FYPO + obofoundry: fypo ols: fypo ontobee: FYPO name: Fission Yeast Phenotype Ontology @@ -9911,7 +9917,7 @@ gaz: biocontext: GAZ bioportal: GAZ fairsharing: FAIRsharing.wkdjpb - obofoundry: GAZ + obofoundry: gaz ols: gaz ontobee: GAZ wikidata: P6778 @@ -10010,7 +10016,7 @@ gecko: aberowl: GECKO bioportal: GECKO fairsharing: FAIRsharing.3da56b - obofoundry: GECKO + obofoundry: gecko ols: gecko ontobee: GECKO name: Genomics Cohorts Knowledge Ontology @@ -10148,7 +10154,7 @@ genepio: aberowl: GENEPIO biocontext: GENEPIO fairsharing: FAIRsharing.y1mmbv - obofoundry: GENEPIO + obofoundry: genepio ols: genepio ontobee: GENEPIO name: Genomic Epidemiology Ontology @@ -10216,7 +10222,7 @@ geno: biocontext: GENO bioportal: GENO fairsharing: FAIRsharing.kpbna7 - obofoundry: GENO + obofoundry: geno ols: geno ontobee: GENO name: Genotype Ontology @@ -10278,9 +10284,9 @@ geogeo: banana_peel: _ contact: email: hoganwr@gmail.com - github: null + github: hoganwr name: Bill Hogan - orcid: null + orcid: 0000-0002-9881-1017 description: An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign @@ -10294,7 +10300,7 @@ geogeo: biocontext: GEO bioportal: GEO miriam: geogeo - obofoundry: GEO + obofoundry: geo ols: geo ontobee: GEO name: Geographical Entity Ontology @@ -10673,7 +10679,7 @@ gno: mappings: aberowl: GNO bioportal: GNO - obofoundry: GNO + obofoundry: gno ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology @@ -10744,7 +10750,7 @@ go: miriam: go n2t: go ncbi: GO - obofoundry: GO + obofoundry: go ols: go ontobee: GO prefixcommons: go @@ -11287,7 +11293,7 @@ gsso: aberowl: GSSO bioportal: GSSO miriam: gsso - obofoundry: GSSO + obofoundry: gsso ols: gsso ontobee: GSSO name: Gender, Sex, and Sexual Orientation Ontology @@ -11457,7 +11463,7 @@ habronattus: homepage: http://www.mesquiteproject.org/ontology/Habronattus/index.html mappings: biocontext: HABRONATTUS - obofoundry: HABRONATTUS + obofoundry: habronattus name: Habronattus courtship preferred_prefix: HABRONATTUS uri_format: http://purl.obolibrary.org/obo/HABRONATTUS_$1 @@ -11497,7 +11503,7 @@ hancestro: biolink: HANCESTRO bioportal: HANCESTRO fairsharing: FAIRsharing.rja8qp - obofoundry: HANCESTRO + obofoundry: hancestro ols: hancestro ontobee: HANCESTRO name: Human Ancestry Ontology @@ -11524,7 +11530,7 @@ hao: biocontext: HAO bioportal: HAO fairsharing: FAIRsharing.kj3m5n - obofoundry: HAO + obofoundry: hao ols: hao ontobee: HAO name: Hymenoptera Anatomy Ontology @@ -11898,7 +11904,7 @@ hom: biocontext: HOM bioportal: HOM fairsharing: FAIRsharing.efv7gw - obofoundry: HOM + obofoundry: hom ols: hom ontobee: HOM name: Homology Ontology @@ -12014,7 +12020,7 @@ hp: fairsharing: FAIRsharing.kbtt7f miriam: hp n2t: hp - obofoundry: HP + obofoundry: hp ols: hp ontobee: HP wikidata: P3841 @@ -12153,7 +12159,7 @@ hsapdv: biolink: HsapDv bioportal: HSAPDV fairsharing: FAIRsharing.c6vhm3 - obofoundry: HsapDv + obofoundry: hsapdv ols: hsapdv ontobee: HSAPDV name: Human Developmental Stages @@ -12200,7 +12206,7 @@ hso: mappings: aberowl: HSO bioportal: HSO - obofoundry: HSO + obofoundry: hso ols: hso ontobee: HSO name: Health Surveillance Ontology @@ -12247,7 +12253,7 @@ htn: mappings: aberowl: HTN bioportal: HTN - obofoundry: HTN + obofoundry: htn ols: htn ontobee: HTN name: Hypertension Ontology @@ -12306,7 +12312,7 @@ iao: go: IAO miriam: iao n2t: iao - obofoundry: IAO + obofoundry: iao ols: iao ontobee: IAO name: Information Artifact Ontology @@ -12515,7 +12521,7 @@ iceo: mappings: aberowl: ICEO bioportal: ICEO - obofoundry: ICEO + obofoundry: iceo ols: iceo ontobee: ICEO name: Integrative and Conjugative Element Ontology @@ -12569,7 +12575,7 @@ ico: biocontext: ICO bioportal: ICO fairsharing: FAIRsharing.b9znd5 - obofoundry: ICO + obofoundry: ico ols: ico ontobee: ICO name: Informed Consent Ontology @@ -12616,7 +12622,7 @@ ido: fairsharing: FAIRsharing.aae3v6 miriam: ido n2t: ido - obofoundry: IDO + obofoundry: ido ols: ido ontobee: IDO name: Infectious Disease Ontology @@ -12684,7 +12690,7 @@ idomal: biocontext: IDOMAL bioportal: IDOMAL fairsharing: FAIRsharing.2q8c28 - obofoundry: IDOMAL + obofoundry: idomal ols: idomal ontobee: IDOMAL name: Malaria Ontology @@ -12774,7 +12780,7 @@ iev: homepage: http://www.inoh.org mappings: biocontext: IEV - obofoundry: IEV + obofoundry: iev prefixcommons: iev name: Event (INOH pathway ontology) pattern: ^\d{7}$ @@ -12991,7 +12997,7 @@ imr: homepage: http://www.inoh.org mappings: biocontext: IMR - obofoundry: IMR + obofoundry: imr prefixcommons: imr name: Molecule role (INOH Protein name/family name ontology) pattern: ^\d{7}$ @@ -13119,7 +13125,7 @@ ino: biolink: INO bioportal: INO fairsharing: FAIRsharing.mm72as - obofoundry: INO + obofoundry: ino ols: ino ontobee: INO name: Interaction Network Ontology @@ -13330,7 +13336,7 @@ interpro: miriam: interpro n2t: interpro ncbi: InterPro - obofoundry: IPR + obofoundry: ipr prefixcommons: interpro uniprot: InterPro wikidata: P2926 @@ -14110,7 +14116,6 @@ labo: - iao - obi - ogms - - omiabis - omrse - opmi description: LABO is an ontology of informational entities formalizing clinical @@ -14122,7 +14127,7 @@ labo: mappings: aberowl: LABO bioportal: LABO - obofoundry: LABO + obofoundry: labo ols: labo ontobee: LABO name: clinical LABoratory Ontology @@ -14193,7 +14198,7 @@ lepao: mappings: aberowl: LEPAO bioportal: LEPAO - obofoundry: LEPAO + obofoundry: lepao ols: lepao name: Lepidoptera Anatomy Ontology pattern: ^\d{7}$ @@ -14481,7 +14486,7 @@ lipro: aberowl: LIPRO biocontext: LIPRO bioportal: LIPRO - obofoundry: LIPRO + obofoundry: lipro name: Lipid Ontology preferred_prefix: LIPRO uri_format: http://purl.obolibrary.org/obo/LIPRO_$1 @@ -14508,7 +14513,7 @@ loggerhead: homepage: http://www.mesquiteproject.org/ontology/Loggerhead/index.html mappings: biocontext: LOGGERHEAD - obofoundry: LOGGERHEAD + obofoundry: loggerhead name: Loggerhead nesting preferred_prefix: LOGGERHEAD uri_format: http://purl.obolibrary.org/obo/LOGGERHEAD_$1 @@ -14685,7 +14690,7 @@ ma: go: MA miriam: ma n2t: ma - obofoundry: MA + obofoundry: ma ols: ma ontobee: MA prefixcommons: ma @@ -14753,7 +14758,7 @@ mamo: fairsharing: FAIRsharing.kbz5jh miriam: mamo n2t: mamo - obofoundry: MAMO + obofoundry: mamo ols: mamo ontobee: MAMO name: Mathematical modeling ontology @@ -14772,7 +14777,7 @@ mao: homepage: http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html mappings: biocontext: MAO - obofoundry: MAO + obofoundry: mao prefixcommons: mao name: Multiple alignment preferred_prefix: MAO @@ -14834,7 +14839,7 @@ mat: aberowl: MAT biocontext: MAT bioportal: MAT - obofoundry: MAT + obofoundry: mat name: Minimal Anatomical Terminology pattern: ^\d{7}$ preferred_prefix: MAT @@ -14899,7 +14904,7 @@ maxo: aberowl: MAXO biolink: MAXO bioportal: MAXO - obofoundry: MAXO + obofoundry: maxo ols: maxo ontobee: MAXO name: Medical Action Ontology @@ -14958,7 +14963,7 @@ mco: mappings: aberowl: MCO bioportal: MCO - obofoundry: MCO + obofoundry: mco ols: mco ontobee: MCO name: Microbial Conditions Ontology @@ -15357,7 +15362,7 @@ mf: biocontext: MF bioportal: MF fairsharing: FAIRsharing.4gm9gt - obofoundry: MF + obofoundry: mf ols: mf ontobee: MF name: Mental Functioning Ontology @@ -15386,7 +15391,7 @@ mfmo: biocontext: MFMO bioportal: MFMO fairsharing: FAIRsharing.669cnk - obofoundry: MFMO + obofoundry: mfmo ols: mfmo ontobee: MFMO name: Mammalian Feeding Muscle Ontology @@ -15410,7 +15415,7 @@ mfo: aberowl: MFO biocontext: MFO bioportal: MFO - obofoundry: MFO + obofoundry: mfo prefixcommons: mfo name: Medaka fish anatomy and development preferred_prefix: MFO @@ -15432,7 +15437,7 @@ mfoem: biocontext: MFOEM bioportal: MFOEM fairsharing: FAIRsharing.dx30m8 - obofoundry: MFOEM + obofoundry: mfoem ols: mfoem ontobee: MFOEM name: Emotion Ontology @@ -15459,7 +15464,7 @@ mfomd: biocontext: MFOMD bioportal: MFOMD fairsharing: FAIRsharing.q053vb - obofoundry: MFOMD + obofoundry: mfomd ols: mfomd ontobee: MFOMD name: Mental Disease Ontology @@ -15590,7 +15595,7 @@ mi: go: PSI-MI miriam: mi n2t: psimi - obofoundry: MI + obofoundry: mi ols: mi ontobee: MI prefixcommons: psi.mi @@ -15643,7 +15648,7 @@ miapa: biocontext: MIAPA bioportal: MIAPA fairsharing: FAIRsharing.ca48xs - obofoundry: MIAPA + obofoundry: miapa ols: miapa ontobee: MIAPA name: Minimum Anformation About a Phylogenetic Analysis Ontology @@ -15669,7 +15674,7 @@ micro: aberowl: MICRO biocontext: MICRO fairsharing: FAIRsharing.brhpb0 - obofoundry: MICRO + obofoundry: micro ols: micro ontobee: MicrO name: Ontology of Prokaryotic Phenotypic and Metabolic Characters @@ -15962,7 +15967,7 @@ mirnao: aberowl: MIRNAO biocontext: MIRNAO bioportal: MIRNAO - obofoundry: MIRNAO + obofoundry: mirnao ontobee: miRNAO name: microRNA Ontology preferred_prefix: MIRNAO @@ -16000,7 +16005,7 @@ miro: biocontext: MIRO bioportal: MIRO fairsharing: FAIRsharing.sjf113 - obofoundry: MIRO + obofoundry: miro ols: miro ontobee: MIRO name: Mosquito insecticide resistance @@ -16101,7 +16106,7 @@ mmo: biocontext: MMO bioportal: MMO fairsharing: FAIRsharing.bgkyd7 - obofoundry: MMO + obofoundry: mmo ols: mmo ontobee: MMO name: Measurement method ontology @@ -16211,7 +16216,7 @@ mmusdv: biolink: MmusDv bioportal: MMUSDV fairsharing: FAIRsharing.zchb68 - obofoundry: MmusDv + obofoundry: mmusdv ols: mmusdv ontobee: MMUSDV name: Mouse Developmental Stages @@ -16242,7 +16247,7 @@ mo: bioportal: MO miriam: mo n2t: mo - obofoundry: MO + obofoundry: mo name: Microarray experimental conditions pattern: ^\w+$ preferred_prefix: MO @@ -16291,7 +16296,7 @@ mod: go: PSI-MOD miriam: mod n2t: mod - obofoundry: MOD + obofoundry: mod ols: mod ontobee: MOD prefixcommons: psi.mod @@ -16382,7 +16387,7 @@ mondo: biocontext: MONDO bioportal: MONDO fairsharing: FAIRsharing.b2979t - obofoundry: MONDO + obofoundry: mondo ols: mondo ontobee: MONDO wikidata: P5270 @@ -16411,7 +16416,7 @@ mop: biocontext: MOP bioportal: MOP fairsharing: FAIRsharing.mct09a - obofoundry: MOP + obofoundry: mop ols: mop ontobee: MOP name: Molecular Process Ontology @@ -16464,7 +16469,7 @@ mp: fairsharing: FAIRsharing.kg1x4z miriam: mp n2t: mp - obofoundry: MP + obofoundry: mp ols: mp ontobee: MP prefixcommons: mp @@ -16492,7 +16497,7 @@ mpath: biocontext: MPATH bioportal: MPATH fairsharing: FAIRsharing.3wbgm0 - obofoundry: MPATH + obofoundry: mpath ols: mpath ontobee: MPATH prefixcommons: mpath @@ -16545,7 +16550,7 @@ mpio: aberowl: MPIO biocontext: MPIO bioportal: MPIO - obofoundry: MPIO + obofoundry: mpio ols: mpio ontobee: MPIO name: Minimum PDDI Information Ontology @@ -16573,7 +16578,7 @@ mro: biocontext: MRO bioportal: MRO fairsharing: FAIRsharing.k893xa - obofoundry: MRO + obofoundry: mro ols: mro ontobee: MRO name: MHC Restriction Ontology @@ -16611,7 +16616,7 @@ ms: bioportal: MS miriam: ms n2t: ms - obofoundry: MS + obofoundry: ms ols: ms ontobee: MS name: Mass spectrometry ontology @@ -16987,7 +16992,7 @@ nbo: biocontext: NBO bioportal: NBO fairsharing: FAIRsharing.pktgc6 - obofoundry: NBO + obofoundry: nbo ols: nbo ontobee: NBO name: Neuro Behavior Ontology @@ -17240,7 +17245,7 @@ ncbitaxon: miriam: taxonomy n2t: taxonomy ncbi: taxon - obofoundry: NCBITaxon + obofoundry: ncbitaxon ols: ncbitaxon ontobee: NCBITaxon prefixcommons: uniprot.taxonomy @@ -17327,7 +17332,7 @@ ncit: fairsharing: FAIRsharing.4cvwxa miriam: ncit n2t: ncit - obofoundry: NCIT + obofoundry: ncit ols: ncit ontobee: NCIT prefixcommons: ncit @@ -17365,7 +17370,7 @@ ncro: biocontext: NCRO bioportal: NCRO fairsharing: FAIRsharing.vppyga - obofoundry: NCRO + obofoundry: ncro ols: ncro ontobee: NCRO name: Non-Coding RNA Ontology @@ -17675,7 +17680,7 @@ nif.cell: aberowl: NIFCELL biocontext: NIF_CELL bioportal: NIFCELL - obofoundry: NIF_CELL + obofoundry: nif_cell name: NIF Cell part_of: nif preferred_prefix: NIF_CELL @@ -17690,7 +17695,7 @@ nif.dysfunction: homepage: http://neuinfo.org/ mappings: biocontext: NIF_DYSFUNCTION - obofoundry: NIF_DYSFUNCTION + obofoundry: nif_dysfunction name: NIF Dysfunction part_of: nif preferred_prefix: NIF_DYSFUNCTION @@ -17735,7 +17740,7 @@ nif.grossanatomy: homepage: http://neuinfo.org/ mappings: biocontext: NIF_GROSSANATOMY - obofoundry: NIF_GROSSANATOMY + obofoundry: nif_grossanatomy name: NIF Gross Anatomy part_of: nif preferred_prefix: NIF_GROSSANATOMY @@ -18240,7 +18245,7 @@ nmr: bioportal: NMR miriam: nmr n2t: nmr - obofoundry: NMR + obofoundry: nmr ols: nmrcv prefixcommons: nmr name: NMR-instrument specific component of metabolomics investigations @@ -18299,7 +18304,7 @@ nomen: mappings: aberowl: NOMEN bioportal: NOMEN - obofoundry: NOMEN + obofoundry: nomen ols: nomen ontobee: NOMEN name: A nomenclatural ontology for biological names @@ -18484,7 +18489,7 @@ oae: biocontext: OAE bioportal: OAE fairsharing: FAIRsharing.tw4q8x - obofoundry: OAE + obofoundry: oae ols: oae ontobee: OAE name: Ontology of Adverse Events @@ -18509,7 +18514,7 @@ oarcs: biocontext: OARCS bioportal: OARCS fairsharing: FAIRsharing.yqn857 - obofoundry: OARCS + obofoundry: oarcs ols: oarcs ontobee: OARCS name: Ontology of Arthropod Circulatory Systems @@ -18539,7 +18544,7 @@ oba: biocontext: OBA bioportal: OBA fairsharing: FAIRsharing.mp0rwf - obofoundry: OBA + obofoundry: oba ols: oba ontobee: OBA name: Ontology of Biological Attributes @@ -18569,7 +18574,7 @@ obcs: biocontext: OBCS bioportal: OBCS fairsharing: FAIRsharing.5p12xh - obofoundry: OBCS + obofoundry: obcs ols: obcs ontobee: OBCS name: Ontology of Biological and Clinical Statistics @@ -18616,7 +18621,7 @@ obi: go: OBI miriam: obi n2t: obi - obofoundry: OBI + obofoundry: obi ols: obi ontobee: OBI prefixcommons: obi @@ -18650,7 +18655,7 @@ obib: biocontext: OBIB bioportal: OBIB fairsharing: FAIRsharing.bxc508 - obofoundry: OBIB + obofoundry: obib ols: obib ontobee: OBIB name: Ontology for Biobanking @@ -18828,7 +18833,7 @@ ogg: biocontext: OGG bioportal: OGG fairsharing: FAIRsharing.zmx7nn - obofoundry: OGG + obofoundry: ogg ols: ogg ontobee: OGG name: The Ontology of Genes and Genomes @@ -18866,7 +18871,7 @@ ogi: aberowl: OGI biocontext: OGI bioportal: OGI - obofoundry: OGI + obofoundry: ogi ols: ogi ontobee: OGI name: Ontology for genetic interval @@ -18911,7 +18916,7 @@ ogms: biocontext: OGMS bioportal: OGMS fairsharing: FAIRsharing.rvz0m9 - obofoundry: OGMS + obofoundry: ogms ols: ogms ontobee: OGMS name: Ontology for General Medical Science @@ -18939,7 +18944,7 @@ ogsf: biocontext: OGSF bioportal: OGSF fairsharing: FAIRsharing.egv2cz - obofoundry: OGSF + obofoundry: ogsf ols: ogsf ontobee: OGSF name: Ontology of Genetic Susceptibility Factor @@ -18965,7 +18970,7 @@ ohd: biocontext: OHD bioportal: OHD fairsharing: FAIRsharing.bg7bb6 - obofoundry: OHD + obofoundry: ohd ols: ohd ontobee: OHD name: Oral Health and Disease Ontology @@ -18991,7 +18996,7 @@ ohmi: biocontext: OHMI bioportal: OHMI fairsharing: FAIRsharing.cz9cnp - obofoundry: OHMI + obofoundry: ohmi ols: ohmi ontobee: OHMI name: Ontology of Host-Microbiome Interactions @@ -19017,7 +19022,7 @@ ohpi: aberowl: OHPI bioportal: OHPI fairsharing: FAIRsharing.vxpUJ6 - obofoundry: OHPI + obofoundry: ohpi ols: ohpi ontobee: OHPI name: Ontology of Host Pathogen Interactions @@ -19056,7 +19061,7 @@ olatdv: biocontext: OLATDV bioportal: OLATDV fairsharing: FAIRsharing.c86z66 - obofoundry: OlatDv + obofoundry: olatdv ols: olatdv ontobee: OLATDV name: Medaka Developmental Stages @@ -19176,7 +19181,7 @@ omiabis: aberowl: OMIABIS biocontext: OMIABIS bioportal: OMIABIS - obofoundry: OMIABIS + obofoundry: omiabis ols: omiabis ontobee: OMIABIS name: Ontologized MIABIS @@ -19274,7 +19279,7 @@ omit: fairsharing: FAIRsharing.mf91p5 miriam: omit n2t: omit - obofoundry: OMIT + obofoundry: omit ols: omit ontobee: OMIT name: Ontology for MicroRNA Target @@ -19302,7 +19307,7 @@ omo: mappings: aberowl: OMO bioportal: OMO - obofoundry: OMO + obofoundry: omo ols: omo ontobee: OMO name: OBO Metadata Ontology @@ -19348,7 +19353,7 @@ omp: biocontext: OMP bioportal: OMP fairsharing: FAIRsharing.cc3f2x - obofoundry: OMP + obofoundry: omp ols: omp ontobee: OMP name: Ontology of Microbial Phenotypes @@ -19378,7 +19383,7 @@ omrse: biocontext: OMRSE bioportal: OMRSE fairsharing: FAIRsharing.z0p37e - obofoundry: OMRSE + obofoundry: omrse ols: omrse ontobee: OMRSE name: Ontology of Medically Related Social Entities @@ -19424,7 +19429,7 @@ one: aberowl: ONE bioportal: ONE fairsharing: FAIRsharing.USxx0K - obofoundry: ONE + obofoundry: one ols: one ontobee: ONE name: Ontology for Nutritional Epidemiology @@ -19460,7 +19465,7 @@ ons: aberowl: ONS bioportal: ONS fairsharing: FAIRsharing.rfec93 - obofoundry: ONS + obofoundry: ons ols: ons ontobee: ONS name: Ontology for Nutritional Studies @@ -19508,7 +19513,7 @@ ontoavida: mappings: aberowl: ONTOAVIDA bioportal: ONTOAVIDA - obofoundry: ONTOAVIDA + obofoundry: ontoavida ols: ontoavida ontobee: ONTOAVIDA name: Ontology for Avida digital evolution platform @@ -19535,7 +19540,7 @@ ontoneo: biocontext: ONTONEO bioportal: ONTONEO fairsharing: FAIRsharing.5a4y1y - obofoundry: ONTONEO + obofoundry: ontoneo ols: ontoneo ontobee: ONTONEO name: Obstetric and Neonatal Ontology @@ -19561,7 +19566,7 @@ oostt: biocontext: OOSTT bioportal: OOSTT fairsharing: FAIRsharing.b4sa0w - obofoundry: OOSTT + obofoundry: oostt ols: oostt ontobee: OOSTT name: Ontology of Organizational Structures of Trauma centers and Trauma systems @@ -19638,7 +19643,7 @@ opl: biocontext: OPL bioportal: OPL fairsharing: FAIRsharing.ez2nhb - obofoundry: OPL + obofoundry: opl ols: opl ontobee: OPL name: Ontology for Parasite LifeCycle @@ -19682,7 +19687,7 @@ opmi: mappings: aberowl: OPMI bioportal: OPMI - obofoundry: OPMI + obofoundry: opmi ols: opmi ontobee: OPMI name: Ontology of Precision Medicine and Investigation @@ -19782,7 +19787,7 @@ ornaseq: mappings: aberowl: ORNASEQ bioportal: ORNASEQ - obofoundry: ORNASEQ + obofoundry: ornaseq ols: ornaseq ontobee: ORNASEQ name: Ontology of RNA Sequencing @@ -20042,7 +20047,7 @@ ovae: biocontext: OVAE bioportal: OVAE fairsharing: FAIRsharing.w4x6n4 - obofoundry: OVAE + obofoundry: ovae ols: ovae ontobee: OVAE name: Ontology of Vaccine Adverse Events @@ -20209,7 +20214,7 @@ pao: homepage: http://www.plantontology.org mappings: biocontext: PAO - obofoundry: PAO + obofoundry: pao name: Plant Anatomy Ontology preferred_prefix: PAO uri_format: http://purl.obolibrary.org/obo/PAO_$1 @@ -20307,7 +20312,7 @@ pato: go: PATO miriam: pato n2t: pato - obofoundry: PATO + obofoundry: pato ols: pato ontobee: PATO prefixcommons: pato @@ -20444,7 +20449,7 @@ pcl: mappings: aberowl: PCL bioportal: PCL - obofoundry: PCL + obofoundry: pcl ols: pcl ontobee: PCL name: Provisional Cell Ontology @@ -20489,7 +20494,7 @@ pco: bioportal: PCO ecoportal: PCO fairsharing: FAIRsharing.vq28qp - obofoundry: PCO + obofoundry: pco ols: pco ontobee: PCO name: Population and Community Ontology @@ -20508,7 +20513,7 @@ pd_st: homepage: http://4dx.embl.de/platy mappings: biocontext: PD_ST - obofoundry: PD_ST + obofoundry: pd_st name: Platynereis stage ontology preferred_prefix: PD_ST uri_format: http://purl.obolibrary.org/obo/PD_ST_$1 @@ -20646,7 +20651,7 @@ pdro: biocontext: PDRO bioportal: PDRO fairsharing: FAIRsharing.9te3ev - obofoundry: PDRO + obofoundry: pdro ols: pdro ontobee: PDRO name: The Prescription of Drugs Ontology @@ -20672,7 +20677,7 @@ pdumdv: biocontext: PDUMDV bioportal: PDUMDV fairsharing: FAIRsharing.493qns - obofoundry: PdumDv + obofoundry: pdumdv ols: pdumdv ontobee: PDUMDV name: Platynereis Developmental Stages @@ -20705,7 +20710,7 @@ peco: biocontext: PECO bioportal: PECO fairsharing: FAIRsharing.6yNXYK - obofoundry: PECO + obofoundry: peco ols: peco ontobee: PECO name: Plant Experimental Conditions Ontology @@ -20885,7 +20890,7 @@ pgdso: homepage: http://www.plantontology.org mappings: biocontext: PGDSO - obofoundry: PGDSO + obofoundry: pgdso name: Plant Growth and Development Stage preferred_prefix: PGDSO uri_format: http://purl.obolibrary.org/obo/PGDSO_$1 @@ -21094,7 +21099,7 @@ phipo: mappings: aberowl: PHIPO bioportal: PHIPO - obofoundry: PHIPO + obofoundry: phipo ols: phipo ontobee: PHIPO name: Pathogen Host Interaction Phenotype Ontology @@ -21362,7 +21367,7 @@ plana: biocontext: PLANA bioportal: PLANA fairsharing: FAIRsharing.g1qrqs - obofoundry: PLANA + obofoundry: plana ols: plana ontobee: PLANA name: Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology @@ -21392,7 +21397,7 @@ planp: mappings: aberowl: PLANP bioportal: PLANP - obofoundry: PLANP + obofoundry: planp ols: planp ontobee: PLANP name: Planarian Phenotype Ontology @@ -21454,7 +21459,7 @@ plo: homepage: http://www.sanger.ac.uk/Users/mb4/PLO/ mappings: biocontext: PLO - obofoundry: PLO + obofoundry: plo name: Plasmodium Life Cycle preferred_prefix: PLO uri_format: http://purl.obolibrary.org/obo/PLO_$1 @@ -21597,7 +21602,7 @@ po: go: PO miriam: po n2t: po - obofoundry: PO + obofoundry: po ols: po ontobee: PO prefixcommons: po @@ -21685,7 +21690,7 @@ poro: biocontext: PORO bioportal: PORO fairsharing: FAIRsharing.93g1th - obofoundry: PORO + obofoundry: poro ols: poro ontobee: PORO name: Porifera Ontology @@ -21728,7 +21733,7 @@ ppo: biocontext: PPO bioportal: PPO fairsharing: FAIRsharing.hakg7c - obofoundry: PPO + obofoundry: ppo ols: ppo ontobee: PPO name: Plant Phenology Ontology @@ -21782,7 +21787,7 @@ pr: go: PR miriam: pr n2t: pr - obofoundry: PR + obofoundry: pr ols: pr ontobee: PR prefixcommons: pr @@ -21907,20 +21912,23 @@ proco: - pato - ro - sbo - description: PROCO covers process chemistry, the chemical field concerned with scaling - up laboratory syntheses to commercially viable processes. + description: PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to + standardly represent entities and relations among entities in the domain of process + chemistry. download_owl: http://purl.obolibrary.org/obo/proco.owl example: '0000001' homepage: https://github.com/proco-ontology/PROCO license: CC BY 4.0 mappings: aberowl: PROCO - obofoundry: PROCO + obofoundry: proco + ols: proco ontobee: PROCO name: Process Chemistry Ontology preferred_prefix: PROCO repository: https://github.com/proco-ontology/PROCO uri_format: http://purl.obolibrary.org/obo/PROCO_$1 + version: PROCO release 20220414 prodom: description: ProDom is a database of protein domain families generated from the global comparison of all available protein sequences. @@ -21966,7 +21974,7 @@ propreo: aberowl: PROPREO biocontext: PROPREO bioportal: PROPREO - obofoundry: PROPREO + obofoundry: propreo prefixcommons: propreo name: Proteomics data and process provenance preferred_prefix: PROPREO @@ -22134,7 +22142,7 @@ psdo: mappings: aberowl: PSDO bioportal: PSDO - obofoundry: PSDO + obofoundry: psdo ols: psdo ontobee: PSDO name: Performance Summary Display Ontology @@ -22206,7 +22214,7 @@ pso: aberowl: PSO bioportal: PSO fairsharing: FAIRsharing.dyj433 - obofoundry: PSO + obofoundry: pso ols: pso ontobee: PSO name: Plant Stress Ontology @@ -22459,7 +22467,7 @@ pw: fairsharing: FAIRsharing.f73xhd miriam: pw n2t: pw - obofoundry: PW + obofoundry: pw ols: pw ontobee: PW prefixcommons: pw @@ -22629,7 +22637,7 @@ rbo: mappings: aberowl: RBO bioportal: RBO - obofoundry: RBO + obofoundry: rbo ols: rbo ontobee: RBO name: Radiation Biology Ontology @@ -22905,7 +22913,7 @@ resid: go: RESID miriam: resid n2t: resid - obofoundry: RESID + obofoundry: resid prefixcommons: resid name: Protein covalent bond pattern: ^AA\d{4}$ @@ -22937,7 +22945,7 @@ rex: biocontext: REX bioportal: REX fairsharing: FAIRsharing.g0a7s0 - obofoundry: REX + obofoundry: rex ols: rex ontobee: REX prefixcommons: rex @@ -23238,7 +23246,7 @@ rnao: biocontext: RNAO bioportal: RNAO fairsharing: FAIRsharing.kqt2h2 - obofoundry: RNAO + obofoundry: rnao ols: rnao ontobee: RNAO prefixcommons: rnao @@ -23280,7 +23288,6 @@ ro: - psdo - pso - rbo - - upa - xpo - zp banana: RO @@ -23308,7 +23315,7 @@ ro: go: RO miriam: ro n2t: ro - obofoundry: RO + obofoundry: ro ols: ro ontobee: RO prefixcommons: ro @@ -23382,7 +23389,7 @@ rs: biocontext: RS bioportal: RS fairsharing: FAIRsharing.vajn3f - obofoundry: RS + obofoundry: rs ols: rs ontobee: RS prefixcommons: rs @@ -23425,7 +23432,7 @@ rxno: biocontext: RXNO bioportal: RXNO fairsharing: FAIRsharing.w4tncg - obofoundry: RXNO + obofoundry: rxno ols: rxno ontobee: RXNO wikidata: P2106 @@ -23571,7 +23578,7 @@ sao: aberowl: SAO biocontext: SAO bioportal: SAO - obofoundry: SAO + obofoundry: sao prefixcommons: sao name: Subcellular Anatomy Ontology pattern: ^\d+$ @@ -23624,7 +23631,7 @@ sbo: fairsharing: FAIRsharing.s19src miriam: sbo n2t: sbo - obofoundry: SBO + obofoundry: sbo ols: sbo ontobee: SBO prefixcommons: sbo @@ -23653,13 +23660,11 @@ scdo: - envo - eupath - exo - - gaz - gsso - hp - hsapdv - ico - ido - - idomal - mp - nbo - ncit @@ -23684,7 +23689,7 @@ scdo: aberowl: SCDO bioportal: SCDO fairsharing: FAIRsharing.kkq6pw - obofoundry: SCDO + obofoundry: scdo ols: scdo ontobee: SCDO name: Sickle Cell Disease Ontology @@ -23980,7 +23985,7 @@ sep: aberowl: SEP biocontext: SEP bioportal: SEP - obofoundry: SEP + obofoundry: sep ontobee: SEP prefixcommons: sep name: Sample processing and separation techniques @@ -24003,7 +24008,7 @@ sepio: aberowl: SEPIO biocontext: SEPIO bioportal: SEPIO - obofoundry: SEPIO + obofoundry: sepio ols: sepio ontobee: SEPIO name: Scientific Evidence and Provenance Information Ontology @@ -24129,7 +24134,7 @@ sibo: biocontext: SIBO bioportal: SIBO fairsharing: FAIRsharing.q09hck - obofoundry: SIBO + obofoundry: sibo ols: sibo ontobee: SIBO name: Social Insect Behavior Ontology @@ -24519,7 +24524,7 @@ so: go: SO miriam: so n2t: so - obofoundry: SO + obofoundry: so ols: so ontobee: SO prefixcommons: so @@ -24543,7 +24548,7 @@ sopharm: aberowl: SOPHARM biocontext: SOPHARM bioportal: SOPHARM - obofoundry: SOPHARM + obofoundry: sopharm name: Suggested Ontology for Pharmacogenomics preferred_prefix: SOPHARM uri_format: http://purl.obolibrary.org/obo/SOPHARM_$1 @@ -24593,7 +24598,7 @@ spd: biocontext: SPD bioportal: SPD fairsharing: FAIRsharing.yecp83 - obofoundry: SPD + obofoundry: spd ols: spd ontobee: SPD prefixcommons: spd @@ -24777,7 +24782,7 @@ stato: biocontext: STATO bioportal: STATO fairsharing: FAIRsharing.na5xp - obofoundry: STATO + obofoundry: stato ols: stato ontobee: STATO name: The Statistical Methods Ontology @@ -25094,7 +25099,7 @@ swo: biocontext: SWO bioportal: SWO fairsharing: FAIRsharing.sp3szt - obofoundry: SWO + obofoundry: swo ols: swo ontobee: SWO prefixcommons: swo @@ -25124,7 +25129,7 @@ symp: biocontext: SYMP bioportal: SYMP fairsharing: FAIRsharing.ay74mj - obofoundry: SYMP + obofoundry: symp ols: symp ontobee: SYMP wikidata: P8656 @@ -25181,7 +25186,7 @@ tads: biocontext: TADS bioportal: TADS fairsharing: FAIRsharing.8wm364 - obofoundry: TADS + obofoundry: tads ols: tads ontobee: TADS name: Tick Anatomy Ontology @@ -25199,7 +25204,7 @@ tahe: deprecated: true mappings: biocontext: TAHE - obofoundry: TAHE + obofoundry: tahe name: Terminology of Anatomy of Human Embryology preferred_prefix: TAHE uri_format: http://purl.obolibrary.org/obo/TAHE_$1 @@ -25212,7 +25217,7 @@ tahh: deprecated: true mappings: biocontext: TAHH - obofoundry: TAHH + obofoundry: tahh name: Terminology of Anatomy of Human Histology preferred_prefix: TAHH uri_format: http://purl.obolibrary.org/obo/TAHH_$1 @@ -25286,7 +25291,7 @@ tao: aberowl: TAO biocontext: TAO bioportal: TAO - obofoundry: TAO + obofoundry: tao prefixcommons: tao name: Teleost Anatomy Ontology pattern: ^\d{7}$ @@ -25326,7 +25331,7 @@ taxrank: biocontext: TAXRANK bioportal: TAXRANK fairsharing: FAIRsharing.p1sejz - obofoundry: TAXRANK + obofoundry: taxrank ols: taxrank ontobee: TAXRANK prefixcommons: taxrank @@ -25434,7 +25439,7 @@ tgma: biocontext: TGMA bioportal: TGMA fairsharing: FAIRsharing.dqnfkg - obofoundry: TGMA + obofoundry: tgma ols: tgma ontobee: TGMA prefixcommons: tgma @@ -25552,7 +25557,7 @@ to: biocontext: TO bioportal: PTO fairsharing: FAIRsharing.w69t6r - obofoundry: TO + obofoundry: to ols: to ontobee: TO name: Plant Trait Ontology @@ -25667,7 +25672,7 @@ trans: biocontext: TRANS bioportal: TRANS fairsharing: FAIRsharing.nygmp7 - obofoundry: TRANS + obofoundry: trans ols: trans ontobee: TRANS name: Pathogen Transmission Ontology @@ -25817,7 +25822,7 @@ tto: biocontext: TTO bioportal: TTO fairsharing: FAIRsharing.1rj558 - obofoundry: TTO + obofoundry: tto ols: tto ontobee: TTO prefixcommons: tto @@ -25856,7 +25861,7 @@ txpo: mappings: aberowl: TXPO bioportal: TXPO - obofoundry: TXPO + obofoundry: txpo ols: txpo ontobee: TXPO name: Toxic Process Ontology @@ -25923,7 +25928,7 @@ uberon: go: UBERON miriam: uberon n2t: uberon - obofoundry: UBERON + obofoundry: uberon ols: uberon ontobee: UBERON wikidata: P1554 @@ -26601,7 +26606,7 @@ uo: fairsharing: FAIRsharing.mjnypw miriam: uo n2t: uo - obofoundry: UO + obofoundry: uo ols: uo ontobee: UO prefixcommons: uo @@ -26633,7 +26638,7 @@ upa: bioportal: UPA edam: '2645' go: UniPathway - obofoundry: UPA + obofoundry: upa ols: upa ontobee: UPA prefixcommons: unipathway @@ -26664,7 +26669,7 @@ upheno: biocontext: UPHENO bioportal: UPHENO fairsharing: FAIRsharing.r41qhx - obofoundry: UPHENO + obofoundry: upheno ols: upheno ontobee: UPHENO name: Unified Phenotype Ontology @@ -26745,7 +26750,7 @@ vario: fairsharing: FAIRsharing.65xkbs miriam: vario n2t: vario - obofoundry: VariO + obofoundry: vario ols: vario ontobee: VariO name: Variation Ontology @@ -26929,7 +26934,7 @@ vhog: aberowl: VHOG biocontext: VHOG bioportal: VHOG - obofoundry: VHOG + obofoundry: vhog prefixcommons: vhog name: Vertebrate Homologous Organ Group Ontology pattern: ^\d{7}$ @@ -27102,7 +27107,7 @@ vo: biocontext: VO bioportal: VO fairsharing: FAIRsharing.zwtww5 - obofoundry: VO + obofoundry: vo ols: vo ontobee: VO prefixcommons: vo @@ -27142,7 +27147,7 @@ vsao: aberowl: VSAO biocontext: VSAO bioportal: VSAO - obofoundry: VSAO + obofoundry: vsao name: Vertebrate Skeletal Anatomy Ontology preferred_prefix: VSAO synonyms: @@ -27207,7 +27212,7 @@ vt: biocontext: VT bioportal: VT fairsharing: FAIRsharing.10gr18 - obofoundry: VT + obofoundry: vt ols: vt ontobee: VT prefixcommons: vt @@ -27233,7 +27238,7 @@ vto: biocontext: VTO bioportal: VTO fairsharing: FAIRsharing.akmeb9 - obofoundry: VTO + obofoundry: vto ols: vto ontobee: VTO name: Vertebrate Taxonomy Ontology @@ -27309,7 +27314,7 @@ wbbt: bioportal: WB-BT fairsharing: FAIRsharing.phk7dd go: WBbt - obofoundry: WBbt + obofoundry: wbbt ols: wbbt ontobee: WBbt prefixcommons: wbbt @@ -27340,7 +27345,7 @@ wbls: bioportal: WB-LS fairsharing: FAIRsharing.sm90nh go: WBls - obofoundry: WBls + obofoundry: wbls ols: wbls ontobee: WBLS prefixcommons: wbls @@ -27371,7 +27376,7 @@ wbphenotype: bioportal: WB-PHENOTYPE fairsharing: FAIRsharing.agvc7y go: WBPhenotype - obofoundry: WBPhenotype + obofoundry: wbphenotype ols: wbphenotype ontobee: WBPhenotype prefixcommons: wbphenotype @@ -27672,7 +27677,7 @@ xao: biocontext: XAO bioportal: XAO fairsharing: FAIRsharing.17zapb - obofoundry: XAO + obofoundry: xao ols: xao ontobee: XAO wikidata: P4495 @@ -27703,7 +27708,7 @@ xco: biocontext: XCO bioportal: XCO fairsharing: FAIRsharing.x39h5y - obofoundry: XCO + obofoundry: xco ols: xco ontobee: XCO prefixcommons: xco @@ -27787,7 +27792,7 @@ xlmod: mappings: aberowl: XLMOD bioportal: XLMOD - obofoundry: XLMOD + obofoundry: xlmod ols: xlmod ontobee: XLMOD name: HUPO-PSI cross-linking and derivatization reagents controlled vocabulary @@ -27855,7 +27860,7 @@ xpo: aberowl: XPO biolink: XPO bioportal: XPO - obofoundry: XPO + obofoundry: xpo ols: xpo ontobee: XPO name: Xenopus Phenotype Ontology @@ -27977,11 +27982,10 @@ ypo: deprecated: true homepage: http://www.yeastgenome.org/ mappings: - obofoundry: YPO + obofoundry: ypo ols: ypo name: Yeast phenotypes preferred_prefix: YPO - uri_format: http://purl.obolibrary.org/obo/YPO_$1 yrcpdr: description: The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations @@ -28013,7 +28017,7 @@ zea: aberowl: ZEA biocontext: ZEA bioportal: ZEA - obofoundry: ZEA + obofoundry: zea prefixcommons: zea name: Maize gross anatomy preferred_prefix: ZEA @@ -28038,7 +28042,7 @@ zeco: biocontext: ZECO bioportal: ZECO fairsharing: FAIRsharing.np2wfz - obofoundry: ZECO + obofoundry: zeco ols: zeco ontobee: ZECO name: Zebrafish Experimental Conditions Ontology @@ -28090,7 +28094,7 @@ zfa: biocontext: ZFA bioportal: ZFA fairsharing: FAIRsharing.s3r6sk - obofoundry: ZFA + obofoundry: zfa ols: zfa ontobee: ZFA prefixcommons: zfa @@ -28151,7 +28155,7 @@ zfs: biocontext: ZFS bioportal: ZFS fairsharing: FAIRsharing.bc8ayj - obofoundry: ZFS + obofoundry: zfs ols: zfs ontobee: ZFS name: Zebrafish developmental stages ontology @@ -28202,7 +28206,7 @@ zp: aberowl: ZP biocontext: ZP bioportal: ZP - obofoundry: ZP + obofoundry: zp ols: zp ontobee: ZP name: Zebrafish Phenotype Ontology diff --git a/exports/sssom/bioregistry.sssom.tsv b/exports/sssom/bioregistry.sssom.tsv index 398153764..8d00c616e 100644 --- a/exports/sssom/bioregistry.sssom.tsv +++ b/exports/sssom/bioregistry.sssom.tsv @@ -10,7 +10,7 @@ bioregistry:4dn.biosource skos:exactMatch miriam:4dn sssom:HumanCurated bioregistry:4dn.biosource skos:exactMatch prefixcommons:4dn sssom:HumanCurated bioregistry:aao skos:exactMatch biocontext:AAO sssom:HumanCurated bioregistry:aao skos:exactMatch fairsharing:FAIRsharing.mxx5rp sssom:HumanCurated -bioregistry:aao skos:exactMatch obofoundry:AAO sssom:HumanCurated +bioregistry:aao skos:exactMatch obofoundry:aao sssom:HumanCurated bioregistry:aao skos:exactMatch prefixcommons:aao sssom:HumanCurated bioregistry:abcd skos:exactMatch fairsharing:FAIRsharing.Z8OKi5 sssom:HumanCurated bioregistry:abs skos:exactMatch biocontext:ABS sssom:HumanCurated @@ -29,7 +29,8 @@ bioregistry:addgene skos:exactMatch prefixcommons:addgene sssom:HumanCurated bioregistry:ado skos:exactMatch aberowl:ADO sssom:HumanCurated bioregistry:ado skos:exactMatch bioportal:ADO sssom:HumanCurated bioregistry:ado skos:exactMatch fairsharing:FAIRsharing.ckd4rf sssom:HumanCurated -bioregistry:ado skos:exactMatch obofoundry:ADO sssom:HumanCurated +bioregistry:ado skos:exactMatch obofoundry:ado sssom:HumanCurated +bioregistry:ado skos:exactMatch ols:ado sssom:HumanCurated bioregistry:ado bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated bioregistry:adw skos:exactMatch aberowl:ADW sssom:HumanCurated bioregistry:adw skos:exactMatch biocontext:ADW sssom:HumanCurated @@ -37,20 +38,19 @@ bioregistry:adw skos:exactMatch bioportal:ADW sssom:HumanCurated bioregistry:adw skos:exactMatch fairsharing:FAIRsharing.t9fvdn sssom:HumanCurated bioregistry:adw skos:exactMatch miriam:adw sssom:HumanCurated bioregistry:adw skos:exactMatch n2t:adw sssom:HumanCurated -bioregistry:adw skos:exactMatch obofoundry:ADW sssom:HumanCurated +bioregistry:adw skos:exactMatch obofoundry:adw sssom:HumanCurated bioregistry:aeo skos:exactMatch aberowl:AEO sssom:HumanCurated bioregistry:aeo skos:exactMatch biocontext:AEO sssom:HumanCurated bioregistry:aeo skos:exactMatch bioportal:AEO sssom:HumanCurated bioregistry:aeo skos:exactMatch fairsharing:FAIRsharing.93ee19 sssom:HumanCurated -bioregistry:aeo skos:exactMatch obofoundry:AEO sssom:HumanCurated +bioregistry:aeo skos:exactMatch obofoundry:aeo sssom:HumanCurated bioregistry:aeo skos:exactMatch ols:aeo sssom:HumanCurated bioregistry:aeo skos:exactMatch ontobee:AEO sssom:HumanCurated -bioregistry:aeo bioregistry.schema:0000018 bioregistry:ehdaa2 sssom:HumanCurated bioregistry:aero skos:exactMatch aberowl:AERO sssom:HumanCurated bioregistry:aero skos:exactMatch biocontext:AERO sssom:HumanCurated bioregistry:aero skos:exactMatch bioportal:AERO sssom:HumanCurated bioregistry:aero skos:exactMatch fairsharing:FAIRsharing.rycy2x sssom:HumanCurated -bioregistry:aero skos:exactMatch obofoundry:AERO sssom:HumanCurated +bioregistry:aero skos:exactMatch obofoundry:aero sssom:HumanCurated bioregistry:affy.probeset skos:exactMatch biocontext:AFFY.PROBESET sssom:HumanCurated bioregistry:affy.probeset skos:exactMatch miriam:affy.probeset sssom:HumanCurated bioregistry:affy.probeset skos:exactMatch n2t:affy.probeset sssom:HumanCurated @@ -70,7 +70,7 @@ bioregistry:agro skos:exactMatch agroportal:AGRO sssom:HumanCurated bioregistry:agro skos:exactMatch biocontext:AGRO sssom:HumanCurated bioregistry:agro skos:exactMatch bioportal:AGRO sssom:HumanCurated bioregistry:agro skos:exactMatch fairsharing:FAIRsharing.m40bhw sssom:HumanCurated -bioregistry:agro skos:exactMatch obofoundry:AGRO sssom:HumanCurated +bioregistry:agro skos:exactMatch obofoundry:agro sssom:HumanCurated bioregistry:agro skos:exactMatch ols:agro sssom:HumanCurated bioregistry:agro skos:exactMatch ontobee:AGRO sssom:HumanCurated bioregistry:agro bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -92,7 +92,7 @@ bioregistry:agrovoc skos:exactMatch ecoportal:AGROVOC sssom:HumanCurated bioregistry:agrovoc skos:exactMatch fairsharing:FAIRsharing.anpj91 sssom:HumanCurated bioregistry:aism skos:exactMatch aberowl:AISM sssom:HumanCurated bioregistry:aism skos:exactMatch bioportal:AISM sssom:HumanCurated -bioregistry:aism skos:exactMatch obofoundry:AISM sssom:HumanCurated +bioregistry:aism skos:exactMatch obofoundry:aism sssom:HumanCurated bioregistry:aism skos:exactMatch ols:aism sssom:HumanCurated bioregistry:aism skos:exactMatch ontobee:AISM sssom:HumanCurated bioregistry:aism bioregistry.schema:0000018 bioregistry:colao sssom:HumanCurated @@ -115,7 +115,7 @@ bioregistry:amoebadb skos:exactMatch n2t:amoebadb sssom:HumanCurated bioregistry:amoebadb skos:exactMatch prefixcommons:amoebadb sssom:HumanCurated bioregistry:amphx skos:exactMatch aberowl:AMPHX sssom:HumanCurated bioregistry:amphx skos:exactMatch bioportal:AMPHX sssom:HumanCurated -bioregistry:amphx skos:exactMatch obofoundry:AMPHX sssom:HumanCurated +bioregistry:amphx skos:exactMatch obofoundry:amphx sssom:HumanCurated bioregistry:amphx skos:exactMatch ols:amphx sssom:HumanCurated bioregistry:amphx skos:exactMatch ontobee:AMPHX sssom:HumanCurated bioregistry:amphx bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated @@ -159,13 +159,13 @@ bioregistry:apo skos:exactMatch aberowl:APO sssom:HumanCurated bioregistry:apo skos:exactMatch biocontext:YPO sssom:HumanCurated bioregistry:apo skos:exactMatch bioportal:APO sssom:HumanCurated bioregistry:apo skos:exactMatch fairsharing:FAIRsharing.dyqz3y sssom:HumanCurated -bioregistry:apo skos:exactMatch obofoundry:APO sssom:HumanCurated +bioregistry:apo skos:exactMatch obofoundry:apo sssom:HumanCurated bioregistry:apo skos:exactMatch ols:apo sssom:HumanCurated bioregistry:apo skos:exactMatch ontobee:APO sssom:HumanCurated bioregistry:apollosv skos:exactMatch aberowl:APOLLO_SV sssom:HumanCurated bioregistry:apollosv skos:exactMatch bioportal:APOLLO-SV sssom:HumanCurated bioregistry:apollosv skos:exactMatch fairsharing:FAIRsharing.ngv2xx sssom:HumanCurated -bioregistry:apollosv skos:exactMatch obofoundry:APOLLO_SV sssom:HumanCurated +bioregistry:apollosv skos:exactMatch obofoundry:apollo_sv sssom:HumanCurated bioregistry:apollosv skos:exactMatch ols:apollo_sv sssom:HumanCurated bioregistry:apollosv skos:exactMatch ontobee:APOLLO_SV sssom:HumanCurated bioregistry:apollosv bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -183,7 +183,7 @@ bioregistry:ark skos:exactMatch n2t:ark sssom:HumanCurated bioregistry:aro skos:exactMatch aberowl:ARO sssom:HumanCurated bioregistry:aro skos:exactMatch biocontext:ARO sssom:HumanCurated bioregistry:aro skos:exactMatch bioportal:ARO sssom:HumanCurated -bioregistry:aro skos:exactMatch obofoundry:ARO sssom:HumanCurated +bioregistry:aro skos:exactMatch obofoundry:aro sssom:HumanCurated bioregistry:aro skos:exactMatch ols:aro sssom:HumanCurated bioregistry:aro skos:exactMatch ontobee:ARO sssom:HumanCurated bioregistry:aro bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -244,7 +244,7 @@ bioregistry:ato skos:exactMatch aberowl:ATO sssom:HumanCurated bioregistry:ato skos:exactMatch biocontext:ATO sssom:HumanCurated bioregistry:ato skos:exactMatch bioportal:ATO sssom:HumanCurated bioregistry:ato skos:exactMatch fairsharing:FAIRsharing.ayjdsm sssom:HumanCurated -bioregistry:ato skos:exactMatch obofoundry:ATO sssom:HumanCurated +bioregistry:ato skos:exactMatch obofoundry:ato sssom:HumanCurated bioregistry:atol skos:exactMatch aberowl:ATOL sssom:HumanCurated bioregistry:atol skos:exactMatch agroportal:ATOL sssom:HumanCurated bioregistry:atol skos:exactMatch bioportal:ATOL sssom:HumanCurated @@ -277,7 +277,7 @@ bioregistry:bbtp skos:exactMatch miriam:bbtp sssom:HumanCurated bioregistry:bcgo skos:exactMatch aberowl:BCGO sssom:HumanCurated bioregistry:bcgo skos:exactMatch biocontext:BCGO sssom:HumanCurated bioregistry:bcgo skos:exactMatch bioportal:BCGO sssom:HumanCurated -bioregistry:bcgo skos:exactMatch obofoundry:BCGO sssom:HumanCurated +bioregistry:bcgo skos:exactMatch obofoundry:bcgo sssom:HumanCurated bioregistry:bcgo skos:exactMatch ontobee:BCGO sssom:HumanCurated bioregistry:bcio skos:exactMatch aberowl:BCI-O sssom:HumanCurated bioregistry:bcio skos:exactMatch bioportal:BCI-O sssom:HumanCurated @@ -288,7 +288,7 @@ bioregistry:bco skos:exactMatch biocontext:BCO sssom:HumanCurated bioregistry:bco skos:exactMatch bioportal:BCO sssom:HumanCurated bioregistry:bco skos:exactMatch ecoportal:BCO sssom:HumanCurated bioregistry:bco skos:exactMatch fairsharing:FAIRsharing.8ktkqy sssom:HumanCurated -bioregistry:bco skos:exactMatch obofoundry:BCO sssom:HumanCurated +bioregistry:bco skos:exactMatch obofoundry:bco sssom:HumanCurated bioregistry:bco skos:exactMatch ols:bco sssom:HumanCurated bioregistry:bco skos:exactMatch ontobee:BCO sssom:HumanCurated bioregistry:bco bioregistry.schema:0000018 bioregistry:fovt sssom:HumanCurated @@ -316,7 +316,7 @@ bioregistry:bfo skos:exactMatch agroportal:BFO sssom:HumanCurated bioregistry:bfo skos:exactMatch biocontext:BFO sssom:HumanCurated bioregistry:bfo skos:exactMatch bioportal:BFO sssom:HumanCurated bioregistry:bfo skos:exactMatch fairsharing:FAIRsharing.wcpd6f sssom:HumanCurated -bioregistry:bfo skos:exactMatch obofoundry:BFO sssom:HumanCurated +bioregistry:bfo skos:exactMatch obofoundry:bfo sssom:HumanCurated bioregistry:bfo skos:exactMatch ols:bfo sssom:HumanCurated bioregistry:bfo skos:exactMatch ontobee:BFO sssom:HumanCurated bioregistry:bfo bioregistry.schema:0000018 bioregistry:ado sssom:HumanCurated @@ -366,7 +366,7 @@ bioregistry:bigg.reaction skos:exactMatch miriam:bigg.reaction sssom:HumanCurate bioregistry:bigg.reaction skos:exactMatch n2t:bigg.reaction sssom:HumanCurated bioregistry:bila skos:exactMatch biocontext:BILA sssom:HumanCurated bioregistry:bila skos:exactMatch fairsharing:FAIRsharing.eqgjeq sssom:HumanCurated -bioregistry:bila skos:exactMatch obofoundry:BILA sssom:HumanCurated +bioregistry:bila skos:exactMatch obofoundry:bila sssom:HumanCurated bioregistry:bindingdb skos:exactMatch biocontext:BINDINGDB sssom:HumanCurated bioregistry:bindingdb skos:exactMatch fairsharing:FAIRsharing.3b36hk sssom:HumanCurated bioregistry:bindingdb skos:exactMatch miriam:bindingdb sssom:HumanCurated @@ -405,7 +405,7 @@ bioregistry:biomodels.kisao skos:exactMatch bioportal:KISAO sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch fairsharing:FAIRsharing.jcg19w sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch miriam:biomodels.kisao sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch n2t:biomodels.kisao sssom:HumanCurated -bioregistry:biomodels.kisao skos:exactMatch obofoundry:KISAO sssom:HumanCurated +bioregistry:biomodels.kisao skos:exactMatch obofoundry:kisao sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch ols:kisao sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch ontobee:KISAO sssom:HumanCurated bioregistry:biomodels.kisao skos:exactMatch prefixcommons:kisao sssom:HumanCurated @@ -472,7 +472,7 @@ bioregistry:bold.taxonomy skos:exactMatch biocontext:BOLD.TAXONOMY sssom:HumanCu bioregistry:bold.taxonomy skos:exactMatch miriam:bold.taxonomy sssom:HumanCurated bioregistry:bold.taxonomy skos:exactMatch n2t:bold.taxonomy sssom:HumanCurated bioregistry:bootstrep skos:exactMatch biocontext:BOOTSTREP sssom:HumanCurated -bioregistry:bootstrep skos:exactMatch obofoundry:BOOTSTREP sssom:HumanCurated +bioregistry:bootstrep skos:exactMatch obofoundry:bootstrep sssom:HumanCurated bioregistry:brenda skos:exactMatch biocontext:BRENDA sssom:HumanCurated bioregistry:brenda skos:exactMatch fairsharing:FAIRsharing.etp533 sssom:HumanCurated bioregistry:brenda skos:exactMatch miriam:brenda sssom:HumanCurated @@ -485,7 +485,7 @@ bioregistry:bspo skos:exactMatch aberowl:BSPO sssom:HumanCurated bioregistry:bspo skos:exactMatch biocontext:BSPO sssom:HumanCurated bioregistry:bspo skos:exactMatch bioportal:BSPO sssom:HumanCurated bioregistry:bspo skos:exactMatch fairsharing:FAIRsharing.newa3z sssom:HumanCurated -bioregistry:bspo skos:exactMatch obofoundry:BSPO sssom:HumanCurated +bioregistry:bspo skos:exactMatch obofoundry:bspo sssom:HumanCurated bioregistry:bspo skos:exactMatch ols:bspo sssom:HumanCurated bioregistry:bspo skos:exactMatch ontobee:BSPO sssom:HumanCurated bioregistry:bspo bioregistry.schema:0000018 bioregistry:aism sssom:HumanCurated @@ -499,7 +499,7 @@ bioregistry:bto skos:exactMatch bioportal:BTO sssom:HumanCurated bioregistry:bto skos:exactMatch fairsharing:FAIRsharing.1414v8 sssom:HumanCurated bioregistry:bto skos:exactMatch miriam:bto sssom:HumanCurated bioregistry:bto skos:exactMatch n2t:bto sssom:HumanCurated -bioregistry:bto skos:exactMatch obofoundry:BTO sssom:HumanCurated +bioregistry:bto skos:exactMatch obofoundry:bto sssom:HumanCurated bioregistry:bto skos:exactMatch ols:bto sssom:HumanCurated bioregistry:bto skos:exactMatch ontobee:BTO sssom:HumanCurated bioregistry:bto skos:exactMatch prefixcommons:bto sssom:HumanCurated @@ -534,12 +534,11 @@ bioregistry:caro skos:exactMatch aberowl:CARO sssom:HumanCurated bioregistry:caro skos:exactMatch biocontext:CARO sssom:HumanCurated bioregistry:caro skos:exactMatch bioportal:CARO sssom:HumanCurated bioregistry:caro skos:exactMatch fairsharing:FAIRsharing.3kcgmr sssom:HumanCurated -bioregistry:caro skos:exactMatch obofoundry:CARO sssom:HumanCurated +bioregistry:caro skos:exactMatch obofoundry:caro sssom:HumanCurated bioregistry:caro skos:exactMatch ols:caro sssom:HumanCurated bioregistry:caro skos:exactMatch ontobee:CARO sssom:HumanCurated bioregistry:caro bioregistry.schema:0000018 bioregistry:aism sssom:HumanCurated bioregistry:caro bioregistry.schema:0000018 bioregistry:colao sssom:HumanCurated -bioregistry:caro bioregistry.schema:0000018 bioregistry:ehdaa2 sssom:HumanCurated bioregistry:caro bioregistry.schema:0000018 bioregistry:lepao sssom:HumanCurated bioregistry:caro bioregistry.schema:0000018 bioregistry:pco sssom:HumanCurated bioregistry:cas skos:exactMatch biocontext:CAS sssom:HumanCurated @@ -593,7 +592,7 @@ bioregistry:cdao skos:exactMatch agroportal:CDAO sssom:HumanCurated bioregistry:cdao skos:exactMatch biocontext:CDAO sssom:HumanCurated bioregistry:cdao skos:exactMatch bioportal:CDAO sssom:HumanCurated bioregistry:cdao skos:exactMatch fairsharing:FAIRsharing.kay31r sssom:HumanCurated -bioregistry:cdao skos:exactMatch obofoundry:CDAO sssom:HumanCurated +bioregistry:cdao skos:exactMatch obofoundry:cdao sssom:HumanCurated bioregistry:cdao skos:exactMatch ols:cdao sssom:HumanCurated bioregistry:cdao skos:exactMatch ontobee:CDAO sssom:HumanCurated bioregistry:cdd skos:exactMatch biocontext:CDD sssom:HumanCurated @@ -603,7 +602,7 @@ bioregistry:cdd skos:exactMatch n2t:cdd sssom:HumanCurated bioregistry:cdd skos:exactMatch prefixcommons:cdd sssom:HumanCurated bioregistry:cdno skos:exactMatch aberowl:CDNO sssom:HumanCurated bioregistry:cdno skos:exactMatch bioportal:CDNO sssom:HumanCurated -bioregistry:cdno skos:exactMatch obofoundry:CDNO sssom:HumanCurated +bioregistry:cdno skos:exactMatch obofoundry:cdno sssom:HumanCurated bioregistry:cdno skos:exactMatch ols:cdno sssom:HumanCurated bioregistry:cdno skos:exactMatch ontobee:CDNO sssom:HumanCurated bioregistry:cdno bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -630,7 +629,7 @@ bioregistry:ceph skos:exactMatch aberowl:CEPH sssom:HumanCurated bioregistry:ceph skos:exactMatch biocontext:CEPH sssom:HumanCurated bioregistry:ceph skos:exactMatch bioportal:CEPH sssom:HumanCurated bioregistry:ceph skos:exactMatch fairsharing:FAIRsharing.p58bm4 sssom:HumanCurated -bioregistry:ceph skos:exactMatch obofoundry:CEPH sssom:HumanCurated +bioregistry:ceph skos:exactMatch obofoundry:ceph sssom:HumanCurated bioregistry:ceph skos:exactMatch ols:ceph sssom:HumanCurated bioregistry:ceph skos:exactMatch ontobee:CEPH sssom:HumanCurated bioregistry:cgd skos:exactMatch biocontext:CGD sssom:HumanCurated @@ -654,7 +653,7 @@ bioregistry:chebi skos:exactMatch cheminf:000407 sssom:HumanCurated bioregistry:chebi skos:exactMatch fairsharing:FAIRsharing.62qk8w sssom:HumanCurated bioregistry:chebi skos:exactMatch miriam:chebi sssom:HumanCurated bioregistry:chebi skos:exactMatch n2t:chebi sssom:HumanCurated -bioregistry:chebi skos:exactMatch obofoundry:CHEBI sssom:HumanCurated +bioregistry:chebi skos:exactMatch obofoundry:chebi sssom:HumanCurated bioregistry:chebi skos:exactMatch ols:chebi sssom:HumanCurated bioregistry:chebi skos:exactMatch ontobee:CHEBI sssom:HumanCurated bioregistry:chebi skos:exactMatch prefixcommons:chebi sssom:HumanCurated @@ -704,7 +703,7 @@ bioregistry:cheminf skos:exactMatch aberowl:CHEMINF sssom:HumanCurated bioregistry:cheminf skos:exactMatch biocontext:CHEMINF sssom:HumanCurated bioregistry:cheminf skos:exactMatch bioportal:CHEMINF sssom:HumanCurated bioregistry:cheminf skos:exactMatch fairsharing:FAIRsharing.sjhvyy sssom:HumanCurated -bioregistry:cheminf skos:exactMatch obofoundry:CHEMINF sssom:HumanCurated +bioregistry:cheminf skos:exactMatch obofoundry:cheminf sssom:HumanCurated bioregistry:cheminf skos:exactMatch ols:cheminf sssom:HumanCurated bioregistry:cheminf skos:exactMatch ontobee:CHEMINF sssom:HumanCurated bioregistry:cheminf bioregistry.schema:0000018 bioregistry:proco sssom:HumanCurated @@ -722,7 +721,7 @@ bioregistry:chickenqtldb skos:exactMatch prefixcommons:chickenqtldb sssom:HumanC bioregistry:chickenqtldb bfo:0000050 bioregistry:qtldb sssom:HumanCurated bioregistry:chiro skos:exactMatch aberowl:CHIRO sssom:HumanCurated bioregistry:chiro skos:exactMatch bioportal:CHIRO sssom:HumanCurated -bioregistry:chiro skos:exactMatch obofoundry:CHIRO sssom:HumanCurated +bioregistry:chiro skos:exactMatch obofoundry:chiro sssom:HumanCurated bioregistry:chiro skos:exactMatch ols:chiro sssom:HumanCurated bioregistry:chiro skos:exactMatch ontobee:CHIRO sssom:HumanCurated bioregistry:chiro bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated @@ -736,7 +735,7 @@ bioregistry:chmo skos:exactMatch aberowl:CHMO sssom:HumanCurated bioregistry:chmo skos:exactMatch biocontext:CHMO sssom:HumanCurated bioregistry:chmo skos:exactMatch bioportal:CHMO sssom:HumanCurated bioregistry:chmo skos:exactMatch fairsharing:FAIRsharing.9j4wh2 sssom:HumanCurated -bioregistry:chmo skos:exactMatch obofoundry:CHMO sssom:HumanCurated +bioregistry:chmo skos:exactMatch obofoundry:chmo sssom:HumanCurated bioregistry:chmo skos:exactMatch ols:chmo sssom:HumanCurated bioregistry:chmo skos:exactMatch ontobee:CHMO sssom:HumanCurated bioregistry:chmo bioregistry.schema:0000018 bioregistry:rbo sssom:HumanCurated @@ -744,14 +743,14 @@ bioregistry:chmo bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated bioregistry:cido skos:exactMatch aberowl:CIDO sssom:HumanCurated bioregistry:cido skos:exactMatch bioportal:CIDO sssom:HumanCurated bioregistry:cido skos:exactMatch fairsharing:FAIRsharing.aVmpKl sssom:HumanCurated -bioregistry:cido skos:exactMatch obofoundry:CIDO sssom:HumanCurated +bioregistry:cido skos:exactMatch obofoundry:cido sssom:HumanCurated bioregistry:cido skos:exactMatch ols:cido sssom:HumanCurated bioregistry:cido skos:exactMatch ontobee:CIDO sssom:HumanCurated bioregistry:cio skos:exactMatch aberowl:CIO sssom:HumanCurated bioregistry:cio skos:exactMatch biocontext:CIO sssom:HumanCurated bioregistry:cio skos:exactMatch bioportal:CIO sssom:HumanCurated bioregistry:cio skos:exactMatch fairsharing:FAIRsharing.e3t0yw sssom:HumanCurated -bioregistry:cio skos:exactMatch obofoundry:CIO sssom:HumanCurated +bioregistry:cio skos:exactMatch obofoundry:cio sssom:HumanCurated bioregistry:cio skos:exactMatch ols:cio sssom:HumanCurated bioregistry:cio skos:exactMatch ontobee:CIO sssom:HumanCurated bioregistry:citexplore skos:exactMatch fairsharing:FAIRsharing.619eqr sssom:HumanCurated @@ -766,14 +765,13 @@ bioregistry:cl skos:exactMatch bioportal:CL sssom:HumanCurated bioregistry:cl skos:exactMatch fairsharing:FAIRsharing.j9y503 sssom:HumanCurated bioregistry:cl skos:exactMatch miriam:cl sssom:HumanCurated bioregistry:cl skos:exactMatch n2t:cl sssom:HumanCurated -bioregistry:cl skos:exactMatch obofoundry:CL sssom:HumanCurated +bioregistry:cl skos:exactMatch obofoundry:cl sssom:HumanCurated bioregistry:cl skos:exactMatch ols:cl sssom:HumanCurated bioregistry:cl skos:exactMatch ontobee:CL sssom:HumanCurated bioregistry:cl skos:exactMatch prefixcommons:cl sssom:HumanCurated bioregistry:cl skos:exactMatch wikidata:P7963 sssom:HumanCurated bioregistry:cl bioregistry.schema:0000018 bioregistry:clo sssom:HumanCurated bioregistry:cl bioregistry.schema:0000018 bioregistry:ecao sssom:HumanCurated -bioregistry:cl bioregistry.schema:0000018 bioregistry:ehdaa2 sssom:HumanCurated bioregistry:cl bioregistry.schema:0000018 bioregistry:go sssom:HumanCurated bioregistry:cl bioregistry.schema:0000018 bioregistry:mco sssom:HumanCurated bioregistry:cl bioregistry.schema:0000018 bioregistry:pcl sssom:HumanCurated @@ -788,7 +786,7 @@ bioregistry:cl bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated bioregistry:cl bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:clao skos:exactMatch aberowl:CLAO sssom:HumanCurated bioregistry:clao skos:exactMatch bioportal:CLAO sssom:HumanCurated -bioregistry:clao skos:exactMatch obofoundry:CLAO sssom:HumanCurated +bioregistry:clao skos:exactMatch obofoundry:clao sssom:HumanCurated bioregistry:clao skos:exactMatch ols:clao sssom:HumanCurated bioregistry:clao skos:exactMatch ontobee:CLAO sssom:HumanCurated bioregistry:clao bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated @@ -818,7 +816,7 @@ bioregistry:clo skos:exactMatch aberowl:CLO sssom:HumanCurated bioregistry:clo skos:exactMatch biocontext:CLO sssom:HumanCurated bioregistry:clo skos:exactMatch bioportal:CLO sssom:HumanCurated bioregistry:clo skos:exactMatch fairsharing:FAIRsharing.4dvtcz sssom:HumanCurated -bioregistry:clo skos:exactMatch obofoundry:CLO sssom:HumanCurated +bioregistry:clo skos:exactMatch obofoundry:clo sssom:HumanCurated bioregistry:clo skos:exactMatch ols:clo sssom:HumanCurated bioregistry:clo skos:exactMatch ontobee:CLO sssom:HumanCurated bioregistry:clo skos:exactMatch prefixcommons:clo sssom:HumanCurated @@ -830,7 +828,7 @@ bioregistry:clo bioregistry.schema:0000017 bioregistry:ncbitaxon sssom:HumanCura bioregistry:clo bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:clyh skos:exactMatch aberowl:CLYH sssom:HumanCurated bioregistry:clyh skos:exactMatch bioportal:CLYH sssom:HumanCurated -bioregistry:clyh skos:exactMatch obofoundry:CLYH sssom:HumanCurated +bioregistry:clyh skos:exactMatch obofoundry:clyh sssom:HumanCurated bioregistry:clyh skos:exactMatch ols:clyh sssom:HumanCurated bioregistry:clyh skos:exactMatch ontobee:CLYH sssom:HumanCurated bioregistry:clyh bioregistry.schema:0000017 bioregistry:iao sssom:HumanCurated @@ -838,13 +836,13 @@ bioregistry:clyh bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated bioregistry:clyh bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:cmf skos:exactMatch aberowl:CMF sssom:HumanCurated bioregistry:cmf skos:exactMatch biocontext:CMF sssom:HumanCurated -bioregistry:cmf skos:exactMatch obofoundry:CMF sssom:HumanCurated +bioregistry:cmf skos:exactMatch obofoundry:cmf sssom:HumanCurated bioregistry:cmf skos:exactMatch ontobee:CMF sssom:HumanCurated bioregistry:cmo skos:exactMatch aberowl:CMO sssom:HumanCurated bioregistry:cmo skos:exactMatch biocontext:CMO sssom:HumanCurated bioregistry:cmo skos:exactMatch bioportal:CMO sssom:HumanCurated bioregistry:cmo skos:exactMatch fairsharing:FAIRsharing.dq78pn sssom:HumanCurated -bioregistry:cmo skos:exactMatch obofoundry:CMO sssom:HumanCurated +bioregistry:cmo skos:exactMatch obofoundry:cmo sssom:HumanCurated bioregistry:cmo skos:exactMatch ols:cmo sssom:HumanCurated bioregistry:cmo skos:exactMatch ontobee:CMO sssom:HumanCurated bioregistry:cmo bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -976,7 +974,7 @@ bioregistry:co_366 skos:exactMatch cropoct:CO_366 sssom:HumanCurated bioregistry:co_366 skos:exactMatch ols:co_366 sssom:HumanCurated bioregistry:cob skos:exactMatch aberowl:COB sssom:HumanCurated bioregistry:cob skos:exactMatch bioportal:COB sssom:HumanCurated -bioregistry:cob skos:exactMatch obofoundry:COB sssom:HumanCurated +bioregistry:cob skos:exactMatch obofoundry:cob sssom:HumanCurated bioregistry:cob skos:exactMatch ols:cob sssom:HumanCurated bioregistry:cob skos:exactMatch ontobee:COB sssom:HumanCurated bioregistry:cog skos:exactMatch biolink:COG sssom:HumanCurated @@ -987,7 +985,7 @@ bioregistry:cog.pathway bfo:0000050 bioregistry:cog sssom:HumanCurated bioregistry:col.taiwan skos:exactMatch wikidata:P3088 sssom:HumanCurated bioregistry:colao skos:exactMatch aberowl:COLAO sssom:HumanCurated bioregistry:colao skos:exactMatch bioportal:COLAO sssom:HumanCurated -bioregistry:colao skos:exactMatch obofoundry:COLAO sssom:HumanCurated +bioregistry:colao skos:exactMatch obofoundry:colao sssom:HumanCurated bioregistry:colao skos:exactMatch ols:colao sssom:HumanCurated bioregistry:colao skos:exactMatch ontobee:COLAO sssom:HumanCurated bioregistry:colao bioregistry.schema:0000017 bioregistry:aism sssom:HumanCurated @@ -1043,7 +1041,7 @@ bioregistry:cpc skos:exactMatch miriam:cpc sssom:HumanCurated bioregistry:cpc skos:exactMatch n2t:cpc sssom:HumanCurated bioregistry:cpga skos:exactMatch biocontext:gro.cpga sssom:HumanCurated bioregistry:cpga skos:exactMatch bioportal:GRO-CPGA sssom:HumanCurated -bioregistry:cpga skos:exactMatch obofoundry:GRO sssom:HumanCurated +bioregistry:cpga skos:exactMatch obofoundry:gro sssom:HumanCurated bioregistry:cpt skos:exactMatch aberowl:CPT sssom:HumanCurated bioregistry:cpt skos:exactMatch biolink:CPT sssom:HumanCurated bioregistry:cpt skos:exactMatch bioportal:CPT sssom:HumanCurated @@ -1055,7 +1053,7 @@ bioregistry:crisprdb skos:exactMatch n2t:crisprdb sssom:HumanCurated bioregistry:cro skos:exactMatch aberowl:CRO sssom:HumanCurated bioregistry:cro skos:exactMatch biocontext:CRO sssom:HumanCurated bioregistry:cro skos:exactMatch bioportal:CRO sssom:HumanCurated -bioregistry:cro skos:exactMatch obofoundry:CRO sssom:HumanCurated +bioregistry:cro skos:exactMatch obofoundry:cro sssom:HumanCurated bioregistry:cro skos:exactMatch ols:cro sssom:HumanCurated bioregistry:cro skos:exactMatch ontobee:CRO sssom:HumanCurated bioregistry:cryoem skos:exactMatch aberowl:CRYOEM sssom:HumanCurated @@ -1104,7 +1102,7 @@ bioregistry:cteno skos:exactMatch aberowl:CTENO sssom:HumanCurated bioregistry:cteno skos:exactMatch biocontext:CTENO sssom:HumanCurated bioregistry:cteno skos:exactMatch bioportal:CTENO sssom:HumanCurated bioregistry:cteno skos:exactMatch fairsharing:FAIRsharing.mgxgza sssom:HumanCurated -bioregistry:cteno skos:exactMatch obofoundry:CTENO sssom:HumanCurated +bioregistry:cteno skos:exactMatch obofoundry:cteno sssom:HumanCurated bioregistry:cteno skos:exactMatch ols:cteno sssom:HumanCurated bioregistry:cteno skos:exactMatch ontobee:CTENO sssom:HumanCurated bioregistry:cteno bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated @@ -1112,7 +1110,7 @@ bioregistry:cteno bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurat bioregistry:cto skos:exactMatch aberowl:CTO sssom:HumanCurated bioregistry:cto skos:exactMatch bioportal:CTO sssom:HumanCurated bioregistry:cto skos:exactMatch fairsharing:FAIRsharing.qp211a sssom:HumanCurated -bioregistry:cto skos:exactMatch obofoundry:CTO sssom:HumanCurated +bioregistry:cto skos:exactMatch obofoundry:cto sssom:HumanCurated bioregistry:cto skos:exactMatch ols:cto sssom:HumanCurated bioregistry:cto skos:exactMatch ontobee:CTO sssom:HumanCurated bioregistry:cubedb skos:exactMatch biocontext:CUBEDB sssom:HumanCurated @@ -1122,7 +1120,7 @@ bioregistry:cvdo skos:exactMatch aberowl:CVDO sssom:HumanCurated bioregistry:cvdo skos:exactMatch biocontext:CVDO sssom:HumanCurated bioregistry:cvdo skos:exactMatch bioportal:CVDO sssom:HumanCurated bioregistry:cvdo skos:exactMatch fairsharing:FAIRsharing.2basyz sssom:HumanCurated -bioregistry:cvdo skos:exactMatch obofoundry:CVDO sssom:HumanCurated +bioregistry:cvdo skos:exactMatch obofoundry:cvdo sssom:HumanCurated bioregistry:cvdo skos:exactMatch ols:cvdo sssom:HumanCurated bioregistry:cvdo skos:exactMatch ontobee:CVDO sssom:HumanCurated bioregistry:d1id skos:exactMatch biocontext:D1ID sssom:HumanCurated @@ -1186,7 +1184,7 @@ bioregistry:dc skos:exactMatch bioportal:DC sssom:HumanCurated bioregistry:dc skos:exactMatch fairsharing:FAIRsharing.3nx7t sssom:HumanCurated bioregistry:dc bioregistry.schema:0000016 bioregistry:dcterms sssom:HumanCurated bioregistry:dc_cl skos:exactMatch biocontext:DC_CL sssom:HumanCurated -bioregistry:dc_cl skos:exactMatch obofoundry:DC_CL sssom:HumanCurated +bioregistry:dc_cl skos:exactMatch obofoundry:dc_cl sssom:HumanCurated bioregistry:dcat skos:exactMatch aberowl:DCAT sssom:HumanCurated bioregistry:dcat skos:exactMatch biocontext:dcat sssom:HumanCurated bioregistry:dcat skos:exactMatch biolink:dcat sssom:HumanCurated @@ -1202,7 +1200,7 @@ bioregistry:ddanat skos:exactMatch aberowl:DDANAT sssom:HumanCurated bioregistry:ddanat skos:exactMatch biocontext:DDANAT sssom:HumanCurated bioregistry:ddanat skos:exactMatch bioportal:DDANAT sssom:HumanCurated bioregistry:ddanat skos:exactMatch fairsharing:FAIRsharing.z656ab sssom:HumanCurated -bioregistry:ddanat skos:exactMatch obofoundry:DDANAT sssom:HumanCurated +bioregistry:ddanat skos:exactMatch obofoundry:ddanat sssom:HumanCurated bioregistry:ddanat skos:exactMatch ols:ddanat sssom:HumanCurated bioregistry:ddanat skos:exactMatch ontobee:DDANAT sssom:HumanCurated bioregistry:ddanat skos:exactMatch prefixcommons:ddanat sssom:HumanCurated @@ -1210,7 +1208,7 @@ bioregistry:ddpheno skos:exactMatch aberowl:DDPHENO sssom:HumanCurated bioregistry:ddpheno skos:exactMatch biocontext:DDPHENO sssom:HumanCurated bioregistry:ddpheno skos:exactMatch bioportal:DDPHENO sssom:HumanCurated bioregistry:ddpheno skos:exactMatch fairsharing:FAIRsharing.9c1p18 sssom:HumanCurated -bioregistry:ddpheno skos:exactMatch obofoundry:DDPHENO sssom:HumanCurated +bioregistry:ddpheno skos:exactMatch obofoundry:ddpheno sssom:HumanCurated bioregistry:ddpheno skos:exactMatch ols:ddpheno sssom:HumanCurated bioregistry:ddpheno skos:exactMatch ontobee:DDPHENO sssom:HumanCurated bioregistry:decipher skos:exactMatch biocontext:DECIPHER sssom:HumanCurated @@ -1256,13 +1254,13 @@ bioregistry:dideo skos:exactMatch aberowl:DIDEO sssom:HumanCurated bioregistry:dideo skos:exactMatch biocontext:DIDEO sssom:HumanCurated bioregistry:dideo skos:exactMatch bioportal:DIDEO sssom:HumanCurated bioregistry:dideo skos:exactMatch fairsharing:FAIRsharing.9y8f0n sssom:HumanCurated -bioregistry:dideo skos:exactMatch obofoundry:DIDEO sssom:HumanCurated +bioregistry:dideo skos:exactMatch obofoundry:dideo sssom:HumanCurated bioregistry:dideo skos:exactMatch ols:dideo sssom:HumanCurated bioregistry:dideo skos:exactMatch ontobee:DIDEO sssom:HumanCurated bioregistry:dinto skos:exactMatch aberowl:DINTO sssom:HumanCurated bioregistry:dinto skos:exactMatch biocontext:DINTO sssom:HumanCurated bioregistry:dinto skos:exactMatch bioportal:DINTO sssom:HumanCurated -bioregistry:dinto skos:exactMatch obofoundry:DINTO sssom:HumanCurated +bioregistry:dinto skos:exactMatch obofoundry:dinto sssom:HumanCurated bioregistry:dinto skos:exactMatch ontobee:DINTO sssom:HumanCurated bioregistry:dip skos:exactMatch biocontext:DIP sssom:HumanCurated bioregistry:dip skos:exactMatch fairsharing:FAIRsharing.qje0v8 sssom:HumanCurated @@ -1271,7 +1269,7 @@ bioregistry:dip skos:exactMatch n2t:dip sssom:HumanCurated bioregistry:dip skos:exactMatch prefixcommons:dip sssom:HumanCurated bioregistry:disdriv skos:exactMatch aberowl:DISDRIV sssom:HumanCurated bioregistry:disdriv skos:exactMatch bioportal:DISDRIV sssom:HumanCurated -bioregistry:disdriv skos:exactMatch obofoundry:DISDRIV sssom:HumanCurated +bioregistry:disdriv skos:exactMatch obofoundry:disdriv sssom:HumanCurated bioregistry:disdriv skos:exactMatch ols:disdriv sssom:HumanCurated bioregistry:diseaseclass bioregistry.schema:0000018 bioregistry:efo sssom:HumanCurated bioregistry:diseasesdb skos:exactMatch wikidata:P557 sssom:HumanCurated @@ -1296,7 +1294,7 @@ bioregistry:doid skos:exactMatch bioportal:DOID sssom:HumanCurated bioregistry:doid skos:exactMatch fairsharing:FAIRsharing.8b6wfq sssom:HumanCurated bioregistry:doid skos:exactMatch miriam:doid sssom:HumanCurated bioregistry:doid skos:exactMatch n2t:doid sssom:HumanCurated -bioregistry:doid skos:exactMatch obofoundry:DOID sssom:HumanCurated +bioregistry:doid skos:exactMatch obofoundry:doid sssom:HumanCurated bioregistry:doid skos:exactMatch ols:doid sssom:HumanCurated bioregistry:doid skos:exactMatch ontobee:DOID sssom:HumanCurated bioregistry:doid skos:exactMatch prefixcommons:do sssom:HumanCurated @@ -1320,7 +1318,7 @@ bioregistry:doqcs.pathway skos:exactMatch n2t:doqcs.pathway sssom:HumanCurated bioregistry:doqcs.pathway skos:exactMatch prefixcommons:doqcs.pathway sssom:HumanCurated bioregistry:dpo skos:exactMatch aberowl:DPO sssom:HumanCurated bioregistry:dpo skos:exactMatch bioportal:DPO sssom:HumanCurated -bioregistry:dpo skos:exactMatch obofoundry:FBcv sssom:HumanCurated +bioregistry:dpo skos:exactMatch obofoundry:dpo sssom:HumanCurated bioregistry:dpo skos:exactMatch ols:dpo sssom:HumanCurated bioregistry:dpo skos:exactMatch ontobee:DPO sssom:HumanCurated bioregistry:dpo bfo:0000050 bioregistry:fbcv sssom:HumanCurated @@ -1343,7 +1341,7 @@ bioregistry:dron skos:exactMatch aberowl:DRON sssom:HumanCurated bioregistry:dron skos:exactMatch biocontext:DRON sssom:HumanCurated bioregistry:dron skos:exactMatch bioportal:DRON sssom:HumanCurated bioregistry:dron skos:exactMatch fairsharing:FAIRsharing.w5ntfd sssom:HumanCurated -bioregistry:dron skos:exactMatch obofoundry:DRON sssom:HumanCurated +bioregistry:dron skos:exactMatch obofoundry:dron sssom:HumanCurated bioregistry:dron skos:exactMatch ols:dron sssom:HumanCurated bioregistry:dron skos:exactMatch ontobee:DRON sssom:HumanCurated bioregistry:dron bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -1374,7 +1372,7 @@ bioregistry:duo skos:exactMatch aberowl:DUO sssom:HumanCurated bioregistry:duo skos:exactMatch biocontext:DUO sssom:HumanCurated bioregistry:duo skos:exactMatch bioportal:DUO sssom:HumanCurated bioregistry:duo skos:exactMatch fairsharing:FAIRsharing.5dnjs2 sssom:HumanCurated -bioregistry:duo skos:exactMatch obofoundry:DUO sssom:HumanCurated +bioregistry:duo skos:exactMatch obofoundry:duo sssom:HumanCurated bioregistry:duo skos:exactMatch ols:duo sssom:HumanCurated bioregistry:duo skos:exactMatch ontobee:DUO sssom:HumanCurated bioregistry:duo bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -1382,7 +1380,7 @@ bioregistry:duo bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated bioregistry:duo bioregistry.schema:0000017 bioregistry:iao sssom:HumanCurated bioregistry:ecao skos:exactMatch aberowl:ECAO sssom:HumanCurated bioregistry:ecao skos:exactMatch bioportal:ECAO sssom:HumanCurated -bioregistry:ecao skos:exactMatch obofoundry:ECAO sssom:HumanCurated +bioregistry:ecao skos:exactMatch obofoundry:ecao sssom:HumanCurated bioregistry:ecao skos:exactMatch ols:ecao sssom:HumanCurated bioregistry:ecao skos:exactMatch ontobee:ECAO sssom:HumanCurated bioregistry:ecao bioregistry.schema:0000017 bioregistry:cl sssom:HumanCurated @@ -1407,14 +1405,14 @@ bioregistry:eco skos:exactMatch bioportal:ECO sssom:HumanCurated bioregistry:eco skos:exactMatch fairsharing:FAIRsharing.wvpgwn sssom:HumanCurated bioregistry:eco skos:exactMatch miriam:eco sssom:HumanCurated bioregistry:eco skos:exactMatch n2t:eco sssom:HumanCurated -bioregistry:eco skos:exactMatch obofoundry:ECO sssom:HumanCurated +bioregistry:eco skos:exactMatch obofoundry:eco sssom:HumanCurated bioregistry:eco skos:exactMatch ols:eco sssom:HumanCurated bioregistry:eco skos:exactMatch ontobee:ECO sssom:HumanCurated bioregistry:eco skos:exactMatch prefixcommons:eco sssom:HumanCurated bioregistry:ecocore skos:exactMatch aberowl:ECOCORE sssom:HumanCurated bioregistry:ecocore skos:exactMatch biocontext:ECOCORE sssom:HumanCurated bioregistry:ecocore skos:exactMatch bioportal:ECOCORE sssom:HumanCurated -bioregistry:ecocore skos:exactMatch obofoundry:ECOCORE sssom:HumanCurated +bioregistry:ecocore skos:exactMatch obofoundry:ecocore sssom:HumanCurated bioregistry:ecocore skos:exactMatch ols:ecocore sssom:HumanCurated bioregistry:ecocore skos:exactMatch ontobee:ECOCORE sssom:HumanCurated bioregistry:ecocore bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -1440,7 +1438,7 @@ bioregistry:ecoliwiki skos:exactMatch n2t:ecoliwiki sssom:HumanCurated bioregistry:ecto skos:exactMatch aberowl:ECTO sssom:HumanCurated bioregistry:ecto skos:exactMatch biolink:ECTO sssom:HumanCurated bioregistry:ecto skos:exactMatch bioportal:ECTO sssom:HumanCurated -bioregistry:ecto skos:exactMatch obofoundry:ECTO sssom:HumanCurated +bioregistry:ecto skos:exactMatch obofoundry:ecto sssom:HumanCurated bioregistry:ecto skos:exactMatch ols:ecto sssom:HumanCurated bioregistry:ecto skos:exactMatch ontobee:ECTO sssom:HumanCurated bioregistry:ecto bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated @@ -1512,18 +1510,18 @@ bioregistry:eggnog skos:exactMatch prefixcommons:eggnog sssom:HumanCurated bioregistry:ehda skos:exactMatch aberowl:EHDA sssom:HumanCurated bioregistry:ehda skos:exactMatch biocontext:EHDA sssom:HumanCurated bioregistry:ehda skos:exactMatch bioportal:EHDA sssom:HumanCurated -bioregistry:ehda skos:exactMatch obofoundry:EHDA sssom:HumanCurated +bioregistry:ehda skos:exactMatch obofoundry:ehda sssom:HumanCurated bioregistry:ehda skos:exactMatch prefixcommons:ehda sssom:HumanCurated bioregistry:ehdaa skos:exactMatch aberowl:EHDAA sssom:HumanCurated bioregistry:ehdaa skos:exactMatch biocontext:EHDAA sssom:HumanCurated bioregistry:ehdaa skos:exactMatch bioportal:EHDAA sssom:HumanCurated -bioregistry:ehdaa skos:exactMatch obofoundry:EHDAA sssom:HumanCurated +bioregistry:ehdaa skos:exactMatch obofoundry:ehdaa sssom:HumanCurated bioregistry:ehdaa skos:exactMatch prefixcommons:ehdaa sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch aberowl:EHDAA2 sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch biocontext:EHDAA2 sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch bioportal:EHDAA2 sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch fairsharing:FAIRsharing.7zxrs6 sssom:HumanCurated -bioregistry:ehdaa2 skos:exactMatch obofoundry:EHDAA2 sssom:HumanCurated +bioregistry:ehdaa2 skos:exactMatch obofoundry:ehdaa2 sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch ols:ehdaa2 sssom:HumanCurated bioregistry:ehdaa2 skos:exactMatch ontobee:EHDAA2 sssom:HumanCurated bioregistry:ehdaa2 bioregistry.schema:0000017 bioregistry:aeo sssom:HumanCurated @@ -1535,12 +1533,12 @@ bioregistry:elm skos:exactMatch miriam:elm sssom:HumanCurated bioregistry:elm skos:exactMatch n2t:elm sssom:HumanCurated bioregistry:emap skos:exactMatch biocontext:EMAP sssom:HumanCurated bioregistry:emap skos:exactMatch bioportal:EMAP sssom:HumanCurated -bioregistry:emap skos:exactMatch obofoundry:EMAP sssom:HumanCurated +bioregistry:emap skos:exactMatch obofoundry:emap sssom:HumanCurated bioregistry:emapa skos:exactMatch aberowl:EMAPA sssom:HumanCurated bioregistry:emapa skos:exactMatch biocontext:EMAPA sssom:HumanCurated bioregistry:emapa skos:exactMatch bioportal:EMAPA sssom:HumanCurated bioregistry:emapa skos:exactMatch fairsharing:FAIRsharing.j0fa1d sssom:HumanCurated -bioregistry:emapa skos:exactMatch obofoundry:EMAPA sssom:HumanCurated +bioregistry:emapa skos:exactMatch obofoundry:emapa sssom:HumanCurated bioregistry:emapa skos:exactMatch ols:emapa sssom:HumanCurated bioregistry:emapa skos:exactMatch ontobee:EMAPA sssom:HumanCurated bioregistry:emdb skos:exactMatch biocontext:EMDB sssom:HumanCurated @@ -1600,7 +1598,7 @@ bioregistry:envo skos:exactMatch bioportal:ENVO sssom:HumanCurated bioregistry:envo skos:exactMatch fairsharing:FAIRsharing.azqskx sssom:HumanCurated bioregistry:envo skos:exactMatch miriam:envo sssom:HumanCurated bioregistry:envo skos:exactMatch n2t:envo sssom:HumanCurated -bioregistry:envo skos:exactMatch obofoundry:ENVO sssom:HumanCurated +bioregistry:envo skos:exactMatch obofoundry:envo sssom:HumanCurated bioregistry:envo skos:exactMatch ols:envo sssom:HumanCurated bioregistry:envo skos:exactMatch ontobee:ENVO sssom:HumanCurated bioregistry:envo bioregistry.schema:0000018 bioregistry:agro sssom:HumanCurated @@ -1625,7 +1623,7 @@ bioregistry:eo skos:exactMatch agroportal:EO sssom:HumanCurated bioregistry:eo skos:exactMatch biocontext:EO sssom:HumanCurated bioregistry:eo skos:exactMatch miriam:eo sssom:HumanCurated bioregistry:eo skos:exactMatch n2t:eo sssom:HumanCurated -bioregistry:eo skos:exactMatch obofoundry:EO sssom:HumanCurated +bioregistry:eo skos:exactMatch obofoundry:eo sssom:HumanCurated bioregistry:eo skos:exactMatch prefixcommons:eo sssom:HumanCurated bioregistry:eo bioregistry.schema:0000018 bioregistry:foodon sssom:HumanCurated bioregistry:eol skos:exactMatch aberowl:EOL sssom:HumanCurated @@ -1641,13 +1639,13 @@ bioregistry:epd skos:exactMatch miriam:epd sssom:HumanCurated bioregistry:epd skos:exactMatch n2t:epd sssom:HumanCurated bioregistry:epio skos:exactMatch aberowl:EPIO sssom:HumanCurated bioregistry:epio skos:exactMatch bioportal:EPIO sssom:HumanCurated -bioregistry:epio skos:exactMatch obofoundry:EPIO sssom:HumanCurated +bioregistry:epio skos:exactMatch obofoundry:epio sssom:HumanCurated bioregistry:epio skos:exactMatch ontobee:EPIO sssom:HumanCurated bioregistry:epio bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated bioregistry:epo skos:exactMatch aberowl:EPO sssom:HumanCurated bioregistry:epo skos:exactMatch biocontext:EPO sssom:HumanCurated bioregistry:epo skos:exactMatch bioportal:EPO sssom:HumanCurated -bioregistry:epo skos:exactMatch obofoundry:EPO sssom:HumanCurated +bioregistry:epo skos:exactMatch obofoundry:epo sssom:HumanCurated bioregistry:epo skos:exactMatch ontobee:EPO sssom:HumanCurated bioregistry:epso skos:exactMatch aberowl:EPSO sssom:HumanCurated bioregistry:epso skos:exactMatch bioportal:EPSO sssom:HumanCurated @@ -1659,7 +1657,7 @@ bioregistry:ero skos:exactMatch aberowl:ERO sssom:HumanCurated bioregistry:ero skos:exactMatch biocontext:ERO sssom:HumanCurated bioregistry:ero skos:exactMatch bioportal:ERO sssom:HumanCurated bioregistry:ero skos:exactMatch fairsharing:FAIRsharing.nwgynk sssom:HumanCurated -bioregistry:ero skos:exactMatch obofoundry:ERO sssom:HumanCurated +bioregistry:ero skos:exactMatch obofoundry:ero sssom:HumanCurated bioregistry:ero skos:exactMatch ols:ero sssom:HumanCurated bioregistry:ero skos:exactMatch ontobee:ERO sssom:HumanCurated bioregistry:erv skos:exactMatch biocontext:ERV sssom:HumanCurated @@ -1675,12 +1673,12 @@ bioregistry:eupath skos:exactMatch aberowl:EUPATH sssom:HumanCurated bioregistry:eupath skos:exactMatch biocontext:EUPATH sssom:HumanCurated bioregistry:eupath skos:exactMatch bioportal:EUPATH sssom:HumanCurated bioregistry:eupath skos:exactMatch fairsharing:FAIRsharing.9rhr9j sssom:HumanCurated -bioregistry:eupath skos:exactMatch obofoundry:EUPATH sssom:HumanCurated +bioregistry:eupath skos:exactMatch obofoundry:eupath sssom:HumanCurated bioregistry:eupath skos:exactMatch ols:eupath sssom:HumanCurated bioregistry:eupath skos:exactMatch ontobee:EUPATH sssom:HumanCurated bioregistry:eupath bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated bioregistry:ev skos:exactMatch biocontext:EV sssom:HumanCurated -bioregistry:ev skos:exactMatch obofoundry:EV sssom:HumanCurated +bioregistry:ev skos:exactMatch obofoundry:ev sssom:HumanCurated bioregistry:ev bioregistry.schema:0000018 bioregistry:cl sssom:HumanCurated bioregistry:exac.gene skos:exactMatch biocontext:EXAC.GENE sssom:HumanCurated bioregistry:exac.gene skos:exactMatch miriam:exac.gene sssom:HumanCurated @@ -1696,7 +1694,7 @@ bioregistry:exo skos:exactMatch biocontext:EXO sssom:HumanCurated bioregistry:exo skos:exactMatch biolink:ExO sssom:HumanCurated bioregistry:exo skos:exactMatch bioportal:EXO sssom:HumanCurated bioregistry:exo skos:exactMatch fairsharing:FAIRsharing.6hna78 sssom:HumanCurated -bioregistry:exo skos:exactMatch obofoundry:ExO sssom:HumanCurated +bioregistry:exo skos:exactMatch obofoundry:exo sssom:HumanCurated bioregistry:exo skos:exactMatch ols:exo sssom:HumanCurated bioregistry:exo skos:exactMatch ontobee:ExO sssom:HumanCurated bioregistry:exo bioregistry.schema:0000018 bioregistry:ecto sssom:HumanCurated @@ -1721,7 +1719,7 @@ bioregistry:fao skos:exactMatch aberowl:FAO sssom:HumanCurated bioregistry:fao skos:exactMatch biocontext:FAO sssom:HumanCurated bioregistry:fao skos:exactMatch bioportal:FAO sssom:HumanCurated bioregistry:fao skos:exactMatch fairsharing:FAIRsharing.xs6t67 sssom:HumanCurated -bioregistry:fao skos:exactMatch obofoundry:FAO sssom:HumanCurated +bioregistry:fao skos:exactMatch obofoundry:fao sssom:HumanCurated bioregistry:fao skos:exactMatch ols:fao sssom:HumanCurated bioregistry:fao skos:exactMatch ontobee:FAO sssom:HumanCurated bioregistry:fao skos:exactMatch prefixcommons:fao sssom:HumanCurated @@ -1729,7 +1727,7 @@ bioregistry:fbbi skos:exactMatch aberowl:FBbi sssom:HumanCurated bioregistry:fbbi skos:exactMatch biocontext:FBbi sssom:HumanCurated bioregistry:fbbi skos:exactMatch bioportal:FBbi sssom:HumanCurated bioregistry:fbbi skos:exactMatch fairsharing:FAIRsharing.ny3z9j sssom:HumanCurated -bioregistry:fbbi skos:exactMatch obofoundry:FBbi sssom:HumanCurated +bioregistry:fbbi skos:exactMatch obofoundry:fbbi sssom:HumanCurated bioregistry:fbbi skos:exactMatch ols:fbbi sssom:HumanCurated bioregistry:fbbi skos:exactMatch ontobee:FBBI sssom:HumanCurated bioregistry:fbbi skos:exactMatch prefixcommons:fbbi sssom:HumanCurated @@ -1737,7 +1735,7 @@ bioregistry:fbbt skos:exactMatch aberowl:FBBT sssom:HumanCurated bioregistry:fbbt skos:exactMatch biocontext:FBbt sssom:HumanCurated bioregistry:fbbt skos:exactMatch bioportal:FB-BT sssom:HumanCurated bioregistry:fbbt skos:exactMatch fairsharing:FAIRsharing.y2qkst sssom:HumanCurated -bioregistry:fbbt skos:exactMatch obofoundry:FBbt sssom:HumanCurated +bioregistry:fbbt skos:exactMatch obofoundry:fbbt sssom:HumanCurated bioregistry:fbbt skos:exactMatch ols:fbbt sssom:HumanCurated bioregistry:fbbt skos:exactMatch ontobee:FBBT sssom:HumanCurated bioregistry:fbbt skos:exactMatch prefixcommons:fbbt sssom:HumanCurated @@ -1746,7 +1744,7 @@ bioregistry:fbcv skos:exactMatch aberowl:FBCV sssom:HumanCurated bioregistry:fbcv skos:exactMatch biocontext:FBcv sssom:HumanCurated bioregistry:fbcv skos:exactMatch bioportal:FB-CV sssom:HumanCurated bioregistry:fbcv skos:exactMatch fairsharing:FAIRsharing.6tgyxf sssom:HumanCurated -bioregistry:fbcv skos:exactMatch obofoundry:FBcv sssom:HumanCurated +bioregistry:fbcv skos:exactMatch obofoundry:fbcv sssom:HumanCurated bioregistry:fbcv skos:exactMatch ols:fbcv sssom:HumanCurated bioregistry:fbcv skos:exactMatch ontobee:FBCV sssom:HumanCurated bioregistry:fbcv skos:exactMatch prefixcommons:fbcv sssom:HumanCurated @@ -1756,7 +1754,7 @@ bioregistry:fbdv skos:exactMatch aberowl:FBDV sssom:HumanCurated bioregistry:fbdv skos:exactMatch biocontext:FBdv sssom:HumanCurated bioregistry:fbdv skos:exactMatch bioportal:FB-DV sssom:HumanCurated bioregistry:fbdv skos:exactMatch fairsharing:FAIRsharing.p52pzj sssom:HumanCurated -bioregistry:fbdv skos:exactMatch obofoundry:FBdv sssom:HumanCurated +bioregistry:fbdv skos:exactMatch obofoundry:fbdv sssom:HumanCurated bioregistry:fbdv skos:exactMatch ols:fbdv sssom:HumanCurated bioregistry:fbdv skos:exactMatch ontobee:FBdv sssom:HumanCurated bioregistry:fbdv skos:exactMatch prefixcommons:fbdv sssom:HumanCurated @@ -1767,13 +1765,13 @@ bioregistry:fbrf bfo:0000050 bioregistry:flybase sssom:HumanCurated bioregistry:fbsp skos:exactMatch aberowl:FB-SP sssom:HumanCurated bioregistry:fbsp skos:exactMatch biocontext:FBSP sssom:HumanCurated bioregistry:fbsp skos:exactMatch bioportal:FB-SP sssom:HumanCurated -bioregistry:fbsp skos:exactMatch obofoundry:FBSP sssom:HumanCurated +bioregistry:fbsp skos:exactMatch obofoundry:fbsp sssom:HumanCurated bioregistry:fbsp bfo:0000050 bioregistry:flybase sssom:HumanCurated bioregistry:fbtc bfo:0000050 bioregistry:flybase sssom:HumanCurated bioregistry:fcb skos:exactMatch miriam:fcb sssom:HumanCurated bioregistry:fideo skos:exactMatch aberowl:FIDEO sssom:HumanCurated bioregistry:fideo skos:exactMatch bioportal:FIDEO sssom:HumanCurated -bioregistry:fideo skos:exactMatch obofoundry:FIDEO sssom:HumanCurated +bioregistry:fideo skos:exactMatch obofoundry:fideo sssom:HumanCurated bioregistry:fideo skos:exactMatch ols:fideo sssom:HumanCurated bioregistry:fideo skos:exactMatch ontobee:FIDEO sssom:HumanCurated bioregistry:fishbase.species skos:exactMatch wikidata:P938 sssom:HumanCurated @@ -1782,7 +1780,7 @@ bioregistry:fix skos:exactMatch aberowl:FIX sssom:HumanCurated bioregistry:fix skos:exactMatch biocontext:FIX sssom:HumanCurated bioregistry:fix skos:exactMatch bioportal:FIX sssom:HumanCurated bioregistry:fix skos:exactMatch fairsharing:FAIRsharing.wwy1ns sssom:HumanCurated -bioregistry:fix skos:exactMatch obofoundry:FIX sssom:HumanCurated +bioregistry:fix skos:exactMatch obofoundry:fix sssom:HumanCurated bioregistry:fix skos:exactMatch ols:fix sssom:HumanCurated bioregistry:fix skos:exactMatch ontobee:FIX sssom:HumanCurated bioregistry:fix skos:exactMatch prefixcommons:fix sssom:HumanCurated @@ -1792,7 +1790,7 @@ bioregistry:flopo skos:exactMatch agroportal:FLOPO sssom:HumanCurated bioregistry:flopo skos:exactMatch biocontext:FLOPO sssom:HumanCurated bioregistry:flopo skos:exactMatch bioportal:FLOPO sssom:HumanCurated bioregistry:flopo skos:exactMatch fairsharing:FAIRsharing.ny9vnm sssom:HumanCurated -bioregistry:flopo skos:exactMatch obofoundry:FLOPO sssom:HumanCurated +bioregistry:flopo skos:exactMatch obofoundry:flopo sssom:HumanCurated bioregistry:flopo skos:exactMatch ols:flopo sssom:HumanCurated bioregistry:flopo skos:exactMatch ontobee:FLOPO sssom:HumanCurated bioregistry:flowrepository skos:exactMatch fairsharing:FAIRsharing.veg2d6 sssom:HumanCurated @@ -1801,7 +1799,7 @@ bioregistry:flowrepository skos:exactMatch n2t:flowrepository sssom:HumanCurated bioregistry:flu skos:exactMatch aberowl:FLU sssom:HumanCurated bioregistry:flu skos:exactMatch biocontext:FLU sssom:HumanCurated bioregistry:flu skos:exactMatch bioportal:FLU sssom:HumanCurated -bioregistry:flu skos:exactMatch obofoundry:FLU sssom:HumanCurated +bioregistry:flu skos:exactMatch obofoundry:flu sssom:HumanCurated bioregistry:flybase skos:exactMatch biocontext:FlyBase sssom:HumanCurated bioregistry:flybase skos:exactMatch fairsharing:FAIRsharing.wrvze3 sssom:HumanCurated bioregistry:flybase skos:exactMatch miriam:fb sssom:HumanCurated @@ -1814,7 +1812,7 @@ bioregistry:fma skos:exactMatch bioportal:FMA sssom:HumanCurated bioregistry:fma skos:exactMatch fairsharing:FAIRsharing.x56jsy sssom:HumanCurated bioregistry:fma skos:exactMatch miriam:fma sssom:HumanCurated bioregistry:fma skos:exactMatch n2t:fma sssom:HumanCurated -bioregistry:fma skos:exactMatch obofoundry:FMA sssom:HumanCurated +bioregistry:fma skos:exactMatch obofoundry:fma sssom:HumanCurated bioregistry:fma skos:exactMatch ols:fma sssom:HumanCurated bioregistry:fma skos:exactMatch ontobee:FMA sssom:HumanCurated bioregistry:fma skos:exactMatch prefixcommons:fma sssom:HumanCurated @@ -1825,7 +1823,7 @@ bioregistry:foaf skos:exactMatch bioportal:FOAF sssom:HumanCurated bioregistry:fobi skos:exactMatch aberowl:FOBI sssom:HumanCurated bioregistry:fobi skos:exactMatch agroportal:FOBI sssom:HumanCurated bioregistry:fobi skos:exactMatch bioportal:FOBI sssom:HumanCurated -bioregistry:fobi skos:exactMatch obofoundry:FOBI sssom:HumanCurated +bioregistry:fobi skos:exactMatch obofoundry:fobi sssom:HumanCurated bioregistry:fobi skos:exactMatch ols:fobi sssom:HumanCurated bioregistry:fobi skos:exactMatch ontobee:FOBI sssom:HumanCurated bioregistry:fobi bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated @@ -1842,7 +1840,7 @@ bioregistry:foodon skos:exactMatch bioportal:FOODON sssom:HumanCurated bioregistry:foodon skos:exactMatch fairsharing:FAIRsharing.dzxae sssom:HumanCurated bioregistry:foodon skos:exactMatch miriam:foodon sssom:HumanCurated bioregistry:foodon skos:exactMatch n2t:foodon sssom:HumanCurated -bioregistry:foodon skos:exactMatch obofoundry:FOODON sssom:HumanCurated +bioregistry:foodon skos:exactMatch obofoundry:foodon sssom:HumanCurated bioregistry:foodon skos:exactMatch ols:foodon sssom:HumanCurated bioregistry:foodon skos:exactMatch ontobee:FOODON sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000018 bioregistry:agro sssom:HumanCurated @@ -1854,7 +1852,6 @@ bioregistry:foodon bioregistry.schema:0000018 bioregistry:ons sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:envo sssom:HumanCurated -bioregistry:foodon bioregistry.schema:0000017 bioregistry:eo sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:ncbitaxon sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:obi sssom:HumanCurated bioregistry:foodon bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated @@ -1863,7 +1860,7 @@ bioregistry:fossilworks.journal skos:exactMatch wikidata:P7720 sssom:HumanCurate bioregistry:fossilworks.taxon skos:exactMatch wikidata:P842 sssom:HumanCurated bioregistry:fovt skos:exactMatch aberowl:FOVT sssom:HumanCurated bioregistry:fovt skos:exactMatch bioportal:FOVT sssom:HumanCurated -bioregistry:fovt skos:exactMatch obofoundry:FOVT sssom:HumanCurated +bioregistry:fovt skos:exactMatch obofoundry:fovt sssom:HumanCurated bioregistry:fovt skos:exactMatch ols:fovt sssom:HumanCurated bioregistry:fovt skos:exactMatch ontobee:FOVT sssom:HumanCurated bioregistry:fovt bioregistry.schema:0000017 bioregistry:bco sssom:HumanCurated @@ -1911,7 +1908,7 @@ bioregistry:fypo skos:exactMatch biocontext:FYPO sssom:HumanCurated bioregistry:fypo skos:exactMatch biolink:FYPO sssom:HumanCurated bioregistry:fypo skos:exactMatch bioportal:FYPO sssom:HumanCurated bioregistry:fypo skos:exactMatch fairsharing:FAIRsharing.4vr0ys sssom:HumanCurated -bioregistry:fypo skos:exactMatch obofoundry:FYPO sssom:HumanCurated +bioregistry:fypo skos:exactMatch obofoundry:fypo sssom:HumanCurated bioregistry:fypo skos:exactMatch ols:fypo sssom:HumanCurated bioregistry:fypo skos:exactMatch ontobee:FYPO sssom:HumanCurated bioregistry:ga4ghdos skos:exactMatch biocontext:GA4GHDOS sssom:HumanCurated @@ -1929,7 +1926,7 @@ bioregistry:gaz skos:exactMatch aberowl:GAZ sssom:HumanCurated bioregistry:gaz skos:exactMatch biocontext:GAZ sssom:HumanCurated bioregistry:gaz skos:exactMatch bioportal:GAZ sssom:HumanCurated bioregistry:gaz skos:exactMatch fairsharing:FAIRsharing.wkdjpb sssom:HumanCurated -bioregistry:gaz skos:exactMatch obofoundry:GAZ sssom:HumanCurated +bioregistry:gaz skos:exactMatch obofoundry:gaz sssom:HumanCurated bioregistry:gaz skos:exactMatch ols:gaz sssom:HumanCurated bioregistry:gaz skos:exactMatch ontobee:GAZ sssom:HumanCurated bioregistry:gaz skos:exactMatch wikidata:P6778 sssom:HumanCurated @@ -1946,7 +1943,7 @@ bioregistry:gdsc skos:exactMatch n2t:gdsc sssom:HumanCurated bioregistry:gecko skos:exactMatch aberowl:GECKO sssom:HumanCurated bioregistry:gecko skos:exactMatch bioportal:GECKO sssom:HumanCurated bioregistry:gecko skos:exactMatch fairsharing:FAIRsharing.3da56b sssom:HumanCurated -bioregistry:gecko skos:exactMatch obofoundry:GECKO sssom:HumanCurated +bioregistry:gecko skos:exactMatch obofoundry:gecko sssom:HumanCurated bioregistry:gecko skos:exactMatch ols:gecko sssom:HumanCurated bioregistry:gecko skos:exactMatch ontobee:GECKO sssom:HumanCurated bioregistry:gemet skos:exactMatch agroportal:GEMET sssom:HumanCurated @@ -1978,7 +1975,7 @@ bioregistry:genefarm skos:exactMatch prefixcommons:genefarm sssom:HumanCurated bioregistry:genepio skos:exactMatch aberowl:GENEPIO sssom:HumanCurated bioregistry:genepio skos:exactMatch biocontext:GENEPIO sssom:HumanCurated bioregistry:genepio skos:exactMatch fairsharing:FAIRsharing.y1mmbv sssom:HumanCurated -bioregistry:genepio skos:exactMatch obofoundry:GENEPIO sssom:HumanCurated +bioregistry:genepio skos:exactMatch obofoundry:genepio sssom:HumanCurated bioregistry:genepio skos:exactMatch ols:genepio sssom:HumanCurated bioregistry:genepio skos:exactMatch ontobee:GENEPIO sssom:HumanCurated bioregistry:genepio bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated @@ -1998,7 +1995,7 @@ bioregistry:geno skos:exactMatch aberowl:GENO sssom:HumanCurated bioregistry:geno skos:exactMatch biocontext:GENO sssom:HumanCurated bioregistry:geno skos:exactMatch bioportal:GENO sssom:HumanCurated bioregistry:geno skos:exactMatch fairsharing:FAIRsharing.kpbna7 sssom:HumanCurated -bioregistry:geno skos:exactMatch obofoundry:GENO sssom:HumanCurated +bioregistry:geno skos:exactMatch obofoundry:geno sssom:HumanCurated bioregistry:geno skos:exactMatch ols:geno sssom:HumanCurated bioregistry:geno skos:exactMatch ontobee:GENO sssom:HumanCurated bioregistry:genpept skos:exactMatch biocontext:GENPEPT sssom:HumanCurated @@ -2016,7 +2013,7 @@ bioregistry:geo skos:exactMatch prefixcommons:geo sssom:HumanCurated bioregistry:geogeo skos:exactMatch biocontext:GEO sssom:HumanCurated bioregistry:geogeo skos:exactMatch bioportal:GEO sssom:HumanCurated bioregistry:geogeo skos:exactMatch miriam:geogeo sssom:HumanCurated -bioregistry:geogeo skos:exactMatch obofoundry:GEO sssom:HumanCurated +bioregistry:geogeo skos:exactMatch obofoundry:geo sssom:HumanCurated bioregistry:geogeo skos:exactMatch ols:geo sssom:HumanCurated bioregistry:geogeo skos:exactMatch ontobee:GEO sssom:HumanCurated bioregistry:geonames skos:exactMatch fairsharing:FAIRsharing.56a0Uj sssom:HumanCurated @@ -2075,7 +2072,7 @@ bioregistry:gmd.ref skos:exactMatch n2t:gmd.ref sssom:HumanCurated bioregistry:gmelin skos:exactMatch wikidata:P1578 sssom:HumanCurated bioregistry:gno skos:exactMatch aberowl:GNO sssom:HumanCurated bioregistry:gno skos:exactMatch bioportal:GNO sssom:HumanCurated -bioregistry:gno skos:exactMatch obofoundry:GNO sssom:HumanCurated +bioregistry:gno skos:exactMatch obofoundry:gno sssom:HumanCurated bioregistry:gno skos:exactMatch ols:gno sssom:HumanCurated bioregistry:gno skos:exactMatch ontobee:GNO sssom:HumanCurated bioregistry:gnpis skos:exactMatch biocontext:GNPIS sssom:HumanCurated @@ -2089,7 +2086,7 @@ bioregistry:go skos:exactMatch bioportal:GO sssom:HumanCurated bioregistry:go skos:exactMatch fairsharing:FAIRsharing.6xq0ee sssom:HumanCurated bioregistry:go skos:exactMatch miriam:go sssom:HumanCurated bioregistry:go skos:exactMatch n2t:go sssom:HumanCurated -bioregistry:go skos:exactMatch obofoundry:GO sssom:HumanCurated +bioregistry:go skos:exactMatch obofoundry:go sssom:HumanCurated bioregistry:go skos:exactMatch ols:go sssom:HumanCurated bioregistry:go skos:exactMatch ontobee:GO sssom:HumanCurated bioregistry:go skos:exactMatch prefixcommons:go sssom:HumanCurated @@ -2180,7 +2177,7 @@ bioregistry:grsdb skos:exactMatch prefixcommons:grsdb sssom:HumanCurated bioregistry:gsso skos:exactMatch aberowl:GSSO sssom:HumanCurated bioregistry:gsso skos:exactMatch bioportal:GSSO sssom:HumanCurated bioregistry:gsso skos:exactMatch miriam:gsso sssom:HumanCurated -bioregistry:gsso skos:exactMatch obofoundry:GSSO sssom:HumanCurated +bioregistry:gsso skos:exactMatch obofoundry:gsso sssom:HumanCurated bioregistry:gsso skos:exactMatch ols:gsso sssom:HumanCurated bioregistry:gsso skos:exactMatch ontobee:GSSO sssom:HumanCurated bioregistry:gsso bioregistry.schema:0000018 bioregistry:ontoavida sssom:HumanCurated @@ -2210,7 +2207,7 @@ bioregistry:gxa.gene skos:exactMatch biocontext:GXA.GENE sssom:HumanCurated bioregistry:gxa.gene skos:exactMatch miriam:gxa.gene sssom:HumanCurated bioregistry:gxa.gene skos:exactMatch n2t:gxa.gene sssom:HumanCurated bioregistry:habronattus skos:exactMatch biocontext:HABRONATTUS sssom:HumanCurated -bioregistry:habronattus skos:exactMatch obofoundry:HABRONATTUS sssom:HumanCurated +bioregistry:habronattus skos:exactMatch obofoundry:habronattus sssom:HumanCurated bioregistry:hamap skos:exactMatch biocontext:HAMAP sssom:HumanCurated bioregistry:hamap skos:exactMatch fairsharing:FAIRsharing.63m4ss sssom:HumanCurated bioregistry:hamap skos:exactMatch miriam:hamap sssom:HumanCurated @@ -2220,14 +2217,14 @@ bioregistry:hancestro skos:exactMatch aberowl:HANCESTRO sssom:HumanCurated bioregistry:hancestro skos:exactMatch biolink:HANCESTRO sssom:HumanCurated bioregistry:hancestro skos:exactMatch bioportal:HANCESTRO sssom:HumanCurated bioregistry:hancestro skos:exactMatch fairsharing:FAIRsharing.rja8qp sssom:HumanCurated -bioregistry:hancestro skos:exactMatch obofoundry:HANCESTRO sssom:HumanCurated +bioregistry:hancestro skos:exactMatch obofoundry:hancestro sssom:HumanCurated bioregistry:hancestro skos:exactMatch ols:hancestro sssom:HumanCurated bioregistry:hancestro skos:exactMatch ontobee:HANCESTRO sssom:HumanCurated bioregistry:hao skos:exactMatch aberowl:HAO sssom:HumanCurated bioregistry:hao skos:exactMatch biocontext:HAO sssom:HumanCurated bioregistry:hao skos:exactMatch bioportal:HAO sssom:HumanCurated bioregistry:hao skos:exactMatch fairsharing:FAIRsharing.kj3m5n sssom:HumanCurated -bioregistry:hao skos:exactMatch obofoundry:HAO sssom:HumanCurated +bioregistry:hao skos:exactMatch obofoundry:hao sssom:HumanCurated bioregistry:hao skos:exactMatch ols:hao sssom:HumanCurated bioregistry:hao skos:exactMatch ontobee:HAO sssom:HumanCurated bioregistry:hcao skos:exactMatch ols:hcao sssom:HumanCurated @@ -2286,7 +2283,7 @@ bioregistry:hom skos:exactMatch aberowl:HOM sssom:HumanCurated bioregistry:hom skos:exactMatch biocontext:HOM sssom:HumanCurated bioregistry:hom skos:exactMatch bioportal:HOM sssom:HumanCurated bioregistry:hom skos:exactMatch fairsharing:FAIRsharing.efv7gw sssom:HumanCurated -bioregistry:hom skos:exactMatch obofoundry:HOM sssom:HumanCurated +bioregistry:hom skos:exactMatch obofoundry:hom sssom:HumanCurated bioregistry:hom skos:exactMatch ols:hom sssom:HumanCurated bioregistry:hom skos:exactMatch ontobee:HOM sssom:HumanCurated bioregistry:homd.seq skos:exactMatch biocontext:HOMD.SEQ sssom:HumanCurated @@ -2314,7 +2311,7 @@ bioregistry:hp skos:exactMatch bioportal:HP_O sssom:HumanCurated bioregistry:hp skos:exactMatch fairsharing:FAIRsharing.kbtt7f sssom:HumanCurated bioregistry:hp skos:exactMatch miriam:hp sssom:HumanCurated bioregistry:hp skos:exactMatch n2t:hp sssom:HumanCurated -bioregistry:hp skos:exactMatch obofoundry:HP sssom:HumanCurated +bioregistry:hp skos:exactMatch obofoundry:hp sssom:HumanCurated bioregistry:hp skos:exactMatch ols:hp sssom:HumanCurated bioregistry:hp skos:exactMatch ontobee:HP sssom:HumanCurated bioregistry:hp skos:exactMatch wikidata:P3841 sssom:HumanCurated @@ -2345,14 +2342,14 @@ bioregistry:hsapdv skos:exactMatch biocontext:HSAPDV sssom:HumanCurated bioregistry:hsapdv skos:exactMatch biolink:HsapDv sssom:HumanCurated bioregistry:hsapdv skos:exactMatch bioportal:HSAPDV sssom:HumanCurated bioregistry:hsapdv skos:exactMatch fairsharing:FAIRsharing.c6vhm3 sssom:HumanCurated -bioregistry:hsapdv skos:exactMatch obofoundry:HsapDv sssom:HumanCurated +bioregistry:hsapdv skos:exactMatch obofoundry:hsapdv sssom:HumanCurated bioregistry:hsapdv skos:exactMatch ols:hsapdv sssom:HumanCurated bioregistry:hsapdv skos:exactMatch ontobee:HSAPDV sssom:HumanCurated bioregistry:hsapdv bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated bioregistry:hsdb skos:exactMatch wikidata:P2062 sssom:HumanCurated bioregistry:hso skos:exactMatch aberowl:HSO sssom:HumanCurated bioregistry:hso skos:exactMatch bioportal:HSO sssom:HumanCurated -bioregistry:hso skos:exactMatch obofoundry:HSO sssom:HumanCurated +bioregistry:hso skos:exactMatch obofoundry:hso sssom:HumanCurated bioregistry:hso skos:exactMatch ols:hso sssom:HumanCurated bioregistry:hso skos:exactMatch ontobee:HSO sssom:HumanCurated bioregistry:hso bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -2366,7 +2363,7 @@ bioregistry:hssp skos:exactMatch n2t:hssp sssom:HumanCurated bioregistry:hssp skos:exactMatch prefixcommons:hssp sssom:HumanCurated bioregistry:htn skos:exactMatch aberowl:HTN sssom:HumanCurated bioregistry:htn skos:exactMatch bioportal:HTN sssom:HumanCurated -bioregistry:htn skos:exactMatch obofoundry:HTN sssom:HumanCurated +bioregistry:htn skos:exactMatch obofoundry:htn sssom:HumanCurated bioregistry:htn skos:exactMatch ols:htn sssom:HumanCurated bioregistry:htn skos:exactMatch ontobee:HTN sssom:HumanCurated bioregistry:huge skos:exactMatch biocontext:HUGE sssom:HumanCurated @@ -2380,7 +2377,7 @@ bioregistry:iao skos:exactMatch bioportal:IAO sssom:HumanCurated bioregistry:iao skos:exactMatch fairsharing:FAIRsharing.gq1xtx sssom:HumanCurated bioregistry:iao skos:exactMatch miriam:iao sssom:HumanCurated bioregistry:iao skos:exactMatch n2t:iao sssom:HumanCurated -bioregistry:iao skos:exactMatch obofoundry:IAO sssom:HumanCurated +bioregistry:iao skos:exactMatch obofoundry:iao sssom:HumanCurated bioregistry:iao skos:exactMatch ols:iao sssom:HumanCurated bioregistry:iao skos:exactMatch ontobee:IAO sssom:HumanCurated bioregistry:iao bioregistry.schema:0000018 bioregistry:agro sssom:HumanCurated @@ -2432,14 +2429,14 @@ bioregistry:iceberg.family skos:exactMatch miriam:iceberg.family sssom:HumanCura bioregistry:iceberg.family skos:exactMatch n2t:iceberg.family sssom:HumanCurated bioregistry:iceo skos:exactMatch aberowl:ICEO sssom:HumanCurated bioregistry:iceo skos:exactMatch bioportal:ICEO sssom:HumanCurated -bioregistry:iceo skos:exactMatch obofoundry:ICEO sssom:HumanCurated +bioregistry:iceo skos:exactMatch obofoundry:iceo sssom:HumanCurated bioregistry:iceo skos:exactMatch ols:iceo sssom:HumanCurated bioregistry:iceo skos:exactMatch ontobee:ICEO sssom:HumanCurated bioregistry:ico skos:exactMatch aberowl:ICO sssom:HumanCurated bioregistry:ico skos:exactMatch biocontext:ICO sssom:HumanCurated bioregistry:ico skos:exactMatch bioportal:ICO sssom:HumanCurated bioregistry:ico skos:exactMatch fairsharing:FAIRsharing.b9znd5 sssom:HumanCurated -bioregistry:ico skos:exactMatch obofoundry:ICO sssom:HumanCurated +bioregistry:ico skos:exactMatch obofoundry:ico sssom:HumanCurated bioregistry:ico skos:exactMatch ols:ico sssom:HumanCurated bioregistry:ico skos:exactMatch ontobee:ICO sssom:HumanCurated bioregistry:ico bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -2453,7 +2450,7 @@ bioregistry:ido skos:exactMatch bioportal:IDO sssom:HumanCurated bioregistry:ido skos:exactMatch fairsharing:FAIRsharing.aae3v6 sssom:HumanCurated bioregistry:ido skos:exactMatch miriam:ido sssom:HumanCurated bioregistry:ido skos:exactMatch n2t:ido sssom:HumanCurated -bioregistry:ido skos:exactMatch obofoundry:IDO sssom:HumanCurated +bioregistry:ido skos:exactMatch obofoundry:ido sssom:HumanCurated bioregistry:ido skos:exactMatch ols:ido sssom:HumanCurated bioregistry:ido skos:exactMatch ontobee:IDO sssom:HumanCurated bioregistry:ido bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -2467,7 +2464,7 @@ bioregistry:idomal skos:exactMatch aberowl:IDOMAL sssom:HumanCurated bioregistry:idomal skos:exactMatch biocontext:IDOMAL sssom:HumanCurated bioregistry:idomal skos:exactMatch bioportal:IDOMAL sssom:HumanCurated bioregistry:idomal skos:exactMatch fairsharing:FAIRsharing.2q8c28 sssom:HumanCurated -bioregistry:idomal skos:exactMatch obofoundry:IDOMAL sssom:HumanCurated +bioregistry:idomal skos:exactMatch obofoundry:idomal sssom:HumanCurated bioregistry:idomal skos:exactMatch ols:idomal sssom:HumanCurated bioregistry:idomal skos:exactMatch ontobee:IDOMAL sssom:HumanCurated bioregistry:idomal bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated @@ -2481,7 +2478,7 @@ bioregistry:idr skos:exactMatch miriam:idr sssom:HumanCurated bioregistry:iedb skos:exactMatch fairsharing:FAIRsharing.c886cd sssom:HumanCurated bioregistry:iedb skos:exactMatch miriam:iedb sssom:HumanCurated bioregistry:iev skos:exactMatch biocontext:IEV sssom:HumanCurated -bioregistry:iev skos:exactMatch obofoundry:IEV sssom:HumanCurated +bioregistry:iev skos:exactMatch obofoundry:iev sssom:HumanCurated bioregistry:iev skos:exactMatch prefixcommons:iev sssom:HumanCurated bioregistry:igsn skos:exactMatch fairsharing:FAIRsharing.Yvc76F sssom:HumanCurated bioregistry:igsn skos:exactMatch miriam:igsn sssom:HumanCurated @@ -2509,7 +2506,7 @@ bioregistry:imgt.ligm skos:exactMatch miriam:imgt.ligm sssom:HumanCurated bioregistry:imgt.ligm skos:exactMatch n2t:imgt.ligm sssom:HumanCurated bioregistry:imgt.ligm skos:exactMatch prefixcommons:imgt.ligm sssom:HumanCurated bioregistry:imr skos:exactMatch biocontext:IMR sssom:HumanCurated -bioregistry:imr skos:exactMatch obofoundry:IMR sssom:HumanCurated +bioregistry:imr skos:exactMatch obofoundry:imr sssom:HumanCurated bioregistry:imr skos:exactMatch prefixcommons:imr sssom:HumanCurated bioregistry:inaturalist.taxon skos:exactMatch wikidata:P3151 sssom:HumanCurated bioregistry:inchi skos:exactMatch biocontext:INCHI sssom:HumanCurated @@ -2527,7 +2524,7 @@ bioregistry:ino skos:exactMatch aberowl:INO sssom:HumanCurated bioregistry:ino skos:exactMatch biolink:INO sssom:HumanCurated bioregistry:ino skos:exactMatch bioportal:INO sssom:HumanCurated bioregistry:ino skos:exactMatch fairsharing:FAIRsharing.mm72as sssom:HumanCurated -bioregistry:ino skos:exactMatch obofoundry:INO sssom:HumanCurated +bioregistry:ino skos:exactMatch obofoundry:ino sssom:HumanCurated bioregistry:ino skos:exactMatch ols:ino sssom:HumanCurated bioregistry:ino skos:exactMatch ontobee:INO sssom:HumanCurated bioregistry:insdc skos:exactMatch biocontext:INSDC sssom:HumanCurated @@ -2561,7 +2558,7 @@ bioregistry:interpro skos:exactMatch biolink:interpro sssom:HumanCurated bioregistry:interpro skos:exactMatch fairsharing:FAIRsharing.pda11d sssom:HumanCurated bioregistry:interpro skos:exactMatch miriam:interpro sssom:HumanCurated bioregistry:interpro skos:exactMatch n2t:interpro sssom:HumanCurated -bioregistry:interpro skos:exactMatch obofoundry:IPR sssom:HumanCurated +bioregistry:interpro skos:exactMatch obofoundry:ipr sssom:HumanCurated bioregistry:interpro skos:exactMatch prefixcommons:interpro sssom:HumanCurated bioregistry:interpro skos:exactMatch wikidata:P2926 sssom:HumanCurated bioregistry:ird.segment skos:exactMatch biocontext:IRD.SEGMENT sssom:HumanCurated @@ -2718,13 +2715,12 @@ bioregistry:knapsack skos:exactMatch wikidata:P2064 sssom:HumanCurated bioregistry:kupo bioregistry.schema:0000018 bioregistry:cl sssom:HumanCurated bioregistry:labo skos:exactMatch aberowl:LABO sssom:HumanCurated bioregistry:labo skos:exactMatch bioportal:LABO sssom:HumanCurated -bioregistry:labo skos:exactMatch obofoundry:LABO sssom:HumanCurated +bioregistry:labo skos:exactMatch obofoundry:labo sssom:HumanCurated bioregistry:labo skos:exactMatch ols:labo sssom:HumanCurated bioregistry:labo skos:exactMatch ontobee:LABO sssom:HumanCurated bioregistry:labo bioregistry.schema:0000017 bioregistry:iao sssom:HumanCurated bioregistry:labo bioregistry.schema:0000017 bioregistry:obi sssom:HumanCurated bioregistry:labo bioregistry.schema:0000017 bioregistry:ogms sssom:HumanCurated -bioregistry:labo bioregistry.schema:0000017 bioregistry:omiabis sssom:HumanCurated bioregistry:labo bioregistry.schema:0000017 bioregistry:omrse sssom:HumanCurated bioregistry:labo bioregistry.schema:0000017 bioregistry:opmi sssom:HumanCurated bioregistry:lbo skos:exactMatch aberowl:LBO sssom:HumanCurated @@ -2736,7 +2732,7 @@ bioregistry:lei skos:exactMatch miriam:lei sssom:HumanCurated bioregistry:lei skos:exactMatch n2t:lei sssom:HumanCurated bioregistry:lepao skos:exactMatch aberowl:LEPAO sssom:HumanCurated bioregistry:lepao skos:exactMatch bioportal:LEPAO sssom:HumanCurated -bioregistry:lepao skos:exactMatch obofoundry:LEPAO sssom:HumanCurated +bioregistry:lepao skos:exactMatch obofoundry:lepao sssom:HumanCurated bioregistry:lepao skos:exactMatch ols:lepao sssom:HumanCurated bioregistry:lepao bioregistry.schema:0000017 bioregistry:aism sssom:HumanCurated bioregistry:lepao bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -2791,10 +2787,10 @@ bioregistry:lipidmaps skos:exactMatch wikidata:P2063 sssom:HumanCurated bioregistry:lipro skos:exactMatch aberowl:LIPRO sssom:HumanCurated bioregistry:lipro skos:exactMatch biocontext:LIPRO sssom:HumanCurated bioregistry:lipro skos:exactMatch bioportal:LIPRO sssom:HumanCurated -bioregistry:lipro skos:exactMatch obofoundry:LIPRO sssom:HumanCurated +bioregistry:lipro skos:exactMatch obofoundry:lipro sssom:HumanCurated bioregistry:lncipedia skos:exactMatch fairsharing:FAIRsharing.84c1a7 sssom:HumanCurated bioregistry:loggerhead skos:exactMatch biocontext:LOGGERHEAD sssom:HumanCurated -bioregistry:loggerhead skos:exactMatch obofoundry:LOGGERHEAD sssom:HumanCurated +bioregistry:loggerhead skos:exactMatch obofoundry:loggerhead sssom:HumanCurated bioregistry:loinc skos:exactMatch aberowl:LOINC sssom:HumanCurated bioregistry:loinc skos:exactMatch biolink:LOINC sssom:HumanCurated bioregistry:loinc skos:exactMatch bioportal:LOINC sssom:HumanCurated @@ -2813,7 +2809,7 @@ bioregistry:ma skos:exactMatch bioportal:MA sssom:HumanCurated bioregistry:ma skos:exactMatch fairsharing:FAIRsharing.pdwqcr sssom:HumanCurated bioregistry:ma skos:exactMatch miriam:ma sssom:HumanCurated bioregistry:ma skos:exactMatch n2t:ma sssom:HumanCurated -bioregistry:ma skos:exactMatch obofoundry:MA sssom:HumanCurated +bioregistry:ma skos:exactMatch obofoundry:ma sssom:HumanCurated bioregistry:ma skos:exactMatch ols:ma sssom:HumanCurated bioregistry:ma skos:exactMatch ontobee:MA sssom:HumanCurated bioregistry:ma skos:exactMatch prefixcommons:ma sssom:HumanCurated @@ -2833,11 +2829,11 @@ bioregistry:mamo skos:exactMatch bioportal:MAMO sssom:HumanCurated bioregistry:mamo skos:exactMatch fairsharing:FAIRsharing.kbz5jh sssom:HumanCurated bioregistry:mamo skos:exactMatch miriam:mamo sssom:HumanCurated bioregistry:mamo skos:exactMatch n2t:mamo sssom:HumanCurated -bioregistry:mamo skos:exactMatch obofoundry:MAMO sssom:HumanCurated +bioregistry:mamo skos:exactMatch obofoundry:mamo sssom:HumanCurated bioregistry:mamo skos:exactMatch ols:mamo sssom:HumanCurated bioregistry:mamo skos:exactMatch ontobee:MAMO sssom:HumanCurated bioregistry:mao skos:exactMatch biocontext:MAO sssom:HumanCurated -bioregistry:mao skos:exactMatch obofoundry:MAO sssom:HumanCurated +bioregistry:mao skos:exactMatch obofoundry:mao sssom:HumanCurated bioregistry:mao skos:exactMatch prefixcommons:mao sssom:HumanCurated bioregistry:massbank skos:exactMatch biocontext:MASSBANK sssom:HumanCurated bioregistry:massbank skos:exactMatch fairsharing:FAIRsharing.dk451a sssom:HumanCurated @@ -2851,7 +2847,7 @@ bioregistry:massive skos:exactMatch n2t:massive sssom:HumanCurated bioregistry:mat skos:exactMatch aberowl:MAT sssom:HumanCurated bioregistry:mat skos:exactMatch biocontext:MAT sssom:HumanCurated bioregistry:mat skos:exactMatch bioportal:MAT sssom:HumanCurated -bioregistry:mat skos:exactMatch obofoundry:MAT sssom:HumanCurated +bioregistry:mat skos:exactMatch obofoundry:mat sssom:HumanCurated bioregistry:matrixdb skos:exactMatch fairsharing:FAIRsharing.91yrz6 sssom:HumanCurated bioregistry:matrixdb skos:exactMatch prefixcommons:matrixdb sssom:HumanCurated bioregistry:matrixdb bioregistry.schema:0000018 bioregistry:complexportal sssom:HumanCurated @@ -2861,7 +2857,7 @@ bioregistry:matrixdb.association skos:exactMatch n2t:matrixdb.association sssom: bioregistry:maxo skos:exactMatch aberowl:MAXO sssom:HumanCurated bioregistry:maxo skos:exactMatch biolink:MAXO sssom:HumanCurated bioregistry:maxo skos:exactMatch bioportal:MAXO sssom:HumanCurated -bioregistry:maxo skos:exactMatch obofoundry:MAXO sssom:HumanCurated +bioregistry:maxo skos:exactMatch obofoundry:maxo sssom:HumanCurated bioregistry:maxo skos:exactMatch ols:maxo sssom:HumanCurated bioregistry:maxo skos:exactMatch ontobee:MAXO sssom:HumanCurated bioregistry:maxo bioregistry.schema:0000018 bioregistry:ecto sssom:HumanCurated @@ -2874,7 +2870,7 @@ bioregistry:maxo bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurate bioregistry:mcc skos:exactMatch bioportal:MCCL sssom:HumanCurated bioregistry:mco skos:exactMatch aberowl:MCO sssom:HumanCurated bioregistry:mco skos:exactMatch bioportal:MCO sssom:HumanCurated -bioregistry:mco skos:exactMatch obofoundry:MCO sssom:HumanCurated +bioregistry:mco skos:exactMatch obofoundry:mco sssom:HumanCurated bioregistry:mco skos:exactMatch ols:mco sssom:HumanCurated bioregistry:mco skos:exactMatch ontobee:MCO sssom:HumanCurated bioregistry:mco bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -2970,34 +2966,34 @@ bioregistry:mf skos:exactMatch aberowl:MF sssom:HumanCurated bioregistry:mf skos:exactMatch biocontext:MF sssom:HumanCurated bioregistry:mf skos:exactMatch bioportal:MF sssom:HumanCurated bioregistry:mf skos:exactMatch fairsharing:FAIRsharing.4gm9gt sssom:HumanCurated -bioregistry:mf skos:exactMatch obofoundry:MF sssom:HumanCurated +bioregistry:mf skos:exactMatch obofoundry:mf sssom:HumanCurated bioregistry:mf skos:exactMatch ols:mf sssom:HumanCurated bioregistry:mf skos:exactMatch ontobee:MF sssom:HumanCurated bioregistry:mfmo skos:exactMatch aberowl:MFMO sssom:HumanCurated bioregistry:mfmo skos:exactMatch biocontext:MFMO sssom:HumanCurated bioregistry:mfmo skos:exactMatch bioportal:MFMO sssom:HumanCurated bioregistry:mfmo skos:exactMatch fairsharing:FAIRsharing.669cnk sssom:HumanCurated -bioregistry:mfmo skos:exactMatch obofoundry:MFMO sssom:HumanCurated +bioregistry:mfmo skos:exactMatch obofoundry:mfmo sssom:HumanCurated bioregistry:mfmo skos:exactMatch ols:mfmo sssom:HumanCurated bioregistry:mfmo skos:exactMatch ontobee:MFMO sssom:HumanCurated bioregistry:mfmo bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:mfo skos:exactMatch aberowl:MFO sssom:HumanCurated bioregistry:mfo skos:exactMatch biocontext:MFO sssom:HumanCurated bioregistry:mfo skos:exactMatch bioportal:MFO sssom:HumanCurated -bioregistry:mfo skos:exactMatch obofoundry:MFO sssom:HumanCurated +bioregistry:mfo skos:exactMatch obofoundry:mfo sssom:HumanCurated bioregistry:mfo skos:exactMatch prefixcommons:mfo sssom:HumanCurated bioregistry:mfoem skos:exactMatch aberowl:MFOEM sssom:HumanCurated bioregistry:mfoem skos:exactMatch biocontext:MFOEM sssom:HumanCurated bioregistry:mfoem skos:exactMatch bioportal:MFOEM sssom:HumanCurated bioregistry:mfoem skos:exactMatch fairsharing:FAIRsharing.dx30m8 sssom:HumanCurated -bioregistry:mfoem skos:exactMatch obofoundry:MFOEM sssom:HumanCurated +bioregistry:mfoem skos:exactMatch obofoundry:mfoem sssom:HumanCurated bioregistry:mfoem skos:exactMatch ols:mfoem sssom:HumanCurated bioregistry:mfoem skos:exactMatch ontobee:MFOEM sssom:HumanCurated bioregistry:mfomd skos:exactMatch aberowl:MFOMD sssom:HumanCurated bioregistry:mfomd skos:exactMatch biocontext:MFOMD sssom:HumanCurated bioregistry:mfomd skos:exactMatch bioportal:MFOMD sssom:HumanCurated bioregistry:mfomd skos:exactMatch fairsharing:FAIRsharing.q053vb sssom:HumanCurated -bioregistry:mfomd skos:exactMatch obofoundry:MFOMD sssom:HumanCurated +bioregistry:mfomd skos:exactMatch obofoundry:mfomd sssom:HumanCurated bioregistry:mfomd skos:exactMatch ols:mfomd sssom:HumanCurated bioregistry:mfomd skos:exactMatch ontobee:MFOMD sssom:HumanCurated bioregistry:mge skos:exactMatch miriam:mge sssom:HumanCurated @@ -3018,7 +3014,7 @@ bioregistry:mi skos:exactMatch biolink:MI sssom:HumanCurated bioregistry:mi skos:exactMatch bioportal:MI sssom:HumanCurated bioregistry:mi skos:exactMatch miriam:mi sssom:HumanCurated bioregistry:mi skos:exactMatch n2t:psimi sssom:HumanCurated -bioregistry:mi skos:exactMatch obofoundry:MI sssom:HumanCurated +bioregistry:mi skos:exactMatch obofoundry:mi sssom:HumanCurated bioregistry:mi skos:exactMatch ols:mi sssom:HumanCurated bioregistry:mi skos:exactMatch ontobee:MI sssom:HumanCurated bioregistry:mi skos:exactMatch prefixcommons:psi.mi sssom:HumanCurated @@ -3026,13 +3022,13 @@ bioregistry:miapa skos:exactMatch aberowl:MIAPA sssom:HumanCurated bioregistry:miapa skos:exactMatch biocontext:MIAPA sssom:HumanCurated bioregistry:miapa skos:exactMatch bioportal:MIAPA sssom:HumanCurated bioregistry:miapa skos:exactMatch fairsharing:FAIRsharing.ca48xs sssom:HumanCurated -bioregistry:miapa skos:exactMatch obofoundry:MIAPA sssom:HumanCurated +bioregistry:miapa skos:exactMatch obofoundry:miapa sssom:HumanCurated bioregistry:miapa skos:exactMatch ols:miapa sssom:HumanCurated bioregistry:miapa skos:exactMatch ontobee:MIAPA sssom:HumanCurated bioregistry:micro skos:exactMatch aberowl:MICRO sssom:HumanCurated bioregistry:micro skos:exactMatch biocontext:MICRO sssom:HumanCurated bioregistry:micro skos:exactMatch fairsharing:FAIRsharing.brhpb0 sssom:HumanCurated -bioregistry:micro skos:exactMatch obofoundry:MICRO sssom:HumanCurated +bioregistry:micro skos:exactMatch obofoundry:micro sssom:HumanCurated bioregistry:micro skos:exactMatch ols:micro sssom:HumanCurated bioregistry:micro skos:exactMatch ontobee:MicrO sssom:HumanCurated bioregistry:micro bioregistry.schema:0000018 bioregistry:mco sssom:HumanCurated @@ -3093,7 +3089,7 @@ bioregistry:miriam.resource skos:exactMatch prefixcommons:miriam.resource sssom: bioregistry:mirnao skos:exactMatch aberowl:MIRNAO sssom:HumanCurated bioregistry:mirnao skos:exactMatch biocontext:MIRNAO sssom:HumanCurated bioregistry:mirnao skos:exactMatch bioportal:MIRNAO sssom:HumanCurated -bioregistry:mirnao skos:exactMatch obofoundry:MIRNAO sssom:HumanCurated +bioregistry:mirnao skos:exactMatch obofoundry:mirnao sssom:HumanCurated bioregistry:mirnao skos:exactMatch ontobee:miRNAO sssom:HumanCurated bioregistry:mirnest skos:exactMatch biocontext:MIRNEST sssom:HumanCurated bioregistry:mirnest skos:exactMatch fairsharing:FAIRsharing.5pfx4r sssom:HumanCurated @@ -3104,7 +3100,7 @@ bioregistry:miro skos:exactMatch aberowl:MIRO sssom:HumanCurated bioregistry:miro skos:exactMatch biocontext:MIRO sssom:HumanCurated bioregistry:miro skos:exactMatch bioportal:MIRO sssom:HumanCurated bioregistry:miro skos:exactMatch fairsharing:FAIRsharing.sjf113 sssom:HumanCurated -bioregistry:miro skos:exactMatch obofoundry:MIRO sssom:HumanCurated +bioregistry:miro skos:exactMatch obofoundry:miro sssom:HumanCurated bioregistry:miro skos:exactMatch ols:miro sssom:HumanCurated bioregistry:miro skos:exactMatch ontobee:MIRO sssom:HumanCurated bioregistry:mirtarbase skos:exactMatch biocontext:MIRTARBASE sssom:HumanCurated @@ -3124,7 +3120,7 @@ bioregistry:mmo skos:exactMatch aberowl:MMO sssom:HumanCurated bioregistry:mmo skos:exactMatch biocontext:MMO sssom:HumanCurated bioregistry:mmo skos:exactMatch bioportal:MMO sssom:HumanCurated bioregistry:mmo skos:exactMatch fairsharing:FAIRsharing.bgkyd7 sssom:HumanCurated -bioregistry:mmo skos:exactMatch obofoundry:MMO sssom:HumanCurated +bioregistry:mmo skos:exactMatch obofoundry:mmo sssom:HumanCurated bioregistry:mmo skos:exactMatch ols:mmo sssom:HumanCurated bioregistry:mmo skos:exactMatch ontobee:MMO sssom:HumanCurated bioregistry:mmp.cat skos:exactMatch biocontext:MMP.CAT sssom:HumanCurated @@ -3146,7 +3142,7 @@ bioregistry:mmusdv skos:exactMatch biocontext:MMUSDV sssom:HumanCurated bioregistry:mmusdv skos:exactMatch biolink:MmusDv sssom:HumanCurated bioregistry:mmusdv skos:exactMatch bioportal:MMUSDV sssom:HumanCurated bioregistry:mmusdv skos:exactMatch fairsharing:FAIRsharing.zchb68 sssom:HumanCurated -bioregistry:mmusdv skos:exactMatch obofoundry:MmusDv sssom:HumanCurated +bioregistry:mmusdv skos:exactMatch obofoundry:mmusdv sssom:HumanCurated bioregistry:mmusdv skos:exactMatch ols:mmusdv sssom:HumanCurated bioregistry:mmusdv skos:exactMatch ontobee:MMUSDV sssom:HumanCurated bioregistry:mo skos:exactMatch aberowl:MO sssom:HumanCurated @@ -3154,7 +3150,7 @@ bioregistry:mo skos:exactMatch biocontext:MO sssom:HumanCurated bioregistry:mo skos:exactMatch bioportal:MO sssom:HumanCurated bioregistry:mo skos:exactMatch miriam:mo sssom:HumanCurated bioregistry:mo skos:exactMatch n2t:mo sssom:HumanCurated -bioregistry:mo skos:exactMatch obofoundry:MO sssom:HumanCurated +bioregistry:mo skos:exactMatch obofoundry:mo sssom:HumanCurated bioregistry:mobidb skos:exactMatch biocontext:MOBIDB sssom:HumanCurated bioregistry:mobidb skos:exactMatch fairsharing:FAIRsharing.jwra3e sssom:HumanCurated bioregistry:mobidb skos:exactMatch miriam:mobidb sssom:HumanCurated @@ -3166,7 +3162,7 @@ bioregistry:mod skos:exactMatch bioportal:PSIMOD sssom:HumanCurated bioregistry:mod skos:exactMatch fairsharing:FAIRsharing.2m4ms9 sssom:HumanCurated bioregistry:mod skos:exactMatch miriam:mod sssom:HumanCurated bioregistry:mod skos:exactMatch n2t:mod sssom:HumanCurated -bioregistry:mod skos:exactMatch obofoundry:MOD sssom:HumanCurated +bioregistry:mod skos:exactMatch obofoundry:mod sssom:HumanCurated bioregistry:mod skos:exactMatch ols:mod sssom:HumanCurated bioregistry:mod skos:exactMatch ontobee:MOD sssom:HumanCurated bioregistry:mod skos:exactMatch prefixcommons:psi.mod sssom:HumanCurated @@ -3184,7 +3180,7 @@ bioregistry:mondo skos:exactMatch aberowl:MONDO sssom:HumanCurated bioregistry:mondo skos:exactMatch biocontext:MONDO sssom:HumanCurated bioregistry:mondo skos:exactMatch bioportal:MONDO sssom:HumanCurated bioregistry:mondo skos:exactMatch fairsharing:FAIRsharing.b2979t sssom:HumanCurated -bioregistry:mondo skos:exactMatch obofoundry:MONDO sssom:HumanCurated +bioregistry:mondo skos:exactMatch obofoundry:mondo sssom:HumanCurated bioregistry:mondo skos:exactMatch ols:mondo sssom:HumanCurated bioregistry:mondo skos:exactMatch ontobee:MONDO sssom:HumanCurated bioregistry:mondo skos:exactMatch wikidata:P5270 sssom:HumanCurated @@ -3192,7 +3188,7 @@ bioregistry:mop skos:exactMatch aberowl:MOP sssom:HumanCurated bioregistry:mop skos:exactMatch biocontext:MOP sssom:HumanCurated bioregistry:mop skos:exactMatch bioportal:MOP sssom:HumanCurated bioregistry:mop skos:exactMatch fairsharing:FAIRsharing.mct09a sssom:HumanCurated -bioregistry:mop skos:exactMatch obofoundry:MOP sssom:HumanCurated +bioregistry:mop skos:exactMatch obofoundry:mop sssom:HumanCurated bioregistry:mop skos:exactMatch ols:mop sssom:HumanCurated bioregistry:mop skos:exactMatch ontobee:MOP sssom:HumanCurated bioregistry:morpheus skos:exactMatch miriam:morpheus sssom:HumanCurated @@ -3202,7 +3198,7 @@ bioregistry:mp skos:exactMatch bioportal:MP sssom:HumanCurated bioregistry:mp skos:exactMatch fairsharing:FAIRsharing.kg1x4z sssom:HumanCurated bioregistry:mp skos:exactMatch miriam:mp sssom:HumanCurated bioregistry:mp skos:exactMatch n2t:mp sssom:HumanCurated -bioregistry:mp skos:exactMatch obofoundry:MP sssom:HumanCurated +bioregistry:mp skos:exactMatch obofoundry:mp sssom:HumanCurated bioregistry:mp skos:exactMatch ols:mp sssom:HumanCurated bioregistry:mp skos:exactMatch ontobee:MP sssom:HumanCurated bioregistry:mp skos:exactMatch prefixcommons:mp sssom:HumanCurated @@ -3212,7 +3208,7 @@ bioregistry:mpath skos:exactMatch aberowl:MPATH sssom:HumanCurated bioregistry:mpath skos:exactMatch biocontext:MPATH sssom:HumanCurated bioregistry:mpath skos:exactMatch bioportal:MPATH sssom:HumanCurated bioregistry:mpath skos:exactMatch fairsharing:FAIRsharing.3wbgm0 sssom:HumanCurated -bioregistry:mpath skos:exactMatch obofoundry:MPATH sssom:HumanCurated +bioregistry:mpath skos:exactMatch obofoundry:mpath sssom:HumanCurated bioregistry:mpath skos:exactMatch ols:mpath sssom:HumanCurated bioregistry:mpath skos:exactMatch ontobee:MPATH sssom:HumanCurated bioregistry:mpath skos:exactMatch prefixcommons:mpath sssom:HumanCurated @@ -3223,14 +3219,14 @@ bioregistry:mpid skos:exactMatch n2t:mpid sssom:HumanCurated bioregistry:mpio skos:exactMatch aberowl:MPIO sssom:HumanCurated bioregistry:mpio skos:exactMatch biocontext:MPIO sssom:HumanCurated bioregistry:mpio skos:exactMatch bioportal:MPIO sssom:HumanCurated -bioregistry:mpio skos:exactMatch obofoundry:MPIO sssom:HumanCurated +bioregistry:mpio skos:exactMatch obofoundry:mpio sssom:HumanCurated bioregistry:mpio skos:exactMatch ols:mpio sssom:HumanCurated bioregistry:mpio skos:exactMatch ontobee:MPIO sssom:HumanCurated bioregistry:mro skos:exactMatch aberowl:MRO sssom:HumanCurated bioregistry:mro skos:exactMatch biocontext:MRO sssom:HumanCurated bioregistry:mro skos:exactMatch bioportal:MRO sssom:HumanCurated bioregistry:mro skos:exactMatch fairsharing:FAIRsharing.k893xa sssom:HumanCurated -bioregistry:mro skos:exactMatch obofoundry:MRO sssom:HumanCurated +bioregistry:mro skos:exactMatch obofoundry:mro sssom:HumanCurated bioregistry:mro skos:exactMatch ols:mro sssom:HumanCurated bioregistry:mro skos:exactMatch ontobee:MRO sssom:HumanCurated bioregistry:ms skos:exactMatch aberowl:MS sssom:HumanCurated @@ -3238,7 +3234,7 @@ bioregistry:ms skos:exactMatch biocontext:MS sssom:HumanCurated bioregistry:ms skos:exactMatch bioportal:MS sssom:HumanCurated bioregistry:ms skos:exactMatch miriam:ms sssom:HumanCurated bioregistry:ms skos:exactMatch n2t:ms sssom:HumanCurated -bioregistry:ms skos:exactMatch obofoundry:MS sssom:HumanCurated +bioregistry:ms skos:exactMatch obofoundry:ms sssom:HumanCurated bioregistry:ms skos:exactMatch ols:ms sssom:HumanCurated bioregistry:ms skos:exactMatch ontobee:MS sssom:HumanCurated bioregistry:ms bioregistry.schema:0000017 bioregistry:pato sssom:HumanCurated @@ -3313,7 +3309,7 @@ bioregistry:nbo skos:exactMatch aberowl:NBO sssom:HumanCurated bioregistry:nbo skos:exactMatch biocontext:NBO sssom:HumanCurated bioregistry:nbo skos:exactMatch bioportal:NBO sssom:HumanCurated bioregistry:nbo skos:exactMatch fairsharing:FAIRsharing.pktgc6 sssom:HumanCurated -bioregistry:nbo skos:exactMatch obofoundry:NBO sssom:HumanCurated +bioregistry:nbo skos:exactMatch obofoundry:nbo sssom:HumanCurated bioregistry:nbo skos:exactMatch ols:nbo sssom:HumanCurated bioregistry:nbo skos:exactMatch ontobee:NBO sssom:HumanCurated bioregistry:nbo bioregistry.schema:0000018 bioregistry:ecto sssom:HumanCurated @@ -3347,7 +3343,7 @@ bioregistry:ncbitaxon skos:exactMatch bioportal:NCBITAXON sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch fairsharing:FAIRsharing.fj07xj sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch miriam:taxonomy sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch n2t:taxonomy sssom:HumanCurated -bioregistry:ncbitaxon skos:exactMatch obofoundry:NCBITaxon sssom:HumanCurated +bioregistry:ncbitaxon skos:exactMatch obofoundry:ncbitaxon sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch ols:ncbitaxon sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch ontobee:NCBITaxon sssom:HumanCurated bioregistry:ncbitaxon skos:exactMatch prefixcommons:uniprot.taxonomy sssom:HumanCurated @@ -3375,7 +3371,7 @@ bioregistry:ncit skos:exactMatch bioportal:NCIT sssom:HumanCurated bioregistry:ncit skos:exactMatch fairsharing:FAIRsharing.4cvwxa sssom:HumanCurated bioregistry:ncit skos:exactMatch miriam:ncit sssom:HumanCurated bioregistry:ncit skos:exactMatch n2t:ncit sssom:HumanCurated -bioregistry:ncit skos:exactMatch obofoundry:NCIT sssom:HumanCurated +bioregistry:ncit skos:exactMatch obofoundry:ncit sssom:HumanCurated bioregistry:ncit skos:exactMatch ols:ncit sssom:HumanCurated bioregistry:ncit skos:exactMatch ontobee:NCIT sssom:HumanCurated bioregistry:ncit skos:exactMatch prefixcommons:ncit sssom:HumanCurated @@ -3388,7 +3384,7 @@ bioregistry:ncro skos:exactMatch aberowl:NCRO sssom:HumanCurated bioregistry:ncro skos:exactMatch biocontext:NCRO sssom:HumanCurated bioregistry:ncro skos:exactMatch bioportal:NCRO sssom:HumanCurated bioregistry:ncro skos:exactMatch fairsharing:FAIRsharing.vppyga sssom:HumanCurated -bioregistry:ncro skos:exactMatch obofoundry:NCRO sssom:HumanCurated +bioregistry:ncro skos:exactMatch obofoundry:ncro sssom:HumanCurated bioregistry:ncro skos:exactMatch ols:ncro sssom:HumanCurated bioregistry:ncro skos:exactMatch ontobee:NCRO sssom:HumanCurated bioregistry:ndc skos:exactMatch biocontext:NDC sssom:HumanCurated @@ -3449,11 +3445,11 @@ bioregistry:niaest skos:exactMatch prefixcommons:niaest sssom:HumanCurated bioregistry:nif.cell skos:exactMatch aberowl:NIFCELL sssom:HumanCurated bioregistry:nif.cell skos:exactMatch biocontext:NIF_CELL sssom:HumanCurated bioregistry:nif.cell skos:exactMatch bioportal:NIFCELL sssom:HumanCurated -bioregistry:nif.cell skos:exactMatch obofoundry:NIF_CELL sssom:HumanCurated +bioregistry:nif.cell skos:exactMatch obofoundry:nif_cell sssom:HumanCurated bioregistry:nif.dysfunction skos:exactMatch biocontext:NIF_DYSFUNCTION sssom:HumanCurated -bioregistry:nif.dysfunction skos:exactMatch obofoundry:NIF_DYSFUNCTION sssom:HumanCurated +bioregistry:nif.dysfunction skos:exactMatch obofoundry:nif_dysfunction sssom:HumanCurated bioregistry:nif.grossanatomy skos:exactMatch biocontext:NIF_GROSSANATOMY sssom:HumanCurated -bioregistry:nif.grossanatomy skos:exactMatch obofoundry:NIF_GROSSANATOMY sssom:HumanCurated +bioregistry:nif.grossanatomy skos:exactMatch obofoundry:nif_grossanatomy sssom:HumanCurated bioregistry:nif.std skos:exactMatch aberowl:NIFSTD sssom:HumanCurated bioregistry:nif.std skos:exactMatch bioportal:NIFSTD sssom:HumanCurated bioregistry:nif.std skos:exactMatch fairsharing:FAIRsharing.vgw1m6 sssom:HumanCurated @@ -3465,7 +3461,7 @@ bioregistry:nmr skos:exactMatch biocontext:NMR sssom:HumanCurated bioregistry:nmr skos:exactMatch bioportal:NMR sssom:HumanCurated bioregistry:nmr skos:exactMatch miriam:nmr sssom:HumanCurated bioregistry:nmr skos:exactMatch n2t:nmr sssom:HumanCurated -bioregistry:nmr skos:exactMatch obofoundry:NMR sssom:HumanCurated +bioregistry:nmr skos:exactMatch obofoundry:nmr sssom:HumanCurated bioregistry:nmr skos:exactMatch ols:nmrcv sssom:HumanCurated bioregistry:nmr skos:exactMatch prefixcommons:nmr sssom:HumanCurated bioregistry:nmrshiftdb2 skos:exactMatch fairsharing:FAIRsharing.nYaZ1N sssom:HumanCurated @@ -3473,7 +3469,7 @@ bioregistry:nmrshiftdb2 skos:exactMatch miriam:nmrshiftdb2 sssom:HumanCurated bioregistry:noaa skos:exactMatch wikidata:P6049 sssom:HumanCurated bioregistry:nomen skos:exactMatch aberowl:NOMEN sssom:HumanCurated bioregistry:nomen skos:exactMatch bioportal:NOMEN sssom:HumanCurated -bioregistry:nomen skos:exactMatch obofoundry:NOMEN sssom:HumanCurated +bioregistry:nomen skos:exactMatch obofoundry:nomen sssom:HumanCurated bioregistry:nomen skos:exactMatch ols:nomen sssom:HumanCurated bioregistry:nomen skos:exactMatch ontobee:NOMEN sssom:HumanCurated bioregistry:noncodev3 skos:exactMatch biocontext:NONCODEV3 sssom:HumanCurated @@ -3505,21 +3501,21 @@ bioregistry:oae skos:exactMatch aberowl:OAE sssom:HumanCurated bioregistry:oae skos:exactMatch biocontext:OAE sssom:HumanCurated bioregistry:oae skos:exactMatch bioportal:OAE sssom:HumanCurated bioregistry:oae skos:exactMatch fairsharing:FAIRsharing.tw4q8x sssom:HumanCurated -bioregistry:oae skos:exactMatch obofoundry:OAE sssom:HumanCurated +bioregistry:oae skos:exactMatch obofoundry:oae sssom:HumanCurated bioregistry:oae skos:exactMatch ols:oae sssom:HumanCurated bioregistry:oae skos:exactMatch ontobee:OAE sssom:HumanCurated bioregistry:oarcs skos:exactMatch aberowl:OARCS sssom:HumanCurated bioregistry:oarcs skos:exactMatch biocontext:OARCS sssom:HumanCurated bioregistry:oarcs skos:exactMatch bioportal:OARCS sssom:HumanCurated bioregistry:oarcs skos:exactMatch fairsharing:FAIRsharing.yqn857 sssom:HumanCurated -bioregistry:oarcs skos:exactMatch obofoundry:OARCS sssom:HumanCurated +bioregistry:oarcs skos:exactMatch obofoundry:oarcs sssom:HumanCurated bioregistry:oarcs skos:exactMatch ols:oarcs sssom:HumanCurated bioregistry:oarcs skos:exactMatch ontobee:OARCS sssom:HumanCurated bioregistry:oba skos:exactMatch aberowl:OBA sssom:HumanCurated bioregistry:oba skos:exactMatch biocontext:OBA sssom:HumanCurated bioregistry:oba skos:exactMatch bioportal:OBA sssom:HumanCurated bioregistry:oba skos:exactMatch fairsharing:FAIRsharing.mp0rwf sssom:HumanCurated -bioregistry:oba skos:exactMatch obofoundry:OBA sssom:HumanCurated +bioregistry:oba skos:exactMatch obofoundry:oba sssom:HumanCurated bioregistry:oba skos:exactMatch ols:oba sssom:HumanCurated bioregistry:oba skos:exactMatch ontobee:OBA sssom:HumanCurated bioregistry:oba bioregistry.schema:0000018 bioregistry:fovt sssom:HumanCurated @@ -3527,7 +3523,7 @@ bioregistry:obcs skos:exactMatch aberowl:OBCS sssom:HumanCurated bioregistry:obcs skos:exactMatch biocontext:OBCS sssom:HumanCurated bioregistry:obcs skos:exactMatch bioportal:OBCS sssom:HumanCurated bioregistry:obcs skos:exactMatch fairsharing:FAIRsharing.5p12xh sssom:HumanCurated -bioregistry:obcs skos:exactMatch obofoundry:OBCS sssom:HumanCurated +bioregistry:obcs skos:exactMatch obofoundry:obcs sssom:HumanCurated bioregistry:obcs skos:exactMatch ols:obcs sssom:HumanCurated bioregistry:obcs skos:exactMatch ontobee:OBCS sssom:HumanCurated bioregistry:obi skos:exactMatch aberowl:OBI sssom:HumanCurated @@ -3536,7 +3532,7 @@ bioregistry:obi skos:exactMatch bioportal:OBI sssom:HumanCurated bioregistry:obi skos:exactMatch fairsharing:FAIRsharing.284e1z sssom:HumanCurated bioregistry:obi skos:exactMatch miriam:obi sssom:HumanCurated bioregistry:obi skos:exactMatch n2t:obi sssom:HumanCurated -bioregistry:obi skos:exactMatch obofoundry:OBI sssom:HumanCurated +bioregistry:obi skos:exactMatch obofoundry:obi sssom:HumanCurated bioregistry:obi skos:exactMatch ols:obi sssom:HumanCurated bioregistry:obi skos:exactMatch ontobee:OBI sssom:HumanCurated bioregistry:obi skos:exactMatch prefixcommons:obi sssom:HumanCurated @@ -3554,7 +3550,7 @@ bioregistry:obib skos:exactMatch aberowl:OBIB sssom:HumanCurated bioregistry:obib skos:exactMatch biocontext:OBIB sssom:HumanCurated bioregistry:obib skos:exactMatch bioportal:OBIB sssom:HumanCurated bioregistry:obib skos:exactMatch fairsharing:FAIRsharing.bxc508 sssom:HumanCurated -bioregistry:obib skos:exactMatch obofoundry:OBIB sssom:HumanCurated +bioregistry:obib skos:exactMatch obofoundry:obib sssom:HumanCurated bioregistry:obib skos:exactMatch ols:obib sssom:HumanCurated bioregistry:obib skos:exactMatch ontobee:OBIB sssom:HumanCurated bioregistry:obo skos:exactMatch biocontext:OBO sssom:HumanCurated @@ -3581,20 +3577,20 @@ bioregistry:ogg skos:exactMatch aberowl:OGG sssom:HumanCurated bioregistry:ogg skos:exactMatch biocontext:OGG sssom:HumanCurated bioregistry:ogg skos:exactMatch bioportal:OGG sssom:HumanCurated bioregistry:ogg skos:exactMatch fairsharing:FAIRsharing.zmx7nn sssom:HumanCurated -bioregistry:ogg skos:exactMatch obofoundry:OGG sssom:HumanCurated +bioregistry:ogg skos:exactMatch obofoundry:ogg sssom:HumanCurated bioregistry:ogg skos:exactMatch ols:ogg sssom:HumanCurated bioregistry:ogg skos:exactMatch ontobee:OGG sssom:HumanCurated bioregistry:ogi skos:exactMatch aberowl:OGI sssom:HumanCurated bioregistry:ogi skos:exactMatch biocontext:OGI sssom:HumanCurated bioregistry:ogi skos:exactMatch bioportal:OGI sssom:HumanCurated -bioregistry:ogi skos:exactMatch obofoundry:OGI sssom:HumanCurated +bioregistry:ogi skos:exactMatch obofoundry:ogi sssom:HumanCurated bioregistry:ogi skos:exactMatch ols:ogi sssom:HumanCurated bioregistry:ogi skos:exactMatch ontobee:OGI sssom:HumanCurated bioregistry:ogms skos:exactMatch aberowl:OGMS sssom:HumanCurated bioregistry:ogms skos:exactMatch biocontext:OGMS sssom:HumanCurated bioregistry:ogms skos:exactMatch bioportal:OGMS sssom:HumanCurated bioregistry:ogms skos:exactMatch fairsharing:FAIRsharing.rvz0m9 sssom:HumanCurated -bioregistry:ogms skos:exactMatch obofoundry:OGMS sssom:HumanCurated +bioregistry:ogms skos:exactMatch obofoundry:ogms sssom:HumanCurated bioregistry:ogms skos:exactMatch ols:ogms sssom:HumanCurated bioregistry:ogms skos:exactMatch ontobee:OGMS sssom:HumanCurated bioregistry:ogms bioregistry.schema:0000018 bioregistry:labo sssom:HumanCurated @@ -3603,27 +3599,27 @@ bioregistry:ogsf skos:exactMatch aberowl:OGSF sssom:HumanCurated bioregistry:ogsf skos:exactMatch biocontext:OGSF sssom:HumanCurated bioregistry:ogsf skos:exactMatch bioportal:OGSF sssom:HumanCurated bioregistry:ogsf skos:exactMatch fairsharing:FAIRsharing.egv2cz sssom:HumanCurated -bioregistry:ogsf skos:exactMatch obofoundry:OGSF sssom:HumanCurated +bioregistry:ogsf skos:exactMatch obofoundry:ogsf sssom:HumanCurated bioregistry:ogsf skos:exactMatch ols:ogsf sssom:HumanCurated bioregistry:ogsf skos:exactMatch ontobee:OGSF sssom:HumanCurated bioregistry:ohd skos:exactMatch aberowl:OHD sssom:HumanCurated bioregistry:ohd skos:exactMatch biocontext:OHD sssom:HumanCurated bioregistry:ohd skos:exactMatch bioportal:OHD sssom:HumanCurated bioregistry:ohd skos:exactMatch fairsharing:FAIRsharing.bg7bb6 sssom:HumanCurated -bioregistry:ohd skos:exactMatch obofoundry:OHD sssom:HumanCurated +bioregistry:ohd skos:exactMatch obofoundry:ohd sssom:HumanCurated bioregistry:ohd skos:exactMatch ols:ohd sssom:HumanCurated bioregistry:ohd skos:exactMatch ontobee:OHD sssom:HumanCurated bioregistry:ohmi skos:exactMatch aberowl:OHMI sssom:HumanCurated bioregistry:ohmi skos:exactMatch biocontext:OHMI sssom:HumanCurated bioregistry:ohmi skos:exactMatch bioportal:OHMI sssom:HumanCurated bioregistry:ohmi skos:exactMatch fairsharing:FAIRsharing.cz9cnp sssom:HumanCurated -bioregistry:ohmi skos:exactMatch obofoundry:OHMI sssom:HumanCurated +bioregistry:ohmi skos:exactMatch obofoundry:ohmi sssom:HumanCurated bioregistry:ohmi skos:exactMatch ols:ohmi sssom:HumanCurated bioregistry:ohmi skos:exactMatch ontobee:OHMI sssom:HumanCurated bioregistry:ohpi skos:exactMatch aberowl:OHPI sssom:HumanCurated bioregistry:ohpi skos:exactMatch bioportal:OHPI sssom:HumanCurated bioregistry:ohpi skos:exactMatch fairsharing:FAIRsharing.vxpUJ6 sssom:HumanCurated -bioregistry:ohpi skos:exactMatch obofoundry:OHPI sssom:HumanCurated +bioregistry:ohpi skos:exactMatch obofoundry:ohpi sssom:HumanCurated bioregistry:ohpi skos:exactMatch ols:ohpi sssom:HumanCurated bioregistry:ohpi skos:exactMatch ontobee:OHPI sssom:HumanCurated bioregistry:oid skos:exactMatch miriam:oid sssom:HumanCurated @@ -3632,7 +3628,7 @@ bioregistry:olatdv skos:exactMatch aberowl:OLATDV sssom:HumanCurated bioregistry:olatdv skos:exactMatch biocontext:OLATDV sssom:HumanCurated bioregistry:olatdv skos:exactMatch bioportal:OLATDV sssom:HumanCurated bioregistry:olatdv skos:exactMatch fairsharing:FAIRsharing.c86z66 sssom:HumanCurated -bioregistry:olatdv skos:exactMatch obofoundry:OlatDv sssom:HumanCurated +bioregistry:olatdv skos:exactMatch obofoundry:olatdv sssom:HumanCurated bioregistry:olatdv skos:exactMatch ols:olatdv sssom:HumanCurated bioregistry:olatdv skos:exactMatch ontobee:OLATDV sssom:HumanCurated bioregistry:om skos:exactMatch aberowl:OM sssom:HumanCurated @@ -3653,7 +3649,7 @@ bioregistry:omia skos:exactMatch prefixcommons:omia sssom:HumanCurated bioregistry:omiabis skos:exactMatch aberowl:OMIABIS sssom:HumanCurated bioregistry:omiabis skos:exactMatch biocontext:OMIABIS sssom:HumanCurated bioregistry:omiabis skos:exactMatch bioportal:OMIABIS sssom:HumanCurated -bioregistry:omiabis skos:exactMatch obofoundry:OMIABIS sssom:HumanCurated +bioregistry:omiabis skos:exactMatch obofoundry:omiabis sssom:HumanCurated bioregistry:omiabis skos:exactMatch ols:omiabis sssom:HumanCurated bioregistry:omiabis skos:exactMatch ontobee:OMIABIS sssom:HumanCurated bioregistry:omiabis bioregistry.schema:0000018 bioregistry:labo sssom:HumanCurated @@ -3673,13 +3669,13 @@ bioregistry:omit skos:exactMatch bioportal:OMIT sssom:HumanCurated bioregistry:omit skos:exactMatch fairsharing:FAIRsharing.mf91p5 sssom:HumanCurated bioregistry:omit skos:exactMatch miriam:omit sssom:HumanCurated bioregistry:omit skos:exactMatch n2t:omit sssom:HumanCurated -bioregistry:omit skos:exactMatch obofoundry:OMIT sssom:HumanCurated +bioregistry:omit skos:exactMatch obofoundry:omit sssom:HumanCurated bioregistry:omit skos:exactMatch ols:omit sssom:HumanCurated bioregistry:omit skos:exactMatch ontobee:OMIT sssom:HumanCurated bioregistry:omit bioregistry.schema:0000018 bioregistry:mco sssom:HumanCurated bioregistry:omo skos:exactMatch aberowl:OMO sssom:HumanCurated bioregistry:omo skos:exactMatch bioportal:OMO sssom:HumanCurated -bioregistry:omo skos:exactMatch obofoundry:OMO sssom:HumanCurated +bioregistry:omo skos:exactMatch obofoundry:omo sssom:HumanCurated bioregistry:omo skos:exactMatch ols:omo sssom:HumanCurated bioregistry:omo skos:exactMatch ontobee:OMO sssom:HumanCurated bioregistry:omo bioregistry.schema:0000018 bioregistry:pcl sssom:HumanCurated @@ -3687,7 +3683,7 @@ bioregistry:omp skos:exactMatch aberowl:OMP sssom:HumanCurated bioregistry:omp skos:exactMatch biocontext:OMP sssom:HumanCurated bioregistry:omp skos:exactMatch bioportal:OMP sssom:HumanCurated bioregistry:omp skos:exactMatch fairsharing:FAIRsharing.cc3f2x sssom:HumanCurated -bioregistry:omp skos:exactMatch obofoundry:OMP sssom:HumanCurated +bioregistry:omp skos:exactMatch obofoundry:omp sssom:HumanCurated bioregistry:omp skos:exactMatch ols:omp sssom:HumanCurated bioregistry:omp skos:exactMatch ontobee:OMP sssom:HumanCurated bioregistry:omp bioregistry.schema:0000018 bioregistry:mco sssom:HumanCurated @@ -3695,7 +3691,7 @@ bioregistry:omrse skos:exactMatch aberowl:OMRSE sssom:HumanCurated bioregistry:omrse skos:exactMatch biocontext:OMRSE sssom:HumanCurated bioregistry:omrse skos:exactMatch bioportal:OMRSE sssom:HumanCurated bioregistry:omrse skos:exactMatch fairsharing:FAIRsharing.z0p37e sssom:HumanCurated -bioregistry:omrse skos:exactMatch obofoundry:OMRSE sssom:HumanCurated +bioregistry:omrse skos:exactMatch obofoundry:omrse sssom:HumanCurated bioregistry:omrse skos:exactMatch ols:omrse sssom:HumanCurated bioregistry:omrse skos:exactMatch ontobee:OMRSE sssom:HumanCurated bioregistry:omrse bioregistry.schema:0000018 bioregistry:labo sssom:HumanCurated @@ -3703,7 +3699,7 @@ bioregistry:oncotree bioregistry.schema:0000018 bioregistry:efo sssom:HumanCurat bioregistry:one skos:exactMatch aberowl:ONE sssom:HumanCurated bioregistry:one skos:exactMatch bioportal:ONE sssom:HumanCurated bioregistry:one skos:exactMatch fairsharing:FAIRsharing.USxx0K sssom:HumanCurated -bioregistry:one skos:exactMatch obofoundry:ONE sssom:HumanCurated +bioregistry:one skos:exactMatch obofoundry:one sssom:HumanCurated bioregistry:one skos:exactMatch ols:one sssom:HumanCurated bioregistry:one skos:exactMatch ontobee:ONE sssom:HumanCurated bioregistry:one bioregistry.schema:0000017 bioregistry:foodon sssom:HumanCurated @@ -3712,7 +3708,7 @@ bioregistry:one bioregistry.schema:0000017 bioregistry:ons sssom:HumanCurated bioregistry:ons skos:exactMatch aberowl:ONS sssom:HumanCurated bioregistry:ons skos:exactMatch bioportal:ONS sssom:HumanCurated bioregistry:ons skos:exactMatch fairsharing:FAIRsharing.rfec93 sssom:HumanCurated -bioregistry:ons skos:exactMatch obofoundry:ONS sssom:HumanCurated +bioregistry:ons skos:exactMatch obofoundry:ons sssom:HumanCurated bioregistry:ons skos:exactMatch ols:ons sssom:HumanCurated bioregistry:ons skos:exactMatch ontobee:ONS sssom:HumanCurated bioregistry:ons bioregistry.schema:0000018 bioregistry:one sssom:HumanCurated @@ -3726,7 +3722,7 @@ bioregistry:ons bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated bioregistry:ons bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:ontoavida skos:exactMatch aberowl:ONTOAVIDA sssom:HumanCurated bioregistry:ontoavida skos:exactMatch bioportal:ONTOAVIDA sssom:HumanCurated -bioregistry:ontoavida skos:exactMatch obofoundry:ONTOAVIDA sssom:HumanCurated +bioregistry:ontoavida skos:exactMatch obofoundry:ontoavida sssom:HumanCurated bioregistry:ontoavida skos:exactMatch ols:ontoavida sssom:HumanCurated bioregistry:ontoavida skos:exactMatch ontobee:ONTOAVIDA sssom:HumanCurated bioregistry:ontoavida bioregistry.schema:0000017 bioregistry:fbcv sssom:HumanCurated @@ -3738,14 +3734,14 @@ bioregistry:ontoneo skos:exactMatch aberowl:ONTONEO sssom:HumanCurated bioregistry:ontoneo skos:exactMatch biocontext:ONTONEO sssom:HumanCurated bioregistry:ontoneo skos:exactMatch bioportal:ONTONEO sssom:HumanCurated bioregistry:ontoneo skos:exactMatch fairsharing:FAIRsharing.5a4y1y sssom:HumanCurated -bioregistry:ontoneo skos:exactMatch obofoundry:ONTONEO sssom:HumanCurated +bioregistry:ontoneo skos:exactMatch obofoundry:ontoneo sssom:HumanCurated bioregistry:ontoneo skos:exactMatch ols:ontoneo sssom:HumanCurated bioregistry:ontoneo skos:exactMatch ontobee:ONTONEO sssom:HumanCurated bioregistry:oostt skos:exactMatch aberowl:OOSTT sssom:HumanCurated bioregistry:oostt skos:exactMatch biocontext:OOSTT sssom:HumanCurated bioregistry:oostt skos:exactMatch bioportal:OOSTT sssom:HumanCurated bioregistry:oostt skos:exactMatch fairsharing:FAIRsharing.b4sa0w sssom:HumanCurated -bioregistry:oostt skos:exactMatch obofoundry:OOSTT sssom:HumanCurated +bioregistry:oostt skos:exactMatch obofoundry:oostt sssom:HumanCurated bioregistry:oostt skos:exactMatch ols:oostt sssom:HumanCurated bioregistry:oostt skos:exactMatch ontobee:OOSTT sssom:HumanCurated bioregistry:opb skos:exactMatch aberowl:OPB sssom:HumanCurated @@ -3759,7 +3755,7 @@ bioregistry:opl skos:exactMatch aberowl:OPL sssom:HumanCurated bioregistry:opl skos:exactMatch biocontext:OPL sssom:HumanCurated bioregistry:opl skos:exactMatch bioportal:OPL sssom:HumanCurated bioregistry:opl skos:exactMatch fairsharing:FAIRsharing.ez2nhb sssom:HumanCurated -bioregistry:opl skos:exactMatch obofoundry:OPL sssom:HumanCurated +bioregistry:opl skos:exactMatch obofoundry:opl sssom:HumanCurated bioregistry:opl skos:exactMatch ols:opl sssom:HumanCurated bioregistry:opl skos:exactMatch ontobee:OPL sssom:HumanCurated bioregistry:opm skos:exactMatch biocontext:OPM sssom:HumanCurated @@ -3768,7 +3764,7 @@ bioregistry:opm skos:exactMatch miriam:opm sssom:HumanCurated bioregistry:opm skos:exactMatch n2t:opm sssom:HumanCurated bioregistry:opmi skos:exactMatch aberowl:OPMI sssom:HumanCurated bioregistry:opmi skos:exactMatch bioportal:OPMI sssom:HumanCurated -bioregistry:opmi skos:exactMatch obofoundry:OPMI sssom:HumanCurated +bioregistry:opmi skos:exactMatch obofoundry:opmi sssom:HumanCurated bioregistry:opmi skos:exactMatch ols:opmi sssom:HumanCurated bioregistry:opmi skos:exactMatch ontobee:OPMI sssom:HumanCurated bioregistry:opmi bioregistry.schema:0000018 bioregistry:labo sssom:HumanCurated @@ -3791,7 +3787,7 @@ bioregistry:oridb.schizo skos:exactMatch miriam:oridb.schizo sssom:HumanCurated bioregistry:oridb.schizo skos:exactMatch n2t:oridb.schizo sssom:HumanCurated bioregistry:ornaseq skos:exactMatch aberowl:ORNASEQ sssom:HumanCurated bioregistry:ornaseq skos:exactMatch bioportal:ORNASEQ sssom:HumanCurated -bioregistry:ornaseq skos:exactMatch obofoundry:ORNASEQ sssom:HumanCurated +bioregistry:ornaseq skos:exactMatch obofoundry:ornaseq sssom:HumanCurated bioregistry:ornaseq skos:exactMatch ols:ornaseq sssom:HumanCurated bioregistry:ornaseq skos:exactMatch ontobee:ORNASEQ sssom:HumanCurated bioregistry:orphanet skos:exactMatch biocontext:Orphanet sssom:HumanCurated @@ -3842,7 +3838,7 @@ bioregistry:ovae skos:exactMatch aberowl:OVAE sssom:HumanCurated bioregistry:ovae skos:exactMatch biocontext:OVAE sssom:HumanCurated bioregistry:ovae skos:exactMatch bioportal:OVAE sssom:HumanCurated bioregistry:ovae skos:exactMatch fairsharing:FAIRsharing.w4x6n4 sssom:HumanCurated -bioregistry:ovae skos:exactMatch obofoundry:OVAE sssom:HumanCurated +bioregistry:ovae skos:exactMatch obofoundry:ovae sssom:HumanCurated bioregistry:ovae skos:exactMatch ols:ovae sssom:HumanCurated bioregistry:ovae skos:exactMatch ontobee:OVAE sssom:HumanCurated bioregistry:owl skos:exactMatch biocontext:owl sssom:HumanCurated @@ -3872,7 +3868,7 @@ bioregistry:panther.pthcmp skos:exactMatch biocontext:PANTHER.PTHCMP sssom:Human bioregistry:panther.pthcmp skos:exactMatch miriam:panther.pthcmp sssom:HumanCurated bioregistry:panther.pthcmp skos:exactMatch n2t:panther.pthcmp sssom:HumanCurated bioregistry:pao skos:exactMatch biocontext:PAO sssom:HumanCurated -bioregistry:pao skos:exactMatch obofoundry:PAO sssom:HumanCurated +bioregistry:pao skos:exactMatch obofoundry:pao sssom:HumanCurated bioregistry:pass2 skos:exactMatch biocontext:PASS2 sssom:HumanCurated bioregistry:pass2 skos:exactMatch miriam:pass2 sssom:HumanCurated bioregistry:pass2 skos:exactMatch n2t:pass2 sssom:HumanCurated @@ -3889,7 +3885,7 @@ bioregistry:pato skos:exactMatch bioportal:PATO sssom:HumanCurated bioregistry:pato skos:exactMatch fairsharing:FAIRsharing.ezwdhz sssom:HumanCurated bioregistry:pato skos:exactMatch miriam:pato sssom:HumanCurated bioregistry:pato skos:exactMatch n2t:pato sssom:HumanCurated -bioregistry:pato skos:exactMatch obofoundry:PATO sssom:HumanCurated +bioregistry:pato skos:exactMatch obofoundry:pato sssom:HumanCurated bioregistry:pato skos:exactMatch ols:pato sssom:HumanCurated bioregistry:pato skos:exactMatch ontobee:PATO sssom:HumanCurated bioregistry:pato skos:exactMatch prefixcommons:pato sssom:HumanCurated @@ -3930,7 +3926,7 @@ bioregistry:pazar skos:exactMatch n2t:pazar sssom:HumanCurated bioregistry:pazar skos:exactMatch prefixcommons:pazar sssom:HumanCurated bioregistry:pcl skos:exactMatch aberowl:PCL sssom:HumanCurated bioregistry:pcl skos:exactMatch bioportal:PCL sssom:HumanCurated -bioregistry:pcl skos:exactMatch obofoundry:PCL sssom:HumanCurated +bioregistry:pcl skos:exactMatch obofoundry:pcl sssom:HumanCurated bioregistry:pcl skos:exactMatch ols:pcl sssom:HumanCurated bioregistry:pcl skos:exactMatch ontobee:PCL sssom:HumanCurated bioregistry:pcl bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -3951,7 +3947,7 @@ bioregistry:pco skos:exactMatch biocontext:PCO sssom:HumanCurated bioregistry:pco skos:exactMatch bioportal:PCO sssom:HumanCurated bioregistry:pco skos:exactMatch ecoportal:PCO sssom:HumanCurated bioregistry:pco skos:exactMatch fairsharing:FAIRsharing.vq28qp sssom:HumanCurated -bioregistry:pco skos:exactMatch obofoundry:PCO sssom:HumanCurated +bioregistry:pco skos:exactMatch obofoundry:pco sssom:HumanCurated bioregistry:pco skos:exactMatch ols:pco sssom:HumanCurated bioregistry:pco skos:exactMatch ontobee:PCO sssom:HumanCurated bioregistry:pco bioregistry.schema:0000018 bioregistry:ecocore sssom:HumanCurated @@ -3965,7 +3961,7 @@ bioregistry:pco bioregistry.schema:0000017 bioregistry:ncbitaxon sssom:HumanCura bioregistry:pco bioregistry.schema:0000017 bioregistry:pato sssom:HumanCurated bioregistry:pco bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated bioregistry:pd_st skos:exactMatch biocontext:PD_ST sssom:HumanCurated -bioregistry:pd_st skos:exactMatch obofoundry:PD_ST sssom:HumanCurated +bioregistry:pd_st skos:exactMatch obofoundry:pd_st sssom:HumanCurated bioregistry:pdb skos:exactMatch biocontext:PDB sssom:HumanCurated bioregistry:pdb skos:exactMatch fairsharing:FAIRsharing.mckkb4 sssom:HumanCurated bioregistry:pdb skos:exactMatch miriam:pdb sssom:HumanCurated @@ -3985,14 +3981,14 @@ bioregistry:pdro skos:exactMatch aberowl:PDRO sssom:HumanCurated bioregistry:pdro skos:exactMatch biocontext:PDRO sssom:HumanCurated bioregistry:pdro skos:exactMatch bioportal:PDRO sssom:HumanCurated bioregistry:pdro skos:exactMatch fairsharing:FAIRsharing.9te3ev sssom:HumanCurated -bioregistry:pdro skos:exactMatch obofoundry:PDRO sssom:HumanCurated +bioregistry:pdro skos:exactMatch obofoundry:pdro sssom:HumanCurated bioregistry:pdro skos:exactMatch ols:pdro sssom:HumanCurated bioregistry:pdro skos:exactMatch ontobee:PDRO sssom:HumanCurated bioregistry:pdumdv skos:exactMatch aberowl:PDUMDV sssom:HumanCurated bioregistry:pdumdv skos:exactMatch biocontext:PDUMDV sssom:HumanCurated bioregistry:pdumdv skos:exactMatch bioportal:PDUMDV sssom:HumanCurated bioregistry:pdumdv skos:exactMatch fairsharing:FAIRsharing.493qns sssom:HumanCurated -bioregistry:pdumdv skos:exactMatch obofoundry:PdumDv sssom:HumanCurated +bioregistry:pdumdv skos:exactMatch obofoundry:pdumdv sssom:HumanCurated bioregistry:pdumdv skos:exactMatch ols:pdumdv sssom:HumanCurated bioregistry:pdumdv skos:exactMatch ontobee:PDUMDV sssom:HumanCurated bioregistry:peco skos:exactMatch aberowl:PECO sssom:HumanCurated @@ -4000,7 +3996,7 @@ bioregistry:peco skos:exactMatch agroportal:PECO sssom:HumanCurated bioregistry:peco skos:exactMatch biocontext:PECO sssom:HumanCurated bioregistry:peco skos:exactMatch bioportal:PECO sssom:HumanCurated bioregistry:peco skos:exactMatch fairsharing:FAIRsharing.6yNXYK sssom:HumanCurated -bioregistry:peco skos:exactMatch obofoundry:PECO sssom:HumanCurated +bioregistry:peco skos:exactMatch obofoundry:peco sssom:HumanCurated bioregistry:peco skos:exactMatch ols:peco sssom:HumanCurated bioregistry:peco skos:exactMatch ontobee:PECO sssom:HumanCurated bioregistry:peco bioregistry.schema:0000018 bioregistry:agro sssom:HumanCurated @@ -4029,7 +4025,7 @@ bioregistry:pfam skos:exactMatch prefixcommons:pfam sssom:HumanCurated bioregistry:pfam skos:exactMatch wikidata:P3519 sssom:HumanCurated bioregistry:pfr skos:exactMatch fairsharing:FAIRsharing.wqsxtg sssom:HumanCurated bioregistry:pgdso skos:exactMatch biocontext:PGDSO sssom:HumanCurated -bioregistry:pgdso skos:exactMatch obofoundry:PGDSO sssom:HumanCurated +bioregistry:pgdso skos:exactMatch obofoundry:pgdso sssom:HumanCurated bioregistry:pgs skos:exactMatch miriam:pgs sssom:HumanCurated bioregistry:pgx skos:exactMatch biocontext:PGX sssom:HumanCurated bioregistry:pgx skos:exactMatch fairsharing:FAIRsharing.65tdnz sssom:HumanCurated @@ -4064,7 +4060,7 @@ bioregistry:phenx skos:exactMatch bioportal:PHENX sssom:HumanCurated bioregistry:phenx skos:exactMatch fairsharing:FAIRsharing.y5jcwa sssom:HumanCurated bioregistry:phipo skos:exactMatch aberowl:PHIPO sssom:HumanCurated bioregistry:phipo skos:exactMatch bioportal:PHIPO sssom:HumanCurated -bioregistry:phipo skos:exactMatch obofoundry:PHIPO sssom:HumanCurated +bioregistry:phipo skos:exactMatch obofoundry:phipo sssom:HumanCurated bioregistry:phipo skos:exactMatch ols:phipo sssom:HumanCurated bioregistry:phipo skos:exactMatch ontobee:PHIPO sssom:HumanCurated bioregistry:phipo bioregistry.schema:0000017 bioregistry:pato sssom:HumanCurated @@ -4117,7 +4113,7 @@ bioregistry:plana skos:exactMatch aberowl:PLANA sssom:HumanCurated bioregistry:plana skos:exactMatch biocontext:PLANA sssom:HumanCurated bioregistry:plana skos:exactMatch bioportal:PLANA sssom:HumanCurated bioregistry:plana skos:exactMatch fairsharing:FAIRsharing.g1qrqs sssom:HumanCurated -bioregistry:plana skos:exactMatch obofoundry:PLANA sssom:HumanCurated +bioregistry:plana skos:exactMatch obofoundry:plana sssom:HumanCurated bioregistry:plana skos:exactMatch ols:plana sssom:HumanCurated bioregistry:plana skos:exactMatch ontobee:PLANA sssom:HumanCurated bioregistry:plana bioregistry.schema:0000018 bioregistry:planp sssom:HumanCurated @@ -4125,7 +4121,7 @@ bioregistry:plana bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated bioregistry:plana bioregistry.schema:0000017 bioregistry:uberon sssom:HumanCurated bioregistry:planp skos:exactMatch aberowl:PLANP sssom:HumanCurated bioregistry:planp skos:exactMatch bioportal:PLANP sssom:HumanCurated -bioregistry:planp skos:exactMatch obofoundry:PLANP sssom:HumanCurated +bioregistry:planp skos:exactMatch obofoundry:planp sssom:HumanCurated bioregistry:planp skos:exactMatch ols:planp sssom:HumanCurated bioregistry:planp skos:exactMatch ontobee:PLANP sssom:HumanCurated bioregistry:planp bioregistry.schema:0000017 bioregistry:go sssom:HumanCurated @@ -4143,7 +4139,7 @@ bioregistry:plasmodb skos:exactMatch miriam:plasmodb sssom:HumanCurated bioregistry:plasmodb skos:exactMatch n2t:plasmodb sssom:HumanCurated bioregistry:plasmodb skos:exactMatch prefixcommons:plasmodb sssom:HumanCurated bioregistry:plo skos:exactMatch biocontext:PLO sssom:HumanCurated -bioregistry:plo skos:exactMatch obofoundry:PLO sssom:HumanCurated +bioregistry:plo skos:exactMatch obofoundry:plo sssom:HumanCurated bioregistry:pmap.cutdb skos:exactMatch biocontext:PMAP.CUTDB sssom:HumanCurated bioregistry:pmap.cutdb skos:exactMatch miriam:pmap.cutdb sssom:HumanCurated bioregistry:pmap.cutdb skos:exactMatch n2t:pmap.cutdb sssom:HumanCurated @@ -4179,7 +4175,7 @@ bioregistry:po skos:exactMatch bioportal:PO sssom:HumanCurated bioregistry:po skos:exactMatch fairsharing:FAIRsharing.3ngg40 sssom:HumanCurated bioregistry:po skos:exactMatch miriam:po sssom:HumanCurated bioregistry:po skos:exactMatch n2t:po sssom:HumanCurated -bioregistry:po skos:exactMatch obofoundry:PO sssom:HumanCurated +bioregistry:po skos:exactMatch obofoundry:po sssom:HumanCurated bioregistry:po skos:exactMatch ols:po sssom:HumanCurated bioregistry:po skos:exactMatch ontobee:PO sssom:HumanCurated bioregistry:po skos:exactMatch prefixcommons:po sssom:HumanCurated @@ -4206,7 +4202,7 @@ bioregistry:poro skos:exactMatch aberowl:PORO sssom:HumanCurated bioregistry:poro skos:exactMatch biocontext:PORO sssom:HumanCurated bioregistry:poro skos:exactMatch bioportal:PORO sssom:HumanCurated bioregistry:poro skos:exactMatch fairsharing:FAIRsharing.93g1th sssom:HumanCurated -bioregistry:poro skos:exactMatch obofoundry:PORO sssom:HumanCurated +bioregistry:poro skos:exactMatch obofoundry:poro sssom:HumanCurated bioregistry:poro skos:exactMatch ols:poro sssom:HumanCurated bioregistry:poro skos:exactMatch ontobee:PORO sssom:HumanCurated bioregistry:poro bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated @@ -4217,7 +4213,7 @@ bioregistry:ppo skos:exactMatch agroportal:PPO sssom:HumanCurated bioregistry:ppo skos:exactMatch biocontext:PPO sssom:HumanCurated bioregistry:ppo skos:exactMatch bioportal:PPO sssom:HumanCurated bioregistry:ppo skos:exactMatch fairsharing:FAIRsharing.hakg7c sssom:HumanCurated -bioregistry:ppo skos:exactMatch obofoundry:PPO sssom:HumanCurated +bioregistry:ppo skos:exactMatch obofoundry:ppo sssom:HumanCurated bioregistry:ppo skos:exactMatch ols:ppo sssom:HumanCurated bioregistry:ppo skos:exactMatch ontobee:PPO sssom:HumanCurated bioregistry:pr skos:exactMatch aberowl:PR sssom:HumanCurated @@ -4227,7 +4223,7 @@ bioregistry:pr skos:exactMatch bioportal:PR sssom:HumanCurated bioregistry:pr skos:exactMatch fairsharing:FAIRsharing.4ndncv sssom:HumanCurated bioregistry:pr skos:exactMatch miriam:pr sssom:HumanCurated bioregistry:pr skos:exactMatch n2t:pr sssom:HumanCurated -bioregistry:pr skos:exactMatch obofoundry:PR sssom:HumanCurated +bioregistry:pr skos:exactMatch obofoundry:pr sssom:HumanCurated bioregistry:pr skos:exactMatch ols:pr sssom:HumanCurated bioregistry:pr skos:exactMatch ontobee:PR sssom:HumanCurated bioregistry:pr skos:exactMatch prefixcommons:pr sssom:HumanCurated @@ -4257,8 +4253,9 @@ bioregistry:probonto skos:exactMatch miriam:probonto sssom:HumanCurated bioregistry:probonto skos:exactMatch n2t:probonto sssom:HumanCurated bioregistry:probonto skos:exactMatch ols:probonto sssom:HumanCurated bioregistry:proco skos:exactMatch aberowl:PROCO sssom:HumanCurated -bioregistry:proco skos:exactMatch obofoundry:PROCO sssom:HumanCurated +bioregistry:proco skos:exactMatch obofoundry:proco sssom:HumanCurated bioregistry:proco skos:exactMatch ontobee:PROCO sssom:HumanCurated +bioregistry:proco skos:exactMatch ols:proco sssom:HumanCurated bioregistry:proco bioregistry.schema:0000017 bioregistry:chebi sssom:HumanCurated bioregistry:proco bioregistry.schema:0000017 bioregistry:cheminf sssom:HumanCurated bioregistry:proco bioregistry.schema:0000017 bioregistry:obi sssom:HumanCurated @@ -4276,7 +4273,7 @@ bioregistry:proglyc skos:exactMatch n2t:proglyc sssom:HumanCurated bioregistry:propreo skos:exactMatch aberowl:PROPREO sssom:HumanCurated bioregistry:propreo skos:exactMatch biocontext:PROPREO sssom:HumanCurated bioregistry:propreo skos:exactMatch bioportal:PROPREO sssom:HumanCurated -bioregistry:propreo skos:exactMatch obofoundry:PROPREO sssom:HumanCurated +bioregistry:propreo skos:exactMatch obofoundry:propreo sssom:HumanCurated bioregistry:propreo skos:exactMatch prefixcommons:propreo sssom:HumanCurated bioregistry:prosite skos:exactMatch biocontext:PROSITE sssom:HumanCurated bioregistry:prosite skos:exactMatch fairsharing:FAIRsharing.vwc6bd sssom:HumanCurated @@ -4313,7 +4310,7 @@ bioregistry:pscdb skos:exactMatch miriam:pscdb sssom:HumanCurated bioregistry:pscdb skos:exactMatch n2t:pscdb sssom:HumanCurated bioregistry:psdo skos:exactMatch aberowl:PSDO sssom:HumanCurated bioregistry:psdo skos:exactMatch bioportal:PSDO sssom:HumanCurated -bioregistry:psdo skos:exactMatch obofoundry:PSDO sssom:HumanCurated +bioregistry:psdo skos:exactMatch obofoundry:psdo sssom:HumanCurated bioregistry:psdo skos:exactMatch ols:psdo sssom:HumanCurated bioregistry:psdo skos:exactMatch ontobee:PSDO sssom:HumanCurated bioregistry:psdo bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -4331,7 +4328,7 @@ bioregistry:psipar skos:exactMatch n2t:psipar sssom:HumanCurated bioregistry:pso skos:exactMatch aberowl:PSO sssom:HumanCurated bioregistry:pso skos:exactMatch bioportal:PSO sssom:HumanCurated bioregistry:pso skos:exactMatch fairsharing:FAIRsharing.dyj433 sssom:HumanCurated -bioregistry:pso skos:exactMatch obofoundry:PSO sssom:HumanCurated +bioregistry:pso skos:exactMatch obofoundry:pso sssom:HumanCurated bioregistry:pso skos:exactMatch ols:pso sssom:HumanCurated bioregistry:pso skos:exactMatch ontobee:PSO sssom:HumanCurated bioregistry:pso bioregistry.schema:0000017 bioregistry:ro sssom:HumanCurated @@ -4374,7 +4371,7 @@ bioregistry:pw skos:exactMatch bioportal:PW sssom:HumanCurated bioregistry:pw skos:exactMatch fairsharing:FAIRsharing.f73xhd sssom:HumanCurated bioregistry:pw skos:exactMatch miriam:pw sssom:HumanCurated bioregistry:pw skos:exactMatch n2t:pw sssom:HumanCurated -bioregistry:pw skos:exactMatch obofoundry:PW sssom:HumanCurated +bioregistry:pw skos:exactMatch obofoundry:pw sssom:HumanCurated bioregistry:pw skos:exactMatch ols:pw sssom:HumanCurated bioregistry:pw skos:exactMatch ontobee:PW sssom:HumanCurated bioregistry:pw skos:exactMatch prefixcommons:pw sssom:HumanCurated @@ -4398,7 +4395,7 @@ bioregistry:rbk skos:exactMatch miriam:rbk sssom:HumanCurated bioregistry:rbk skos:exactMatch n2t:rbk sssom:HumanCurated bioregistry:rbo skos:exactMatch aberowl:RBO sssom:HumanCurated bioregistry:rbo skos:exactMatch bioportal:RBO sssom:HumanCurated -bioregistry:rbo skos:exactMatch obofoundry:RBO sssom:HumanCurated +bioregistry:rbo skos:exactMatch obofoundry:rbo sssom:HumanCurated bioregistry:rbo skos:exactMatch ols:rbo sssom:HumanCurated bioregistry:rbo skos:exactMatch ontobee:RBO sssom:HumanCurated bioregistry:rbo bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -4445,7 +4442,7 @@ bioregistry:reproduceme skos:exactMatch ols:reproduceme sssom:HumanCurated bioregistry:resid skos:exactMatch biocontext:RESID sssom:HumanCurated bioregistry:resid skos:exactMatch miriam:resid sssom:HumanCurated bioregistry:resid skos:exactMatch n2t:resid sssom:HumanCurated -bioregistry:resid skos:exactMatch obofoundry:RESID sssom:HumanCurated +bioregistry:resid skos:exactMatch obofoundry:resid sssom:HumanCurated bioregistry:resid skos:exactMatch prefixcommons:resid sssom:HumanCurated bioregistry:reto skos:exactMatch aberowl:RETO sssom:HumanCurated bioregistry:reto skos:exactMatch bioportal:RETO sssom:HumanCurated @@ -4455,7 +4452,7 @@ bioregistry:rex skos:exactMatch aberowl:REX sssom:HumanCurated bioregistry:rex skos:exactMatch biocontext:REX sssom:HumanCurated bioregistry:rex skos:exactMatch bioportal:REX sssom:HumanCurated bioregistry:rex skos:exactMatch fairsharing:FAIRsharing.g0a7s0 sssom:HumanCurated -bioregistry:rex skos:exactMatch obofoundry:REX sssom:HumanCurated +bioregistry:rex skos:exactMatch obofoundry:rex sssom:HumanCurated bioregistry:rex skos:exactMatch ols:rex sssom:HumanCurated bioregistry:rex skos:exactMatch ontobee:REX sssom:HumanCurated bioregistry:rex skos:exactMatch prefixcommons:rex sssom:HumanCurated @@ -4517,7 +4514,7 @@ bioregistry:rnao skos:exactMatch aberowl:RNAO sssom:HumanCurated bioregistry:rnao skos:exactMatch biocontext:RNAO sssom:HumanCurated bioregistry:rnao skos:exactMatch bioportal:RNAO sssom:HumanCurated bioregistry:rnao skos:exactMatch fairsharing:FAIRsharing.kqt2h2 sssom:HumanCurated -bioregistry:rnao skos:exactMatch obofoundry:RNAO sssom:HumanCurated +bioregistry:rnao skos:exactMatch obofoundry:rnao sssom:HumanCurated bioregistry:rnao skos:exactMatch ols:rnao sssom:HumanCurated bioregistry:rnao skos:exactMatch ontobee:RNAO sssom:HumanCurated bioregistry:rnao skos:exactMatch prefixcommons:rnao sssom:HumanCurated @@ -4529,7 +4526,7 @@ bioregistry:ro skos:exactMatch bioportal:OBOREL sssom:HumanCurated bioregistry:ro skos:exactMatch fairsharing:FAIRsharing.cp0ybc sssom:HumanCurated bioregistry:ro skos:exactMatch miriam:ro sssom:HumanCurated bioregistry:ro skos:exactMatch n2t:ro sssom:HumanCurated -bioregistry:ro skos:exactMatch obofoundry:RO sssom:HumanCurated +bioregistry:ro skos:exactMatch obofoundry:ro sssom:HumanCurated bioregistry:ro skos:exactMatch ols:ro sssom:HumanCurated bioregistry:ro skos:exactMatch ontobee:RO sssom:HumanCurated bioregistry:ro skos:exactMatch prefixcommons:ro sssom:HumanCurated @@ -4564,7 +4561,6 @@ bioregistry:ro bioregistry.schema:0000018 bioregistry:proco sssom:HumanCurated bioregistry:ro bioregistry.schema:0000018 bioregistry:psdo sssom:HumanCurated bioregistry:ro bioregistry.schema:0000018 bioregistry:pso sssom:HumanCurated bioregistry:ro bioregistry.schema:0000018 bioregistry:rbo sssom:HumanCurated -bioregistry:ro bioregistry.schema:0000018 bioregistry:upa sssom:HumanCurated bioregistry:ro bioregistry.schema:0000018 bioregistry:xpo sssom:HumanCurated bioregistry:ro bioregistry.schema:0000018 bioregistry:zp sssom:HumanCurated bioregistry:rouge skos:exactMatch biocontext:ROUGE sssom:HumanCurated @@ -4580,7 +4576,7 @@ bioregistry:rs skos:exactMatch aberowl:RS sssom:HumanCurated bioregistry:rs skos:exactMatch biocontext:RS sssom:HumanCurated bioregistry:rs skos:exactMatch bioportal:RS sssom:HumanCurated bioregistry:rs skos:exactMatch fairsharing:FAIRsharing.vajn3f sssom:HumanCurated -bioregistry:rs skos:exactMatch obofoundry:RS sssom:HumanCurated +bioregistry:rs skos:exactMatch obofoundry:rs sssom:HumanCurated bioregistry:rs skos:exactMatch ols:rs sssom:HumanCurated bioregistry:rs skos:exactMatch ontobee:RS sssom:HumanCurated bioregistry:rs skos:exactMatch prefixcommons:rs sssom:HumanCurated @@ -4589,7 +4585,7 @@ bioregistry:rxno skos:exactMatch aberowl:RXNO sssom:HumanCurated bioregistry:rxno skos:exactMatch biocontext:RXNO sssom:HumanCurated bioregistry:rxno skos:exactMatch bioportal:RXNO sssom:HumanCurated bioregistry:rxno skos:exactMatch fairsharing:FAIRsharing.w4tncg sssom:HumanCurated -bioregistry:rxno skos:exactMatch obofoundry:RXNO sssom:HumanCurated +bioregistry:rxno skos:exactMatch obofoundry:rxno sssom:HumanCurated bioregistry:rxno skos:exactMatch ols:rxno sssom:HumanCurated bioregistry:rxno skos:exactMatch ontobee:RXNO sssom:HumanCurated bioregistry:rxno skos:exactMatch wikidata:P2106 sssom:HumanCurated @@ -4618,7 +4614,7 @@ bioregistry:salk bioregistry.schema:0000018 bioregistry:efo sssom:HumanCurated bioregistry:sao skos:exactMatch aberowl:SAO sssom:HumanCurated bioregistry:sao skos:exactMatch biocontext:SAO sssom:HumanCurated bioregistry:sao skos:exactMatch bioportal:SAO sssom:HumanCurated -bioregistry:sao skos:exactMatch obofoundry:SAO sssom:HumanCurated +bioregistry:sao skos:exactMatch obofoundry:sao sssom:HumanCurated bioregistry:sao skos:exactMatch prefixcommons:sao sssom:HumanCurated bioregistry:sasbdb skos:exactMatch biocontext:SASBDB sssom:HumanCurated bioregistry:sasbdb skos:exactMatch fairsharing:FAIRsharing.i1F3Hb sssom:HumanCurated @@ -4630,7 +4626,7 @@ bioregistry:sbo skos:exactMatch bioportal:SBO sssom:HumanCurated bioregistry:sbo skos:exactMatch fairsharing:FAIRsharing.s19src sssom:HumanCurated bioregistry:sbo skos:exactMatch miriam:sbo sssom:HumanCurated bioregistry:sbo skos:exactMatch n2t:sbo sssom:HumanCurated -bioregistry:sbo skos:exactMatch obofoundry:SBO sssom:HumanCurated +bioregistry:sbo skos:exactMatch obofoundry:sbo sssom:HumanCurated bioregistry:sbo skos:exactMatch ols:sbo sssom:HumanCurated bioregistry:sbo skos:exactMatch ontobee:SBO sssom:HumanCurated bioregistry:sbo skos:exactMatch prefixcommons:sbo sssom:HumanCurated @@ -4639,7 +4635,7 @@ bioregistry:sbo bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated bioregistry:scdo skos:exactMatch aberowl:SCDO sssom:HumanCurated bioregistry:scdo skos:exactMatch bioportal:SCDO sssom:HumanCurated bioregistry:scdo skos:exactMatch fairsharing:FAIRsharing.kkq6pw sssom:HumanCurated -bioregistry:scdo skos:exactMatch obofoundry:SCDO sssom:HumanCurated +bioregistry:scdo skos:exactMatch obofoundry:scdo sssom:HumanCurated bioregistry:scdo skos:exactMatch ols:scdo sssom:HumanCurated bioregistry:scdo skos:exactMatch ontobee:SCDO sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:apollosv sssom:HumanCurated @@ -4653,13 +4649,11 @@ bioregistry:scdo bioregistry.schema:0000017 bioregistry:duo sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:envo sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:eupath sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:exo sssom:HumanCurated -bioregistry:scdo bioregistry.schema:0000017 bioregistry:gaz sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:gsso sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:hp sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:hsapdv sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:ico sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:ido sssom:HumanCurated -bioregistry:scdo bioregistry.schema:0000017 bioregistry:idomal sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:mp sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:nbo sssom:HumanCurated bioregistry:scdo bioregistry.schema:0000017 bioregistry:ncit sssom:HumanCurated @@ -4708,13 +4702,13 @@ bioregistry:seed.reaction skos:exactMatch n2t:seed.reaction sssom:HumanCurated bioregistry:sep skos:exactMatch aberowl:SEP sssom:HumanCurated bioregistry:sep skos:exactMatch biocontext:SEP sssom:HumanCurated bioregistry:sep skos:exactMatch bioportal:SEP sssom:HumanCurated -bioregistry:sep skos:exactMatch obofoundry:SEP sssom:HumanCurated +bioregistry:sep skos:exactMatch obofoundry:sep sssom:HumanCurated bioregistry:sep skos:exactMatch ontobee:SEP sssom:HumanCurated bioregistry:sep skos:exactMatch prefixcommons:sep sssom:HumanCurated bioregistry:sepio skos:exactMatch aberowl:SEPIO sssom:HumanCurated bioregistry:sepio skos:exactMatch biocontext:SEPIO sssom:HumanCurated bioregistry:sepio skos:exactMatch bioportal:SEPIO sssom:HumanCurated -bioregistry:sepio skos:exactMatch obofoundry:SEPIO sssom:HumanCurated +bioregistry:sepio skos:exactMatch obofoundry:sepio sssom:HumanCurated bioregistry:sepio skos:exactMatch ols:sepio sssom:HumanCurated bioregistry:sepio skos:exactMatch ontobee:SEPIO sssom:HumanCurated bioregistry:sgd skos:exactMatch biocontext:SGD sssom:HumanCurated @@ -4741,7 +4735,7 @@ bioregistry:sibo skos:exactMatch aberowl:SIBO sssom:HumanCurated bioregistry:sibo skos:exactMatch biocontext:SIBO sssom:HumanCurated bioregistry:sibo skos:exactMatch bioportal:SIBO sssom:HumanCurated bioregistry:sibo skos:exactMatch fairsharing:FAIRsharing.q09hck sssom:HumanCurated -bioregistry:sibo skos:exactMatch obofoundry:SIBO sssom:HumanCurated +bioregistry:sibo skos:exactMatch obofoundry:sibo sssom:HumanCurated bioregistry:sibo skos:exactMatch ols:sibo sssom:HumanCurated bioregistry:sibo skos:exactMatch ontobee:SIBO sssom:HumanCurated bioregistry:sider.drug skos:exactMatch biocontext:SIDER.DRUG sssom:HumanCurated @@ -4811,7 +4805,7 @@ bioregistry:so skos:exactMatch bioportal:SO sssom:HumanCurated bioregistry:so skos:exactMatch fairsharing:FAIRsharing.6bc7h9 sssom:HumanCurated bioregistry:so skos:exactMatch miriam:so sssom:HumanCurated bioregistry:so skos:exactMatch n2t:so sssom:HumanCurated -bioregistry:so skos:exactMatch obofoundry:SO sssom:HumanCurated +bioregistry:so skos:exactMatch obofoundry:so sssom:HumanCurated bioregistry:so skos:exactMatch ols:so sssom:HumanCurated bioregistry:so skos:exactMatch ontobee:SO sssom:HumanCurated bioregistry:so skos:exactMatch prefixcommons:so sssom:HumanCurated @@ -4819,7 +4813,7 @@ bioregistry:so bioregistry.schema:0000018 bioregistry:pcl sssom:HumanCurated bioregistry:sopharm skos:exactMatch aberowl:SOPHARM sssom:HumanCurated bioregistry:sopharm skos:exactMatch biocontext:SOPHARM sssom:HumanCurated bioregistry:sopharm skos:exactMatch bioportal:SOPHARM sssom:HumanCurated -bioregistry:sopharm skos:exactMatch obofoundry:SOPHARM sssom:HumanCurated +bioregistry:sopharm skos:exactMatch obofoundry:sopharm sssom:HumanCurated bioregistry:soybase skos:exactMatch biocontext:SOYBASE sssom:HumanCurated bioregistry:soybase skos:exactMatch fairsharing:FAIRsharing.z4agsr sssom:HumanCurated bioregistry:soybase skos:exactMatch miriam:soybase sssom:HumanCurated @@ -4828,7 +4822,7 @@ bioregistry:spd skos:exactMatch aberowl:SPD sssom:HumanCurated bioregistry:spd skos:exactMatch biocontext:SPD sssom:HumanCurated bioregistry:spd skos:exactMatch bioportal:SPD sssom:HumanCurated bioregistry:spd skos:exactMatch fairsharing:FAIRsharing.yecp83 sssom:HumanCurated -bioregistry:spd skos:exactMatch obofoundry:SPD sssom:HumanCurated +bioregistry:spd skos:exactMatch obofoundry:spd sssom:HumanCurated bioregistry:spd skos:exactMatch ols:spd sssom:HumanCurated bioregistry:spd skos:exactMatch ontobee:SPD sssom:HumanCurated bioregistry:spd skos:exactMatch prefixcommons:spd sssom:HumanCurated @@ -4855,7 +4849,7 @@ bioregistry:stato skos:exactMatch aberowl:STATO sssom:HumanCurated bioregistry:stato skos:exactMatch biocontext:STATO sssom:HumanCurated bioregistry:stato skos:exactMatch bioportal:STATO sssom:HumanCurated bioregistry:stato skos:exactMatch fairsharing:FAIRsharing.na5xp sssom:HumanCurated -bioregistry:stato skos:exactMatch obofoundry:STATO sssom:HumanCurated +bioregistry:stato skos:exactMatch obofoundry:stato sssom:HumanCurated bioregistry:stato skos:exactMatch ols:stato sssom:HumanCurated bioregistry:stato skos:exactMatch ontobee:STATO sssom:HumanCurated bioregistry:stato bioregistry.schema:0000018 bioregistry:ontoavida sssom:HumanCurated @@ -4924,7 +4918,7 @@ bioregistry:swo skos:exactMatch aberowl:SWO sssom:HumanCurated bioregistry:swo skos:exactMatch biocontext:SWO sssom:HumanCurated bioregistry:swo skos:exactMatch bioportal:SWO sssom:HumanCurated bioregistry:swo skos:exactMatch fairsharing:FAIRsharing.sp3szt sssom:HumanCurated -bioregistry:swo skos:exactMatch obofoundry:SWO sssom:HumanCurated +bioregistry:swo skos:exactMatch obofoundry:swo sssom:HumanCurated bioregistry:swo skos:exactMatch ols:swo sssom:HumanCurated bioregistry:swo skos:exactMatch ontobee:SWO sssom:HumanCurated bioregistry:swo skos:exactMatch prefixcommons:swo sssom:HumanCurated @@ -4932,7 +4926,7 @@ bioregistry:symp skos:exactMatch aberowl:SYMP sssom:HumanCurated bioregistry:symp skos:exactMatch biocontext:SYMP sssom:HumanCurated bioregistry:symp skos:exactMatch bioportal:SYMP sssom:HumanCurated bioregistry:symp skos:exactMatch fairsharing:FAIRsharing.ay74mj sssom:HumanCurated -bioregistry:symp skos:exactMatch obofoundry:SYMP sssom:HumanCurated +bioregistry:symp skos:exactMatch obofoundry:symp sssom:HumanCurated bioregistry:symp skos:exactMatch ols:symp sssom:HumanCurated bioregistry:symp skos:exactMatch ontobee:SYMP sssom:HumanCurated bioregistry:symp skos:exactMatch wikidata:P8656 sssom:HumanCurated @@ -4946,13 +4940,13 @@ bioregistry:tads skos:exactMatch aberowl:TADS sssom:HumanCurated bioregistry:tads skos:exactMatch biocontext:TADS sssom:HumanCurated bioregistry:tads skos:exactMatch bioportal:TADS sssom:HumanCurated bioregistry:tads skos:exactMatch fairsharing:FAIRsharing.8wm364 sssom:HumanCurated -bioregistry:tads skos:exactMatch obofoundry:TADS sssom:HumanCurated +bioregistry:tads skos:exactMatch obofoundry:tads sssom:HumanCurated bioregistry:tads skos:exactMatch ols:tads sssom:HumanCurated bioregistry:tads skos:exactMatch ontobee:TADS sssom:HumanCurated bioregistry:tahe skos:exactMatch biocontext:TAHE sssom:HumanCurated -bioregistry:tahe skos:exactMatch obofoundry:TAHE sssom:HumanCurated +bioregistry:tahe skos:exactMatch obofoundry:tahe sssom:HumanCurated bioregistry:tahh skos:exactMatch biocontext:TAHH sssom:HumanCurated -bioregistry:tahh skos:exactMatch obofoundry:TAHH sssom:HumanCurated +bioregistry:tahh skos:exactMatch obofoundry:tahh sssom:HumanCurated bioregistry:tair.gene skos:exactMatch biocontext:TAIR.GENE sssom:HumanCurated bioregistry:tair.gene skos:exactMatch miriam:tair.gene sssom:HumanCurated bioregistry:tair.gene skos:exactMatch n2t:tair.gene sssom:HumanCurated @@ -4968,7 +4962,7 @@ bioregistry:tair.protein skos:exactMatch prefixcommons:tair.protein sssom:HumanC bioregistry:tao skos:exactMatch aberowl:TAO sssom:HumanCurated bioregistry:tao skos:exactMatch biocontext:TAO sssom:HumanCurated bioregistry:tao skos:exactMatch bioportal:TAO sssom:HumanCurated -bioregistry:tao skos:exactMatch obofoundry:TAO sssom:HumanCurated +bioregistry:tao skos:exactMatch obofoundry:tao sssom:HumanCurated bioregistry:tao skos:exactMatch prefixcommons:tao sssom:HumanCurated bioregistry:tarbase skos:exactMatch biocontext:TARBASE sssom:HumanCurated bioregistry:tarbase skos:exactMatch fairsharing:FAIRsharing.a0k4cd sssom:HumanCurated @@ -4978,7 +4972,7 @@ bioregistry:taxrank skos:exactMatch aberowl:TAXRANK sssom:HumanCurated bioregistry:taxrank skos:exactMatch biocontext:TAXRANK sssom:HumanCurated bioregistry:taxrank skos:exactMatch bioportal:TAXRANK sssom:HumanCurated bioregistry:taxrank skos:exactMatch fairsharing:FAIRsharing.p1sejz sssom:HumanCurated -bioregistry:taxrank skos:exactMatch obofoundry:TAXRANK sssom:HumanCurated +bioregistry:taxrank skos:exactMatch obofoundry:taxrank sssom:HumanCurated bioregistry:taxrank skos:exactMatch ols:taxrank sssom:HumanCurated bioregistry:taxrank skos:exactMatch ontobee:TAXRANK sssom:HumanCurated bioregistry:taxrank skos:exactMatch prefixcommons:taxrank sssom:HumanCurated @@ -4998,7 +4992,7 @@ bioregistry:tgma skos:exactMatch aberowl:TGMA sssom:HumanCurated bioregistry:tgma skos:exactMatch biocontext:TGMA sssom:HumanCurated bioregistry:tgma skos:exactMatch bioportal:TGMA sssom:HumanCurated bioregistry:tgma skos:exactMatch fairsharing:FAIRsharing.dqnfkg sssom:HumanCurated -bioregistry:tgma skos:exactMatch obofoundry:TGMA sssom:HumanCurated +bioregistry:tgma skos:exactMatch obofoundry:tgma sssom:HumanCurated bioregistry:tgma skos:exactMatch ols:tgma sssom:HumanCurated bioregistry:tgma skos:exactMatch ontobee:TGMA sssom:HumanCurated bioregistry:tgma skos:exactMatch prefixcommons:tgma sssom:HumanCurated @@ -5010,7 +5004,7 @@ bioregistry:to skos:exactMatch agroportal:TO sssom:HumanCurated bioregistry:to skos:exactMatch biocontext:TO sssom:HumanCurated bioregistry:to skos:exactMatch bioportal:PTO sssom:HumanCurated bioregistry:to skos:exactMatch fairsharing:FAIRsharing.w69t6r sssom:HumanCurated -bioregistry:to skos:exactMatch obofoundry:TO sssom:HumanCurated +bioregistry:to skos:exactMatch obofoundry:to sssom:HumanCurated bioregistry:to skos:exactMatch ols:to sssom:HumanCurated bioregistry:to skos:exactMatch ontobee:TO sssom:HumanCurated bioregistry:to bioregistry.schema:0000018 bioregistry:agro sssom:HumanCurated @@ -5034,7 +5028,7 @@ bioregistry:trans skos:exactMatch aberowl:TRANS sssom:HumanCurated bioregistry:trans skos:exactMatch biocontext:TRANS sssom:HumanCurated bioregistry:trans skos:exactMatch bioportal:TRANS sssom:HumanCurated bioregistry:trans skos:exactMatch fairsharing:FAIRsharing.nygmp7 sssom:HumanCurated -bioregistry:trans skos:exactMatch obofoundry:TRANS sssom:HumanCurated +bioregistry:trans skos:exactMatch obofoundry:trans sssom:HumanCurated bioregistry:trans skos:exactMatch ols:trans sssom:HumanCurated bioregistry:trans skos:exactMatch ontobee:TRANS sssom:HumanCurated bioregistry:transyt skos:exactMatch miriam:transyt sssom:HumanCurated @@ -5065,13 +5059,13 @@ bioregistry:tto skos:exactMatch aberowl:TTO sssom:HumanCurated bioregistry:tto skos:exactMatch biocontext:TTO sssom:HumanCurated bioregistry:tto skos:exactMatch bioportal:TTO sssom:HumanCurated bioregistry:tto skos:exactMatch fairsharing:FAIRsharing.1rj558 sssom:HumanCurated -bioregistry:tto skos:exactMatch obofoundry:TTO sssom:HumanCurated +bioregistry:tto skos:exactMatch obofoundry:tto sssom:HumanCurated bioregistry:tto skos:exactMatch ols:tto sssom:HumanCurated bioregistry:tto skos:exactMatch ontobee:TTO sssom:HumanCurated bioregistry:tto skos:exactMatch prefixcommons:tto sssom:HumanCurated bioregistry:txpo skos:exactMatch aberowl:TXPO sssom:HumanCurated bioregistry:txpo skos:exactMatch bioportal:TXPO sssom:HumanCurated -bioregistry:txpo skos:exactMatch obofoundry:TXPO sssom:HumanCurated +bioregistry:txpo skos:exactMatch obofoundry:txpo sssom:HumanCurated bioregistry:txpo skos:exactMatch ols:txpo sssom:HumanCurated bioregistry:txpo skos:exactMatch ontobee:TXPO sssom:HumanCurated bioregistry:uberon skos:exactMatch aberowl:UBERON sssom:HumanCurated @@ -5080,7 +5074,7 @@ bioregistry:uberon skos:exactMatch bioportal:UBERON sssom:HumanCurated bioregistry:uberon skos:exactMatch fairsharing:FAIRsharing.4c0b6b sssom:HumanCurated bioregistry:uberon skos:exactMatch miriam:uberon sssom:HumanCurated bioregistry:uberon skos:exactMatch n2t:uberon sssom:HumanCurated -bioregistry:uberon skos:exactMatch obofoundry:UBERON sssom:HumanCurated +bioregistry:uberon skos:exactMatch obofoundry:uberon sssom:HumanCurated bioregistry:uberon skos:exactMatch ols:uberon sssom:HumanCurated bioregistry:uberon skos:exactMatch ontobee:UBERON sssom:HumanCurated bioregistry:uberon skos:exactMatch wikidata:P1554 sssom:HumanCurated @@ -5206,7 +5200,7 @@ bioregistry:uo skos:exactMatch bioportal:UO sssom:HumanCurated bioregistry:uo skos:exactMatch fairsharing:FAIRsharing.mjnypw sssom:HumanCurated bioregistry:uo skos:exactMatch miriam:uo sssom:HumanCurated bioregistry:uo skos:exactMatch n2t:uo sssom:HumanCurated -bioregistry:uo skos:exactMatch obofoundry:UO sssom:HumanCurated +bioregistry:uo skos:exactMatch obofoundry:uo sssom:HumanCurated bioregistry:uo skos:exactMatch ols:uo sssom:HumanCurated bioregistry:uo skos:exactMatch ontobee:UO sssom:HumanCurated bioregistry:uo skos:exactMatch prefixcommons:uo sssom:HumanCurated @@ -5217,7 +5211,7 @@ bioregistry:uo bioregistry.schema:0000018 bioregistry:scdo sssom:HumanCurated bioregistry:upa skos:exactMatch aberowl:UPA sssom:HumanCurated bioregistry:upa skos:exactMatch biocontext:UNIPATHWAY sssom:HumanCurated bioregistry:upa skos:exactMatch bioportal:UPA sssom:HumanCurated -bioregistry:upa skos:exactMatch obofoundry:UPA sssom:HumanCurated +bioregistry:upa skos:exactMatch obofoundry:upa sssom:HumanCurated bioregistry:upa skos:exactMatch ols:upa sssom:HumanCurated bioregistry:upa skos:exactMatch ontobee:UPA sssom:HumanCurated bioregistry:upa skos:exactMatch prefixcommons:unipathway sssom:HumanCurated @@ -5226,7 +5220,7 @@ bioregistry:upheno skos:exactMatch aberowl:UPHENO sssom:HumanCurated bioregistry:upheno skos:exactMatch biocontext:UPHENO sssom:HumanCurated bioregistry:upheno skos:exactMatch bioportal:UPHENO sssom:HumanCurated bioregistry:upheno skos:exactMatch fairsharing:FAIRsharing.r41qhx sssom:HumanCurated -bioregistry:upheno skos:exactMatch obofoundry:UPHENO sssom:HumanCurated +bioregistry:upheno skos:exactMatch obofoundry:upheno sssom:HumanCurated bioregistry:upheno skos:exactMatch ols:upheno sssom:HumanCurated bioregistry:upheno skos:exactMatch ontobee:UPHENO sssom:HumanCurated bioregistry:uspto skos:exactMatch biocontext:USPTO sssom:HumanCurated @@ -5248,7 +5242,7 @@ bioregistry:vario skos:exactMatch bioportal:VARIO sssom:HumanCurated bioregistry:vario skos:exactMatch fairsharing:FAIRsharing.65xkbs sssom:HumanCurated bioregistry:vario skos:exactMatch miriam:vario sssom:HumanCurated bioregistry:vario skos:exactMatch n2t:vario sssom:HumanCurated -bioregistry:vario skos:exactMatch obofoundry:VariO sssom:HumanCurated +bioregistry:vario skos:exactMatch obofoundry:vario sssom:HumanCurated bioregistry:vario skos:exactMatch ols:vario sssom:HumanCurated bioregistry:vario skos:exactMatch ontobee:VariO sssom:HumanCurated bioregistry:vbase2 skos:exactMatch biocontext:VBASE2 sssom:HumanCurated @@ -5283,7 +5277,7 @@ bioregistry:vgnc skos:exactMatch miriam:vgnc sssom:HumanCurated bioregistry:vhog skos:exactMatch aberowl:VHOG sssom:HumanCurated bioregistry:vhog skos:exactMatch biocontext:VHOG sssom:HumanCurated bioregistry:vhog skos:exactMatch bioportal:VHOG sssom:HumanCurated -bioregistry:vhog skos:exactMatch obofoundry:VHOG sssom:HumanCurated +bioregistry:vhog skos:exactMatch obofoundry:vhog sssom:HumanCurated bioregistry:vhog skos:exactMatch prefixcommons:vhog sssom:HumanCurated bioregistry:viaf skos:exactMatch miriam:viaf sssom:HumanCurated bioregistry:viaf skos:exactMatch n2t:viaf sssom:HumanCurated @@ -5314,7 +5308,7 @@ bioregistry:vo skos:exactMatch aberowl:VO sssom:HumanCurated bioregistry:vo skos:exactMatch biocontext:VO sssom:HumanCurated bioregistry:vo skos:exactMatch bioportal:VO sssom:HumanCurated bioregistry:vo skos:exactMatch fairsharing:FAIRsharing.zwtww5 sssom:HumanCurated -bioregistry:vo skos:exactMatch obofoundry:VO sssom:HumanCurated +bioregistry:vo skos:exactMatch obofoundry:vo sssom:HumanCurated bioregistry:vo skos:exactMatch ols:vo sssom:HumanCurated bioregistry:vo skos:exactMatch ontobee:VO sssom:HumanCurated bioregistry:vo skos:exactMatch prefixcommons:vo sssom:HumanCurated @@ -5323,7 +5317,7 @@ bioregistry:void skos:exactMatch biocontext:void sssom:HumanCurated bioregistry:vsao skos:exactMatch aberowl:VSAO sssom:HumanCurated bioregistry:vsao skos:exactMatch biocontext:VSAO sssom:HumanCurated bioregistry:vsao skos:exactMatch bioportal:VSAO sssom:HumanCurated -bioregistry:vsao skos:exactMatch obofoundry:VSAO sssom:HumanCurated +bioregistry:vsao skos:exactMatch obofoundry:vsao sssom:HumanCurated bioregistry:vso skos:exactMatch aberowl:VSO sssom:HumanCurated bioregistry:vso skos:exactMatch bioportal:VSO sssom:HumanCurated bioregistry:vso skos:exactMatch fairsharing:FAIRsharing.jjb2p2 sssom:HumanCurated @@ -5333,7 +5327,7 @@ bioregistry:vt skos:exactMatch agroportal:VT sssom:HumanCurated bioregistry:vt skos:exactMatch biocontext:VT sssom:HumanCurated bioregistry:vt skos:exactMatch bioportal:VT sssom:HumanCurated bioregistry:vt skos:exactMatch fairsharing:FAIRsharing.10gr18 sssom:HumanCurated -bioregistry:vt skos:exactMatch obofoundry:VT sssom:HumanCurated +bioregistry:vt skos:exactMatch obofoundry:vt sssom:HumanCurated bioregistry:vt skos:exactMatch ols:vt sssom:HumanCurated bioregistry:vt skos:exactMatch ontobee:VT sssom:HumanCurated bioregistry:vt skos:exactMatch prefixcommons:vt sssom:HumanCurated @@ -5342,7 +5336,7 @@ bioregistry:vto skos:exactMatch aberowl:VTO sssom:HumanCurated bioregistry:vto skos:exactMatch biocontext:VTO sssom:HumanCurated bioregistry:vto skos:exactMatch bioportal:VTO sssom:HumanCurated bioregistry:vto skos:exactMatch fairsharing:FAIRsharing.akmeb9 sssom:HumanCurated -bioregistry:vto skos:exactMatch obofoundry:VTO sssom:HumanCurated +bioregistry:vto skos:exactMatch obofoundry:vto sssom:HumanCurated bioregistry:vto skos:exactMatch ols:vto sssom:HumanCurated bioregistry:vto skos:exactMatch ontobee:VTO sssom:HumanCurated bioregistry:vz skos:exactMatch prefixcommons:vz sssom:HumanCurated @@ -5354,7 +5348,7 @@ bioregistry:wbbt skos:exactMatch biocontext:WBbt sssom:HumanCurated bioregistry:wbbt skos:exactMatch biolink:WBbt sssom:HumanCurated bioregistry:wbbt skos:exactMatch bioportal:WB-BT sssom:HumanCurated bioregistry:wbbt skos:exactMatch fairsharing:FAIRsharing.phk7dd sssom:HumanCurated -bioregistry:wbbt skos:exactMatch obofoundry:WBbt sssom:HumanCurated +bioregistry:wbbt skos:exactMatch obofoundry:wbbt sssom:HumanCurated bioregistry:wbbt skos:exactMatch ols:wbbt sssom:HumanCurated bioregistry:wbbt skos:exactMatch ontobee:WBbt sssom:HumanCurated bioregistry:wbbt skos:exactMatch prefixcommons:wbbt sssom:HumanCurated @@ -5363,7 +5357,7 @@ bioregistry:wbls skos:exactMatch biocontext:WBLS sssom:HumanCurated bioregistry:wbls skos:exactMatch biolink:WBls sssom:HumanCurated bioregistry:wbls skos:exactMatch bioportal:WB-LS sssom:HumanCurated bioregistry:wbls skos:exactMatch fairsharing:FAIRsharing.sm90nh sssom:HumanCurated -bioregistry:wbls skos:exactMatch obofoundry:WBls sssom:HumanCurated +bioregistry:wbls skos:exactMatch obofoundry:wbls sssom:HumanCurated bioregistry:wbls skos:exactMatch ols:wbls sssom:HumanCurated bioregistry:wbls skos:exactMatch ontobee:WBLS sssom:HumanCurated bioregistry:wbls skos:exactMatch prefixcommons:wbls sssom:HumanCurated @@ -5372,7 +5366,7 @@ bioregistry:wbphenotype skos:exactMatch aberowl:WBPHENOTYPE sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch biocontext:WBPhenotype sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch bioportal:WB-PHENOTYPE sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch fairsharing:FAIRsharing.agvc7y sssom:HumanCurated -bioregistry:wbphenotype skos:exactMatch obofoundry:WBPhenotype sssom:HumanCurated +bioregistry:wbphenotype skos:exactMatch obofoundry:wbphenotype sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch ols:wbphenotype sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch ontobee:WBPhenotype sssom:HumanCurated bioregistry:wbphenotype skos:exactMatch prefixcommons:wbphenotype sssom:HumanCurated @@ -5427,7 +5421,7 @@ bioregistry:xao skos:exactMatch aberowl:XAO sssom:HumanCurated bioregistry:xao skos:exactMatch biocontext:XAO sssom:HumanCurated bioregistry:xao skos:exactMatch bioportal:XAO sssom:HumanCurated bioregistry:xao skos:exactMatch fairsharing:FAIRsharing.17zapb sssom:HumanCurated -bioregistry:xao skos:exactMatch obofoundry:XAO sssom:HumanCurated +bioregistry:xao skos:exactMatch obofoundry:xao sssom:HumanCurated bioregistry:xao skos:exactMatch ols:xao sssom:HumanCurated bioregistry:xao skos:exactMatch ontobee:XAO sssom:HumanCurated bioregistry:xao skos:exactMatch wikidata:P4495 sssom:HumanCurated @@ -5436,7 +5430,7 @@ bioregistry:xco skos:exactMatch aberowl:XCO sssom:HumanCurated bioregistry:xco skos:exactMatch biocontext:XCO sssom:HumanCurated bioregistry:xco skos:exactMatch bioportal:XCO sssom:HumanCurated bioregistry:xco skos:exactMatch fairsharing:FAIRsharing.x39h5y sssom:HumanCurated -bioregistry:xco skos:exactMatch obofoundry:XCO sssom:HumanCurated +bioregistry:xco skos:exactMatch obofoundry:xco sssom:HumanCurated bioregistry:xco skos:exactMatch ols:xco sssom:HumanCurated bioregistry:xco skos:exactMatch ontobee:XCO sssom:HumanCurated bioregistry:xco skos:exactMatch prefixcommons:xco sssom:HumanCurated @@ -5454,14 +5448,14 @@ bioregistry:xl skos:exactMatch ols:xl sssom:HumanCurated bioregistry:xl skos:exactMatch ontobee:XL sssom:HumanCurated bioregistry:xlmod skos:exactMatch aberowl:XLMOD sssom:HumanCurated bioregistry:xlmod skos:exactMatch bioportal:XLMOD sssom:HumanCurated -bioregistry:xlmod skos:exactMatch obofoundry:XLMOD sssom:HumanCurated +bioregistry:xlmod skos:exactMatch obofoundry:xlmod sssom:HumanCurated bioregistry:xlmod skos:exactMatch ols:xlmod sssom:HumanCurated bioregistry:xlmod skos:exactMatch ontobee:XLMOD sssom:HumanCurated bioregistry:xml skos:exactMatch biocontext:xml sssom:HumanCurated bioregistry:xpo skos:exactMatch aberowl:XPO sssom:HumanCurated bioregistry:xpo skos:exactMatch biolink:XPO sssom:HumanCurated bioregistry:xpo skos:exactMatch bioportal:XPO sssom:HumanCurated -bioregistry:xpo skos:exactMatch obofoundry:XPO sssom:HumanCurated +bioregistry:xpo skos:exactMatch obofoundry:xpo sssom:HumanCurated bioregistry:xpo skos:exactMatch ols:xpo sssom:HumanCurated bioregistry:xpo skos:exactMatch ontobee:XPO sssom:HumanCurated bioregistry:xpo bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated @@ -5488,7 +5482,7 @@ bioregistry:yid skos:exactMatch biocontext:YID sssom:HumanCurated bioregistry:yid skos:exactMatch miriam:yid sssom:HumanCurated bioregistry:yid skos:exactMatch n2t:yid sssom:HumanCurated bioregistry:ymdb skos:exactMatch fairsharing:FAIRsharing.tawpg2 sssom:HumanCurated -bioregistry:ypo skos:exactMatch obofoundry:YPO sssom:HumanCurated +bioregistry:ypo skos:exactMatch obofoundry:ypo sssom:HumanCurated bioregistry:ypo skos:exactMatch ols:ypo sssom:HumanCurated bioregistry:yrcpdr skos:exactMatch biocontext:YRCPDR sssom:HumanCurated bioregistry:yrcpdr skos:exactMatch fairsharing:FAIRsharing.karvzj sssom:HumanCurated @@ -5497,13 +5491,13 @@ bioregistry:yrcpdr skos:exactMatch n2t:yrcpdr sssom:HumanCurated bioregistry:zea skos:exactMatch aberowl:ZEA sssom:HumanCurated bioregistry:zea skos:exactMatch biocontext:ZEA sssom:HumanCurated bioregistry:zea skos:exactMatch bioportal:ZEA sssom:HumanCurated -bioregistry:zea skos:exactMatch obofoundry:ZEA sssom:HumanCurated +bioregistry:zea skos:exactMatch obofoundry:zea sssom:HumanCurated bioregistry:zea skos:exactMatch prefixcommons:zea sssom:HumanCurated bioregistry:zeco skos:exactMatch aberowl:ZECO sssom:HumanCurated bioregistry:zeco skos:exactMatch biocontext:ZECO sssom:HumanCurated bioregistry:zeco skos:exactMatch bioportal:ZECO sssom:HumanCurated bioregistry:zeco skos:exactMatch fairsharing:FAIRsharing.np2wfz sssom:HumanCurated -bioregistry:zeco skos:exactMatch obofoundry:ZECO sssom:HumanCurated +bioregistry:zeco skos:exactMatch obofoundry:zeco sssom:HumanCurated bioregistry:zeco skos:exactMatch ols:zeco sssom:HumanCurated bioregistry:zeco skos:exactMatch ontobee:ZECO sssom:HumanCurated bioregistry:zeco bioregistry.schema:0000018 bioregistry:mco sssom:HumanCurated @@ -5512,7 +5506,7 @@ bioregistry:zfa skos:exactMatch aberowl:ZFA sssom:HumanCurated bioregistry:zfa skos:exactMatch biocontext:ZFA sssom:HumanCurated bioregistry:zfa skos:exactMatch bioportal:ZFA sssom:HumanCurated bioregistry:zfa skos:exactMatch fairsharing:FAIRsharing.s3r6sk sssom:HumanCurated -bioregistry:zfa skos:exactMatch obofoundry:ZFA sssom:HumanCurated +bioregistry:zfa skos:exactMatch obofoundry:zfa sssom:HumanCurated bioregistry:zfa skos:exactMatch ols:zfa sssom:HumanCurated bioregistry:zfa skos:exactMatch ontobee:ZFA sssom:HumanCurated bioregistry:zfa skos:exactMatch prefixcommons:zfa sssom:HumanCurated @@ -5527,7 +5521,7 @@ bioregistry:zfs skos:exactMatch aberowl:ZFS sssom:HumanCurated bioregistry:zfs skos:exactMatch biocontext:ZFS sssom:HumanCurated bioregistry:zfs skos:exactMatch bioportal:ZFS sssom:HumanCurated bioregistry:zfs skos:exactMatch fairsharing:FAIRsharing.bc8ayj sssom:HumanCurated -bioregistry:zfs skos:exactMatch obofoundry:ZFS sssom:HumanCurated +bioregistry:zfs skos:exactMatch obofoundry:zfs sssom:HumanCurated bioregistry:zfs skos:exactMatch ols:zfs sssom:HumanCurated bioregistry:zfs skos:exactMatch ontobee:ZFS sssom:HumanCurated bioregistry:zinc skos:exactMatch biocontext:ZINC sssom:HumanCurated @@ -5537,7 +5531,7 @@ bioregistry:zinc skos:exactMatch wikidata:P2084 sssom:HumanCurated bioregistry:zp skos:exactMatch aberowl:ZP sssom:HumanCurated bioregistry:zp skos:exactMatch biocontext:ZP sssom:HumanCurated bioregistry:zp skos:exactMatch bioportal:ZP sssom:HumanCurated -bioregistry:zp skos:exactMatch obofoundry:ZP sssom:HumanCurated +bioregistry:zp skos:exactMatch obofoundry:zp sssom:HumanCurated bioregistry:zp skos:exactMatch ols:zp sssom:HumanCurated bioregistry:zp skos:exactMatch ontobee:ZP sssom:HumanCurated bioregistry:zp bioregistry.schema:0000017 bioregistry:bfo sssom:HumanCurated diff --git a/exports/tables/summary.tex b/exports/tables/summary.tex index b14b61008..4c955a8de 100644 --- a/exports/tables/summary.tex +++ b/exports/tables/summary.tex @@ -1,17 +1,17 @@ \begin{table} \centering -\caption{Overview statistics of the Bioregistry on 2022-07-29.} +\caption{Overview statistics of the Bioregistry on 2022-07-30.} \label{tab:bioregistry-summary} \begin{tabular}{lr} \toprule Category & Count \\ \midrule - Version & 0.5.51-dev \\ + Version & 0.5.53-dev \\ Registries Surveyed & 23 \\ Registries Aligned & 22 \\ Prefixes & 1419 \\ Synonyms & 393 \\ - Cross-registry Mappings & 6810 \\ + Cross-registry Mappings & 6812 \\ Curated Mismatches & 25 \\ Collections and Contexts & 7 \\ Direct Contributors & 28 \\ diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 56b01baf6..c1180ec8c 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -191,7 +191,22 @@ "description": "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO has been integrated into Uberon.", "id": "876", "name": "Amphibian gross Anatomy Ontology", - "prefix": "FAIRsharing.mxx5rp" + "prefix": "FAIRsharing.mxx5rp", + "publications": [ + { + "doi": "10.1186/2041-1480-5-21", + "pubmed_id": 25009735, + "title": "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon" + }, + { + "doi": "10.1142/9789812772435_0035", + "pubmed_id": null, + "title": "AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS" + } + ], + "subjects": [ + "Anatomy" + ] }, "mappings": { "biocontext": "AAO", @@ -522,7 +537,8 @@ "aberowl": "ADO", "bioportal": "ADO", "fairsharing": "FAIRsharing.ckd4rf", - "obofoundry": "ado" + "obofoundry": "ado", + "ols": "ado" }, "obofoundry": { "contact": "alpha.tom.kodamullil@scai.fraunhofer.de", @@ -542,6 +558,15 @@ "preferredPrefix": "ADO", "prefix": "ado", "repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO" + }, + "ols": { + "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", + "download": "http://purl.obolibrary.org/obo/ado.owl", + "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", + "name": "Alzheimer's Disease Ontology (ADO)", + "prefix": "ado", + "version": "2.0.0", + "version.iri": "http://purl.obolibrary.org/obo/ado/releases/2022-06-11/ado.owl" } }, "adw": { @@ -568,7 +593,12 @@ "description": "An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.", "id": "1038", "name": "Animal natural history and life history", - "prefix": "FAIRsharing.t9fvdn" + "prefix": "FAIRsharing.t9fvdn", + "publications": [], + "subjects": [ + "Anatomy", + "Life Science" + ] }, "mappings": { "aberowl": "ADW", @@ -637,6 +667,13 @@ "id": "1175", "name": "Anatomical Entity Ontology", "prefix": "FAIRsharing.93ee19", + "publications": [ + { + "doi": "10.3389/fgene.2012.00018", + "pubmed_id": 22347883, + "title": "The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs." + } + ], "subjects": [ "Anatomy", "Life Science" @@ -712,7 +749,14 @@ "description": "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.", "id": "221", "name": "Adverse Event Reporting ontology", - "prefix": "FAIRsharing.rycy2x" + "prefix": "FAIRsharing.rycy2x", + "publications": [], + "subjects": [ + "Medicine", + "Health Science", + "Biomedical Science", + "Preclinical Studies" + ] }, "mappings": { "aberowl": "AERO", @@ -3032,7 +3076,9 @@ "description": "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource", "id": "583", "name": "Amphibian Taxonomy Ontology", - "prefix": "FAIRsharing.ayjdsm" + "prefix": "FAIRsharing.ayjdsm", + "publications": [], + "subjects": [] }, "mappings": { "aberowl": "ATO", @@ -4357,7 +4403,11 @@ "description": "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource.", "id": "1035", "name": "Bilateria anatomy", - "prefix": "FAIRsharing.eqgjeq" + "prefix": "FAIRsharing.eqgjeq", + "publications": [], + "subjects": [ + "Anatomy" + ] }, "mappings": { "biocontext": "BILA", @@ -8196,6 +8246,7 @@ "id": "668", "name": "Cephalopod Ontology", "prefix": "FAIRsharing.p58bm4", + "publications": [], "subjects": [] }, "mappings": { @@ -19201,6 +19252,13 @@ "id": "199", "name": "Edinburgh human developmental anatomy abstract version 2", "prefix": "FAIRsharing.7zxrs6", + "publications": [ + { + "doi": "10.1111/j.1469-7580.2012.01566.x", + "pubmed_id": 22973865, + "title": "A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1-20)." + } + ], "subjects": [ "Anatomy", "Life Science", @@ -20867,6 +20925,18 @@ "id": "1166", "name": "eagle-i Research Resource Ontology", "prefix": "FAIRsharing.nwgynk", + "publications": [ + { + "doi": "10.1109/JCDL.2017.7991571", + "pubmed_id": 29599662, + "title": "Automating data citation: the eagle-i experience." + }, + { + "doi": "10.1093/database/bar067", + "pubmed_id": 22434835, + "title": "Research resources: curating the new eagle-i discovery system." + } + ], "subjects": [ "Life Science", "Biomedical Science" @@ -22384,6 +22454,7 @@ "id": "1241", "name": "Physico-chemical methods and properties", "prefix": "FAIRsharing.wwy1ns", + "publications": [], "subjects": [ "Chemistry" ] @@ -22804,6 +22875,18 @@ "id": "683", "name": "Foundational Model of Anatomy", "prefix": "FAIRsharing.x56jsy", + "publications": [ + { + "doi": "10.1016/j.jbi.2003.11.007", + "pubmed_id": 14759820, + "title": "A reference ontology for biomedical informatics: the Foundational Model of Anatomy." + }, + { + "doi": "10.1016/j.artmed.2016.04.003", + "pubmed_id": 27235801, + "title": "From frames to OWL2: Converting the Foundational Model of Anatomy." + } + ], "subjects": [ "Anatomy", "Radiology", @@ -24151,6 +24234,7 @@ "id": "384", "name": "Gazetteer", "prefix": "FAIRsharing.wkdjpb", + "publications": [], "subjects": [ "Environmental Science" ] @@ -31104,6 +31188,18 @@ "id": "549", "name": "Infection Disease Ontology Malaria", "prefix": "FAIRsharing.2q8c28", + "publications": [ + { + "doi": "10.1186/2041-1480-4-16", + "pubmed_id": 24034841, + "title": "IDOMAL: the malaria ontology revisited." + }, + { + "doi": "10.1186/1475-2875-9-230", + "pubmed_id": 20698959, + "title": "IDOMAL: an ontology for malaria." + } + ], "subjects": [ "Molecular Infection Biology", "Life Science", @@ -39362,6 +39458,13 @@ "id": "720", "name": "Mosquito Insecticide Resistance Ontology", "prefix": "FAIRsharing.sjf113", + "publications": [ + { + "doi": "10.1371/journal.pntd.0000465", + "pubmed_id": 19547750, + "title": "MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors." + } + ], "subjects": [ "Life Science" ] @@ -53755,6 +53858,7 @@ "mappings": { "aberowl": "PROCO", "obofoundry": "proco", + "ols": "proco", "ontobee": "PROCO" }, "obofoundry": { @@ -53781,6 +53885,15 @@ "prefix": "proco", "repository": "https://github.com/proco-ontology/PROCO" }, + "ols": { + "description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.", + "download": "http://purl.obolibrary.org/obo/proco.owl", + "homepage": "https://github.com/proco-ontology/PROCO", + "name": "PROCO: PROcess Chemistry Ontology", + "prefix": "proco", + "version": "PROCO release 20220414", + "version.iri": "http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl" + }, "ontobee": { "library": "Library", "name": "Process Chemistry Ontology", @@ -56296,6 +56409,7 @@ "id": "1085", "name": "Physico-chemical process", "prefix": "FAIRsharing.g0a7s0", + "publications": [], "subjects": [ "Chemistry", "Life Science" @@ -57143,6 +57257,18 @@ "id": "65", "name": "RNA Ontology", "prefix": "FAIRsharing.kqt2h2", + "publications": [ + { + "doi": "10.1261/rna.2343206", + "pubmed_id": 16484377, + "title": "The RNA Ontology Consortium: an open invitation to the RNA community." + }, + { + "doi": "10.3233/AO-2011-0082", + "pubmed_id": null, + "title": "The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data" + } + ], "subjects": [ "Biochemistry", "Life Science" @@ -57227,6 +57353,7 @@ "uri_format": "http://purl.obolibrary.org/obo/RO_$1" }, "bioportal": { + "name": "Relations Ontology", "prefix": "OBOREL" }, "example": "0002533", @@ -58262,12 +58389,30 @@ "example": "0000728", "fairsharing": { "abbreviation": "SCDO", - "description": "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD.", + "description": "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. ", "id": "888", "name": "Sickle Cell Disease Ontology", "prefix": "FAIRsharing.kkq6pw", - "publications": [], - "subjects": [] + "publications": [ + { + "doi": "10.1093/database/baac014", + "pubmed_id": 35363306, + "title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation." + }, + { + "doi": "10.1089/omi.2020.0153", + "pubmed_id": 33021900, + "title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications." + }, + { + "doi": "10.1093/database/baz118", + "pubmed_id": 31769834, + "title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation." + } + ], + "subjects": [ + "Biomedical Science" + ] }, "mappings": { "aberowl": "SCDO", @@ -59350,6 +59495,7 @@ "id": "596", "name": "Social Inset Behavior Ontology", "prefix": "FAIRsharing.q09hck", + "publications": [], "subjects": [] }, "mappings": { @@ -62055,6 +62201,13 @@ "id": "222", "name": "Tick Gross Anatomy", "prefix": "FAIRsharing.8wm364", + "publications": [ + { + "doi": "10.1111/j.1365-2583.2008.00781.x", + "pubmed_id": 18237287, + "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase." + } + ], "subjects": [ "Anatomy", "Life Science" @@ -62782,6 +62935,13 @@ "id": "15", "name": "Mosquito gross anatomy", "prefix": "FAIRsharing.dqnfkg", + "publications": [ + { + "doi": "10.1111/j.1365-2583.2008.00781.x", + "pubmed_id": 18237287, + "title": "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase." + } + ], "subjects": [ "Anatomy", "Life Science" @@ -65868,6 +66028,33 @@ "id": "546", "name": "Variation Ontology", "prefix": "FAIRsharing.65xkbs", + "publications": [ + { + "doi": "10.1101/gr.157495.113", + "pubmed_id": 24162187, + "title": "Variation Ontology for annotation of variation effects and mechanisms." + }, + { + "doi": "10.1007/s00439-015-1529-6", + "pubmed_id": 25616435, + "title": "Types and effects of protein variations." + }, + { + "doi": "10.1186/2041-1480-5-9", + "pubmed_id": 24533660, + "title": "Variation ontology: annotator guide." + }, + { + "doi": "10.1002/humu.22954", + "pubmed_id": 26773573, + "title": "VariOtator, a Software Tool for Variation Annotation with the Variation Ontology." + }, + { + "doi": "10.1186/s12864-018-5262-0", + "pubmed_id": 30591019, + "title": "Systematics for types and effects of DNA variations." + } + ], "subjects": [ "Genetics" ] diff --git a/src/bioregistry/data/external/aberowl/raw.json b/src/bioregistry/data/external/aberowl/raw.json index 337895804..ee65074f9 100644 --- a/src/bioregistry/data/external/aberowl/raw.json +++ b/src/bioregistry/data/external/aberowl/raw.json @@ -1 +1 @@ -[{"acronym":"BANDARQ","name":"CapsaBandarQ.com Capsa Online, Agen Bandar Q, Domino 99, Qiu Qiu Online, BandarQ","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"ONTOPARON_SOCIAL","name":"Ontology of amyotrophic lateral sclerosis, social module","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"GEOSPECIES","name":"GeoSpecies Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":8,"download_url":"media/ontologies/GEOSPECIES/1/geospecies.owl","submission_id":1,"domain":null,"description":"This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. 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In addition, literature data from Semantic MEDLINE (SM) has been extracted and integrated in the GTO to provide scientific evidence accordingly.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2015-02-25T00:00:00Z","date_created":"2015-02-25T23:27:57Z","home_page":"http://qianzhu-lab.umbc.edu/","version":null,"has_ontology_language":"OWL","nb_classes":0,"nb_individuals":0,"nb_properties":0,"max_depth":0,"max_children":0,"avg_children":0,"classifiable":false,"nb_inconsistent":0,"indexed":false,"md5sum":null}},{"acronym":"TUNIGO-SLIM","name":"Tunicate GO Slim","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"ONTONEO-CORE","name":"OntONeo-core","status":"Unloadable","topics":null,"species":null,"submission":{"id":64,"download_url":"media/ontologies/ONTONEO-CORE/1/ontoneo-core.owl","submission_id":1,"domain":null,"description":"Collect the basic information required to work with Obstetric and Neonatal 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\r\nLineage(s)\r\n

\r\nA class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage. \r\n

\r\nAnnotations\r\n

\r\nSpecific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
\r\nDEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
\r\nFULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
\r\nICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
\r\nICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
\r\nClass Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
\r\nPreferred_Name: A human-friendly and commonly used name in plain English.
\r\nSynonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
\r\nUMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they \"understand\" the meaning of the language of biomedicine and health.\r\n

\r\nRelationships (Object Properties)\r\n

\r\nRelationships are properties by which one class is related to another class in the ontology. For example, \"Population_Group\" (a class) has_susceptibility_to_disease (a relationship) \"Immune_Disorder\" (a class). This box may be empty if no relationship has been used for modeling. \r\n

\r\nDatatype Properties\r\n

\r\nDatatype Properties are properties by which a class is related to a datatype. 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The BIM ontology is represented in three parts; (i) image vocabularies - which holds vocabularies for the annotation of an image and/or region of interests (ROI) inside an image, as well as vocabularies to represent the pre and post processing states of an image, (ii) text entities - covers annotations from the text that are associated with an image (e.g. image captions) and provides semantic representation for NLP algorithm outputs, (iii) a provenance model - that contributes towards the maintenance of annotation versioning. 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Allotrope Merged Ontology Suite

\r\n\r\n

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

\r\n\r\n

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

\r\n\r\n

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
\r\nrights: http://purl.allotrope.org/voc/copyright

\r\n \r\n

Please get the latest version of AFO from http://purl.allotrope.org

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Therefore, we aimed to present a novel classification in this regard.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2019-07-10T00:00:00Z","date_created":"2019-07-11T01:50:19Z","home_page":null,"version":null,"has_ontology_language":"OWL","nb_classes":407,"nb_individuals":0,"nb_properties":0,"max_depth":5,"max_children":76,"avg_children":7,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"HANCESTRO","name":"Human Ancestry Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":5076,"download_url":"media/ontologies/HANCESTRO/9/hancestro.owl","submission_id":9,"domain":"organisms","description":"The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.","documentation":null,"publication":null,"publications":[{"id":"https://www.ncbi.nlm.nih.gov/pubmed/29448949","title":"A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog"}],"products":[{"id":"hancestro.owl","title":"HANCESTRO","description":"The full version of HANCESTRO in OWL format","ontology_purl":"http://purl.obolibrary.org/obo/hancestro.owl"},{"id":"hancestro_bfo.owl","title":"HANCESTRO BFO","description":"Version of HANCESTRO with BFO upper hierarchy for easier integration with other ontologies","ontology_purl":"http://purl.obolibrary.org/obo/hancestro_bfo.owl"}],"taxon":null,"date_released":"2022-05-16T12:17:15.575923Z","date_created":"2022-05-16T12:17:15.575939Z","home_page":"https://github.com/EBISPOT/ancestro","version":null,"has_ontology_language":"OWL","nb_classes":583,"nb_individuals":0,"nb_properties":9,"max_depth":5,"max_children":240,"avg_children":19,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":"3b8ab54b8b659ea5112de7d481b888ee"}},{"acronym":"HCPCS","name":"Healthcare Common Procedure Coding System","status":"Classified","topics":null,"species":null,"submission":{"id":331,"download_url":"media/ontologies/HCPCS/9/hcpcs.umls","submission_id":9,"domain":null,"description":"Healthcare Common Procedure Coding System","documentation":"http://cms.hhs.gov","publication":"http://cms.hhs.gov","publications":null,"products":null,"taxon":null,"date_released":"2017-02-06T21:25:59Z","date_created":"2017-02-06T21:25:59Z","home_page":"http://cms.hhs.gov","version":"2016AB","has_ontology_language":"UMLS","nb_classes":5946,"nb_individuals":0,"nb_properties":20,"max_depth":0,"max_children":0,"avg_children":0,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"HCPCS-mod","name":"HCPCS modifiers","status":"Unloadable","topics":null,"species":null,"submission":{"id":588,"download_url":"media/ontologies/HCPCS-mod/1/hcpcs-mod.owl","submission_id":1,"domain":null,"description":"Modifiers denote that a certain procedure/service has been altered by a particular circumstance, but not changed in its definition, therefore the same code is used and a modifier is added to denote what has been altered.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2012-09-18T07:00:00Z","date_created":"2012-09-18T19:17:54Z","home_page":null,"version":"unknown","has_ontology_language":"OWL","nb_classes":11,"nb_individuals":7,"nb_properties":18,"max_depth":1,"max_children":10,"avg_children":5,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"INCENTIVE-VARS","name":"INCENTIVE Variables","status":"Classified","topics":null,"species":null,"submission":{"id":5216,"download_url":"media/ontologies/INCENTIVE-VARS/8/incentive-vars.skos","submission_id":8,"domain":null,"description":"Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). 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\r\nLineage(s)\r\n

\r\nA class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage. \r\n

\r\nAnnotations\r\n

\r\nSpecific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
\r\nDEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
\r\nFULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
\r\nICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
\r\nICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
\r\nClass Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
\r\nPreferred_Name: A human-friendly and commonly used name in plain English.
\r\nSynonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
\r\nUMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they \"understand\" the meaning of the language of biomedicine and health.\r\n

\r\nRelationships (Object Properties)\r\n

\r\nRelationships are properties by which one class is related to another class in the ontology. For example, \"Population_Group\" (a class) has_susceptibility_to_disease (a relationship) \"Immune_Disorder\" (a class). This box may be empty if no relationship has been used for modeling. \r\n

\r\nDatatype Properties\r\n

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To illustrate the BIM ontology’s utility, we provide three annotation cases generated by BIM in conjunction with the SEBI image annotation engine.","documentation":"http://cbakerlab.unbsj.ca/unbvps/BIM","publication":"https://code.google.com/p/bio-ont/","publications":null,"products":null,"taxon":null,"date_released":"2014-09-26T00:00:00Z","date_created":"2015-10-08T22:02:57Z","home_page":"https://sites.google.com/site/bimontology/","version":"1.3","has_ontology_language":"OWL","nb_classes":125,"nb_individuals":34,"nb_properties":73,"max_depth":3,"max_children":50,"avg_children":6,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"RBMS","name":"RBMS Controlled Vocabularies","status":"Unloadable","topics":null,"species":null,"submission":{"id":704,"download_url":"media/ontologies/RBMS/1/rbms.skos","submission_id":1,"domain":null,"description":"These thesauri provide standardized vocabulary for retrieving special collections materials by form, genre, or by various physical characteristics that are typically of interest to researchers and special collections librarians, and for relating materials to individuals or corporate bodies.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2016-06-16T00:00:00Z","date_created":"2017-07-13T22:41:49Z","home_page":"http://rbms.info/vocabularies/","version":"1.0","has_ontology_language":"SKOS","nb_classes":0,"nb_individuals":0,"nb_properties":0,"max_depth":0,"max_children":0,"avg_children":0,"classifiable":false,"nb_inconsistent":0,"indexed":false,"md5sum":null}},{"acronym":"QIBO","name":"Quantitative Imaging Biomarker Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":707,"download_url":"media/ontologies/QIBO/2/qibo.owl","submission_id":2,"domain":null,"description":"An ontology that describes various concepts in quantitative imaging biomarkers. ","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2011-10-06T07:00:00Z","date_created":"2011-10-06T18:15:59Z","home_page":null,"version":"unknown","has_ontology_language":"OWL","nb_classes":0,"nb_individuals":0,"nb_properties":0,"max_depth":0,"max_children":0,"avg_children":0,"classifiable":false,"nb_inconsistent":0,"indexed":false,"md5sum":null}},{"acronym":"Python acronym","name":"Python name","status":"Unknown","topics":["Python Topic"],"species":["Python species"],"submission":null},{"acronym":"EPO","name":"Early Pregnancy Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":767,"download_url":"media/ontologies/EPO/1/epo.owl","submission_id":1,"domain":null,"description":"The early pregnancy ontology contains the concepts to describe ectopic pregnancy ultrasound images, organized into several subsumption hierarchies for types of ectopic pregnancies and the signs, anatomical structures and technical elements of imaging associated with ectopic pregnancy.\r\nVersion 1.1 was used for ultrasound image annotations (Dhombres et al. Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy. J Biomed Semantics, 2017)\r\n","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2016-05-28T00:00:00Z","date_created":"2016-06-03T17:38:39Z","home_page":null,"version":"1.1","has_ontology_language":"OWL","nb_classes":1388,"nb_individuals":0,"nb_properties":48,"max_depth":20,"max_children":80,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"EHDAA","name":"Human Developmental Anatomy Ontology, abstract version 1","status":"Classified","topics":null,"species":null,"submission":{"id":427,"download_url":"media/ontologies/EHDAA/6/ehdaa.obo","submission_id":6,"domain":null,"description":"A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2011-02-15T08:00:00Z","date_created":"2011-02-16T02:06:55Z","home_page":"http://genex.hgu.mrc.ac.uk/","version":"unknown","has_ontology_language":"OBO","nb_classes":2314,"nb_individuals":0,"nb_properties":1,"max_depth":0,"max_children":1,"avg_children":1,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"COVID19","name":"COVID-19 Surveillance Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":4237,"download_url":"media/ontologies/COVID19/3/covid19.owl","submission_id":3,"domain":null,"description":"The COVID-19 Surveillance Ontology is an application ontology used to support SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) surveillance in primary care. The ontology facilitates monitoring of COVID-19 cases and related respiratory conditions using data from multiple brands of computerised medical record systems.","documentation":null,"publication":"https://publichealth.jmir.org/2020/4/e21434/","publications":null,"products":null,"taxon":null,"date_released":"2020-08-05T00:00:00Z","date_created":"2021-01-28T13:39:11Z","home_page":"https://orchid.phc.ox.ac.uk/index.php/cov-19/","version":"V1.0","has_ontology_language":"OWL","nb_classes":32,"nb_individuals":0,"nb_properties":0,"max_depth":2,"max_children":11,"avg_children":6,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"ADMF","name":"alzhaimer dessiese main factors","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"CONTSONTO","name":"Continuity of care","status":"Classified","topics":null,"species":null,"submission":{"id":4348,"download_url":"media/ontologies/CONTSONTO/4/contsonto.owl","submission_id":4,"domain":null,"description":"The Ontology of Continuity of care (ContSOnto) is an emerging research area consisting of the extension of a healthcare ontology to inform the continuity of care domain. This field is positioned at the confluence of health informatics, nursing informatics, process modelling, and artificial intelligence. This research relating to ContSOnto is underpinned by health informatics standard ISO 13940 Systems of Concepts for Continuity of Care ContSOnto focuses on how information flows from different information systems across and between services for clinical applications and health care professionals to use. Figure 14.2 provides an illustration (see https://contsys.org/pages/Guest%20blog/FormalOntology)of how the different classes and relationships in the standard are represented. Subject of care refers to the individual service user and health care actors can be human or non-human, for example, a health care professional or an organisation.","documentation":"https://contsys.org/pages/Guest%20blog/FormalOntology","publication":"https://contsys.org/pages/Guest%20blog/FormalOntology","publications":null,"products":null,"taxon":null,"date_released":"2021-01-02T00:00:00Z","date_created":"2021-03-11T21:31:40Z","home_page":"http://purl.org/net/for-coc","version":"1.4","has_ontology_language":"OWL","nb_classes":153,"nb_individuals":0,"nb_properties":132,"max_depth":8,"max_children":19,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"COP","name":"Core Ontology of Phenotypes","status":"Classified","topics":["phenotype"],"species":[],"submission":{"id":4404,"download_url":"media/ontologies/COP/1/cop.owl","submission_id":1,"domain":null,"description":"COP is a core ontology, which can be used to specify phenotype algorithms as ontologies (Phenotype Algorithm Specification Ontology, PASO).","documentation":null,"publication":"Uciteli, A; Beger, C; Kirsten, T; Meineke, FA; Herre, H: Ontological Modelling and Reasoning of Phenotypes. 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Concepts are labeled in English and Korean translations are also provided.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2021-11-02T00:00:00Z","date_created":"2022-03-11T13:25:18Z","home_page":null,"version":"2","has_ontology_language":"OWL","nb_classes":262,"nb_individuals":513,"nb_properties":7,"max_depth":6,"max_children":13,"avg_children":4,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"ETHIOPIADISEASES","name":"EthiopiaDiseasesList","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"COVID19-IBO","name":"Covid19 Impact on Banking Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":4651,"download_url":"media/ontologies/COVID19-IBO/6/covid19-ibo.owl","submission_id":6,"domain":null,"description":"Covid19 Impact on Banking Ontology (Covid19-IBO) provides semantic information about the impact of the Covid-19 on the banking sector of 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covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2020-05-14T00:00:00Z","date_created":"2020-06-22T14:31:16Z","home_page":null,"version":"Version Release: 1.0.0","has_ontology_language":"OWL","nb_classes":2268,"nb_individuals":6,"nb_properties":8,"max_depth":16,"max_children":245,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"COVID-19-ONT-PM","name":"COVID-19OntologyInPatternMedicine","status":"Classified","topics":null,"species":null,"submission":{"id":5008,"download_url":"media/ontologies/COVID-19-ONT-PM/9/covid-19-ont-pm.owl","submission_id":9,"domain":null,"description":"This ontology focuses on the aspects of the scientific findings in the COVID-19 fields in order to help the efforts against the outbreak of the pandemic. \r\nIt is expected, through the ontology, to understand the medical conditions and make medical decisions in more integrated or systematic ways, by the engineerized or calculatable methods, rahter than the experience-based ways, usually used in the Traditional Information-Pieces-Accumulation Medicine(TIPAM).\r\nThe researches of the ontology involve the exploratory works of the Pattern Medicine(PM) and so called the Generalized Biomedical Dynamics(GBMD) , especially concentrating to the relations between the molecular and clinic levels.\r\n\r\nPlease pay attention to the background researches or the pilot project related to this ontolgy, and the introduction and publications, as well. \r\nThe relative artcle under going is at stie:\r\n\r\nhttps://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/","documentation":"https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/","publication":"https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/","publications":null,"products":null,"taxon":null,"date_released":"2021-08-20T00:00:00Z","date_created":"2022-04-05T03:13:03Z","home_page":"https://blog.51.ca/u-345129/2020/11/13/the-preliminary-researches-on-the-data-dynamics-of-covid-19/","version":"007","has_ontology_language":"OWL","nb_classes":299,"nb_individuals":6,"nb_properties":11,"max_depth":9,"max_children":39,"avg_children":5,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"ETHANC","name":"ETHANC","status":"Classified","topics":null,"species":null,"submission":{"id":4646,"download_url":"media/ontologies/ETHANC/16/ethanc.skos","submission_id":16,"domain":null,"description":"Antenatal 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Allotrope Merged Ontology Suite

\r\n\r\n

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

\r\n\r\n

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

\r\n\r\n

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
\r\nrights: http://purl.allotrope.org/voc/copyright

\r\n \r\n

Please get the latest version of AFO from http://purl.allotrope.org

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Developed by the IRD and the Fiocruz.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2018-10-12T00:00:00Z","date_created":"2018-10-12T11:14:09Z","home_page":null,"version":null,"has_ontology_language":"OWL","nb_classes":49,"nb_individuals":0,"nb_properties":19,"max_depth":4,"max_children":9,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"HAMIDEHSGH","name":"Inherited Retinal Dystrophy","status":"Classified","topics":null,"species":null,"submission":{"id":2746,"download_url":"media/ontologies/HAMIDEHSGH/1/hamidehsgh.owl","submission_id":1,"domain":null,"description":"Inherited retinal dystrophy (IRD) as one of the rare ocular diseases encompasses different types of hereditary retinal degenerations appearing by involvement of the different layers of the posterior ocular segment. In respect of the importance of the classification systems regarding the recorded history of biologic and natural sciences, there is no classification regarding the IRD diagnoses. Therefore, we aimed to present a novel classification in this regard.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2019-07-10T00:00:00Z","date_created":"2019-07-11T01:50:19Z","home_page":null,"version":null,"has_ontology_language":"OWL","nb_classes":407,"nb_individuals":0,"nb_properties":0,"max_depth":5,"max_children":76,"avg_children":7,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"HANCESTRO","name":"Human Ancestry Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":5076,"download_url":"media/ontologies/HANCESTRO/9/hancestro.owl","submission_id":9,"domain":"organisms","description":"The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.","documentation":null,"publication":null,"publications":[{"id":"https://www.ncbi.nlm.nih.gov/pubmed/29448949","title":"A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog"}],"products":[{"id":"hancestro.owl","title":"HANCESTRO","description":"The full version of HANCESTRO in OWL format","ontology_purl":"http://purl.obolibrary.org/obo/hancestro.owl"},{"id":"hancestro_bfo.owl","title":"HANCESTRO BFO","description":"Version of HANCESTRO with BFO upper hierarchy for easier integration with other ontologies","ontology_purl":"http://purl.obolibrary.org/obo/hancestro_bfo.owl"}],"taxon":null,"date_released":"2022-05-16T12:17:15.575923Z","date_created":"2022-05-16T12:17:15.575939Z","home_page":"https://github.com/EBISPOT/ancestro","version":null,"has_ontology_language":"OWL","nb_classes":583,"nb_individuals":0,"nb_properties":9,"max_depth":5,"max_children":240,"avg_children":19,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":"3b8ab54b8b659ea5112de7d481b888ee"}},{"acronym":"HCPCS","name":"Healthcare Common Procedure Coding System","status":"Classified","topics":null,"species":null,"submission":{"id":331,"download_url":"media/ontologies/HCPCS/9/hcpcs.umls","submission_id":9,"domain":null,"description":"Healthcare Common Procedure Coding System","documentation":"http://cms.hhs.gov","publication":"http://cms.hhs.gov","publications":null,"products":null,"taxon":null,"date_released":"2017-02-06T21:25:59Z","date_created":"2017-02-06T21:25:59Z","home_page":"http://cms.hhs.gov","version":"2016AB","has_ontology_language":"UMLS","nb_classes":5946,"nb_individuals":0,"nb_properties":20,"max_depth":0,"max_children":0,"avg_children":0,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"INCENTIVE-VARS","name":"INCENTIVE Variables","status":"Classified","topics":null,"species":null,"submission":{"id":5216,"download_url":"media/ontologies/INCENTIVE-VARS/8/incentive-vars.skos","submission_id":8,"domain":null,"description":"Controlled vocabularies allow an accurate and controlled approach in describing physical and digital assets (e.g., data). One of such controlled vocabulary is INCENTIVE Variables. 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As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels.\r\nIMGT®, the international ImMunoGeneTics information system®, has been built on IMGT-ONTOLOGY.\r\n\r\nThe version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION.","documentation":"http://www.imgt.org/IMGTindex/ontology.php","publication":"http://www.imgt.org/IMGTindex/ontology.php","publications":null,"products":null,"taxon":null,"date_released":"2013-07-17T07:00:00Z","date_created":"2013-07-17T15:30:29Z","home_page":"http://www.imgt.org/","version":"1.0.2","has_ontology_language":"OWL","nb_classes":1415,"nb_individuals":0,"nb_properties":42,"max_depth":8,"max_children":61,"avg_children":4,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"H1_NMOABA_2_0","name":"NeuroMorpho.Org Allen Brain Atlas ontology v.2.0","status":"Classified","topics":null,"species":null,"submission":{"id":272,"download_url":"media/ontologies/H1_NMOABA_2_0/1/h1_nmoaba_2_0.owl","submission_id":1,"domain":null,"description":"Light version of the Allen Brain Atlas ontology that is customized for the NeuroMorpho.Org brain regions. 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The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. Once complete, we anticipate that the ontology will: 1) be the most comprehensive collection of knowledge on SCD, 2) facilitate exploration of new scientific questions and ideas, 3) facilitate seamless data sharing and collaborations including meta-analysis within the SCD community, 4) support the building of databasing and clinical informatics in SCD.", + "description": "The Sickle Cell Disease Ontology (SCDO) project is a collaboration between H3ABioNet (Pan African Bioinformatics Network) and SPAN (Sickle Cell Disease Pan African Network). The SCDO is currently under development and its purpose is to: 1) establish community standardized SCD terms and descriptions, 2) establish canonical and hierarchical representation of knowledge on SCD, 3) links to other ontologies and bodies of work such as DO, PhenX MeSH, ICD, NCI’s thesaurus, SNOMED and OMIM. ", "id": "888", "name": "Sickle Cell Disease Ontology", - "publications": [], - "subjects": [] + "publications": [ + { + "doi": "10.1093/database/baac014", + "pubmed_id": 35363306, + "title": "The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation." + }, + { + "doi": "10.1089/omi.2020.0153", + "pubmed_id": 33021900, + "title": "The Sickle Cell Disease Ontology: Enabling Collaborative Research and Co-Designing of New Planetary Health Applications." + }, + { + "doi": "10.1093/database/baz118", + "pubmed_id": 31769834, + "title": "The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation." + } + ], + "subjects": [ + "Biomedical Science" + ] }, "FAIRsharing.kn0d5v": { "abbreviation": "DC_CL", diff --git a/src/bioregistry/data/external/ols/processed.json b/src/bioregistry/data/external/ols/processed.json index 93ce307f3..a0bf669e3 100644 --- a/src/bioregistry/data/external/ols/processed.json +++ b/src/bioregistry/data/external/ols/processed.json @@ -1,4 +1,13 @@ { + "ado": { + "description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining.", + "download": "http://purl.obolibrary.org/obo/ado.owl", + "homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO", + "name": "Alzheimer's Disease Ontology (ADO)", + "prefix": "ado", + "version": "2.0.0", + "version.iri": "http://purl.obolibrary.org/obo/ado/releases/2022-06-11/ado.owl" + }, "aeo": { "description": "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology", "download": "http://purl.obolibrary.org/obo/aeo.owl", @@ -137,6 +146,14 @@ "version": "2022-02-18", "version.iri": "http://purl.obolibrary.org/obo/caro/releases/2022-02-18/caro.owl" }, + "ccf": { + "description": "This ontology provides a view of the Uberon anatomy ontology and the Cell Ontology based on expert reviewed content provided by the HuBMaP project. Cell Ontology terms are linked to sets of expert-specified cell type markers, recorded using HGNC identifiers and metadata.", + "download": "https://purl.org/ccf/2.0/ccf.owl", + "name": "Common Coordinate Framework (CCF) Ontology", + "prefix": "ccf", + "version": "2.0.1", + "version.iri": "http://purl.org/ccf/releases/2.0.1/ccf.owl" + }, "cco": { "contact": "vladimir.n.mironov@gmail.com", "description": "The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects.", @@ -1856,6 +1873,15 @@ "prefix": "probonto", "version": "2.5.0" }, + "proco": { + "description": "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.", + "download": "http://purl.obolibrary.org/obo/proco.owl", + "homepage": "https://github.com/proco-ontology/PROCO", + "name": "PROCO: PROcess Chemistry Ontology", + "prefix": "proco", + "version": "PROCO release 20220414", + "version.iri": "http://purl.obolibrary.org/obo/proco/releases/2022-04-11/proco.owl" + }, "prov": { "download": "https://www.w3.org/ns/prov-o", "homepage": "https://www.w3.org/TR/prov-o/", @@ -2004,6 +2030,12 @@ "version": "$Revision$", "version.iri": "http://purl.obolibrary.org/obo/sepio-v20170929.owl" }, + "shareloc": { + "description": "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc.", + "download": "https://raw.githubusercontent.com/imodpasteur/ShareLoc.XYZ/ontology/shareloc.owl", + "name": "ShareLoc", + "prefix": "shareloc" + }, "sibo": { "description": "Social Behavior in insects", "download": "http://purl.obolibrary.org/obo/sibo.owl",