From 895bca5315726fc217e1393d9f102eb1ad341752 Mon Sep 17 00:00:00 2001 From: AlanSimmons Date: Wed, 4 Dec 2024 13:30:57 -0500 Subject: [PATCH] version --- docs/contexts/index.MD | 110 +++++++++++++++++++---------------------- docs/lang/en.json | 5 +- docs/version/index.MD | 57 +++++++++++++++++++++ 3 files changed, 113 insertions(+), 59 deletions(-) create mode 100644 docs/version/index.MD diff --git a/docs/contexts/index.MD b/docs/contexts/index.MD index 3c0b6cd..f97c247 100644 --- a/docs/contexts/index.MD +++ b/docs/contexts/index.MD @@ -121,68 +121,62 @@ The base context includes summaries of genes from [RefSeq](https://www.ncbi.nlm. A separate script (refseq.py) adds RefSeq summaries to the UBKG. This import assumes that GenCode has been ingested. -### Azimuth-Cell Ontology mappings -The HuBMAP project is building a mapping between tissue codings from Azimuth and Cell Ontology (CL). -The AZ-CL mappings will be added to UBKG contexts as needed. - -| SAB | Description | Type of data | platform | Citations | Citation Reference | License | -|------------------------------------------------------------|--------------------------------------------------------|--------------|-----------------|:----------|:-------------------|:--------| -| [AZ](https://azimuth.hubmapconsortium.org/) | Azimuth cell annotations mapped to Cell Ontology terms | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | - ### HuBMAP/SenNet context The HuBMAP/SenNet context appends to the UBKG base set assertions from the following SABs: -| SAB | Description | Type of data | platform | Citations | Citation Reference | License | License Reference | -|-------------------------------------------------------------|-----------------------------------------------------------------------------------|--------------|-------------------------------------------------------------------------|:------------------------------------------------------------|:----------------------------------------------|:-----------------------------------------------------------|:------------------------------------------------------------------------------------------------------------| -| [HRA](https://humanatlas.io/) | Human Reference Atlas | ontology | Globus | [PMID:34750582 ](https://pubmed.ncbi.nlm.nih.gov/34750582/) | | Data Use Agreement | [Reference](https://hubmapconsortium.org/wp-content/uploads/2020/06/DUA_FINAL_2020_02_03_for_Signature.pdf) | -| [HRAVS](https://bioportal.bioontology.org/ontologies/HRAVS) | Human Reference Atlas Value Set | ontology | NCBO BioPortal | | | | | -| [HUBMAP](https://hubmapconsortium.org/) | the application ontology supporting the infrastructure of the HuBMAP Consortium | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | | -| [SENNET](https://sennetconsortium.org/) | the application ontology supporting the infrastructure of the SenNet Consortium | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | | -| [CEDAR](https://metadatacenter.org/) | Custom HuBMAP/SenNet metadata templates built from CEDAR templates | reference | Globus | [PMID:26112029](https://pubmed.ncbi.nlm.nih.gov/26112029/) | [Reference](https://metadatacenter.org/#cite) | | | -| HMFIELD | Custom legacy HuBMAP metadata | reference | custom | | | | | -| CEDAR-ENTITY | Custom mappings between CEDAR templates and HuBMAP and SenNet provenance entities | reference | custom | | | | | -| [PCL](https://obofoundry.org/ontology/pcl.html) | Provisional Cell Ontology | ontology | OBO Foundry | | | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://obofoundry.org/ontology/pcl.html) | +| SAB | Description | Type of data | platform | Citations | Citation Reference | License | License Reference | +|-------------------------------------------------------------|-----------------------------------------------------------------------------------|--------------|-------------------------------------------------------------------------|:------------------------------------------------------------|:----------------------------------------------|:-------------------|:------------------------------------------------------------------------------------------------------------| +| [AZ](https://azimuth.hubmapconsortium.org/) | Azimuth cell annotations mapped to Cell Ontology codes | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | +| [HRA](https://humanatlas.io/) | Human Reference Atlas | ontology | Globus | [PMID:34750582 ](https://pubmed.ncbi.nlm.nih.gov/34750582/) | | Data Use Agreement | [Reference](https://hubmapconsortium.org/wp-content/uploads/2020/06/DUA_FINAL_2020_02_03_for_Signature.pdf) | +| [HRAVS](https://bioportal.bioontology.org/ontologies/HRAVS) | Human Reference Atlas Value Set | ontology | NCBO BioPortal | | | | | +| [HUBMAP](https://hubmapconsortium.org/) | the application ontology supporting the infrastructure of the HuBMAP Consortium | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | | +| [SENNET](https://sennetconsortium.org/) | the application ontology supporting the infrastructure of the SenNet Consortium | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | | | | +| [CEDAR](https://metadatacenter.org/) | Custom HuBMAP/SenNet metadata templates built from CEDAR templates | reference | Globus | [PMID:26112029](https://pubmed.ncbi.nlm.nih.gov/26112029/) | [Reference](https://metadatacenter.org/#cite) | | | +| HMFIELD | Custom legacy HuBMAP metadata | reference | custom | | | | | +| CEDAR-ENTITY | Custom mappings between CEDAR templates and HuBMAP and SenNet provenance entities | reference | custom | | | | | +| STELLAR | STELLAR cell annotations mapped to Cell Ontology codes | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | [PMID:36280720](https://pubmed.ncbi.nlm.nih.gov/36280720/) +| DCT | DeepCellType cell annotations mapped to Cell Ontology codes | ontology | [SimpleKnowledge](https://github.com/x-atlas-consortia/SimpleKnowledge) | | ### Data Distillery context The Data Distillery context appends to the UBKG base set assertions to support participants in [Data Distillery](https://commonfund.nih.gov/dataecosystem/highlights), a project of the National Institute of Health's [Common Fund Data Ecosystem](https://commonfund.nih.gov/dataecosystem) (CFDE). SABs include: -| Data Coordinating Center / Domain | SAB | Description | Type of data | platform | Citations | Citation Reference | License | Licensing Reference | -|--------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------|----------------------------------------------------------------------------------------|--------------|----------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------| -| Data Distillery Support Mappings | [CLINVAR](https://www.ncbi.nlm.nih.gov/clinvar/) | NCBI ClinVar - associations between genes and diseases or phenotypes | reference | Globus | [PMID:31777943](https://pubmed.ncbi.nlm.nih.gov/31777943/),[PMID:30311387](https://pubmed.ncbi.nlm.nih.gov/30311387/),[PMID:29165669](https://pubmed.ncbi.nlm.nih.gov/29165669/)
,[PMID:26582918](https://pubmed.ncbi.nlm.nih.gov/26582918/),[PMID:24234437](https://pubmed.ncbi.nlm.nih.gov/24234437/),[NBK174587](https://www.ncbi.nlm.nih.gov/books/NBK174587/) | [Reference](https://www.ncbi.nlm.nih.gov/clinvar/intro/) | Public Domain | [Reference](https://www.ncbi.nlm.nih.gov/clinvar/intro/) | -| | [CMAP](https://www.broadinstitute.org/connectivity-map-cmap) | Broad Institute's Connectivity Map - associations between genes and chemicals or drugs | reference | Globus | [PMID:29195078](https://pubmed.ncbi.nlm.nih.gov/29195078/) | [Reference](https://clue.io/connectopedia/pdf/how_to_cite_cmap) | Public access | [Reference](https://www.broadinstitute.org/principles-disseminating-scientific-innovations) | -| | HPOMP | HPO-MP mapping | reference | Globus | MP: [PMID:26467479](https://pubmed.ncbi.nlm.nih.gov/22961259/)
HPO: [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/) | [MP](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[HPO](https://hpo.jax.org/app/citation) | MP: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
HPO: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HPO/index.html) | [MP](https://obofoundry.org/ontology/mp.html) | -| | HGNCHPO | human genotype - phenotype mapping | reference | Globus | HGNC: [PMID:36243972](https://pubmed.ncbi.nlm.nih.gov/36243972/)
HPO: [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/) | [HGNC](https://www.genenames.org/about/license/)
[HPO](https://hpo.jax.org/app/citation) | HGNC: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/index.html)
HPO: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HPO/index.html) | | -| | HCOP (_formerly HCOPHGNC_) | human - mouse orthologs | reference | Globus | MGD: [PMID:33231642](https://pubmed.ncbi.nlm.nih.gov/33231642/)
HGNC: [PMID:36243972](https://pubmed.ncbi.nlm.nih.gov/36243972/) | [MGD](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[HGNC](https://www.genenames.org/about/license/) | MGD: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
HGNC: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/index.html) | [MGD](https://www.informatics.jax.org/mgihome/other/copyright.shtml) | -| | MPMGI (_formerly HCOPMP_) | mouse genotype-phenotype mapping | reference | Globus | MGD: [PMID:33231642](https://pubmed.ncbi.nlm.nih.gov/33231642/)
MP: [PMID:26467479](https://pubmed.ncbi.nlm.nih.gov/22961259/) | [MGD](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[MP](https://www.informatics.jax.org/mgihome/other/citation.shtml) | MGD: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
MP: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [MGD](https://www.informatics.jax.org/mgihome/other/copyright.shtml)
[MP](https://obofoundry.org/ontology/mp.html) | -| | RATHCOP | ENSEMBL Human to ENSEMBL Rat ortholog_ | reference | Globus | [PMID:36318249](https://pubmed.ncbi.nlm.nih.gov/36318249/) | [Reference](http://useast.ensembl.org/info/about/publications.html) | [Apache 2.0 ](https://www.apache.org/licenses/LICENSE-2.0) | [Reference](http://useast.ensembl.org/info/about/legal/code_licence.html) | -| | [MSIGDB](https://www.gsea-msigdb.org/gsea/msigdb) | Molecular Signatures Database | reference | Globus | [PMID:16199517](https://pubmed.ncbi.nlm.nih.gov/16199517/),[PMID:21546393](https://pubmed.ncbi.nlm.nih.gov/21546393/),[PMID:26771021](https://pubmed.ncbi.nlm.nih.gov/26771021/),[PMID:37704782](https://pubmed.ncbi.nlm.nih.gov/37704782/) | [Reference](https://www.gsea-msigdb.org/gsea/msigdb/index.jsp) | [CC BY](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.gsea-msigdb.org/gsea/msigdb_license_terms.jsp) | -| | HSCLO | Chromosome Location Ontology | ontology | Globus | [bioArXiv](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | | [CC BY NC ND 4.0 ](https://creativecommons.org/licenses/by-nc-nd/4.0/) | [Reference](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | -| | GENCODEHSCLO | GENCODE-HSCLO mapping | reference | Globus | GENCODE:[PMID:33270111](https://pubmed.ncbi.nlm.nih.gov/33270111/)
HSCLO: [bioArXiv](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | [GENCODE]([Reference](https://www.gencodegenes.org/pages/publications.html)) | GENCODE: [open access ](https://www.gencodegenes.org/pages/data_access.html)
HSCLO: [CC BY NC ND 4.0 ](https://creativecommons.org/licenses/by-nc-nd/4.0/) | [HSCLO](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | -| | [WP](https://www.wikipathways.org/) | WikiPathways gene-gene interactions | reference | Globus | [PMID:37941138](https://pubmed.ncbi.nlm.nih.gov/37941138/),[PMID:18651794](https://pubmed.ncbi.nlm.nih.gov/18651794/) | [Reference](https://www.wikipathways.org/cite.html) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/) | [Reference](https://www.wikipathways.org/cite.html) | -| | [CLINGEN](https://clinicalgenome.org/) | Clinical Genome selected datasets | reference | Globus | [PMID:26014595](https://pubmed.ncbi.nlm.nih.gov/26014595/) | [Reference](https://clinicalgenome.org/docs/terms-of-use/) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/) | [Reference](https://clinicalgenome.org/docs/terms-of-use/) | -| | [STRING](https://string-db.org/) | StringDB Protein-Protein Interaction Network | reference | Globus | [PMID:36370105](https://pubmed.ncbi.nlm.nih.gov/36370105/) | [Reference](https://string-db.org/cgi/about?footer_active_subpage=references) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://string-db.org/cgi/access?footer_active_subpage=licensing) | -| [4DNucleome](https://www.4dnucleome.org/) | [4DN](https://www.4dnucleome.org/) | 4D Nucleome | result | Globus | [PMID:28905911 ](https://pubmed.ncbi.nlm.nih.gov/28905911/),[PMID:35501320](https://pubmed.ncbi.nlm.nih.gov/35501320/) | [Reference](https://data.4dnucleome.org/) | Freely available | [Reference](https://data.4dnucleome.org/) | -| [Extracellular RNA Communication Consortium (ERCC)](https://exrna.org/) | [ERCCRBP](https://exrna.org/) | exRNA RNA Binding Proteins | result | Globus | [PMID:26320938](https://pubmed.ncbi.nlm.nih.gov/26320938/) | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | Pre-publication data sharing | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | -| | [ERCCREG](https://exrna.org/) | Regulatory Elements | result | Globus | [PMID:26320938](https://pubmed.ncbi.nlm.nih.gov/26320938/) | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | Pre-publication data sharing | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | -| [GlyGen](https://www.glygen.org/) | [FALDO](https://bioportal.bioontology.org/ontologies/FALDO) | Feature Annotation Description Ontology | ontology | NCBO BioPortal | | | | | -| | [UNIPROT](https://ftp.uniprot.org/pub/databases/uniprot/) | Universal Protein Resource | ontology | UniProt FTP | | | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://ftp.uniprot.org/pub/databases/uniprot/LICENSE) | -| | [GLYCORDF](https://github.com/glycoinfo/GlycoRDF) | Glycomics | ontology | GitHub | [PMID:24280648 ](https://pubmed.ncbi.nlm.nih.gov/24280648/) | [Reference](https://github.com/glycoinfo/GlycoRDF) | | | -| | [GLYCOCOO](https://github.com/glycoinfo/GlycoCoO) | Glycoconjugate | ontology | GitHub | | | | | -| | GLYCANS | Glycans data | result | Globus | [PMID:31616925](https://pubmed.ncbi.nlm.nih.gov/31616925/) | [Reference](https://www.glygen.org/how-to-cite/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.glygen.org/license/) | -| | PROTEOFORM | Proteoform | result | Globus | [PMID:31616925](https://pubmed.ncbi.nlm.nih.gov/31616925/) | [Reference](https://www.glygen.org/how-to-cite/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.glygen.org/license/) | -| [Genotype Tissue Expression (GTEx)](https://gtexportal.org/home/) | GTEXCOEXP | Co-expression | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | -| | GTEXEQTL | Expression | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | -| | GTEXEXP | Expression quantitative trait loci (eQTL) | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | -| [Human BioMolecular Atlas Program (HuBMAP) ](https://hubmapconsortium.org/) | HMAZ | HuBMAP Azimuth Cell Expression Summary | result | Globus | [PMID:31597973](https://pubmed.ncbi.nlm.nih.gov/31597973/) | [Reference](https://hubmapconsortium.org/acknowledgement-in-publications/) | Data Use Agreement | [Reference](https://hubmapconsortium.org/wp-content/uploads/2020/06/DUA_FINAL_2020_02_03_for_Signature.pdf) | -| [Illuminating the Druggable Genome (IDG)](https://commonfund.nih.gov/idg) | IDGP | Compound-protein interactions | result | Globus | | | Open | [Reference](https://druggablegenome.net/IDGPolicies) | -| | IDGD | Compound-disease interactions | result | Globus | | | Open | [Reference](https://druggablegenome.net/IDGPolicies) | -| [Gabriella Miller Kids First](https://commonfund.nih.gov/KidsFirst) | KF | | result | Globus | | | | | -| [Library of Integrated Network-Based Cellular Signatures (LINCS)](https://commonfund.nih.gov/LINCS/) | LINCS | | result | Globus | | | freely available | [Reference](https://commonfund.nih.gov/LINCS) | -| [Molecular Transducers of Physical Activity Consortium (MoTrPAC)](https://commonfund.nih.gov/MolecularTransducers) | MOTRPAC | | result | Globus | | | | | -| [Metabolomics Workbench (MW)](https://commonfund.nih.gov/metabolomics/) | MW | Cell-metabolite mappings | result | Globus | [PMID:26467476](https://pubmed.ncbi.nlm.nih.gov/26467476/) | [Reference](https://www.metabolomicsworkbench.org/) | public domain | [Reference](https://www.metabolomicsworkbench.org/data/datasharing.php) | -| [Stimulating Peripheral Activity to Relieve Conditions (SPARC)](https://commonfund.nih.gov/Sparc/) | [NPO](https://bioportal.bioontology.org/ontologies/NPOKB) | Neuron Phenotype Ontology | ontology | NCBO BioPortal | | | | | -| | [NPOSCKAN](https://github.com/SciCrunch/NIF-Ontology/releases) | NPOSCKAN | ontology | GitHub | | | | | -| [Reactome](https://reactome.org/) | REACTOME | Pathways | reference | Globus | [PMID:37941124 ](https://pubmed.ncbi.nlm.nih.gov/37941124/) | [Reference](https://reactome.org/cite) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/),[CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://reactome.org/license) | -| [DisGenet](https://www.disgenet.org/) | DGN | Disease-gene associations | reference | Globus | [PMID:31680165](https://pubmed.ncbi.nlm.nih.gov/31680165/) | [Reference](https://www.disgenet.org/citation) | [CC-BY-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) | [Reference](https://www.disgenet.org/terms-of-use/) | -| [Biomarker Partnership Project](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/) | BIOMARKER | Biomarkers | reference | Globus | [PMID:35925813](https://pubmed.ncbi.nlm.nih.gov/35925813/),[PMID:34015823](https://pubmed.ncbi.nlm.nih.gov/34015823/),[PMID:32142370](https://pubmed.ncbi.nlm.nih.gov/32142370/) | [Reference](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data) | - +| Data Coordinating Center / Domain | SAB | Description | Type of data | platform | Citations | Citation Reference | License | Licensing Reference | +|--------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------|-----------------------------------------------------------------------------------------------|--------------|----------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------| +| Data Distillery Support Mappings | [CLINVAR](https://www.ncbi.nlm.nih.gov/clinvar/) | NCBI ClinVar - associations between genes and diseases or phenotypes | reference | Globus | [PMID:31777943](https://pubmed.ncbi.nlm.nih.gov/31777943/),[PMID:30311387](https://pubmed.ncbi.nlm.nih.gov/30311387/),[PMID:29165669](https://pubmed.ncbi.nlm.nih.gov/29165669/)
,[PMID:26582918](https://pubmed.ncbi.nlm.nih.gov/26582918/),[PMID:24234437](https://pubmed.ncbi.nlm.nih.gov/24234437/),[NBK174587](https://www.ncbi.nlm.nih.gov/books/NBK174587/) | [Reference](https://www.ncbi.nlm.nih.gov/clinvar/intro/) | Public Domain | [Reference](https://www.ncbi.nlm.nih.gov/clinvar/intro/) | +| | [CMAP](https://www.broadinstitute.org/connectivity-map-cmap) | Broad Institute's Connectivity Map - associations between genes and chemicals or drugs | reference | Globus | [PMID:29195078](https://pubmed.ncbi.nlm.nih.gov/29195078/) | [Reference](https://clue.io/connectopedia/pdf/how_to_cite_cmap) | Public access | [Reference](https://www.broadinstitute.org/principles-disseminating-scientific-innovations) | +| | HPOMP | HPO-MP mapping | reference | Globus | MP: [PMID:26467479](https://pubmed.ncbi.nlm.nih.gov/22961259/)
HPO: [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/) | [MP](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[HPO](https://hpo.jax.org/app/citation) | MP: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
HPO: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HPO/index.html) | [MP](https://obofoundry.org/ontology/mp.html) | +| | HGNCHPO | human genotype - phenotype mapping | reference | Globus | HGNC: [PMID:36243972](https://pubmed.ncbi.nlm.nih.gov/36243972/)
HPO: [PMID:37953324](https://pubmed.ncbi.nlm.nih.gov/37953324/) | [HGNC](https://www.genenames.org/about/license/)
[HPO](https://hpo.jax.org/app/citation) | HGNC: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/index.html)
HPO: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HPO/index.html) | | +| | HCOP (_formerly HCOPHGNC_) | human - mouse orthologs | reference | Globus | MGD: [PMID:33231642](https://pubmed.ncbi.nlm.nih.gov/33231642/)
HGNC: [PMID:36243972](https://pubmed.ncbi.nlm.nih.gov/36243972/) | [MGD](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[HGNC](https://www.genenames.org/about/license/) | MGD: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
HGNC: [UMLS restriction level 0](https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/index.html) | [MGD](https://www.informatics.jax.org/mgihome/other/copyright.shtml) | +| | MPMGI (_formerly HCOPMP_) | mouse genotype-phenotype mapping | reference | Globus | MGD: [PMID:33231642](https://pubmed.ncbi.nlm.nih.gov/33231642/)
MP: [PMID:26467479](https://pubmed.ncbi.nlm.nih.gov/22961259/) | [MGD](https://www.informatics.jax.org/mgihome/other/citation.shtml)
[MP](https://www.informatics.jax.org/mgihome/other/citation.shtml) | MGD: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/)
MP: [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [MGD](https://www.informatics.jax.org/mgihome/other/copyright.shtml)
[MP](https://obofoundry.org/ontology/mp.html) | +| | RATHCOP | ENSEMBL Human to ENSEMBL Rat ortholog_ | reference | Globus | [PMID:36318249](https://pubmed.ncbi.nlm.nih.gov/36318249/) | [Reference](http://useast.ensembl.org/info/about/publications.html) | [Apache 2.0 ](https://www.apache.org/licenses/LICENSE-2.0) | [Reference](http://useast.ensembl.org/info/about/legal/code_licence.html) | +| | [MSIGDB](https://www.gsea-msigdb.org/gsea/msigdb) | Molecular Signatures Database | reference | Globus | [PMID:16199517](https://pubmed.ncbi.nlm.nih.gov/16199517/),[PMID:21546393](https://pubmed.ncbi.nlm.nih.gov/21546393/),[PMID:26771021](https://pubmed.ncbi.nlm.nih.gov/26771021/),[PMID:37704782](https://pubmed.ncbi.nlm.nih.gov/37704782/) | [Reference](https://www.gsea-msigdb.org/gsea/msigdb/index.jsp) | [CC BY](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.gsea-msigdb.org/gsea/msigdb_license_terms.jsp) | +| | HSCLO | Chromosome Location Ontology | ontology | Globus | [bioArXiv](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | | [CC BY NC ND 4.0 ](https://creativecommons.org/licenses/by-nc-nd/4.0/) | [Reference](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | +| | GENCODEHSCLO | GENCODE-HSCLO mapping | reference | Globus | GENCODE:[PMID:33270111](https://pubmed.ncbi.nlm.nih.gov/33270111/)
HSCLO: [bioArXiv](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | [GENCODE]([Reference](https://www.gencodegenes.org/pages/publications.html)) | GENCODE: [open access ](https://www.gencodegenes.org/pages/data_access.html)
HSCLO: [CC BY NC ND 4.0 ](https://creativecommons.org/licenses/by-nc-nd/4.0/) | [HSCLO](https://www.biorxiv.org/content/10.1101/2024.02.15.580505v1) | +| | [WP](https://www.wikipathways.org/) | WikiPathways gene-gene interactions | reference | Globus | [PMID:37941138](https://pubmed.ncbi.nlm.nih.gov/37941138/),[PMID:18651794](https://pubmed.ncbi.nlm.nih.gov/18651794/) | [Reference](https://www.wikipathways.org/cite.html) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/) | [Reference](https://www.wikipathways.org/cite.html) | +| | [CLINGEN](https://clinicalgenome.org/) | Clinical Genome selected datasets | reference | Globus | [PMID:26014595](https://pubmed.ncbi.nlm.nih.gov/26014595/) | [Reference](https://clinicalgenome.org/docs/terms-of-use/) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/) | [Reference](https://clinicalgenome.org/docs/terms-of-use/) | +| | [STRING](https://string-db.org/) | StringDB Protein-Protein Interaction Network | reference | Globus | [PMID:36370105](https://pubmed.ncbi.nlm.nih.gov/36370105/) | [Reference](https://string-db.org/cgi/about?footer_active_subpage=references) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://string-db.org/cgi/access?footer_active_subpage=licensing) | +| [4DNucleome](https://www.4dnucleome.org/) | [4DN](https://www.4dnucleome.org/) | 4D Nucleome | result | Globus | [PMID:28905911 ](https://pubmed.ncbi.nlm.nih.gov/28905911/),[PMID:35501320](https://pubmed.ncbi.nlm.nih.gov/35501320/) | [Reference](https://data.4dnucleome.org/) | Freely available | [Reference](https://data.4dnucleome.org/) | +| [Extracellular RNA Communication Consortium (ERCC)](https://exrna.org/) | [ERCCRBP](https://exrna.org/) | exRNA RNA Binding Proteins | result | Globus | [PMID:26320938](https://pubmed.ncbi.nlm.nih.gov/26320938/) | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | Pre-publication data sharing | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | +| | [ERCCREG](https://exrna.org/) | Regulatory Elements | result | Globus | [PMID:26320938](https://pubmed.ncbi.nlm.nih.gov/26320938/) | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | Pre-publication data sharing | [Reference](https://exrna.org/resources/data/data-access-policy-summary/) | +| [GlyGen](https://www.glygen.org/) | [FALDO](https://bioportal.bioontology.org/ontologies/FALDO) | Feature Annotation Description Ontology | ontology | NCBO BioPortal | | | | | +| | [UNIPROT](https://ftp.uniprot.org/pub/databases/uniprot/) | Universal Protein Resource | ontology | UniProt FTP | | | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://ftp.uniprot.org/pub/databases/uniprot/LICENSE) | +| | [GLYCORDF](https://github.com/glycoinfo/GlycoRDF) | Glycomics | ontology | GitHub | [PMID:24280648 ](https://pubmed.ncbi.nlm.nih.gov/24280648/) | [Reference](https://github.com/glycoinfo/GlycoRDF) | | | +| | [GLYCOCOO](https://github.com/glycoinfo/GlycoCoO) | Glycoconjugate | ontology | GitHub | | | | | +| | GLYCANS | Glycans data | result | Globus | [PMID:31616925](https://pubmed.ncbi.nlm.nih.gov/31616925/) | [Reference](https://www.glygen.org/how-to-cite/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.glygen.org/license/) | +| | PROTEOFORM | Proteoform | result | Globus | [PMID:31616925](https://pubmed.ncbi.nlm.nih.gov/31616925/) | [Reference](https://www.glygen.org/how-to-cite/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://www.glygen.org/license/) | +| [Genotype Tissue Expression (GTEx)](https://gtexportal.org/home/) | GTEXCOEXP | Co-expression | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | +| | GTEXEQTL | Expression | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | +| | GTEXEXP | Expression quantitative trait loci (eQTL) | result | Globus | [PMID:23715323 ](https://pubmed.ncbi.nlm.nih.gov/23715323/) | [Reference](https://gtexportal.org/home/aboutAdultGtex#staticTextPublicationPolicy) | Public | [Reference](https://gtexportal.org/home/license) | +| [Human BioMolecular Atlas Program (HuBMAP) ](https://hubmapconsortium.org/) | HMAZ | HuBMAP Azimuth Cell Expression Summary | result | Globus | [PMID:31597973](https://pubmed.ncbi.nlm.nih.gov/31597973/) | [Reference](https://hubmapconsortium.org/acknowledgement-in-publications/) | Data Use Agreement | [Reference](https://hubmapconsortium.org/wp-content/uploads/2020/06/DUA_FINAL_2020_02_03_for_Signature.pdf) | +| [Illuminating the Druggable Genome (IDG)](https://commonfund.nih.gov/idg) | IDGP | Compound-protein interactions | result | Globus | | | Open | [Reference](https://druggablegenome.net/IDGPolicies) | +| | IDGD | Compound-disease interactions | result | Globus | | | Open | [Reference](https://druggablegenome.net/IDGPolicies) | +| [Gabriella Miller Kids First](https://commonfund.nih.gov/KidsFirst) | KF | | result | Globus | | | | | +| [Library of Integrated Network-Based Cellular Signatures (LINCS)](https://commonfund.nih.gov/LINCS/) | LINCS | | result | Globus | | | freely available | [Reference](https://commonfund.nih.gov/LINCS) | +| [Molecular Transducers of Physical Activity Consortium (MoTrPAC)](https://commonfund.nih.gov/MolecularTransducers) | MOTRPAC | | result | Globus | | | | | +| [Metabolomics Workbench (MW)](https://commonfund.nih.gov/metabolomics/) | MW | Cell-metabolite mappings | result | Globus | [PMID:26467476](https://pubmed.ncbi.nlm.nih.gov/26467476/) | [Reference](https://www.metabolomicsworkbench.org/) | public domain | [Reference](https://www.metabolomicsworkbench.org/data/datasharing.php) | +| [Stimulating Peripheral Activity to Relieve Conditions (SPARC)](https://commonfund.nih.gov/Sparc/) | [NPO](https://bioportal.bioontology.org/ontologies/NPOKB) | Neuron Phenotype Ontology | ontology | NCBO BioPortal | | | | | +| | [NPOSCKAN](https://github.com/SciCrunch/NIF-Ontology/releases) | NPOSCKAN | ontology | GitHub | | | | | +| [Reactome](https://reactome.org/) | REACTOME | Pathways | reference | Globus | [PMID:37941124 ](https://pubmed.ncbi.nlm.nih.gov/37941124/) | [Reference](https://reactome.org/cite) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/),[CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://reactome.org/license) | +| [DisGenet](https://www.disgenet.org/) | DGN | Disease-gene associations | reference | Globus | [PMID:31680165](https://pubmed.ncbi.nlm.nih.gov/31680165/) | [Reference](https://www.disgenet.org/citation) | [CC-BY-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) | [Reference](https://www.disgenet.org/terms-of-use/) | +| [Biomarker Partnership Project](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/) | BIOMARKER | Biomarkers | reference | Globus | [PMID:35925813](https://pubmed.ncbi.nlm.nih.gov/35925813/),[PMID:34015823](https://pubmed.ncbi.nlm.nih.gov/34015823/),[PMID:32142370](https://pubmed.ncbi.nlm.nih.gov/32142370/) | [Reference](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/) | [CC BY 4.0 ](https://creativecommons.org/licenses/by/4.0/) | [Reference](https://hivelab.biochemistry.gwu.edu/biomarker-partnership/data) | +| [Open Targets](https://www.opentargets.org/) | OTG | Human genetics and genomics data for systematic drug target identification and prioritisation | reference | Globus | [PMID:36399499](https://pubmed.ncbi.nlm.nih.gov/36399499/) | [Reference](https://platform-docs.opentargets.org/citation) | [CC0](https://creativecommons.org/publicdomain/zero/1.0/) | [Reference](https://platform-docs.opentargets.org/licence) | diff --git a/docs/lang/en.json b/docs/lang/en.json index f119c2b..86ee10f 100644 --- a/docs/lang/en.json +++ b/docs/lang/en.json @@ -28,7 +28,10 @@ "name": "Formats", "href": "/formats" }, - + { + "name": "Version", + "href": "/version" + }, { "name": "Deployment", "href": "/deployment" diff --git a/docs/version/index.MD b/docs/version/index.MD new file mode 100644 index 0000000..5289498 --- /dev/null +++ b/docs/version/index.MD @@ -0,0 +1,57 @@ +# Unified Biomedical Knowledge Graph (UBKG) + +## Version Information + +A UBKG context comprises data imported from a large number of sources (SABs). +Source data comes in a variety of file formats, with varying frequencies of update: + +- Some data sources, such as Cell Ontology (CL), are updated frequently. +- Some data sources, such as the UMLS, are updated biannually, or infrequently. +- Some sources are static. + +# UBKG Context Release + +The release of a UBKG context will include a text file of Release Notes in the Zip archive of the context's distribution. +The release notes will include a "release date" for the entire context. + +The release date for a UBKG context corresponds to when the zipped Docker neo4j distribution of the context was made available in the public +download site. + +# SAB versioning +SABs vary greatly in how they represent version. Although some SABs have an explicit version identifier, many have no real version information. +SABs without explicit version date include all sources from the CFDE Data Coordinating Centers +that participated in the initial release of the Data Distillery. + +The UBKG assigns versions to SABs using the following algorithm: + +## OWL files +If the SAB source is an OWL file (includes OWL/RDF, OWL/XML, RDF, Turtle, SKOS): +1. Open the file in Protégé. +2. If there is a date or version identifier in the **Ontology Version IRI**, use that identifier. +3. If there is nothing in the Ontology Version IRI, check the **dc:date property**. Use this date, if one exists. +4, If there is nothing in **dc:date**, use the release date shown in the source of the OWL. (This is applicable to files from NCBOBioPortal.) +5. If no other date or version is available, use the date on which the file was downloaded. + +## Edge/Node files +If the SAB source is a set of files in UBKG edge/node format in Globus, use the latest file date of the edge and node files in Globus. + +## SimpleKnowledge spreadsheet +If the SAB source is a SimpleKnowledge spreadsheet, use the date when the file was pushed to the SimpleKnowledge GitHub repo. + +## Custom downloads +If the SAB source was extracted from a website (e.g., UniProtKB; GENCODE; RefSeq): +1.If the source indicates a version (e.g., in a README in the FTP folder, header in the file, etc.), use the version indicated. +2. If no version information available, use the download date. + +# UBKGSOURCE and versioning + +A UBKG context contains version information for its source SABs in a special ontology with SAB **UBKGSOURCE**. + +The UBKGSOURCE ontology combines for each SAB information from the [Contexts](https://ubkg.docs.xconsortia.org/contexts/) regarding +licensing and citations along with details on: +1. The version of the SAB ingested into the UBKG context +2. The date on which the SAB source was downloaded for ingestion + +# sources endpoint +The UBKG API provides the [sources](https://smart-api.info/ui/96e5b5c0b0efeef5b93ea98ac2794837#/default/sources_get) endpoint that translates information from the UBKGSOURCE ontology for the SABs in a UBKG context. +The SmartAPI page for the UBKG API describes the schema of the response of the **sources** endpoint. \ No newline at end of file