From 1fbe68f47c6e5418a53e77862b6b39d6871eb9cc Mon Sep 17 00:00:00 2001 From: Suhaib Mohammed Date: Fri, 19 Oct 2018 10:45:54 +0100 Subject: [PATCH] Feature/configuration update (#13) * Update release numbers- Ensembl 94 EnsemblGenomes 41 Wormbase 11 * added bacteria enesmbl links to scala code and removed unigene from a-l * removed attribute that doesnt exist for oryza_nivara populus_trichocarpa saccharomyces_cerevisiae * removed bacteria ensembl urls --- annsrcs/ensembl/aegilops_tauschii | 2 +- annsrcs/ensembl/amborella_trichopoda | 2 +- annsrcs/ensembl/anas_platyrhynchos | 2 +- annsrcs/ensembl/anolis_carolinensis | 3 +-- annsrcs/ensembl/anopheles_gambiae | 3 +-- annsrcs/ensembl/arabidopsis_lyrata | 2 +- annsrcs/ensembl/arabidopsis_thaliana | 2 +- annsrcs/ensembl/aspergillus_fumigatus | 2 +- annsrcs/ensembl/beta_vulgaris | 2 +- annsrcs/ensembl/bos_taurus | 3 +-- annsrcs/ensembl/brachypodium_distachyon | 2 +- annsrcs/ensembl/brassica_napus | 2 +- annsrcs/ensembl/brassica_oleracea | 2 +- annsrcs/ensembl/brassica_rapa | 2 +- annsrcs/ensembl/caenorhabditis_elegans | 2 +- annsrcs/ensembl/canis_familiaris | 2 +- annsrcs/ensembl/chlamydomonas_reinhardtii | 2 +- annsrcs/ensembl/chlorocebus_sabaeus | 2 +- annsrcs/ensembl/chondrus_crispus | 2 +- annsrcs/ensembl/ciona_intestinalis | 3 +-- annsrcs/ensembl/ciona_savignyi | 3 +-- annsrcs/ensembl/corchorus_capsularis | 2 +- annsrcs/ensembl/cyanidioschyzon_merolae | 2 +- annsrcs/ensembl/danio_rerio | 2 +- annsrcs/ensembl/dasypus_novemcinctus | 2 +- annsrcs/ensembl/drosophila_melanogaster | 2 +- annsrcs/ensembl/equus_caballus | 3 +-- annsrcs/ensembl/galdieria_sulphuraria | 2 +- annsrcs/ensembl/gallus_gallus | 3 +-- annsrcs/ensembl/glycine_max | 2 +- annsrcs/ensembl/gorilla_gorilla | 2 +- annsrcs/ensembl/homo_sapiens | 2 +- annsrcs/ensembl/hordeum_vulgare | 2 +- annsrcs/ensembl/leersia_perrieri | 2 +- annsrcs/ensembl/macaca_mulatta | 2 +- annsrcs/ensembl/medicago_truncatula | 2 +- annsrcs/ensembl/monodelphis_domestica | 2 +- annsrcs/ensembl/mus_musculus | 2 +- annsrcs/ensembl/musa_acuminata | 2 +- annsrcs/ensembl/ornithorhynchus_anatinus | 2 +- annsrcs/ensembl/oryctolagus_cuniculus | 2 +- annsrcs/ensembl/oryza_barthii | 2 +- annsrcs/ensembl/oryza_brachyantha | 2 +- annsrcs/ensembl/oryza_glaberrima | 2 +- annsrcs/ensembl/oryza_glumaepatula | 2 +- annsrcs/ensembl/oryza_indica | 2 +- annsrcs/ensembl/oryza_longistaminata | 2 +- annsrcs/ensembl/oryza_meridionalis | 2 +- annsrcs/ensembl/oryza_nivara | 4 +--- annsrcs/ensembl/oryza_punctata | 2 +- annsrcs/ensembl/oryza_rufipogon | 2 +- annsrcs/ensembl/oryza_sativa | 2 +- annsrcs/ensembl/ostreococcus_lucimarinus | 2 +- annsrcs/ensembl/ovis_aries | 2 +- annsrcs/ensembl/pan_troglodytes | 2 +- annsrcs/ensembl/papio_anubis | 2 +- annsrcs/ensembl/physcomitrella_patens | 2 +- annsrcs/ensembl/pongo_abelii | 2 +- annsrcs/ensembl/populus_trichocarpa | 5 +---- annsrcs/ensembl/prunus_persica | 2 +- annsrcs/ensembl/rattus_norvegicus | 2 +- annsrcs/ensembl/saccharomyces_cerevisiae | 5 ++--- annsrcs/ensembl/schizosaccharomyces_pombe | 2 +- annsrcs/ensembl/selaginella_moellendorffii | 2 +- annsrcs/ensembl/setaria_italica | 2 +- annsrcs/ensembl/solanum_lycopersicum | 2 +- annsrcs/ensembl/solanum_tuberosum | 2 +- annsrcs/ensembl/sorghum_bicolor | 2 +- annsrcs/ensembl/sus_scrofa | 2 +- annsrcs/ensembl/tetraodon_nigroviridis | 2 +- annsrcs/ensembl/theobroma_cacao | 2 +- annsrcs/ensembl/trifolium_pratense | 2 +- annsrcs/ensembl/triticum_aestivum | 2 +- annsrcs/ensembl/triticum_urartu | 2 +- annsrcs/ensembl/vitis_vinifera | 2 +- annsrcs/ensembl/xenopus_tropicalis | 2 +- annsrcs/ensembl/yarrowia_lipolytica | 2 +- annsrcs/ensembl/zea_mays | 2 +- annsrcs/wbps/caenorhabditis_elegans | 2 +- annsrcs/wbps/schistosoma_mansoni | 2 +- src/atlas/AtlasSpecies.sc | 2 +- src/pipeline/retrieve/BioMart.sc | 12 ++++++------ 82 files changed, 88 insertions(+), 101 deletions(-) diff --git a/annsrcs/ensembl/aegilops_tauschii b/annsrcs/ensembl/aegilops_tauschii index 699158f..6e4fdab 100644 --- a/annsrcs/ensembl/aegilops_tauschii +++ b/annsrcs/ensembl/aegilops_tauschii @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=aegilops tauschii databaseName=plants diff --git a/annsrcs/ensembl/amborella_trichopoda b/annsrcs/ensembl/amborella_trichopoda index 4eb840c..b7067ba 100644 --- a/annsrcs/ensembl/amborella_trichopoda +++ b/annsrcs/ensembl/amborella_trichopoda @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=amborella trichopoda databaseName=plants diff --git a/annsrcs/ensembl/anas_platyrhynchos b/annsrcs/ensembl/anas_platyrhynchos index c4338ee..c3b4922 100644 --- a/annsrcs/ensembl/anas_platyrhynchos +++ b/annsrcs/ensembl/anas_platyrhynchos @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=anas platyrhynchos databaseName=ensembl diff --git a/annsrcs/ensembl/anolis_carolinensis b/annsrcs/ensembl/anolis_carolinensis index e7eb341..b45b2e3 100644 --- a/annsrcs/ensembl/anolis_carolinensis +++ b/annsrcs/ensembl/anolis_carolinensis @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=anolis carolinensis databaseName=ensembl @@ -26,6 +26,5 @@ property.mirbase_id=mirbase_id property.ortholog=dnovemcinctus_homolog_ensembl_gene,cintestinalis_homolog_ensembl_gene,csavignyi_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ggallus_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,btaurus_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,ecaballus_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.refseq=refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot diff --git a/annsrcs/ensembl/anopheles_gambiae b/annsrcs/ensembl/anopheles_gambiae index d2d51de..1d5e28b 100644 --- a/annsrcs/ensembl/anopheles_gambiae +++ b/annsrcs/ensembl/anopheles_gambiae @@ -1,5 +1,5 @@ software.name=metazoa -software.version=39 +software.version=41 url=http://metazoa.ensembl.org/biomart/martservice? organism=anopheles gambiae databaseName=metazoa @@ -20,5 +20,4 @@ property.interpro=interpro property.interproterm=interpro_description property.refseq=refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot diff --git a/annsrcs/ensembl/arabidopsis_lyrata b/annsrcs/ensembl/arabidopsis_lyrata index afd41c3..1f84609 100644 --- a/annsrcs/ensembl/arabidopsis_lyrata +++ b/annsrcs/ensembl/arabidopsis_lyrata @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=arabidopsis lyrata databaseName=plants diff --git a/annsrcs/ensembl/arabidopsis_thaliana b/annsrcs/ensembl/arabidopsis_thaliana index 27dc9ce..e262ea0 100644 --- a/annsrcs/ensembl/arabidopsis_thaliana +++ b/annsrcs/ensembl/arabidopsis_thaliana @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=arabidopsis thaliana databaseName=plants diff --git a/annsrcs/ensembl/aspergillus_fumigatus b/annsrcs/ensembl/aspergillus_fumigatus index 706a108..d5e4d72 100644 --- a/annsrcs/ensembl/aspergillus_fumigatus +++ b/annsrcs/ensembl/aspergillus_fumigatus @@ -1,5 +1,5 @@ software.name=fungi -software.version=39 +software.version=41 url=http://fungi.ensembl.org/biomart/martservice? organism=aspergillus fumigatus databaseName=fungi diff --git a/annsrcs/ensembl/beta_vulgaris b/annsrcs/ensembl/beta_vulgaris index c631937..e8ed297 100644 --- a/annsrcs/ensembl/beta_vulgaris +++ b/annsrcs/ensembl/beta_vulgaris @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=beta vulgaris databaseName=plants diff --git a/annsrcs/ensembl/bos_taurus b/annsrcs/ensembl/bos_taurus index a61c69c..c9156b3 100644 --- a/annsrcs/ensembl/bos_taurus +++ b/annsrcs/ensembl/bos_taurus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=bos taurus databaseName=ensembl @@ -27,7 +27,6 @@ property.mirbase_id=mirbase_id property.ortholog=acarolinensis_homolog_ensembl_gene,dnovemcinctus_homolog_ensembl_gene,cintestinalis_homolog_ensembl_gene,csavignyi_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ggallus_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,ecaballus_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.refseq=refseq_mrna,refseq_ncrna,refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot arrayDesign.A-AFFY-128=affy_bovine diff --git a/annsrcs/ensembl/brachypodium_distachyon b/annsrcs/ensembl/brachypodium_distachyon index 942a5c5..3c98917 100644 --- a/annsrcs/ensembl/brachypodium_distachyon +++ b/annsrcs/ensembl/brachypodium_distachyon @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=brachypodium distachyon databaseName=plants diff --git a/annsrcs/ensembl/brassica_napus b/annsrcs/ensembl/brassica_napus index 4716b7e..830e2e1 100644 --- a/annsrcs/ensembl/brassica_napus +++ b/annsrcs/ensembl/brassica_napus @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=brassica napus databaseName=plants diff --git a/annsrcs/ensembl/brassica_oleracea b/annsrcs/ensembl/brassica_oleracea index c0b41d6..d3c0cf4 100644 --- a/annsrcs/ensembl/brassica_oleracea +++ b/annsrcs/ensembl/brassica_oleracea @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=brassica oleracea databaseName=plants diff --git a/annsrcs/ensembl/brassica_rapa b/annsrcs/ensembl/brassica_rapa index 789e2fd..bd2678c 100644 --- a/annsrcs/ensembl/brassica_rapa +++ b/annsrcs/ensembl/brassica_rapa @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=brassica rapa databaseName=plants diff --git a/annsrcs/ensembl/caenorhabditis_elegans b/annsrcs/ensembl/caenorhabditis_elegans index bf69f91..fc1da0b 100644 --- a/annsrcs/ensembl/caenorhabditis_elegans +++ b/annsrcs/ensembl/caenorhabditis_elegans @@ -1,5 +1,5 @@ software.name=metazoa -software.version=39 +software.version=41 url=http://metazoa.ensembl.org/biomart/martservice? organism=caenorhabditis elegans datasetName=celegans_eg_gene diff --git a/annsrcs/ensembl/canis_familiaris b/annsrcs/ensembl/canis_familiaris index 4ef8611..90383d7 100644 --- a/annsrcs/ensembl/canis_familiaris +++ b/annsrcs/ensembl/canis_familiaris @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=canis familiaris databaseName=ensembl diff --git a/annsrcs/ensembl/chlamydomonas_reinhardtii b/annsrcs/ensembl/chlamydomonas_reinhardtii index d8b709a..ebadb93 100644 --- a/annsrcs/ensembl/chlamydomonas_reinhardtii +++ b/annsrcs/ensembl/chlamydomonas_reinhardtii @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=chlamydomonas reinhardtii databaseName=plants diff --git a/annsrcs/ensembl/chlorocebus_sabaeus b/annsrcs/ensembl/chlorocebus_sabaeus index 0b69974..f8baaae 100644 --- a/annsrcs/ensembl/chlorocebus_sabaeus +++ b/annsrcs/ensembl/chlorocebus_sabaeus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=chlorocebus sabaeus databaseName=ensembl diff --git a/annsrcs/ensembl/chondrus_crispus b/annsrcs/ensembl/chondrus_crispus index c163072..43c4c1a 100644 --- a/annsrcs/ensembl/chondrus_crispus +++ b/annsrcs/ensembl/chondrus_crispus @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=chondrus crispus databaseName=plants diff --git a/annsrcs/ensembl/ciona_intestinalis b/annsrcs/ensembl/ciona_intestinalis index 26f7bff..ea956e2 100644 --- a/annsrcs/ensembl/ciona_intestinalis +++ b/annsrcs/ensembl/ciona_intestinalis @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=ciona intestinalis databaseName=ensembl @@ -26,7 +26,6 @@ property.mirbase_id=mirbase_id property.ortholog=acarolinensis_homolog_ensembl_gene,dnovemcinctus_homolog_ensembl_gene,csavignyi_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ggallus_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,btaurus_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,ecaballus_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.refseq=refseq_mrna,refseq_ncrna,refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot arrayDesign.A-AFFY-106=affy_cint06a520380f diff --git a/annsrcs/ensembl/ciona_savignyi b/annsrcs/ensembl/ciona_savignyi index bf882fe..451041a 100644 --- a/annsrcs/ensembl/ciona_savignyi +++ b/annsrcs/ensembl/ciona_savignyi @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=ciona savignyi databaseName=ensembl @@ -23,6 +23,5 @@ property.mirbase_accession=mirbase_accession property.mirbase_id=mirbase_id property.ortholog=acarolinensis_homolog_ensembl_gene,dnovemcinctus_homolog_ensembl_gene,cintestinalis_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ggallus_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,btaurus_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,ecaballus_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot diff --git a/annsrcs/ensembl/corchorus_capsularis b/annsrcs/ensembl/corchorus_capsularis index b066764..7975ba1 100644 --- a/annsrcs/ensembl/corchorus_capsularis +++ b/annsrcs/ensembl/corchorus_capsularis @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=corchorus capsularis databaseName=plants diff --git a/annsrcs/ensembl/cyanidioschyzon_merolae b/annsrcs/ensembl/cyanidioschyzon_merolae index 4ca9b32..ab48b0c 100644 --- a/annsrcs/ensembl/cyanidioschyzon_merolae +++ b/annsrcs/ensembl/cyanidioschyzon_merolae @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=cyanidioschyzon merolae databaseName=plants diff --git a/annsrcs/ensembl/danio_rerio b/annsrcs/ensembl/danio_rerio index b533eee..002b398 100644 --- a/annsrcs/ensembl/danio_rerio +++ b/annsrcs/ensembl/danio_rerio @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=danio rerio databaseName=ensembl diff --git a/annsrcs/ensembl/dasypus_novemcinctus b/annsrcs/ensembl/dasypus_novemcinctus index e97f711..43b3169 100644 --- a/annsrcs/ensembl/dasypus_novemcinctus +++ b/annsrcs/ensembl/dasypus_novemcinctus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=dasypus novemcinctus databaseName=ensembl diff --git a/annsrcs/ensembl/drosophila_melanogaster b/annsrcs/ensembl/drosophila_melanogaster index 3bc9378..52f834f 100644 --- a/annsrcs/ensembl/drosophila_melanogaster +++ b/annsrcs/ensembl/drosophila_melanogaster @@ -1,5 +1,5 @@ software.name=metazoa -software.version=39 +software.version=41 url=http://metazoa.ensembl.org/biomart/martservice? organism=drosophila melanogaster databaseName=metazoa diff --git a/annsrcs/ensembl/equus_caballus b/annsrcs/ensembl/equus_caballus index be7d4ba..bf984c6 100644 --- a/annsrcs/ensembl/equus_caballus +++ b/annsrcs/ensembl/equus_caballus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=equus caballus databaseName=ensembl @@ -26,6 +26,5 @@ property.mirbase_id=mirbase_id property.ortholog=acarolinensis_homolog_ensembl_gene,dnovemcinctus_homolog_ensembl_gene,cintestinalis_homolog_ensembl_gene,csavignyi_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ggallus_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,btaurus_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.refseq=refseq_mrna,refseq_ncrna,refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot diff --git a/annsrcs/ensembl/galdieria_sulphuraria b/annsrcs/ensembl/galdieria_sulphuraria index 3b112d1..2161b0f 100644 --- a/annsrcs/ensembl/galdieria_sulphuraria +++ b/annsrcs/ensembl/galdieria_sulphuraria @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=galdieria sulphuraria databaseName=plants diff --git a/annsrcs/ensembl/gallus_gallus b/annsrcs/ensembl/gallus_gallus index 4c9bf09..0125221 100644 --- a/annsrcs/ensembl/gallus_gallus +++ b/annsrcs/ensembl/gallus_gallus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=gallus gallus databaseName=ensembl @@ -27,6 +27,5 @@ property.mirbase_id=mirbase_id property.ortholog=acarolinensis_homolog_ensembl_gene,dnovemcinctus_homolog_ensembl_gene,cintestinalis_homolog_ensembl_gene,csavignyi_homolog_ensembl_gene,celegans_homolog_ensembl_gene,ptroglodytes_homolog_ensembl_gene,btaurus_homolog_ensembl_gene,cfamiliaris_homolog_ensembl_gene,aplatyrhynchos_homolog_ensembl_gene,dmelanogaster_homolog_ensembl_gene,ggorilla_homolog_ensembl_gene,ecaballus_homolog_ensembl_gene,hsapiens_homolog_ensembl_gene,mmulatta_homolog_ensembl_gene,mmusculus_homolog_ensembl_gene,panubis_homolog_ensembl_gene,mdomestica_homolog_ensembl_gene,pabelii_homolog_ensembl_gene,sscrofa_homolog_ensembl_gene,oanatinus_homolog_ensembl_gene,ocuniculus_homolog_ensembl_gene,rnorvegicus_homolog_ensembl_gene,scerevisiae_homolog_ensembl_gene,oaries_homolog_ensembl_gene,tnigroviridis_homolog_ensembl_gene,csabaeus_homolog_ensembl_gene,xtropicalis_homolog_ensembl_gene,drerio_homolog_ensembl_gene property.refseq=refseq_mrna,refseq_ncrna,refseq_peptide property.symbol=external_gene_name -property.unigene=unigene property.uniprot=uniprotsptrembl,uniprotswissprot arrayDesign.A-AFFY-103=affy_chicken diff --git a/annsrcs/ensembl/glycine_max b/annsrcs/ensembl/glycine_max index a5cfaf2..6ae4a02 100644 --- a/annsrcs/ensembl/glycine_max +++ b/annsrcs/ensembl/glycine_max @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=glycine max databaseName=plants diff --git a/annsrcs/ensembl/gorilla_gorilla b/annsrcs/ensembl/gorilla_gorilla index f636f45..f3b8775 100644 --- a/annsrcs/ensembl/gorilla_gorilla +++ b/annsrcs/ensembl/gorilla_gorilla @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=gorilla gorilla databaseName=ensembl diff --git a/annsrcs/ensembl/homo_sapiens b/annsrcs/ensembl/homo_sapiens index c6beabd..66f00ba 100644 --- a/annsrcs/ensembl/homo_sapiens +++ b/annsrcs/ensembl/homo_sapiens @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=homo sapiens databaseName=ensembl diff --git a/annsrcs/ensembl/hordeum_vulgare b/annsrcs/ensembl/hordeum_vulgare index c63e11f..311d302 100644 --- a/annsrcs/ensembl/hordeum_vulgare +++ b/annsrcs/ensembl/hordeum_vulgare @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=hordeum vulgare databaseName=plants diff --git a/annsrcs/ensembl/leersia_perrieri b/annsrcs/ensembl/leersia_perrieri index 2431b7b..fec5ac1 100644 --- a/annsrcs/ensembl/leersia_perrieri +++ b/annsrcs/ensembl/leersia_perrieri @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=leersia perrieri databaseName=plants diff --git a/annsrcs/ensembl/macaca_mulatta b/annsrcs/ensembl/macaca_mulatta index 70bfb0c..99bf00d 100644 --- a/annsrcs/ensembl/macaca_mulatta +++ b/annsrcs/ensembl/macaca_mulatta @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=macaca mulatta databaseName=ensembl diff --git a/annsrcs/ensembl/medicago_truncatula b/annsrcs/ensembl/medicago_truncatula index 16ca419..a2d4028 100644 --- a/annsrcs/ensembl/medicago_truncatula +++ b/annsrcs/ensembl/medicago_truncatula @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=medicago truncatula databaseName=plants diff --git a/annsrcs/ensembl/monodelphis_domestica b/annsrcs/ensembl/monodelphis_domestica index 099723f..2709524 100644 --- a/annsrcs/ensembl/monodelphis_domestica +++ b/annsrcs/ensembl/monodelphis_domestica @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=monodelphis domestica databaseName=ensembl diff --git a/annsrcs/ensembl/mus_musculus b/annsrcs/ensembl/mus_musculus index df3ca51..837c136 100644 --- a/annsrcs/ensembl/mus_musculus +++ b/annsrcs/ensembl/mus_musculus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=mus musculus databaseName=ensembl diff --git a/annsrcs/ensembl/musa_acuminata b/annsrcs/ensembl/musa_acuminata index bc19807..2809d28 100644 --- a/annsrcs/ensembl/musa_acuminata +++ b/annsrcs/ensembl/musa_acuminata @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=musa acuminata databaseName=plants diff --git a/annsrcs/ensembl/ornithorhynchus_anatinus b/annsrcs/ensembl/ornithorhynchus_anatinus index ed851a2..0017400 100644 --- a/annsrcs/ensembl/ornithorhynchus_anatinus +++ b/annsrcs/ensembl/ornithorhynchus_anatinus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=ornithorhynchus anatinus databaseName=ensembl diff --git a/annsrcs/ensembl/oryctolagus_cuniculus b/annsrcs/ensembl/oryctolagus_cuniculus index c142591..482ff94 100644 --- a/annsrcs/ensembl/oryctolagus_cuniculus +++ b/annsrcs/ensembl/oryctolagus_cuniculus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=oryctolagus cuniculus databaseName=ensembl diff --git a/annsrcs/ensembl/oryza_barthii b/annsrcs/ensembl/oryza_barthii index a5bddd4..707e6f8 100644 --- a/annsrcs/ensembl/oryza_barthii +++ b/annsrcs/ensembl/oryza_barthii @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza barthii databaseName=plants diff --git a/annsrcs/ensembl/oryza_brachyantha b/annsrcs/ensembl/oryza_brachyantha index 9c4f435..76a177d 100644 --- a/annsrcs/ensembl/oryza_brachyantha +++ b/annsrcs/ensembl/oryza_brachyantha @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza brachyantha databaseName=plants diff --git a/annsrcs/ensembl/oryza_glaberrima b/annsrcs/ensembl/oryza_glaberrima index 3a44e20..a997bc0 100644 --- a/annsrcs/ensembl/oryza_glaberrima +++ b/annsrcs/ensembl/oryza_glaberrima @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza glaberrima databaseName=plants diff --git a/annsrcs/ensembl/oryza_glumaepatula b/annsrcs/ensembl/oryza_glumaepatula index f3fa6f6..be37bef 100644 --- a/annsrcs/ensembl/oryza_glumaepatula +++ b/annsrcs/ensembl/oryza_glumaepatula @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza glumaepatula databaseName=plants diff --git a/annsrcs/ensembl/oryza_indica b/annsrcs/ensembl/oryza_indica index 57e6ff9..c620d33 100644 --- a/annsrcs/ensembl/oryza_indica +++ b/annsrcs/ensembl/oryza_indica @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza indica databaseName=plants diff --git a/annsrcs/ensembl/oryza_longistaminata b/annsrcs/ensembl/oryza_longistaminata index f983228..4d0f785 100644 --- a/annsrcs/ensembl/oryza_longistaminata +++ b/annsrcs/ensembl/oryza_longistaminata @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza longistaminata databaseName=plants diff --git a/annsrcs/ensembl/oryza_meridionalis b/annsrcs/ensembl/oryza_meridionalis index 77da9a1..55ea04e 100644 --- a/annsrcs/ensembl/oryza_meridionalis +++ b/annsrcs/ensembl/oryza_meridionalis @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza meridionalis databaseName=plants diff --git a/annsrcs/ensembl/oryza_nivara b/annsrcs/ensembl/oryza_nivara index 350cbc7..0d76f29 100644 --- a/annsrcs/ensembl/oryza_nivara +++ b/annsrcs/ensembl/oryza_nivara @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza nivara databaseName=plants @@ -16,8 +16,6 @@ property.go=go_id property.goterm=name_1006 property.interpro=interpro property.interproterm=interpro_description -property.refseq=refseq_peptide property.symbol=wikigene_name property.uniprot=uniprotsptrembl property.symbol=external_gene_name -#chromosomeName=1,2,3,4,5,6,7,8,9,10,11,12 diff --git a/annsrcs/ensembl/oryza_punctata b/annsrcs/ensembl/oryza_punctata index 17be4d7..57d0ca3 100644 --- a/annsrcs/ensembl/oryza_punctata +++ b/annsrcs/ensembl/oryza_punctata @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza punctata databaseName=plants diff --git a/annsrcs/ensembl/oryza_rufipogon b/annsrcs/ensembl/oryza_rufipogon index d6f5836..c5fa818 100644 --- a/annsrcs/ensembl/oryza_rufipogon +++ b/annsrcs/ensembl/oryza_rufipogon @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza rufipogon databaseName=plants diff --git a/annsrcs/ensembl/oryza_sativa b/annsrcs/ensembl/oryza_sativa index 9675170..07cd020 100644 --- a/annsrcs/ensembl/oryza_sativa +++ b/annsrcs/ensembl/oryza_sativa @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=oryza sativa databaseName=plants diff --git a/annsrcs/ensembl/ostreococcus_lucimarinus b/annsrcs/ensembl/ostreococcus_lucimarinus index 629ebfe..2c04f22 100644 --- a/annsrcs/ensembl/ostreococcus_lucimarinus +++ b/annsrcs/ensembl/ostreococcus_lucimarinus @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=ostreococcus lucimarinus databaseName=plants diff --git a/annsrcs/ensembl/ovis_aries b/annsrcs/ensembl/ovis_aries index 55220b7..efb0ab4 100644 --- a/annsrcs/ensembl/ovis_aries +++ b/annsrcs/ensembl/ovis_aries @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=homo sapiens databaseName=ensembl diff --git a/annsrcs/ensembl/pan_troglodytes b/annsrcs/ensembl/pan_troglodytes index 5ac3f57..b146421 100644 --- a/annsrcs/ensembl/pan_troglodytes +++ b/annsrcs/ensembl/pan_troglodytes @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=pan troglodytes databaseName=ensembl diff --git a/annsrcs/ensembl/papio_anubis b/annsrcs/ensembl/papio_anubis index bc2b8db..aa3e8df 100644 --- a/annsrcs/ensembl/papio_anubis +++ b/annsrcs/ensembl/papio_anubis @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=papio anubis databaseName=ensembl diff --git a/annsrcs/ensembl/physcomitrella_patens b/annsrcs/ensembl/physcomitrella_patens index f10422e..80b8ad6 100644 --- a/annsrcs/ensembl/physcomitrella_patens +++ b/annsrcs/ensembl/physcomitrella_patens @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=physcomitrella patens databaseName=plants diff --git a/annsrcs/ensembl/pongo_abelii b/annsrcs/ensembl/pongo_abelii index 15f9d04..36e5d38 100644 --- a/annsrcs/ensembl/pongo_abelii +++ b/annsrcs/ensembl/pongo_abelii @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=pongo abelii databaseName=ensembl diff --git a/annsrcs/ensembl/populus_trichocarpa b/annsrcs/ensembl/populus_trichocarpa index 4ec0901..f0fb869 100644 --- a/annsrcs/ensembl/populus_trichocarpa +++ b/annsrcs/ensembl/populus_trichocarpa @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=populus trichocarpa databaseName=plants @@ -14,12 +14,9 @@ property.ensprotein=ensembl_peptide_id property.enstranscript=ensembl_transcript_id property.go=go_id property.goterm=name_1006 -property.po=po_id -property.poterm=po_name_1006 property.interpro=interpro property.interproterm=interpro_description property.refseq=refseq_peptide property.symbol=external_gene_name property.uniprot=uniprotsptrembl,uniprotswissprot arrayDesign.A-AFFY-131=affy_poplar 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diff --git a/annsrcs/ensembl/prunus_persica b/annsrcs/ensembl/prunus_persica index 7c83055..22b9902 100644 --- a/annsrcs/ensembl/prunus_persica +++ b/annsrcs/ensembl/prunus_persica @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=prunus persica databaseName=plants diff --git a/annsrcs/ensembl/rattus_norvegicus b/annsrcs/ensembl/rattus_norvegicus index 8ab3d72..ef00c5f 100644 --- a/annsrcs/ensembl/rattus_norvegicus +++ b/annsrcs/ensembl/rattus_norvegicus @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=rattus norvegicus databaseName=ensembl diff --git a/annsrcs/ensembl/saccharomyces_cerevisiae b/annsrcs/ensembl/saccharomyces_cerevisiae index 34d4de6..511392b 100644 --- a/annsrcs/ensembl/saccharomyces_cerevisiae +++ b/annsrcs/ensembl/saccharomyces_cerevisiae @@ -1,5 +1,5 @@ software.name=fungi -software.version=39 +software.version=41 url=http://fungi.ensembl.org/biomart/martservice? organism=saccharomyces cerevisiae databaseName=fungi @@ -17,8 +17,7 @@ property.go=go_id property.goterm=name_1006 property.interpro=interpro property.interproterm=interpro_description -property.symbol=external_gene_name -property.uniprot=uniprotsptrembl,uniprotswissprot +property.uniprot=uniprotswissprot arrayDesign.A-AFFY-27=affy_yg_s98 arrayDesign.A-AFFY-47=affy_yeast_2 diff --git a/annsrcs/ensembl/schizosaccharomyces_pombe b/annsrcs/ensembl/schizosaccharomyces_pombe index ccb2505..dd5f913 100644 --- a/annsrcs/ensembl/schizosaccharomyces_pombe +++ b/annsrcs/ensembl/schizosaccharomyces_pombe @@ -1,5 +1,5 @@ software.name=fungi -software.version=39 +software.version=41 url=http://fungi.ensembl.org/biomart/martservice? organism=schizosaccharomyces pombe databaseName=fungi diff --git a/annsrcs/ensembl/selaginella_moellendorffii b/annsrcs/ensembl/selaginella_moellendorffii index 934e04e..2d818ad 100644 --- a/annsrcs/ensembl/selaginella_moellendorffii +++ b/annsrcs/ensembl/selaginella_moellendorffii @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=selaginella moellendorffii databaseName=plants diff --git a/annsrcs/ensembl/setaria_italica b/annsrcs/ensembl/setaria_italica index 766ffea..dd2dd3c 100644 --- a/annsrcs/ensembl/setaria_italica +++ b/annsrcs/ensembl/setaria_italica @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=setaria italica databaseName=plants diff --git a/annsrcs/ensembl/solanum_lycopersicum b/annsrcs/ensembl/solanum_lycopersicum index 9aaee54..866e676 100644 --- a/annsrcs/ensembl/solanum_lycopersicum +++ b/annsrcs/ensembl/solanum_lycopersicum @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=solanum lycopersicum databaseName=plants diff --git a/annsrcs/ensembl/solanum_tuberosum b/annsrcs/ensembl/solanum_tuberosum index 4faa77e..e90318e 100644 --- a/annsrcs/ensembl/solanum_tuberosum +++ b/annsrcs/ensembl/solanum_tuberosum @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=solanum tuberosum databaseName=plants diff --git a/annsrcs/ensembl/sorghum_bicolor b/annsrcs/ensembl/sorghum_bicolor index 5d6cce8..db4e29c 100644 --- a/annsrcs/ensembl/sorghum_bicolor +++ b/annsrcs/ensembl/sorghum_bicolor @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=sorghum bicolor databaseName=plants diff --git a/annsrcs/ensembl/sus_scrofa b/annsrcs/ensembl/sus_scrofa index 1a92e59..878b731 100644 --- a/annsrcs/ensembl/sus_scrofa +++ b/annsrcs/ensembl/sus_scrofa @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=sus scrofa databaseName=ensembl diff --git a/annsrcs/ensembl/tetraodon_nigroviridis b/annsrcs/ensembl/tetraodon_nigroviridis index 43e8899..49bdd44 100644 --- a/annsrcs/ensembl/tetraodon_nigroviridis +++ b/annsrcs/ensembl/tetraodon_nigroviridis @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=tetraodon nigroviridis databaseName=ensembl diff --git a/annsrcs/ensembl/theobroma_cacao b/annsrcs/ensembl/theobroma_cacao index ec3daeb..1e910b3 100644 --- a/annsrcs/ensembl/theobroma_cacao +++ b/annsrcs/ensembl/theobroma_cacao @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=theobroma cacao databaseName=plants diff --git a/annsrcs/ensembl/trifolium_pratense b/annsrcs/ensembl/trifolium_pratense index 30de933..49df413 100644 --- a/annsrcs/ensembl/trifolium_pratense +++ b/annsrcs/ensembl/trifolium_pratense @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=trifolium pratense databaseName=plants diff --git a/annsrcs/ensembl/triticum_aestivum b/annsrcs/ensembl/triticum_aestivum index 4b01917..8c49af4 100644 --- a/annsrcs/ensembl/triticum_aestivum +++ b/annsrcs/ensembl/triticum_aestivum @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=triticum aestivum databaseName=plants diff --git a/annsrcs/ensembl/triticum_urartu b/annsrcs/ensembl/triticum_urartu index 8f8c825..8b967c0 100644 --- a/annsrcs/ensembl/triticum_urartu +++ b/annsrcs/ensembl/triticum_urartu @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=triticum urartu databaseName=plants diff --git a/annsrcs/ensembl/vitis_vinifera b/annsrcs/ensembl/vitis_vinifera index 9d4e241..fb69877 100644 --- a/annsrcs/ensembl/vitis_vinifera +++ b/annsrcs/ensembl/vitis_vinifera @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=vitis vinifera databaseName=plants diff --git a/annsrcs/ensembl/xenopus_tropicalis b/annsrcs/ensembl/xenopus_tropicalis index b5db4ac..ecc6102 100644 --- a/annsrcs/ensembl/xenopus_tropicalis +++ b/annsrcs/ensembl/xenopus_tropicalis @@ -1,5 +1,5 @@ software.name=ensembl -software.version=92 +software.version=94 url=http://www.ensembl.org/biomart/martservice? organism=xenopus tropicalis databaseName=ensembl diff --git a/annsrcs/ensembl/yarrowia_lipolytica b/annsrcs/ensembl/yarrowia_lipolytica index 43ff82c..31e27be 100644 --- a/annsrcs/ensembl/yarrowia_lipolytica +++ b/annsrcs/ensembl/yarrowia_lipolytica @@ -1,5 +1,5 @@ software.name=fungi -software.version=39 +software.version=41 url=http://fungi.ensembl.org/biomart/martservice? organism=yarrowia lipolytica databaseName=fungi diff --git a/annsrcs/ensembl/zea_mays b/annsrcs/ensembl/zea_mays index c35e9fc..144eac4 100644 --- a/annsrcs/ensembl/zea_mays +++ b/annsrcs/ensembl/zea_mays @@ -1,5 +1,5 @@ software.name=plants -software.version=39 +software.version=41 url=http://plants.ensembl.org/biomart/martservice? organism=zea mays databaseName=plants diff --git a/annsrcs/wbps/caenorhabditis_elegans b/annsrcs/wbps/caenorhabditis_elegans index 8912d65..43fa69d 100644 --- a/annsrcs/wbps/caenorhabditis_elegans +++ b/annsrcs/wbps/caenorhabditis_elegans @@ -1,5 +1,5 @@ software.name=parasite -software.version=10 +software.version=11 url=http://parasite.wormbase.org/biomart/martservice? organism=caenorhabditis elegans datasetName=wbps_gene diff --git a/annsrcs/wbps/schistosoma_mansoni b/annsrcs/wbps/schistosoma_mansoni index cef4715..c02f203 100644 --- a/annsrcs/wbps/schistosoma_mansoni +++ b/annsrcs/wbps/schistosoma_mansoni @@ -1,5 +1,5 @@ software.name=parasite -software.version=10 +software.version=11 url=http://parasite.wormbase.org/biomart/martservice? organism=schistosoma mansoni datasetName=wbps_gene diff --git a/src/atlas/AtlasSpecies.sc b/src/atlas/AtlasSpecies.sc index ef4e981..4ecee08 100644 --- a/src/atlas/AtlasSpecies.sc +++ b/src/atlas/AtlasSpecies.sc @@ -49,7 +49,7 @@ object AtlasSpeciesFactory { "metazoa" -> List(("Ensembl Genomes", "https://metazoa.ensembl.org/")), "fungi" -> List(("Ensembl Genomes", "https://fungi.ensembl.org/")), "parasite" -> List(("Wormbase ParaSite", "https://parasite.wormbase.org/")), - "plants" -> List(("Gramene", "http://ensembl.gramene.org/"),("Ensembl Genomes", "https://plants.ensembl.org/")), + "plants" -> List(("Gramene", "https://ensembl.gramene.org/"),("Ensembl Genomes", "https://plants.ensembl.org/")), "protists" -> List(("Ensembl Genomes", "https://protists.ensembl.org/")) ) ) diff --git a/src/pipeline/retrieve/BioMart.sc b/src/pipeline/retrieve/BioMart.sc index 10c130c..e07ec98 100644 --- a/src/pipeline/retrieve/BioMart.sc +++ b/src/pipeline/retrieve/BioMart.sc @@ -10,12 +10,12 @@ import $file.^.^.property.AtlasProperty def request(databaseName: String,properties: Map[String, String]) : HttpRequest = { val base = databaseName match { - case "metazoa" => "http://metazoa.ensembl.org" - case "plants" => "http://plants.ensembl.org" - case "fungi" => "http://fungi.ensembl.org" - case "parasite" => "http://parasite.wormbase.org" - case "protists" => "http://protists.ensembl.org" - case _ => "http://www.ensembl.org" + case "metazoa" => "https://metazoa.ensembl.org" + case "plants" => "https://plants.ensembl.org" + case "fungi" => "https://fungi.ensembl.org" + case "parasite" => "https://parasite.wormbase.org" + case "protists" => "https://protists.ensembl.org" + case _ => "https://www.ensembl.org" } Http(base+"/biomart/martservice").params(properties).timeout(connTimeoutMs = 5000, readTimeoutMs = 1000000) }