From 4eaaa33296939edfdbb1881c18885958302c92d2 Mon Sep 17 00:00:00 2001 From: Magali Ruffier <mr6@ebi.ac.uk> Date: Mon, 23 Oct 2017 13:11:49 +0100 Subject: [PATCH] config update for 91 --- misc-scripts/xref_mapping/xref_config.ini | 248 +++++++++++++++++++++- 1 file changed, 238 insertions(+), 10 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index ad769686e1..bd2f9168de 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -784,7 +784,7 @@ priority = 1 prio_descr = parser = CCDSParser release_uri = -data_uri = script:host=>mysql-ens-genebuild-prod-5,dbname=>rishi_ccds_human_88,port=>4531,tran_name=>ENST, +data_uri = script:host=>mysql-ens-genebuild-prod-4,dbname=>osagie_human_cdsonly_clone_2017_09,port=>4530,tran_name=>ENST, [source CCDS::mus_musculus] # Used by mus_musculus @@ -795,7 +795,7 @@ priority = 1 prio_descr = parser = CCDSParser release_uri = -data_uri = script:host=>mysql-ens-genebuild-prod-5,dbname=>rishi_ccds_mouse_88,port=>4531,tran_name=>ENSMUST, +data_uri = script:host=>mysql-ens-genebuild-prod-4,dbname=>osagie_mouse_cdsonly_clone_2017_09,port=>4530,tran_name=>ENSMUST, [source Celera_Pep::anopheles_gambiae] # Used by anopheles_gambiae @@ -1036,16 +1036,49 @@ parser = CGNCParser release_uri = data_uri = http://birdgenenames.org/cgnc/downloads.jsp?file=standard -[source VGNC::MULTI] +[source VGNC::pan_troglodytes] # Used by pan_troglodytes name = VGNC download = Y order = 29 priority = 1 prio_descr = -parser = HGNCParser +parser = VGNCParser +release_uri = +data_uri = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/chimpanzee/chimpanzee_vgnc_gene_set_All.txt + +[source VGNC::bos_taurus] +# Used by bos_taurus +name = VGNC +download = Y +order = 29 +priority = 1 +prio_descr = +parser = VGNCParser +release_uri = +data_uri = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/cow/cow_vgnc_gene_set_All.txt + +[source VGNC::canis_familiaris] +# Used by canis_familiaris +name = VGNC +download = Y +order = 29 +priority = 1 +prio_descr = +parser = VGNCParser +release_uri = +data_uri = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/dog/dog_vgnc_gene_set_All.txt + +[source VGNC::equus_caballus] +# Used by equus_caballus +name = VGNC +download = Y +order = 29 +priority = 1 +prio_descr = +parser = VGNCParser release_uri = -data_uri = file:VGNC_to_Ensembl_mapping.txt.gz +data_uri = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/horse/horse_vgnc_gene_set_All.txt [source VGNC::MULTI#01] name = VGNC @@ -1126,7 +1159,7 @@ priority = 2 prio_descr = ccds parser = HGNC_CCDSParser release_uri = -data_uri = script:wget=>http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>mysql-ens-genebuild-prod-5,dbname=>rishi_ccds_human_88,port=>4531,tran_name=>ENST, +data_uri = script:wget=>http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>mysql-ens-genebuild-prod-4,dbname=>osagie_human_cdsonly_clone_2017_09,port=>4530,tran_name=>ENST, [source HGNC::homo_sapiens#07] @@ -2234,7 +2267,7 @@ priority = 2 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = -data_uri = script:host=>mysql-ens-genebuild-prod-5,dbname=>rishi_ccds_human_88,port=>4531,tran_name=>ENST, +data_uri = script:host=>mysql-ens-genebuild-prod-4,dbname=>osagie_human_cdsonly_clone_2017_09,port=>4530,tran_name=>ENST, [source RefSeq_dna::homo_sapiens#01] # Used by homo_sapiens @@ -2280,7 +2313,7 @@ priority = 2 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = -data_uri = script:host=>mysql-ens-genebuild-prod-5,dbname=>rishi_ccds_mouse_88,port=>4531,tran_name=>ENSMUST, +data_uri = script:host=>mysql-ens-genebuild-prod-4,dbname=>osagie_mouse_cdsonly_clone_2017_09,port=>4530,tran_name=>ENSMUST, [source RefSeq_dna::pan_troglodytes] @@ -5238,6 +5271,198 @@ source = Ribosomal_Protein_Gene_DB::anopheles_gambiae source = AnoXcel::anopheles_gambiae source = ArrayExpress::EG +[species aotus_nancymaae] +taxonomy_id = 37293 +aliases = aotus_nancymaae +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species cebus_capucinus] +taxonomy_id = 9516 +aliases = cebus_capucinus +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species cercocebus_atys] +taxonomy_id = 9531 +aliases = cercocebus_atys +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species colobus_angolensis_palliatus] +taxonomy_id = 336983 +aliases = colobus_angolensis_palliatus +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species macaca_fascicularis] +taxonomy_id = 9541 +aliases = macaca_fascicularis +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species macaca_nemestrina] +taxonomy_id = 9545 +aliases = macaca_nemestrina +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species mandrillus_leucophaeus] +taxonomy_id = 9568 +aliases = mandrillus_leucophaeus +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species pan_paniscus] +taxonomy_id = 9597 +aliases = pan_paniscus +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species propithecus_coquereli] +taxonomy_id = 379532 +aliases = propithecus_coquereli +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species rhinopithecus_bieti] +taxonomy_id = 61621 +aliases = rhinopithecus_bieti +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species rhinopithecus_roxellana] +taxonomy_id = 61622 +aliases = rhinopithecus_bieti +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species saimiri_boliviensis_boliviensis] +taxonomy_id = 39432 +aliases = saimiri_boliviensis_boliviensis +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = RefSeq_import::otherfeatures +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species apis_mellifera] taxonomy_id = 7460 aliases = amellifera, apismellifera, honeybee @@ -5610,6 +5835,7 @@ source = ArrayExpress::EG [species bos_taurus] taxonomy_id = 9913 aliases = bostaurus, btaurus, cow +source = VGNC::bos_taurus source = EntrezGene::MULTI source = Reactome::MULTI source = RNACentral::MULTI @@ -5643,6 +5869,7 @@ source = ArrayExpress::MULTI [species canis_familiaris] taxonomy_id = 9615 aliases = canisfamiliaris, cfamiliaris, dog, doggy +source = VGNC::canis_familiaris source = EntrezGene::MULTI source = Reactome::MULTI source = RNACentral::MULTI @@ -6082,6 +6309,7 @@ source = ArrayExpress::MULTI [species equus_caballus] taxonomy_id = 9796 aliases = horse +source = VGNC::equus_caballus source = EntrezGene::MULTI source = Reactome::MULTI source = RNACentral::MULTI @@ -6680,7 +6908,7 @@ source = ArrayExpress::MULTI [species pan_troglodytes] taxonomy_id = 9598 aliases = pantroglodytes, ptroglodytes, chimpanzee, chimp -source = VGNC::MULTI +source = VGNC::pan_troglodytes source = EntrezGene::MULTI source = Reactome::MULTI source = RNACentral::MULTI @@ -7090,7 +7318,7 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI -[species tarsius_syrichta] +[species carlito_syrichta] taxonomy_id = 1868482 aliases = tarsier, bonyfingers source = EntrezGene::MULTI -- GitLab