From 1388eb12fe13f13c8bf1a64fadc1791d1ee0062e Mon Sep 17 00:00:00 2001 From: Magali Ruffier <mr6@ebi.ac.uk> Date: Fri, 31 Aug 2018 15:06:12 +0100 Subject: [PATCH] ENSCORESW-2805: remove empty fields --- misc-scripts/xref_mapping/xref_config.ini | 422 ---------------------- 1 file changed, 422 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 8bf57a2ad7..3779841b41 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -27,10 +27,6 @@ name = EC_NUMBER download = N order = 50 priority = 70 -prio_descr = -parser = -release_uri = -data_uri = [source BioGRID::drosophila_melanogaster] # Used by drosophila_melanogaster @@ -38,9 +34,7 @@ name = BioGRID download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source DEDb::drosophila_melanogaster] @@ -51,7 +45,6 @@ order = 50 priority = 1 prio_descr = Drosophila melanogaster Exon DataBase parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source EPD::drosophila_melanogaster] @@ -60,9 +53,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source EPD::drosophila_pseudoobscura] @@ -71,9 +62,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source EPD::drosophila_simulans] @@ -82,9 +71,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.org/genomes/dsim/current/gff/dsim-all-r1.4.gff.gz [source EPD::drosophila_sechellia] @@ -93,9 +80,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz [source EPD::drosophila_mojavensis] @@ -104,9 +89,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz [source EPD::drosophila_virilis] @@ -115,9 +98,7 @@ name = EPD download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz [source FlyAtlas::drosophila_melanogaster] @@ -126,9 +107,7 @@ name = FlyAtlas download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyAtlas::drosophila_pseudoobscura] @@ -137,9 +116,7 @@ name = FlyAtlas download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source FlyExpress::drosophila_melanogaster] @@ -148,9 +125,7 @@ name = FlyExpress download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyReactome::drosophila_melanogaster] @@ -159,9 +134,7 @@ name = FlyReactome download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source GenomeRNAi::drosophila_melanogaster] @@ -170,9 +143,7 @@ name = GenomeRNAi download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source InteractiveFly::drosophila_melanogaster] @@ -181,9 +152,7 @@ name = InteractiveFly download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source MEROPS::drosophila_melanogaster] @@ -192,9 +161,7 @@ name = MEROPS download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source MEROPS::drosophila_grimshawi] @@ -203,9 +170,7 @@ name = MEROPS download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/current/gff/dgri-all-*.gff.gz [source MEROPS::drosophila_virilis] @@ -214,9 +179,7 @@ name = MEROPS download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dvir_1.2/gff/dvir-all-r1.2.gff.gz [source miRBase::drosophila_melanogaster] @@ -225,9 +188,7 @@ name = miRBase download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source miRBase::drosophila_pseudoobscura] @@ -236,9 +197,7 @@ name = miRBase download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source MitoDrome::drosophila_melanogaster] @@ -247,9 +206,7 @@ name = MitoDrome download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source TransFac::drosophila_melanogaster] @@ -258,9 +215,7 @@ name = TransFac download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source TransFac::drosophila_pseudoobscura] @@ -269,9 +224,7 @@ name = TransFac download = N order = 50 priority = 1 -prio_descr = parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source flybase_annotation_id::drosophila_melanogaster] @@ -282,7 +235,6 @@ order = 50 priority = 1 prio_descr = Annotation ID assigned by FlyBase parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source flybase_gene_id::drosophila_melanogaster] @@ -294,7 +246,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source flybase_gene_id::drosophila_pseudoobscura] @@ -306,7 +257,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source flybase_gene_id::drosophila_grimshawi] @@ -318,7 +268,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dgri_r1.3/gff/dgri-all-r1.3.gff.gz [source flybase_gene_id::drosophila_willistoni] @@ -330,7 +279,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dwil_r1.3/gff/dwil-all-r1.3.gff.gz [source flybase_gene_id::drosophila_ananassae] @@ -342,7 +290,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dana_r1.3/gff/dana-all-r1.3.gff.gz [source flybase_gene_id::drosophila_yakuba] @@ -354,7 +301,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dyak_r1.3/gff/dyak-all-r1.3.gff.gz [source flybase_gene_id::drosophila_simulans] @@ -366,7 +312,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/genomes/dsim/current/gff/dsim-all-r1.4.gff.gz [source flybase_gene_id::drosophila_sechellia] @@ -378,7 +323,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz [source flybase_gene_id::drosophila_erecta] @@ -390,7 +334,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dere_r1.3/gff/dere-all-r1.3.gff.gz [source flybase_gene_id::drosophila_persimilis] @@ -402,7 +345,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dper_r1.3/gff/dper-all-r1.3.gff.gz [source flybase_gene_id::drosophila_mojavensis] @@ -414,7 +356,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz [source flybase_gene_id::drosophila_virilis] @@ -426,7 +367,6 @@ priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro -release_uri = data_uri = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz [source flybase_transcript_id::drosophila_melanogaster] @@ -437,7 +377,6 @@ order = 50 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source flybase_translation_id::drosophila_melanogaster] @@ -448,7 +387,6 @@ order = 50 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseCGID_gene::drosophila_melanogaster] @@ -459,7 +397,6 @@ order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseCGID_transcript::drosophila_melanogaster] @@ -470,7 +407,6 @@ order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseCGID_translation::drosophila_melanogaster] @@ -481,7 +417,6 @@ order = 50 priority = 1 prio_descr = FlyBase_Annotation_IDs parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseName_gene::drosophila_melanogaster] @@ -492,7 +427,6 @@ order = 50 priority = 1 prio_descr = Name assigned to gene in FlyBase gff parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseName_transcript::drosophila_melanogaster] @@ -503,7 +437,6 @@ order = 50 priority = 1 prio_descr = Transcript name in FlyBase gff parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source FlyBaseName_translations::drosophila_melanogaster] @@ -514,7 +447,6 @@ order = 50 priority = 1 prio_descr = Translation name in FlyBase gff parser = FlybaseParser -release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz [source PHIbase::MULTI] @@ -522,10 +454,8 @@ name = PHIbase download = Y order = 50 priority = 1 -prio_descr = parser = PHIbaseParser dependent_on = Uniprot/SWISSPROT,Uniprot/SPTREMBL -release_uri = data_uri = http://www.phi-base.org/PHI-export.php [source ArrayExpress::MULTI] @@ -534,9 +464,7 @@ name = ArrayExpress download = Y order = 50 priority = 1 -prio_descr = parser = ArrayExpressParser -release_uri = data_uri = script:project=>ensembl, #data_uri = script:wget=>http://www.ebi.ac.uk/gxa/dataExport/organisms,project=>ensembl,host=>mysql-ens-genebuild-prod-3,port=>4529,dbname=>kb15_jaculus_jaculus_core_89_1, @@ -545,9 +473,7 @@ name = ArrayExpress download = Y order = 50 priority = 1 -prio_descr = parser = ArrayExpressParser -release_uri = data_uri = script:project=>ensemblgenomes, [source CCDS::homo_sapiens] @@ -556,9 +482,7 @@ name = CCDS download = Y order = 10 priority = 1 -prio_descr = parser = CCDSParser -release_uri = 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] @@ -567,9 +491,7 @@ name = CCDS download = Y order = 10 priority = 1 -prio_descr = parser = CCDSParser -release_uri = data_uri = script:host=>mysql-ens-genebuild-prod-4,dbname=>osagie_mouse_cdsonly_clone_2017_09,port=>4530,tran_name=>ENSMUST, [source DBASS5::homo_sapiens] @@ -580,7 +502,6 @@ order = 50 priority = 1 prio_descr = Database of aberrant 5\' splice sites. parser = DBASSParser -release_uri = data_uri = http://www.dbass.soton.ac.uk/dbass5/download.aspx?item=genes [source DBASS3::homo_sapiens] @@ -591,7 +512,6 @@ order = 50 priority = 1 prio_descr = Database of aberrant 3\' splice sites. parser = DBASSParser -release_uri = data_uri = http://www.dbass.soton.ac.uk/dbass3/download.aspx?item=genes [source EntrezGene::MULTI] @@ -600,9 +520,7 @@ name = EntrezGene download = Y order = 10 priority = 1 -prio_descr = parser = EntrezGeneParser -release_uri = data_uri = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz [source EntrezGene_trans_name] @@ -611,10 +529,7 @@ name = EntrezGene_trans_name download = N order = 70 priority = 1 -prio_descr = parser = comes via official naming -release_uri = -data_uri = [source WikiGene::MULTI] # used via the EntrezGeneParser, for all species @@ -622,9 +537,7 @@ name = WikiGene download = N order = 100 priority = 1 -prio_descr = parser = EntrezGeneParser -release_uri = data_uri = comes via EntrezGene [source GO::MULTI] @@ -649,7 +562,6 @@ priority = 1 prio_descr = main parser = GOSlimParser dependent_on = GO -release_uri = data_uri = script:host=>mysql-eg-staging-1.ebi.ac.uk,port=>4160,dbname=>ensemblgenomes_ontology_21_74, [source GO::saccharomyces_cerevisiae] @@ -661,7 +573,6 @@ priority = 1 prio_descr = main parser = GOParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,SGD -release_uri = data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.sgd.gz data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz @@ -673,7 +584,6 @@ order = 50 priority = 1 prio_descr = Human Protein Atlas (HPA) database parser = HPAParser -release_uri = data_uri = http://www.proteinatlas.org/download/xref.php [source LRG_HGNC_notransfer] @@ -681,10 +591,7 @@ name = LRG_HGNC_notransfer download = N order = 30 priority = 5 -prio_descr = parser = HGNCParser -release_uri = -data_uri = [source VGNC::pan_troglodytes] # Used by pan_troglodytes @@ -692,9 +599,7 @@ 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/vgnc_gene_set_All.txt.gz [source VGNC::bos_taurus] @@ -703,9 +608,7 @@ 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/vgnc_gene_set_All.txt.gz [source VGNC::canis_familiaris] @@ -714,9 +617,7 @@ 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/vgnc_gene_set_All.txt.gz [source VGNC::equus_caballus] @@ -725,9 +626,7 @@ 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/vgnc_gene_set_All.txt.gz [source HGNC::homo_sapiens#01] @@ -738,7 +637,6 @@ order = 30 priority = 2 prio_descr = ccds parser = HGNC_CCDSParser -release_uri = data_uri = script:wget=>https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&col=md_prot_id&col=gd_lsdb_links&col=gd_ccds_ids&status=Approved&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&hgnc_dbtag=on&submit=submit,host=>mysql-ens-core-prod-1,dbname=>homo_sapiens_ccds_91_38,port=>4524,tran_name=>ENST, @@ -750,8 +648,6 @@ order = 30 priority = 1 prio_descr = ensembl_manual parser = HGNCParser -release_uri = -data_uri = [source HGNC::homo_sapiens#02] @@ -763,7 +659,6 @@ priority = 4 prio_descr = entrezgene_manual parser = HGNCParser dependent_on = EntrezGene,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide -release_uri = data_uri = script:wget=>https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit,host=>mysql-ens-core-prod-1,dbname=>homo_sapiens_ccds_91_38,port=>4524, @@ -775,8 +670,6 @@ order = 30 priority = 5 prio_descr = refseq_manual parser = HGNCParser -release_uri = -data_uri = [source HGNC::homo_sapiens#08] # used by #02 @@ -786,8 +679,6 @@ order = 30 priority = 100 prio_descr = desc_only parser = HGNCParser -release_uri = -data_uri = [source Interpro::CORE] # Used by capitella_teleta, crassostrea_gigas, helobdella_robusta, lottia_gigantea, rhodnius_prolixus, tetranychus_urticae @@ -805,10 +696,7 @@ name = MIM_GENE download = N order = 40 priority = 1 -prio_descr = parser = MIMParser -release_uri = -data_uri = [source MIM_MORBID::homo_sapiens] # MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM @@ -816,10 +704,7 @@ name = MIM_MORBID download = N order = 40 priority = 1 -prio_descr = parser = MIMParser -release_uri = -data_uri = [source MIM::homo_sapiens] # Used by homo_sapiens @@ -827,9 +712,7 @@ name = MIM download = Y order = 10 priority = 1 -prio_descr = parser = MIMParser -release_uri = data_uri = http://data.omim.org/downloads/s4mpHKpNRgugjDKWuUAJMw/omim.txt.gz [source MIM2GENE::homo_sapiens] @@ -838,10 +721,8 @@ name = MIM2GENE download = Y order = 60 priority = 1 -prio_descr = parser = Mim2GeneParser dependent_on = MIM,EntrezGene -release_uri = data_uri = ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen [source MGI::mus_musculus#04] @@ -851,8 +732,6 @@ download = N order = 30 priority = 4 prio_descr = uniprot -parser = -release_uri = data_uri = taken from uniprot files [source MGI::mus_musculus#01] @@ -863,7 +742,6 @@ order = 30 priority = 1 prio_descr = official parser = MGIParser -release_uri = data_uri = http://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt [source MGI::mus_musculus#05] @@ -874,7 +752,6 @@ order = 1 priority = 10 prio_descr = descriptions parser = MGI_Desc_Parser -release_uri = data_uri = http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt [source MGI::mus_musculus#03] @@ -885,7 +762,6 @@ order = 35 priority = 3 prio_descr = ccds parser = MGI_CCDS_Parser -release_uri = data_uri = ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse/CCDS.current.txt [source Reactome::MULTI] @@ -926,7 +802,6 @@ order = 20 priority = 1 prio_descr = uniprot parser = ReactomeParser -release_uri = [source RGD::rattus_norvegicus] # Used by rattus_norvegicus @@ -934,10 +809,8 @@ name = RGD download = Y order = 30 priority = 2 -prio_descr = parser = RGDParser dependent_on = RefSeq_dna,RefSeq_peptide -release_uri = data_uri = ftp://ftp.rgd.mcw.edu/pub/data_release/GENES_RAT.txt [source RGD::rattus_norvegicus#02] @@ -948,17 +821,13 @@ order = 30 priority = 1 prio_descr = direct_xref parser = done_in_RGDParser -release_uri = -data_uri = [source RGD_trans_name] name = RGD_trans_name download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source RefSeq_dna::MULTI-vertebrate] # Used by vertebrates @@ -1034,7 +903,6 @@ order = 20 priority = 1 prio_descr = refseq parser = RefSeqParser -release_uri = [source RefSeq_mRNA::MULTI] # Special source used in RefSeqParser. No species uses this source. @@ -1045,7 +913,6 @@ order = 20 priority = 3 prio_descr = refseq parser = RefSeqParser -release_uri = [source RefSeq_mRNA::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1055,7 +922,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_peptide::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1065,7 +931,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_mRNA_predicted::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1075,7 +940,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_peptide_predicted::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1085,7 +949,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_import::otherfeatures] # Import RefSeq models from otherfeatures database @@ -1096,7 +959,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = data_uri = script:project=>ensembl, #data_uri = script:project=>ensembl,host=>ens-staging1,dbname=>homo_sapiens_core_70_37,ofhost=>ens-staging1,ofdbname=>homo_sapiens_otherfeatures_70_37, @@ -1109,7 +971,6 @@ order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser -release_uri = [source RefSeq_ncRNA::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1119,7 +980,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_ncRNA_predicted::otherfeatures] # Special source used in RefSeqCoordinateParser. No species uses this source. @@ -1129,7 +989,6 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = [source RefSeq_mRNA_predicted::MULTI] # Special source used in RefSeqParser. No species uses this source. @@ -1139,7 +998,6 @@ order = 20 priority = 2 prio_descr = refseq parser = RefSeqParser -release_uri = [source RefSeq_ncRNA_predicted::MULTI] # Special source used in RefSeqParser. No species uses this source. @@ -1149,7 +1007,6 @@ order = 20 priority = 1 prio_descr = refseq parser = RefSeqParser -release_uri = [source RefSeq_peptide::MULTI-fungi] # Used by saccharomyces_cerevisiae @@ -1157,7 +1014,6 @@ name = RefSeq_peptide download = Y order = 30 priority = 2 -prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/fungi/fungi*.protein.gpff.gz @@ -1167,7 +1023,6 @@ name = RefSeq_peptide download = Y order = 30 priority = 2 -prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/plant/plant*.protein.gpff.gz @@ -1178,7 +1033,6 @@ name = RefSeq_peptide download = Y order = 30 priority = 2 -prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/complete/complete*.protein.gpff.gz @@ -1189,7 +1043,6 @@ name = RefSeq_peptide download = Y order = 30 priority = 2 -prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/protozoa/protozoa*.protein.gpff.gz @@ -1200,7 +1053,6 @@ name = RefSeq_peptide download = Y order = 30 priority = 2 -prio_descr = parser = RefSeqGPFFParser release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/invertebrate/invertebrate*.protein.gpff.gz @@ -1213,7 +1065,6 @@ order = 30 priority = 2 prio_descr = refseq parser = RefSeqGPFFParser -release_uri = [source RefSeq_peptide::MULTI-vertebrate] # Used by vertebrates @@ -1233,9 +1084,7 @@ name = SGD_GENE download = N order = 10 priority = 1 -prio_descr = parser = SGDParser -release_uri = [source SGD_TRANSLATION::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae @@ -1243,9 +1092,7 @@ name = SGD_TRANSLATION download = N order = 10 priority = 1 -prio_descr = parser = SGDParser -release_uri = [source SGD_TRANSCRIPT::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae @@ -1253,9 +1100,7 @@ name = SGD_TRANSCRIPT download = N order = 10 priority = 1 -prio_descr = parser = SGDParser -release_uri = [source SGD::saccharomyces_cerevisiae] # Used by saccharomyces_cerevisiae @@ -1263,9 +1108,7 @@ name = SGD download = Y order = 10 priority = 1 -prio_descr = parser = SGDParser -release_uri = data_uri = http://downloads.yeastgenome.org/curation/chromosomal_feature/SGD_features.tab [source PomBase_GENE::schizosaccharomyces_pombe] @@ -1274,9 +1117,7 @@ name = PomBase_GENE download = N order = 10 priority = 1 -prio_descr = parser = PomBaseParser -release_uri = [source PomBase_TRANSCRIPT::schizosaccharomyces_pombe] # Used by schizosaccharomyces_pombe @@ -1284,9 +1125,7 @@ name = PomBase_TRANSCRIPT download = N order = 10 priority = 1 -prio_descr = parser = PomBaseParser -release_uri = [source PomBase::schizosaccharomyces_pombe] # Used by schizosaccharomyces_pombe @@ -1294,9 +1133,7 @@ name = PomBase download = Y order = 10 priority = 1 -prio_descr = parser = PomBaseParser -release_uri = data_uri = http://www.ebi.ac.uk/~mcdowall/PomBaseFeatureDescriptions_For-v65.txt [source PGSC_GENE::solanum_tuberosum] @@ -1305,9 +1142,7 @@ name = PGSC_GENE download = Y order = 10 priority = 1 -prio_descr = parser = PGSCParser -release_uri = data_uri = http://solanaceae.plantbiology.msu.edu/data/PGSC_DM_v3.4_gene_func.txt.zip [source PHYTOZOME_GMAX_GENE::glycine_max] @@ -1316,9 +1151,7 @@ name = PHYTOZOME_GMAX_GENE download = Y order = 10 priority = 1 -prio_descr = parser = PhytozomeGmaxParser -release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v8.0/early_release/Gmax_v1.1/annotation/Gmax_v1.1_189_annotation_info.txt.gz [source UCSC::MULTI] @@ -1336,7 +1169,6 @@ name = UCSC_hg38 download = Y order = 70 priority = 1 -prio_descr = parser = UCSC_human_parser release_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/README.txt data_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/knownGene.txt.gz @@ -1347,7 +1179,6 @@ name = UCSC_mm10 download = Y order = 70 priority = 1 -prio_descr = parser = UCSC_mouse_parser release_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/README.txt data_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz @@ -1358,9 +1189,7 @@ name = protein_id_predicted download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source UniProt::protein_id] # Special source used in UniProtParser. No species uses this source. @@ -1368,9 +1197,7 @@ name = protein_id download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source UniProt::PDB] # Special source used in UniProtParser. No species uses this source. @@ -1378,16 +1205,13 @@ name = PDB download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source Uniprot/SPTREMBL::MULTI-invertebrate] name = Uniprot/SPTREMBL download = Y order = 20 priority = 3 -prio_descr = parser = UniProtParser dependent_on = MIM release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/reldate.txt @@ -1414,7 +1238,6 @@ order = 20 priority = 10 prio_descr = protein_evidence_gt_2 parser = UniProtParser -release_uri = status = LOWEVIDENCE @@ -1424,9 +1247,7 @@ name = Uniprot/SPTREMBL_predicted download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source Uniprot/SWISSPROT::MULTI] # Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus @@ -1461,8 +1282,6 @@ order = 22 priority = 1 prio_descr = direct parser = UniProtParser -release_uri = -data_uri = [source Uniprot/SPTREMBL::DIRECT] # Special source used in UniProtParser for direct mappings from Uniprot @@ -1472,8 +1291,6 @@ order = 22 priority = 1 prio_descr = direct parser = UniProtParser -release_uri = -data_uri = [source Uniprot/SWISSPROT::MULTI-predicted] @@ -1482,9 +1299,7 @@ name = Uniprot/SWISSPROT_predicted download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source Uniprot_gn] # Special source used in UniProtParser foir gene names.. @@ -1492,10 +1307,7 @@ name = Uniprot_gn download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = -data_uri = [source Uniprot/SPTREMBL::drosophila_melanogaster] # Used by drosophila_melanogaster @@ -1503,7 +1315,6 @@ name = Uniprot/SPTREMBL download = Y order = 20 priority = 1 -prio_descr = parser = UniProtParser_descriptions_only release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz @@ -1514,9 +1325,7 @@ name = EMBL_predicted download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source Uniprot::EMBL] # Special source used in UniProtParser. No species uses this source. @@ -1524,9 +1333,7 @@ name = EMBL download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source Uniprot::ChEMBL] # Special source used in UniProtParser. No species uses this source. @@ -1534,9 +1341,7 @@ name = ChEMBL download = N order = 20 priority = 1 -prio_descr = parser = UniProtParser -release_uri = [source UniParc::MULTI] @@ -1544,9 +1349,7 @@ name = UniParc download = Y order = 20 priority = 1 -prio_descr = parser = ChecksumParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis [source RNACentral::MULTI] @@ -1554,9 +1357,7 @@ name = RNAcentral download = Y order = 1 priority = 1 -prio_descr = parser = ChecksumParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/md5/md5.tsv.gz [source PIGGY_trans_name] @@ -1564,36 +1365,28 @@ name = PIGGY_trans_name download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source HGNC_trans_name] name = HGNC_trans_name download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source VGNC_trans_name] name = VGNC_trans_name download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source MGI_automatic_transcript::mus_musculus] name = MGI_automatic_transcript_notransfer download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source MGI_trans_name] # Used homo_sapiens,mus_musculus @@ -1601,28 +1394,21 @@ name = MGI_trans_name download = N order = 70 priority = 1 -prio_descr = parser = comes via official naming -release_uri = -data_uri = [source Clone_based_ensembl_transcript::homo_sapiens] name = Clone_based_ensembl_transcript download = N order = 50 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source Clone_based_ensembl_gene::homo_sapiens] name = Clone_based_ensembl_gene download = N order = 50 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source Xenopus_Jamboree::xenopus_tropicalis] # Used by xenopus_tropicalis @@ -1630,9 +1416,7 @@ name = Xenbase download = Y order = 20 priority = 1 -prio_descr = parser = XenopusJamboreeParser -release_uri = data_uri = ftp://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt [source ZFIN_ID::danio_rerio#01] @@ -1643,7 +1427,6 @@ order = 31 priority = 1 prio_descr = uniprot/refseq parser = ZFINParser -release_uri = data_uri = http://zfin.org/data_transfer/Downloads/refseq.txt data_uri = http://zfin.org/data_transfer/Downloads/uniprot.txt data_uri = http://zfin.org/data_transfer/Downloads/aliases.txt @@ -1657,7 +1440,6 @@ order = 1 priority = 10 prio_descr = description_only parser = ZFINDescParser -release_uri = data_uri = ftp://zfin.org/pub/transfer/MEOW/zfin_genes.txt [source ZFIN_ID_trans_name] @@ -1665,9 +1447,7 @@ name = ZFIN_ID_trans_name download = N order = 49 priority = 1 -prio_descr = parser = done_in_official_naming -release_uri = [source cint_aniseed_v1::ciona_intestinalis] # Used by ciona_intestinalis @@ -1675,9 +1455,7 @@ name = cint_aniseed_v1 download = Y order = 50 priority = 1 -prio_descr = parser = JGI_ProteinParser -release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v1.0/ciona.prot.fasta.gz [source cint_jgi_v1::ciona_intestinalis] @@ -1686,9 +1464,7 @@ name = cint_jgi_v1 download = Y order = 50 priority = 1 -prio_descr = parser = JGI_ProteinParser -release_uri = data_uri = ftp://ftp.jgi-psf.org/pub/JGI_data/Ciona/v1.0/ciona.prot.fasta.gz [source RFAM::MULTI] @@ -1697,9 +1473,7 @@ name = RFAM download = Y order = 70 priority = 1 -prio_descr = parser = RFAMParser -release_uri = data_uri = script:wget=>ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz, #data_uri = script:wget=>ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz,host=>mysql-ens-genebuild-prod-3,port=>4529,dbname=>kb15_mesocricetus_auratus_core_89_1, @@ -1708,9 +1482,7 @@ name = RFAM download = Y order = 70 priority = 1 -prio_descr = parser = CoreXrefParser -release_uri = data_uri = script:object_type=>gene,project=>ensemblgenomes,copy_description_from_object=>1, @@ -1720,9 +1492,7 @@ name = miRBase download = Y order = 70 priority = 1 -prio_descr = parser = miRBaseParser -release_uri = data_uri = ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz [source miRBase_trans_name] @@ -1731,10 +1501,7 @@ name = miRBase_trans_name download = N order = 70 priority = 1 -prio_descr = parser = comes via official naming -release_uri = -data_uri = [source RFAM_trans_name] # Used homo_sapiens,mus_musculus @@ -1742,10 +1509,7 @@ name = RFAM_trans_name download = N order = 70 priority = 1 -prio_descr = parser = comes via official naming -release_uri = -data_uri = [source Uniprot_gn_trans_name] # Used by merged species: homo_sapiens,mus_musculus, danio_rerio and sus_scrofa @@ -1753,10 +1517,7 @@ name = Uniprot_gn_trans_name download = N order = 70 priority = 1 -prio_descr = parser = comes via official naming -release_uri = -data_uri = [source RNAMMER::MULTI] @@ -1765,9 +1526,7 @@ name = RNAMMER download = Y order = 70 priority = 1 -prio_descr = parser = CoreXrefParser -release_uri = data_uri = script:biotype=>rRNA,object_type=>gene,project=>ensemblgenomes,copy_description_from_object=>1, @@ -1777,9 +1536,7 @@ name = TRNASCAN_SE download = Y order = 70 priority = 1 -prio_descr = parser = CoreXrefParser -release_uri = data_uri = script:biotype=>tRNA,object_type=>gene,project=>ensemblgenomes,copy_description_from_object=>1, [source ncRNA_EG::EG] @@ -1789,9 +1546,7 @@ name = ncRNA_EG download = Y order = 70 priority = 1 -prio_descr = parser = CoreXrefParser -release_uri = data_uri = script:logic_name=>ncrna_eg,object_type=>gene,project=>ensemblgenomes,copy_description_from_object=>1, [source misc_EG::EG] @@ -1800,9 +1555,7 @@ name = misc_EG download = Y order = 70 priority = 1 -prio_descr = parser = EG_DBParser -release_uri = data_uri = script:host=>mysql-eg-pan-prod.ebi.ac.uk,port=>4276,dbname=>EG_Xrefs, [source ENA_GENE::MULTI] @@ -1811,10 +1564,6 @@ name = ENA_GENE download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source CADRE::MULTI] # Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri @@ -1822,10 +1571,6 @@ name = CADRE download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source CADRE_AFum_A1163::MULTI] # Used by aspergillus_fumigatusa1163 @@ -1833,10 +1578,6 @@ name = CADRE_Afum_A1163 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source AspGD::MULTI] # Used by aspergillus_nidulans @@ -1844,10 +1585,6 @@ name = AspGD download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source GeneDB::MULTI] # Used by plasmodium_falciparum, trypanosoma_brucei, leishmania_major, schistosoma_mansoni @@ -1855,10 +1592,6 @@ name = GeneDB download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source GeneDB_Spombe::MULTI] # Used by schizosaccharomyces_pombe @@ -1866,10 +1599,6 @@ name = GeneDB_Spombe download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source phatr_jgi_v2::MULTI] # Used by Pt @@ -1877,10 +1606,6 @@ name = phatr_jgi_v2 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source phatr_jgi_v2_bd::MULTI] # Used by Pt @@ -1888,10 +1613,6 @@ name = phatr_jgi_v2_bd download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source thaps_jgi_v2::MULTI] # Used by Tp @@ -1899,10 +1620,6 @@ name = thaps_jgi_v2 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source physo1_jgi_v1.1_gene::MULTI] # Used by Pt @@ -1910,10 +1627,6 @@ name = physo1_jgi_v1.1_gene download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source PGD_GENE::MULTI] # Used by Tp @@ -1921,10 +1634,6 @@ name = PGD_GENE download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source physo1_jgi_v1.1::MULTI] # Used by Pt @@ -1932,10 +1641,6 @@ name = physo1_jgi_v1.1 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source physo1_jgi_v1.1_transcript::MULTI] # Used by Pt @@ -1943,10 +1648,6 @@ name = physo1_jgi_v1.1_transcript download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source phyra_jgi_v1.1_gene::MULTI] # Used by Pt @@ -1954,10 +1655,6 @@ name = phyra_jgi_v1.1_gene download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source phyra_jgi_v1.1::MULTI] # Used by Pt @@ -1965,10 +1662,6 @@ name = phyra_jgi_v1.1 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source phyra_jgi_v1.1_transcript::MULTI] # Used by Pt @@ -1976,10 +1669,6 @@ name = phyra_jgi_v1.1_transcript download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_Magnaporthe_DB::MULTI] # Used by magnaporthe_oryzae, magnaporthe_poae and gaeumannomyces_graminis @@ -1987,9 +1676,7 @@ name = BROAD_Magnaporthe_DB download = Y order = 70 priority = 1 -prio_descr = parser = Broad_MagnaportheDBParser -release_uri = data_uri = http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/download/?sp=EAGenomeSummary&sp=SGae_graminis_V2&sp=S.gz [source BROAD_P_infestans::MULTI] @@ -1998,10 +1685,6 @@ name = BROAD_P_infestans download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_P_infestans_GENE::MULTI] # Used by phytophthora_infestans @@ -2009,10 +1692,6 @@ name = BROAD_P_infestans_GENE download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_P_infestans_TRANSCRIPT::MULTI] # Used by phytophthora_infestans @@ -2020,10 +1699,6 @@ name = BROAD_P_infestans_TRANSCRIPT download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source thaps_jgi_v2_bd::MULTI] @@ -2032,10 +1707,6 @@ name = thaps_jgi_v2_bd download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_U_maydis::MULTI] @@ -2044,10 +1715,6 @@ name = BROAD_U_maydis download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_F_oxysporum::MULTI] # Used by fusarium_oxysporum @@ -2055,10 +1722,6 @@ name = BROAD_F_oxysporum download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_g_zeae::MULTI] # Used by gibberella_zeae @@ -2066,10 +1729,6 @@ name = BROAD_G_zeae download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source BROAD_G_moniliformis::MULTI] # Used by gibberella_moniliformis @@ -2077,10 +1736,6 @@ name = BROAD_G_moniliformis download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source SCHISTODB::MULTI] # Used by schistosoma_mansoni @@ -2088,10 +1743,6 @@ name = SCHISTODB download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source triad_jgi_v1.0::MULTI] # Used by trichoplax_adhaerens @@ -2099,19 +1750,13 @@ name = triad_jgi_v1.0 download = N order = 70 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source wormbase::celegans] name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.RELEASE.xrefs.txt.gz [source wormbase::cbriggsae] @@ -2119,9 +1764,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/c_briggsae/PRJNA10731/c_briggsae.PRJNA10731.RELEASE.xrefs.txt.gz [source wormbase::cbrenneri] @@ -2129,9 +1772,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/c_brenneri/PRJNA20035/c_brenneri.PRJNA20035.RELEASE.xrefs.txt.gz [source wormbase::cremanei] @@ -2139,9 +1780,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/c_remanei/PRJNA53967/c_remanei.PRJNA53967.RELEASE.xrefs.txt.gz [source wormbase::cjaponica] @@ -2149,9 +1788,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/c_japonica/PRJNA12591/c_japonica.PRJNA12591.RELEASE.xrefs.txt.gz [source wormbase::ppacificus] @@ -2159,9 +1796,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/p_pacificus/PRJNA12644/p_pacificus.PRJNA12644.RELEASE.xrefs.txt.gz [source wormbase::sratti] @@ -2169,9 +1804,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/s_ratti/PRJEB125/s_ratti.PRJEB125.RELEASE.xrefs.txt.gz @@ -2180,9 +1813,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/b_malayi/PRJNA10729/b_malayi.PRJNA10729.RELEASE.xrefs.txt.gz [source wormbase::ovolvulus] @@ -2190,9 +1821,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/o_volvulus/PRJEB513/o_volvulus.PRJEB513.RELEASE.xrefs.txt.gz [source wormbase::tmuris] @@ -2200,9 +1829,7 @@ name = wormbase_all download = Y order = 50 priority = 1 -prio_descr = parser = WormbaseDirectParser -release_uri = data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/RELEASE/species/t_muris/PRJNA10729/t_muris.PRJEB126.RELEASE.xrefs.txt.gz [source wormpep_id::wormbase] @@ -2211,10 +1838,7 @@ name = wormpep_id download = N order = 50 priority = 1 -prio_descr = parser = comes from WormbaseDirectParser -release_uri = -data_uri = [source wormbase_gene::wormbase] # Used by wormbase core species @@ -2222,10 +1846,7 @@ name = wormbase_gene download = N order = 50 priority = 1 -prio_descr = parser = comes from WormbaseDirectParser -release_uri = -data_uri = [source wormbase_locus::wormbase] # Used by wormbase core species @@ -2233,10 +1854,7 @@ name = wormbase_locus download = N order = 50 priority = 1 -prio_descr = parser = comes from WormbaseDirectParser -release_uri = -data_uri = [source wormbase_gseqname::wormbase] # Used by wormbase core species @@ -2244,10 +1862,7 @@ name = wormbase_gseqname download = N order = 50 priority = 1 -prio_descr = parser = comes from WormbaseDirectParser -release_uri = -data_uri = [source wormbase_transcript::wormbase] # Used by wormbase core species @@ -2255,10 +1870,7 @@ name = wormbase_transcript download = N order = 50 priority = 1 -prio_descr = parser = comes from WormbaseDirectParser -release_uri = -data_uri = [source Gramene_Pathway::arabidopsis_thaliana] # Used by Arabidopsis thaliana, Gramene-specific @@ -2266,9 +1878,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/aracyc.tab.gz [source Gramene_Pathway::brachypodium_distachyon] @@ -2277,9 +1887,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/brachycyc.tab.gz [source Gramene_Pathway::solanum_lycopersicum] @@ -2288,9 +1896,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/lycocyc.tab.gz [source Gramene_Pathway::zea_mays] @@ -2299,9 +1905,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/maizecyc.tab.gz [source Gramene_Pathway::populus_trichocarpa] @@ -2310,9 +1914,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/poplarcyc.tab.gz [source Gramene_Pathway::solanum_tuberosum] @@ -2321,9 +1923,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/potatocyc.tab.gz [source Gramene_Pathway::oryza_sativa] @@ -2332,9 +1932,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/ricecyc.tab.gz [source Gramene_Pathway::sorghum_bicolor] @@ -2343,9 +1941,7 @@ name = Gramene_Pathway download = Y order = 50 priority = 1 -prio_descr = parser = GramenePathwayParser -release_uri = data_uri = ftp://ftp.gramene.org/pub/gramene/ensemblgenomes/xrefs/pathways/sorghumcyc.tab.gz @@ -2358,7 +1954,6 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = data_uri = http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=co data_uri = ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/po_temporal_gene_arabidopsis_tair.assoc @@ -2371,7 +1966,6 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = data_uri = http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=co data_uri = ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/po_anatomy_gene_arabidopsis_tair.assoc @@ -2381,9 +1975,7 @@ name = TAIR_LOCUS download = Y order = 1 priority = 1 -prio_descr = parser = TAIRIDParser -release_uri = data_uri = ftp://ftp.arabidopsis.org/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated [source TAIR_LOCUS_MODEL::arabidopsis_thaliana] @@ -2392,10 +1984,7 @@ name = TAIR_LOCUS_MODEL download = N order = 1 priority = 1 -prio_descr = parser = TAIRIDParser -release_uri = -data_uri = [source TAIR_SYMBOL::arabidopsis_thaliana] # Used by arabidopsis_thaliana @@ -2403,10 +1992,7 @@ name = TAIR_SYMBOL download = N order = 1 priority = 1 -prio_descr = parser = TAIRIDParser -release_uri = -data_uri = [source TAIR_TRANSLATION::arabidopsis_thaliana] # Used by arabidopsis_thaliana @@ -2414,10 +2000,6 @@ name = TAIR_TRANSLATION download = N order = 1 priority = 1 -prio_descr = -parser = -release_uri = -data_uri = [source NASC_GENE_ID::arabidopsis_thaliana] # Used by arabidopsis_thaliana @@ -2425,10 +2007,7 @@ name = NASC_GENE_ID download = N order = 1 priority = 1 -prio_descr = parser = TAIRIDParser -release_uri = -data_uri = [source CommunityGO::arabidopsis_thaliana] # Used by Arabidopsis thaliana, Gramene-specific @@ -2439,7 +2018,6 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.tair.gz -- GitLab