From e80867540e3fd565d968c629fca3b2106c5f8a0f Mon Sep 17 00:00:00 2001 From: Arnaud Kerhornou <arnaud@ebi.ac.uk> Date: Wed, 3 Oct 2012 14:39:28 +0000 Subject: [PATCH] Added musa acuminata, solanum tuberosum species; added two new sources, phytozome_gmax and pgsc; added UniParc source to plants genomes --- misc-scripts/xref_mapping/xref_config.ini | 71 ++++++++++++++++++++++- 1 file changed, 70 insertions(+), 1 deletion(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 3aae7df863..d2a4dbdf7b 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -1058,7 +1058,7 @@ prio_descr = main parser = GOSlimParser dependent_on = GO release_uri = -data_uri = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensemblgenomes_ontology_14_68, +data_uri = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensemblgenomes_ontology_16_69, [source GO::homo_sapiens] # Used by homo_sapiens @@ -2337,6 +2337,28 @@ parser = PomBaseParser release_uri = data_uri = http://www.ebi.ac.uk/~mcdowall/PomBaseFeatureDescriptions_For-v65.txt +[source PGSC::solanum_tuberosum] +# Used by solanum_tuberosum +name = PGSC +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] +# Used by glycine_max +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] # Special source used in UCSCParser. No species uses this source. name = UCSC @@ -6012,6 +6034,7 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI [species glycine_max] taxonomy_id = 3847 @@ -6026,6 +6049,8 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = PHYTOZOME_GMAX_GENE::glycine_max +source = UniParc::MULTI [species oryza_glaberrima] taxonomy_id = 4538 @@ -6040,6 +6065,7 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI [species brassica_rapa] taxonomy_id = 51351 @@ -6058,6 +6084,7 @@ source = RNAMMER::MULTI source = TRNASCAN_SE::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI [species oryza_brachyantha] taxonomy_id = 4533 @@ -6076,6 +6103,7 @@ source = RNAMMER::MULTI source = TRNASCAN_SE::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI [species setaria_italica] taxonomy_id = 4555 @@ -6094,6 +6122,7 @@ source = RNAMMER::MULTI source = TRNASCAN_SE::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI [species solanum_lycopersicum] taxonomy_id = 4081 @@ -6112,6 +6141,46 @@ source = RNAMMER::MULTI source = TRNASCAN_SE::MULTI source = goslim_goa::EG source = ArrayExpress::EG +source = UniParc::MULTI + +[species solanum_tuberosum] +taxonomy_id = 4113 +aliases = Solanum tuberosum +source = EntrezGene::MULTI +source = GO::MULTI +source = InterproGO::MULTI +source = Interpro::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_peptide::MULTI-Plants +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = RFAM::EG +source = miRBase::MULTI +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = goslim_goa::EG +source = ArrayExpress::EG +source = PGSC::solanum_tuberosum +source = UniParc::MULTI + +[species musa_acuminata] +taxonomy_id = 214687 +aliases = Musa acuminata +source = EntrezGene::MULTI +source = GO::MULTI +source = InterproGO::MULTI +source = Interpro::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_peptide::MULTI-Plants +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = RFAM::EG +source = miRBase::MULTI +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = goslim_goa::EG +source = ArrayExpress::EG +source = UniParc::MULTI [species amphimedon_queenslandica] taxonomy_id = 400682 -- GitLab