From 9124211a69a4f493723c40b2132ec3e32bb21a22 Mon Sep 17 00:00:00 2001 From: Arnaud Kerhornou <arnaud@ebi.ac.uk> Date: Thu, 20 Dec 2012 13:40:00 +0000 Subject: [PATCH] Have added all plants missing species, plus all gramene plants species --- misc-scripts/xref_mapping/xref_config.ini | 523 ++++++++++++++++++++++ 1 file changed, 523 insertions(+) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 3e75d744aa..f4726c52a5 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -6166,6 +6166,529 @@ source = goslim_goa::EG source = ArrayExpress::EG source = UniParc::MULTI +[species hordeum_vulgare] +taxonomy_id = 112509 +aliases = Hordeum vulgare, barley +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 = goslim_goa::EG +source = ArrayExpress::EG +source = UniParc::MULTI +source = RFAM::EG +source = miRBase::MULTI +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI + +[species arabidopsis_lyrata] +taxonomy_id = 59689 +aliases = Arabidopsis lyrata,alyrata,arabidopsislyrata,lyrate rockcress +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species arabidopsis_thaliana] +taxonomy_id = 3702 +aliases = Arabidopsis thaliana,athaliana,arabidopsisthaliana,thale cress,thale-cress,mouse-ear cress +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = IPI::arabidopsis_thaliana +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = UniGene::arabidopsis_thaliana +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species brachypodium_distachyon] +taxonomy_id = 15368 +aliases = Brachypodium distachyon,bdistachyon,brachypodiumdistachyon +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = UniGene::brachypodium_distachyon +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species chlamydomonas_reinhardtii] +taxonomy_id = 3055 +taxonomy_id = 906914 +aliases = Chlamydomonas reinhardtii,creinhardtii,chlamydomonasreinhardtii,green algae +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = UniGene::chlamydomonas_reinhardtii +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species cyanidioschyzon_merolae] +taxonomy_id = 45157 +aliases = Cyanidioschyzon merolae,cmerolae,cyanidioschyzonmerolae,red algae +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = miRBase::MULTI +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species leersia_perrieri] +taxonomy_id = 77586 +aliases = Leersia perrieri,lperrieri,leersiaperrieri +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_barthii] +taxonomy_id = 65489 +aliases = Oryza barthii,obarthii,oryzabarthii,African wild rice +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_glumaepatula] +taxonomy_id = 40148 +aliases = Oryza glumaepatula,oglumaepatula,oryzaglumaepatula +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_granulata] +taxonomy_id = 110450 +aliases = Oryza granulata,ogranulata,oryzagranulata +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_longistaminata] +taxonomy_id = 4528 +aliases = Oryza longistaminata,olongistaminata,oryzalongistaminata,red rice +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_meridionalis] +taxonomy_id = 40149 +aliases = Oryza meridionalis,omeridionalis,oryzameridionalis +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +#[species oryza_minutabb] +#taxonomy_id = 63629 +#aliases = Oryza minutabb,ominutabb,oryzaminutabb +#source = ArrayExpress::EG +#source = EntrezGene::MULTI +#source = GO::MULTI +#source = goslim_goa::EG +#source = Interpro::MULTI +#source = InterproGO::MULTI +#source = miRBase::MULTI +#source = RefSeq_dna::MULTI-Plants +#source = RefSeq_mRNA_predicted::MULTI +#source = RefSeq_peptide::MULTI-Plants +#source = RFAM::EG +#source = RNAMMER::MULTI +#source = TRNASCAN_SE::MULTI +#source = UniParc::MULTI +#source = Uniprot/SPTREMBL::MULTI +#source = Uniprot/SWISSPROT::MULTI +# +#[species oryza_minutacc] +#taxonomy_id = 63629 +#aliases = Oryza minutacc,ominutacc,oryzaminutacc +#source = ArrayExpress::EG +#source = EntrezGene::MULTI +#source = GO::MULTI +#source = goslim_goa::EG +#source = Interpro::MULTI +#source = InterproGO::MULTI +#source = miRBase::MULTI +#source = RefSeq_dna::MULTI-Plants +#source = RefSeq_mRNA_predicted::MULTI +#source = RefSeq_peptide::MULTI-Plants +#source = RFAM::EG +#source = RNAMMER::MULTI +#source = TRNASCAN_SE::MULTI +#source = UniParc::MULTI +#source = Uniprot/SPTREMBL::MULTI +#source = Uniprot/SWISSPROT::MULTI + +[species oryza_nivara] +taxonomy_id = 4536 +aliases = Oryza nivara,onivara,oryzanivara +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_officinalis] +taxonomy_id = 4535 +aliases = Oryza officinalis,oofficinalis,oryzaofficinalis +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_punctata] +taxonomy_id = 4537 +aliases = Oryza punctata,opunctata,oryzapunctata +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +#[species oryza_rufipogon3s] +#taxonomy_id = 4529 +#aliases = Oryza rufipogon3s,orufipogon3s,oryzarufipogon3s,red rice,common wild rice +#source = ArrayExpress::EG +#source = EntrezGene::MULTI +#source = GO::MULTI +#source = goslim_goa::EG +#source = Interpro::MULTI +#source = InterproGO::MULTI +#source = miRBase::MULTI +#source = RefSeq_dna::MULTI-Plants +#source = RefSeq_mRNA_predicted::MULTI +#source = RefSeq_peptide::MULTI-Plants +#source = RFAM::EG +#source = RNAMMER::MULTI +#source = TRNASCAN_SE::MULTI +#source = UniParc::MULTI +#source = Uniprot/SPTREMBL::MULTI +#source = Uniprot/SWISSPROT::MULTI +# +#[species oryza_rufipogon_fpc] +#taxonomy_id = 4529 +#aliases = Oryza rufipogon,orufipogon,oryzarufipogon,red rice,common wild rice +#source = ArrayExpress::EG +#source = EntrezGene::MULTI +#source = GO::MULTI +#source = goslim_goa::EG +#source = Interpro::MULTI +#source = InterproGO::MULTI +#source = miRBase::MULTI +#source = RefSeq_dna::MULTI-Plants +#source = RefSeq_mRNA_predicted::MULTI +#source = RefSeq_peptide::MULTI-Plants +#source = RFAM::EG +#source = RNAMMER::MULTI +#source = TRNASCAN_SE::MULTI +#source = UniParc::MULTI +#source = Uniprot/SPTREMBL::MULTI +#source = Uniprot/SWISSPROT::MULTI + +[species oryza_sativa_indica] +taxonomy_id = 39946 +aliases = Oryza sativa,osativa,oryzasativa,rice,Indian rice +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species oryza_sativa_japonica] +taxonomy_id = 39947 +aliases = Oryza sativa,osativa,oryzasativa,rice,Japanese rice +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species physcomitrella_patens] +taxonomy_id = 3218 +taxonomy_id = 145481 +taxonomy_id = 487794 +aliases = Physcomitrella patens,ppatens,physcomitrellapatens,moss,Physcomitrella patens subsp. patens,Physcomitrella patens subsp. magdalenae +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniGene::physcomitrella_patens +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species populus_trichocarpa] +taxonomy_id = 3694 +aliases = Populus trichocarpa,ptrichocarpa,populustrichocarpa,poplar,black cottonwood +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniGene::populus_trichocarpa +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species selaginella_moellendorffii] +taxonomy_id = 88036 +aliases = Selaginella moellendorffii,smoellendorffii,selaginellamoellendorffii,club moss +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniGene::selaginella_moellendorffii +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species sorghum_bicolor] +taxonomy_id = 4558 +taxonomy_id = 91525 +taxonomy_id = 171959 +aliases = Sorghum bicolor,sbicolor,sorghumbicolor,sorghum,milo,broomcorn,shattercane,chicken cornSorghum bicolor subsp. verticilliflorum,Sorghum bicolor subsp. x drummondii +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniGene::sorghum_bicolor +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + +[species zea_mays] +taxonomy_id = 4577 +taxonomy_id = 112001 +taxonomy_id = 381124 +taxonomy_id = 334825 +taxonomy_id = 4579 +taxonomy_id = 76912 +aliases = Zea mays,zmays,zeamays,corn,maize +source = ArrayExpress::EG +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = miRBase::MULTI +source = RefSeq_dna::MULTI-Plants +source = RefSeq_mRNA_predicted::MULTI +source = RefSeq_peptide::MULTI-Plants +source = RFAM::EG +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = UniGene::zea_mays +source = UniParc::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI + [species amphimedon_queenslandica] taxonomy_id = 400682 aliases = sponge, aqueenslandica, amphimedon_queenslandica -- GitLab