Have added all plants missing species, plus all gramene plants species

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