diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 4d33b82b91d594842a7f38e585320a56374ce6f4..9d84cf0b100c5f98350a5f0e6f364b302744bcee 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -763,7 +763,7 @@ 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=>ens-production,dbname=>mr6_human_core, +#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, [source ArrayExpress::EG] name = ArrayExpress @@ -4204,8 +4204,7 @@ 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=>ens-production,dbname=>mr6_pig_core, - +#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, [source RFAM::EG] name = RFAM @@ -5674,6 +5673,36 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species cavia_aperea] +taxonomy_id = 37548 +aliases = brazilian guinea pig +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + +[species chinchilla_lanigera] +taxonomy_id = 34839 +aliases = chinchilla, long-tailed chinchilla +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species chlorocebus_sabaeus] taxonomy_id = 60711 aliases = Chlorocebus sabeus,vervet monkey,African Green Monkey,AGM,vervet,chlorocebus_sabeus,Chlorocebus sabaeus @@ -6101,6 +6130,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species fukomys_damarensis] +taxonomy_id = 885580 +aliases = damara mole rat +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species gadus_morhua] taxonomy_id = 8049 aliases = cod,gmorhua,gadus_morhua,gmor,atlantic_cod,gadmor @@ -6170,6 +6214,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species heterocephalus_glaber] +taxonomy_id = 9999 +aliases = naked mole rat +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species homo_sapiens] taxonomy_id = 9606 @@ -6231,6 +6290,22 @@ source = Uniprot/SWISSPROT::MULTI source = PUBMED::ixodes_scapularis source = ArrayExpress::EG +[species jaculus_jaculus] +taxonomy_id = 51337 +aliases = jerboa, lesser egyptian jerboa +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + + [species latimeria_chalumnae] taxonomy_id = 7897 aliases = coelacanth, lchalumnae, living fossil, lamineria @@ -6330,6 +6405,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species mesocricetus_auratus] +taxonomy_id = 10036 +aliases = golden hamster +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species microcebus_murinus] taxonomy_id = 30608 aliases = mouse lemur, mmur, mmurinus, mouse_lemur, microcebus murinus @@ -6347,6 +6437,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species microtus_ochrogaster] +taxonomy_id = 79684 +aliases = prairie vole +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species monodelphis_domestica] taxonomy_id = 13616 aliases = mdomestica, mono, monodelphis, monodelphisdomestica, opossum, possum @@ -6423,6 +6528,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species nannospalax_galili] +taxonomy_id = 1026970 +aliases = mountain blind mole rat +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species ochotona_princeps] taxonomy_id = 9978 aliases = pika, American pika @@ -6439,6 +6559,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species octodon_degus] +taxonomy_id = 10160 +aliases = common degu, brush-tailed rat +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species oreochromis_niloticus] taxonomy_id = 8128 aliases = oreochromis_niloticus, tilapia, nile tilapia, Tilapia, Nile tilapia @@ -6606,6 +6741,21 @@ source = RFAM::MULTI source = miRBase::MULTI source = ArrayExpress::MULTI +[species peromyscus_maniculatus_bairdii] +taxonomy_id = 230844 +aliases = northern american deer mouse, deer mouse +source = EntrezGene::MULTI +source = Reactome::MULTI +source = RNACentral::MULTI +source = RefSeq_dna::MULTI-vertebrate_mammalian +source = RefSeq_peptide::MULTI-vertebrate_mammalian +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::MULTI +source = miRBase::MULTI +source = ArrayExpress::MULTI + [species petromyzon_marinus] taxonomy_id = 7757 aliases = lamprey, sea lamprey, pmarinus