xref sources for rodent species

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