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Commit 8933c0b7 authored by Magali Ruffier's avatar Magali Ruffier
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xref sources for rodent species

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misc-scripts/xref_mapping/xref_config.ini
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− 3
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......@@ -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
......
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