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Commit 31458563 authored by Alessandro Vullo's avatar Alessandro Vullo
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Entries for spotted gar (Lepisosteous oculatus) and cave fish (Astyanax mexicanus). 

Updated to ensembl ontology 78.
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misc-scripts/xref_mapping/xref_config.ini
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− 6
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......@@ -885,7 +885,7 @@ release_uri =
data_uri = http://www.dbass.soton.ac.uk/dbass3/download.aspx?item=genes
[source EntrezGene::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
name = EntrezGene
download = Y
order = 10
......@@ -931,7 +931,7 @@ release_uri =
data_uri = ftp://fantom.gsc.riken.jp/FANTOM3/DDBJ/DDBJ_fantom3_HTC_accession.txt.gz
[source GO::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, drosophila_grimshawi, drosophila_willistoni, drosophila_ananassae, drosophila_yakuba, drosophila_simulans, drosophila_sechellia, drosophila_erecta, drosophila_persimilis, drosophila_mojavensis, drosophila_virilis, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
name = GO
download = Y
order = 80
......@@ -1004,7 +1004,7 @@ prio_descr = main
parser = GOSlimParser
dependent_on = GO
release_uri =
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_77,
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_78,
[source goslim_goa::EG]
# Used by Ensembl Genomes
......@@ -1345,7 +1345,7 @@ release_uri =
data_uri = file:Mus_musculus/Segments/Seg_xrefs.txt
[source Interpro::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes__scapularis, loxodonta_africana, macaca_mulatta, microcebus_murinus, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, ottolemur_garnetti, pan_troglodytes,pongo_abelii, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, sorex_araneus, ictidomys_tridecemlineatus,sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes__scapularis, loxodonta_africana, macaca_mulatta, microcebus_murinus, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, ottolemur_garnetti, pan_troglodytes,pongo_abelii, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, sorex_araneus, ictidomys_tridecemlineatus,sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum, lepisosteus_oculatus
name = Interpro
download = Y
order = 70
......@@ -2270,6 +2270,28 @@ parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.rna.fna.gz
[source RefSeq_dna::lepisosteus_oculatus]
# Used by lepisosteus_oculatus
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Lepisosteus_oculatus/RNA/rna.gbk.gz
[source RefSeq_dna::astyanax_mexicanus]
# Used by astyanax_mexicanus
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Astyanax_mexicanus/RNA/rna.gbk.gz
[source RefSeq_peptide::MULTI-fungi]
# Used by saccharomyces_cerevisiae
name = RefSeq_peptide
......@@ -2860,6 +2882,28 @@ parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/rat.protein.gpff.gz
[source RefSeq_peptide::lepisosteus_oculatus]
# Used by lepisosteus_oculatus
name = RefSeq_peptide
download = Y
order = 20
priority = 1
prio_descr =
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Lepisosteus_oculatus/protein/protein.gbk.gz
[source RefSeq_peptide::astyanax_mexicanus]
# Used by astyanax_mexicanus
name = RefSeq_peptide
download = Y
order = 20
priority = 1
prio_descr =
parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/genomes/Astyanax_mexicanus/protein/protein.gbk.gz
[source SGD_GENE::saccharomyces_cerevisiae]
# Used by saccharomyces_cerevisiae
name = SGD_GENE
......@@ -3642,7 +3686,7 @@ parser = UniProtAltParser
release_uri =
[source Uniprot/SPTREMBL::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
name = Uniprot/SPTREMBL
download = Y
order = 20
......@@ -3677,7 +3721,7 @@ parser = UniProtAltParser
release_uri =
[source Uniprot/SWISSPROT::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii, rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana, lepisosteus_oculatus
name = Uniprot/SWISSPROT
download = Y
order = 20
......@@ -5152,6 +5196,24 @@ source = TRNASCAN_SE::MULTI
source = RNAMMER::MULTI
source = ArrayExpress::EG
[species astyanax_mexicanus]
taxonomy_id = 7994
aliases = cave fish, Mexican tetra
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::astyanax_mexicanus
source = RefSeq_peptide::astyanax_mexicanus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = UniParc::MULTI
source = RFAM::MULTI
source = miRBase::MULTI
source = ArrayExpress::MULTI
[species neosartorya_fischeri]
taxonomy_id = 36630
taxonomy_id = 331117
......@@ -6084,6 +6146,24 @@ source = RefSeq_dna::MULTI-vertebrate_other
source = RefSeq_peptide::MULTI-vertebrate_other
source = ArrayExpress::MULTI
[species lepisosteus_oculatus]
taxonomy_id = 7918
aliases = spotted gar
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::lepisosteus_oculatus
source = RefSeq_peptide::lepisosteus_oculatus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/SWISSPROT::DIRECT
source = UniParc::MULTI
source = RFAM::MULTI
source = miRBase::MULTI
source = ArrayExpress::MULTI
[species loxodonta_africana]
taxonomy_id = 9785
aliases = elephant, lafricana, loxodontaafricana
......
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