From 314585638fd878d50d6750eee658ddeadf662e19 Mon Sep 17 00:00:00 2001 From: Alessandro Vullo <avullo@ebi.ac.uk> Date: Wed, 22 Oct 2014 14:24:30 +0100 Subject: [PATCH] Entries for spotted gar (Lepisosteous oculatus) and cave fish (Astyanax mexicanus). Updated to ensembl ontology 78. --- misc-scripts/xref_mapping/xref_config.ini | 92 +++++++++++++++++++++-- 1 file changed, 86 insertions(+), 6 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 6fe2af2a78..8bc4edf206 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -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 -- GitLab