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Commit fa3c2f72 authored by Arnaud Kerhornou's avatar Arnaud Kerhornou
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Added 2 diatom species and the necessary soruces for them, and added a source goslim_goa::EG

parent 30cb34cb
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Showing with 138 additions and 15 deletions
misc-scripts/xref_mapping/xref_config.ini
View file @ fa3c2f72
......@@ -654,7 +654,7 @@ data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/
#data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
[source EntrezGene::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana
name = EntrezGene
download = Y
order = 10
......@@ -962,7 +962,7 @@ release_uri =
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
[source GO::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, 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_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, canis_familiaris, 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_pygmaeus,saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri,phaeodactylum_tricornutum,thalassiosira_pseudonana
name = GO
download = Y
order = 80
......@@ -1018,6 +1018,16 @@ parser = GOSlimParser
release_uri =
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_58,
[source goslim_goa::EG]
# Used by Ensembl Genomes
name = goslim_goa
download = Y
order = 120
priority = 1
prio_descr = main
parser = GOSlimParser
release_uri =
data_uri = script:host=>mysql-eg-staging-1,port=>4160,dbname=>ensembl_ontology_58,
[source GO::homo_sapiens]
# Used by homo_sapiens
......@@ -1364,7 +1374,7 @@ release_uri =
data_uri = file:Illumina_V2/Human-6_v2_sequence.csv
[source Interpro::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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, pan_troglodytes,pongo_pygmaeus, oryzias_latipes, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,thalassiosira_pseudonana, phaeodactylum_tricornutum
name = Interpro
download = Y
order = 70
......@@ -1517,6 +1527,39 @@ parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/fungi/fungi*.rna.fna.gz
[source RefSeq_dna::MULTI-complete]
# Used by phaeodactylum_tricornutum
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/complete/complete*.rna.fna.gz
[source RefSeq_dna::MULTI-complete]
# Used by thalassiosira_pseudonana
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/complete/complete*.rna.fna.gz
[source RefSeq_dna::MULTI-protozoa]
# Used by dictyostelium_discoideum
name = RefSeq_dna
download = Y
order = 20
priority = 2
prio_descr = refseq
parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/protozoa/protozoa*.rna.fna.gz
[source RefSeq_dna::MULTI-invertebrate]
# Used by drosophila_melanogaster
name = RefSeq_dna
......@@ -1728,6 +1771,40 @@ parser = RefSeqGPFFParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/release/fungi/fungi*.protein.gpff.gz
[source RefSeq_peptide::MULTI-complete]
# Used by phaeodactylum_tricornutum
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/refseq/release/complete/complete*.protein.gpff.gz
[source RefSeq_peptide::MULTI-complete]
# Used by thalassiosira_pseudonana
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/refseq/release/complete/complete*.protein.gpff.gz
[source RefSeq_peptide::MULTI-protozoa]
# Used by dictyostelium_discoideum
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/refseq/release/protozoa/protozoa*.protein.gpff.gz
[source RefSeq_peptide::MULTI-invertebrate]
# Used by caenorhabditis_elegans, ciona_savignyi, drosophila_melanogaster
name = RefSeq_peptide
......@@ -2231,7 +2308,7 @@ parser = UniProtParser
release_uri =
[source Uniprot/SPTREMBL::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana
name = Uniprot/SPTREMBL
download = Y
order = 20
......@@ -2252,7 +2329,7 @@ parser = UniProtParser
release_uri =
[source Uniprot/SWISSPROT::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, 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_pygmaeus, rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum , thalassiosira_pseudonana
name = Uniprot/SWISSPROT
download = Y
order = 20
......@@ -2327,7 +2404,7 @@ release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldat
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz
[source Uniprot/Varsplic::MULTI]
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis
# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, echinops_telfairi, erinaceus_europaeus, felis_catus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, ixodes_scapularis, loxodonta_africana, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, ornithorhynchus_anatinus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_pygmaeus,rattus_norvegicus, saccharomyces_cerevisiae, spermophilus_tridecemlineatus, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, phaeodactylum_tricornutum, thalassiosira_pseudonana
name = Uniprot/Varsplic
download = Y
order = 30
......@@ -2820,7 +2897,7 @@ taxonomy_id = 344612
aliases = aspergillusclavatus, aclavatus, Aspergillus clavatus, Aspergillus clavatus NRRL 1
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -2838,7 +2915,7 @@ taxonomy_id = 332952
aliases = aspergillusflavus, aflavus, Aspergillus flavus, Aspergillus flavus NRRL3357
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -2851,11 +2928,10 @@ source = TRNASCAN-SE::MULTI-asp
source = RNAMMER::MULTI-asp
[species aspergillus_fumigatus]
taxonomy_id = 5085
taxonomy_id = 330879
aliases = aspergillusfumigatus, afumigatus, Aspergillus fumigatus, Aspergillus fumigatus Af293,Sartorya fumigata,sartoryafumigata,sfumigata
source = EntrezGene::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
......@@ -2871,7 +2947,7 @@ taxonomy_id = 162425
taxonomy_id = 227321
aliases = aspergillusnidulans, anidulans, Aspergillus nidulellus, aspergillusnidulellus, anidulellus, Emericella nidulans, emericellanidulans, enidulans, Aspergillus nidulans FGSC A4
source = EntrezGene::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
source = RefSeq_peptide::MULTI-fungi
......@@ -2888,7 +2964,7 @@ taxonomy_id = 425011
aliases = aspergillusniger, aniger, Aspergillus niger, Aspergillus niger CBS 513.88
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -2906,6 +2982,7 @@ taxonomy_id = 510516
aliases = aspergillusoryzae, aoryzae, Aspergillus oryzae, Aspergillus oryzae RIB40
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -2923,7 +3000,7 @@ taxonomy_id = 341663
aliases = aspergillusterreus, aterreus, Aspergillus terreus, Aspergillus terreus NIH2624
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -2941,7 +3018,7 @@ taxonomy_id = 331117
aliases = neosartoryafischeri, nfischeri, Neosartorya fischeri, Neosartorya fischeri NRRL 181
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -3098,6 +3175,21 @@ source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species dictyostelium_discoideum]
taxonomy_id = 366501
taxonomy_id = 44689
aliases = dictyostelium, dictyostelium_discoideum,Slime_mold
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-protozoa
source = RefSeq_peptide::MULTI-protozoa
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
[species dipodomys_ordii]
taxonomy_id = 10020
aliases = kangaroorat, roorat
......@@ -3701,7 +3793,7 @@ taxonomy_id = 4932
aliases = saccharomyces, saccharomycescerevisiae, scerevisiae, yeast
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-fungi
......@@ -3711,6 +3803,37 @@ source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
[species phaeodactylum_tricornutum]
taxonomy_id = 2850
taxonomy_id = 556484
aliases = diatom, phaeodactlyum_tricornutum, phaeodactlyum,
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
[species thalassiosira_pseudonana]
taxonomy_id = 35128
taxonomy_id = 296543
aliases = diatom,thalassiosira_pseudonana,thalassiosira
source = EntrezGene::MULTI
source = GO::MULTI
source = goslim_goa::EG
source = InterproGO::MULTI
source = Interpro::MULTI
source = RefSeq_dna::MULTI-complete
source = RefSeq_peptide::MULTI-complete
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
#source = Uniprot/Varsplic::MULTI
[species spermophilus_tridecemlineatus]
taxonomy_id = 43179
aliases = squirrel, thirteen-lined ground squirrel
......
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