Commit b077f0ae authored by Karyn Megy's avatar Karyn Megy
Browse files

Adding Ixodes info., modif. Anoph, Aedes and Culex info.

parent d1d24b77
......@@ -150,6 +150,19 @@ parser = VbDirectParser
release_uri =
data_uri = file:Aedes_aegypti/UCR/UCR_GillMgMT_0.2k_v2.txt
[source Aedes_ManualAnnotation::aedes_aegypti]
# Used by aedes_aegypti
name = Aedes_ManualAnnotation
download = Y
order = 40
priority = 1
prio_descr =
parser = AedesCAPParser
release_uri =
#data_uri = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels.fa
data_uri = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels_ALL_descr.fa
#data_uri = file:Aedes_aegypti/Aedes_AaeL1-2_ManualModels_DescrOnly_descr.fa
[source AedesGenBank::aedes_aegypti]
# Used by aedes_aegypti
name = AedesGenBank
......@@ -161,6 +174,17 @@ parser = AedesGenBankParser
release_uri =
data_uri = file:AedesGenBank/Aedes_proteinID.fa
[source Ixodes_ManualAnnotation::ixodes_scapularis]
# Used by ixodes_scapularis
name = Ixodes_ManualAnnotation
download = Y
order = 40
priority = 1
prio_descr =
parser = IxodesCAPParser
release_uri =
data_uri = file:Ixodes_scapularis/ixodes_CAP.fa
[source AgilentCGH::homo_sapiens]
# Used by homo_sapiens
name = AgilentCGH
......@@ -227,6 +251,17 @@ parser = AnophelesSymbolParser
release_uri =
data_uri = file:Anopheles_symbol/GeneName_translation_UniqID.txt
[source VB_Community_Symbol::anopheles_gambiae]
# Used by anopheles_gambiae
name = VB_Community_Symbol
download = Y
order = 40
priority = 1
prio_descr =
parser = VBCommunitySymbolParser
release_uri =
data_uri = file:VB_Community_Symbols/xref_Anopheles_symbol_lookup
[source bdgpinsituexpr::drosophila_melanogaster]
# Used by drosophila_melanogaster
name = bdgpinsituexpr
......@@ -280,7 +315,7 @@ priority = 1
prio_descr =
parser = CeleraProteinParser
release_uri =
data_uri = file:Celera_Pep/consensus-proteins_xref.fasta
data_uri = file:Celera/consensus-proteins_xref.fasta
[source Celera_Trans::anopheles_gambiae]
# Used by anopheles_gambiae
......@@ -291,7 +326,7 @@ priority = 1
prio_descr =
parser = CeleraTranscriptParser
release_uri =
data_uri = file:Celera_trans/consensus-transcripts_xref.fasta
data_uri = file:Celera/consensus-transcripts_xref.fasta
[source Codelink::homo_sapiens]
# Used by homo_sapiens
......@@ -406,7 +441,7 @@ 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, 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
name = EntrezGene
download = Y
order = 10
......@@ -583,7 +618,7 @@ data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/
[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, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, gallus_gallus, gasterosteus_aculeatus, 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, 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
name = GO
download = Y
order = 80
......@@ -962,7 +997,7 @@ 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, 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
name = Interpro
download = Y
order = 70
......@@ -1701,6 +1736,18 @@ release_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/*.LOG
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Monodelphis_domestica/Mdm.data.gz
[source UniGene::ixodes_scapularis]
# Used by ixodes_scapularis
name = UniGene
download = Y
order = 30
priority = 1
prio_descr =
parser = UniGeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.seq.uniq.gz
data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Ixodes_scapularis/Isc.data.gz
[source UniGene::mus_musculus]
# Used by mus_musculus
name = UniGene
......@@ -1805,7 +1852,7 @@ 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, 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
name = Uniprot/SPTREMBL
download = Y
order = 20
......@@ -1869,7 +1916,7 @@ 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, 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
name = Uniprot/Varsplic
download = Y
order = 30
......@@ -2118,7 +2165,15 @@ parser = ncRNA_DBParser
release_uri =
data_uri = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs,
[source ncRNA::culex_pipiens]
name = ncRNA_Culex
download = Y
order = 70
priority = 1
prio_descr =
parser = ncRNAParser
release_uri =
data_uri = file:/lustre/work1/ensembl/kmegy/Culex/Xrefs/culex_ncRNAxref_sw4.txt
[source wormpep_id::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
......@@ -2291,9 +2346,10 @@ source = ARRAY_JHSPH_AG_GAMBER_15k_v1::anopheles_gambiae
source = ARRAY_JHSPH_GAM3_0_21k_v1::anopheles_gambiae
source = ARRAY_LIV_GAMDETOX_0_25k_v1::anopheles_gambiae
source = ARRAY_LIV_GAMDETOX_0_25k_v2::anopheles_gambiae
source = Anopheles_symbol::anopheles_gambiae
#source = Anopheles_symbol::anopheles_gambiae
source = Celera_Pep::anopheles_gambiae
source = Celera_Trans::anopheles_gambiae
source = VB_Community_Symbol::anopheles_gambiae
source = EntrezGene::MULTI
source = GO::MULTI
source = InterproGO::MULTI
......@@ -2401,6 +2457,18 @@ source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::MULTI
[species culex_pipiens]
#taxonomy_id = 7175 c. pipiens
taxonomy_id = 7176 c.quinquefasciatus
aliases = cpipiens, culex, culexpipiens, culex quinquefasciatus, cquinquefasciatus, culexquinquefasciatus
source = EntrezGene::MULTI
source = GO::MULTI
source = Interpro::MULTI
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = ncRNA::culex_pipiens
[species danio_rerio]
taxonomy_id = 7955
aliases = danio, daniorerio, drerio, zebrafish
......@@ -2591,6 +2659,19 @@ source = ncRNA::MULTI
source = UCSC::homo_sapiens
source = HGNC_curated_transcript::homo_sapiens
[species ixodes_scapularis]
taxonomy_id = 6945
aliases = ixodes, ixodesscapularis
source = Ixodes_ManualAnnotation::ixodes_scapularis
source = EntrezGene::MULTI
source = GO::MULTI
source = InterproGO::MULTI
source = Interpro::MULTI
source = UniGene::ixodes_scapularis
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
[species loxodonta_africana]
taxonomy_id = 9785
aliases = elephant, lafricana, loxodontaafricana
......
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