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Commit 95d7d298 authored by Kevin Howe's avatar Kevin Howe
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Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources

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3 merge requests!49Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources,!49Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources,!49Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources
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misc-scripts/xref_mapping/xref_config.ini
+ 203
− 26
View file @ 95d7d298
......@@ -3719,6 +3719,17 @@ prio_descr =
parser = UniProtAltParser
release_uri =
[source Uniprot/SPTREMBL::MULTI-invertebrate]
name = Uniprot/SPTREMBL
download = Y
order = 20
priority = 1
prio_descr =
parser = UniProtAltParser
dependent_on = MIM
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/reldate.txt
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_invertebrates.dat.gz
[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, ficedula_albicollis, 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
......@@ -3767,6 +3778,18 @@ release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldat
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
[source Uniprot/SWISSPROT::MULTI-invertebrate]
name = Uniprot/SWISSPROT
download = Y
order = 20
priority = 2
prio_descr = sequence_mapped
parser = UniProtAltParser
dependent_on = MIM
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/reldate.txt
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_invertebrates.dat.gz
#
# Direct Uniprot mapping.
# Note these have to be done LAST so that we get all
......@@ -4560,7 +4583,7 @@ parser =
release_uri =
data_uri =
[source wormbase::caenorhabditis_elegans]
[source wormbase::celegans]
name = wormbase_all
download = Y
order = 50
......@@ -4568,10 +4591,80 @@ priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.sanger.ac.uk/pub2/wormbase/releases/WS230/species/c_elegans/c_elegans.WS230.xrefs.txt.gz
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS245.xrefs.txt.gz
[source wormpep_id::caenorhabditis_elegans]
# Used by caenorhabditis_elegans
[source wormbase::cbriggsae]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/c_briggsae/PRJNA10731/c_briggsae.PRJNA10731.WS245.xrefs.txt.gz
[source wormbase::cbrenneri]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/c_brenneri/PRJNA20035/c_brenneri.PRJNA20035.WS245.xrefs.txt.gz
[source wormbase::cremanei]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/c_remanei/PRJNA53967/c_remanei.PRJNA53967.WS245.xrefs.txt.gz
[source wormbase::cjaponica]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/c_japonica/PRJNA12591/c_japonica.PRJNA12591.WS245.xrefs.txt.gz
[source wormbase::ppacificus]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/p_pacificus/PRJNA12644/p_pacificus.PRJNA12644.WS245.xrefs.txt.gz
[source wormbase::bmalayi]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/b_malayi/PRJNA10729/b_malayi.PRJNA10729.WS245.xrefs.txt.gz
[source wormbase::ovolvulus]
name = wormbase_all
download = Y
order = 50
priority = 1
prio_descr =
parser = WormbaseDirectParser
release_uri =
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/wormbase/releases/WS245/species/o_volvulus/PRJEB513/o_volvulus.PRJEB513.WS245.xrefs.txt.gz
[source wormpep_id::wormbase]
# Used by wormbase core species
name = wormpep_id
download = N
order = 50
......@@ -4581,8 +4674,8 @@ parser = comes from WormbaseDirectParser
release_uri =
data_uri =
[source wormbase_gene::caenorhabditis_elegans]
# Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser
[source wormbase_gene::wormbase]
# Used by wormbase core species
name = wormbase_gene
download = N
order = 50
......@@ -4592,8 +4685,8 @@ parser = comes from WormbaseDirectParser
release_uri =
data_uri =
[source wormbase_locus::caenorhabditis_elegans]
# Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser
[source wormbase_locus::wormbase]
# Used by wormbase core species
name = wormbase_locus
download = N
order = 50
......@@ -4604,7 +4697,7 @@ release_uri =
data_uri =
[source wormbase_gseqname::wormbase]
# Used by caenorhabditis_elegans comes from WormbaseDirectParser
# Used by wormbase core species
name = wormbase_gseqname
download = N
order = 50
......@@ -4614,8 +4707,8 @@ parser = comes from WormbaseDirectParser
release_uri =
data_uri =
[source wormbase_transcript::caenorhabditis_elegans]
# Used by caenorhabditis_elegans comes from WormbaseDatabaseStableIDParser
[source wormbase_transcript::wormbase]
# Used by wormbase core species
name = wormbase_transcript
download = N
order = 50
......@@ -5519,21 +5612,6 @@ source = RFAM::MULTI
source = miRBase::MULTI
source = ArrayExpress::MULTI
[species caenorhabditis_elegans]
taxonomy_id = 6239
aliases = caenorhabditiselegans, celegans, elegans
source = EntrezGene::MULTI
source = GO::caenorhabditis_elegans
source = goslim_goa::EG
source = RefSeq_dna::caenorhabditis_elegans
source = RefSeq_peptide::caenorhabditis_elegans
source = UniGene::caenorhabditis_elegans
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = UniParc::MULTI
source = wormbase::caenorhabditis_elegans
source = ArrayExpress::EG
[species callithrix_jacchus]
taxonomy_id = 9483
aliases = Marmoset, marmoset, white-tufted-ear marmoset, callithrixjacchus, callithrix_jacchus
......@@ -8447,3 +8525,102 @@ source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = UniParc::MULTI
[species caenorhabditis_elegans]
taxonomy_id = 6239
aliases = caenorhabditiselegans, celegans, elegans
source = EntrezGene::MULTI
source = GO::caenorhabditis_elegans
source = goslim_goa::EG
source = RefSeq_dna::caenorhabditis_elegans
source = RefSeq_peptide::caenorhabditis_elegans
source = UniGene::caenorhabditis_elegans
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::celegans
source = ArrayExpress::EG
[species caenorhabditis_briggsae]
taxonomy_id = 6238
aliases = caenorhabditis_briggae_prjna10731
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::cbriggsae
[species caenorhabditis_remanei]
taxonomy_id = 31234
aliases = caenorhabditis_remanei_prjna53967
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::cremanei
[species caenorhabditis_brenneri]
taxonomy_id = 135651
aliases = caenorhabditis_brenneri_prjna20035
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::cbrenneri
[species caenorhabditis_japonica]
taxonomy_id = 281687
aliases = caenorhabditis_japonica_prjna12591
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::cjaponica
[species brugia_malayi]
taxonomy_id = 6279
aliases = brugia_malayi_prjna10729
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::bmalayi
[species onchocerca_volvulus]
taxonomy_id = 6282
aliases = onchocerca_volvulus_prjeb513
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::ovolvulus
[species pristionchus_pacificus]
taxonomy_id = 54126
aliases = pristionchus_pacificus_prjna12644
source = EntrezGene::MULTI
source = GO::MULTI
source = RefSeq_dna::MULTI-invertebrate
source = RefSeq_peptide::MULTI-invertebrate
source = Uniprot/SPTREMBL::MULTI-invertebrate
source = Uniprot/SWISSPROT::MULTI-invertebrate
source = UniParc::MULTI
source = wormbase::ppacificus
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