From 95d7d298ae49c96555289e33caba44e95a77b8f9 Mon Sep 17 00:00:00 2001 From: Kevin Howe <klh@ebi.ac.uk> Date: Tue, 16 Dec 2014 15:08:50 +0000 Subject: [PATCH] Added UniProt MULTI-invertebrate sources, and cleaned up WormBase sources --- misc-scripts/xref_mapping/xref_config.ini | 229 +++++++++++++++++++--- 1 file changed, 203 insertions(+), 26 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 504e9696c1..7f2f854f27 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -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 -- GitLab