diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 439849981acd438198d1b27ef7f29acdc4c89b2d..59a6a3a252222d991cb03ef117b4e4dff8e330af 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -96,7 +96,7 @@ priority = 1 prio_descr = parser = FlybaseParser release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz +data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source EPD::drosophila_simulans] # Used by the 12 drosophila genomes @@ -162,7 +162,7 @@ priority = 1 prio_descr = parser = FlybaseParser release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz +data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source FlyExpress::drosophila_melanogaster] # Used by drosophila_melanogaster @@ -230,17 +230,6 @@ parser = FlybaseParser release_uri = data_uri = ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/current/gff/dgri-all-*.gff.gz -[source MEROPS::drosophila_erecta] -# Used by the 12 drosophila genomes -name = MEROPS -download = N -order = 50 -priority = 1 -prio_descr = -parser = FlybaseParser -release_uri = -data_uri = ftp://ftp.flybase.org/releases/current/dere_1.3/gff/dere-all-r1.3.gff.gz - [source MEROPS::drosophila_virilis] # Used by the 12 drosophila genomes name = MEROPS @@ -272,7 +261,7 @@ priority = 1 prio_descr = parser = FlybaseParser release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz +data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source MitoDrome::drosophila_melanogaster] # Used by drosophila_melanogaster @@ -305,7 +294,7 @@ priority = 1 prio_descr = parser = FlybaseParser release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz +data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source flybase_annotation_id::drosophila_melanogaster] # Used by drosophila_melanogaster @@ -322,7 +311,7 @@ data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5. # Used by drosophila_melanogaster name = flybase_gene_id download = Y -order = 100 +order = 75 priority = 1 prio_descr = ID assigned by FlyBase parser = FlybaseParser @@ -340,7 +329,7 @@ prio_descr = ID assigned by FlyBase parser = FlybaseParser dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,Interpro release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/current/gff/dpse-all-r2.29.gff.gz +data_uri = ftp://ftp.flybase.net/genomes/Drosophila_pseudoobscura/dpse/gff/dpse-all-r2.30.gff.gz [source flybase_gene_id::drosophila_grimshawi] # Used by drosophila_grimshawi @@ -1049,7 +1038,7 @@ prio_descr = main parser = GOSlimParser dependent_on = GO release_uri = -data_uri = script:host=>mysql-eg-pan-1.ebi.ac.uk,port=>4276,dbname=>ensemblgenomes_ontology_16_69, +data_uri = script:host=>mysql-eg-staging-2.ebi.ac.uk,port=>4275,dbname=>ensemblgenomes_ontology_18_71, [source GO::homo_sapiens] # Used by homo_sapiens @@ -1118,15 +1107,17 @@ data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_assoc data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source GO::drosophila_melanogaster] -# Used by FlyBase +# Used by drosophila_melanogaster name = GO -download = N -order = 50 +download = Y +order = 85 priority = 1 prio_descr = flybasego -parser = FlybaseParser +parser = GOParser +dependent_on = Uniprot/SPTREMBL,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide,flybase_gene_id release_uri = -data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz +data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.fb.gz +data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz [source HPA::homo_sapiens] # Used by homo_sapiens @@ -1655,7 +1646,7 @@ order = 20 priority = 1 prio_descr = otherfeatures parser = RefSeqCoordinateParser -release_uri = +release_uri = data_uri = script:project=>ensembl, #data_uri = script:project=>ensembl,host=>ens-staging1,dbname=>homo_sapiens_core_70_37,ofhost=>ens-staging1,ofdbname=>homo_sapiens_otherfeatures_70_37, @@ -2925,7 +2916,6 @@ release_uri = data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Zea_mays/Zm.seq.uniq.gz data_uri = ftp://ftp.ncbi.nih.gov/repository/UniGene/Zea_mays/Zm.data.gz - [source UniProt::protein_id-predicted] # Special source used in UniProtAltParser. No species uses this source. name = protein_id_predicted @@ -3044,28 +3034,6 @@ parser = UniProtAltParser release_uri = data_uri = -[source Uniprot/SWISSPROT::drosophila_melanogaster] -# Used by drosophila_melanogaster -name = Uniprot/SWISSPROT -download = Y -order = 20 -priority = 1 -prio_descr = -parser = UniProtParser_descriptions_only -release_uri = -data_uri = ftp://ftp.ebi.ac.uk/pub/databases/integr8/uniprot/proteomes/17.D_melanogaster.dat.gz - -[source Uniprot/SWISSPROT::drosophila_pseudoobscura] -# Used by drosophila_pseudoobscura -name = Uniprot/SWISSPROT -download = Y -order = 20 -priority = 1 -prio_descr = -parser = UniProtParser_descriptions_only -release_uri = -data_uri = ftp://ftp.ebi.ac.uk/pub/databases/integr8/uniprot/proteomes/25396.D_pseudoobscura.dat.gz - [source Uniprot/SPTREMBL::drosophila_melanogaster] # Used by drosophila_melanogaster name = Uniprot/SPTREMBL @@ -4014,7 +3982,7 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = +release_uri = data_uri = http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=co data_uri = ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/po_temporal_gene_arabidopsis_tair.assoc @@ -4027,7 +3995,7 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = +release_uri = data_uri = http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=co data_uri = ftp://ftp.arabidopsis.org/home/tair/Ontologies/Plant_Ontology/po_anatomy_gene_arabidopsis_tair.assoc @@ -4039,7 +4007,7 @@ order = 1 priority = 1 prio_descr = parser = TAIRIDParser -release_uri = +release_uri = data_uri = ftp://ftp.arabidopsis.org/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated [source TAIR_LOCUS_MODEL::arabidopsis_thaliana] @@ -4071,7 +4039,7 @@ download = N order = 1 priority = 1 prio_descr = -parser = +parser = release_uri = data_uri = @@ -4084,7 +4052,7 @@ priority = 1 prio_descr = parser = TAIRIDParser release_uri = -data_uri = +data_uri = [source CommunityGO::arabidopsis_thaliana] # Used by Arabidopsis thaliana, Gramene-specific @@ -4095,7 +4063,7 @@ priority = 1 prio_descr = main dependent_on = TAIR_TRANSLATION parser = TAIROntologyParser -release_uri = +release_uri = data_uri = http://archive.geneontology.org/latest-termdb/go_daily-termdb.obo-xml.gz data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.tair.gz @@ -4480,18 +4448,15 @@ aliases = schistosomamansoni, smansoni, Schistosoma mansoni, Schistosoma source = EntrezGene::MULTI source = GO::MULTI source = goslim_goa::EG -source = InterproGO::MULTI source = Interpro::MULTI +source = InterproGO::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = RFAM::EG -source = miRBase::MULTI -source = RNAMMER::MULTI -source = TRNASCAN_SE::MULTI +source = UniParc::MULTI source = misc_EG::EG -source = ArrayExpress::EG +source = ArrayExpress::EG [species leishmania_major] taxonomy_id = 5664 @@ -4858,7 +4823,6 @@ source = Uniprot/SWISSPROT::MULTI source = UniParc::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate -source = GO::MULTI source = GO::drosophila_melanogaster source = goslim_goa::EG source = InterproGO::MULTI @@ -4866,7 +4830,7 @@ source = ArrayExpress::EG source = flybase_gene_id::drosophila_melanogaster [species drosophila_pseudoobscura] -taxonomy_id = 7237 +taxonomy_id = 46245 aliases = dpseudoobscura, drosophila, drosophilapseudoobscura source = EntrezGene::MULTI source = Interpro::MULTI @@ -4881,71 +4845,73 @@ source = InterproGO::MULTI source = ArrayExpress::EG source = flybase_gene_id::drosophila_pseudoobscura -[species drosophila_grimshawi] -taxonomy_id = 7222 -aliases = dgrimshawi, drosophila, drosophilagrimshawi +[species drosophila_ananassae] +taxonomy_id = 7217 +aliases = dananassae, drosophila, drosophilaananassae source = EntrezGene::MULTI -source = GO::MULTI -source = goslim_goa::MULTI source = Interpro::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_grimshawi -source = MEROPS::drosophila_grimshawi -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_ananassae -[species drosophila_willistoni] -taxonomy_id = 7260 -aliases = dwillistoni, drosophila, drosophilawillistoni +[species drosophila_erecta] +taxonomy_id = 7220 +aliases = derecta, drosophila, drosophilaerecta source = EntrezGene::MULTI source = Interpro::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -#source = Uniprot/SPTREMBL::drosophila_melanogaster -#source = Uniprot/SWISSPROT::drosophila_willistoni -#source = Uniprot/Varsplic::MULTI??? -source = flybase_gene_id::drosophila_willistoni -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_erecta -[species drosophila_ananassae] -taxonomy_id = 7217 -aliases = dananassae, drosophila, drosophilaananassae +[species drosophila_grimshawi] +taxonomy_id = 7222 +aliases = dgrimshawi, drosophila, drosophilagrimshawi source = EntrezGene::MULTI -source = GO::MULTI -source = goslim_goa::MULTI source = Interpro::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_ananassae -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_grimshawi -[species drosophila_yakuba] -taxonomy_id = 7245 -aliases = dyakuba, drosophila, drosophilayakuba +[species drosophila_mojavensis] +taxonomy_id = 7230 +aliases = dmojavensis, drosophila, drosophilamojavensis source = EntrezGene::MULTI source = Interpro::MULTI -source = GO::MULTI -source = goslim_goa::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_yakuba -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_mojavensis -[species drosophila_simulans] -taxonomy_id = 7240 -aliases = dsimulans, drosophila, drosophilasimulans +[species drosophila_persimilis] +taxonomy_id = 7234 +aliases = dpersimilis, drosophila, drosophilapersimilis source = EntrezGene::MULTI source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI @@ -4957,69 +4923,87 @@ source = GO::MULTI source = goslim_goa::EG source = InterproGO::MULTI source = ArrayExpress::EG -source = flybase_gene_id::drosophila_simulans +source = flybase_gene_id::drosophila_persimilis [species drosophila_sechellia] taxonomy_id = 7238 aliases = dsechellia, drosophila, drosophilasechellia source = EntrezGene::MULTI source = Interpro::MULTI -source = GO::MULTI -source = goslim_goa::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG source = flybase_gene_id::drosophila_sechellia -source = EPD::drosophila_sechellia -source = ArrayExpress::EG -[species drosophila_erecta] -taxonomy_id = 7220 -aliases = derecta, drosophila, drosophilaerecta +[species drosophila_simulans] +taxonomy_id = 7240 +aliases = dsimulans, drosophila, drosophilasimulans source = EntrezGene::MULTI source = Interpro::MULTI -source = GO::MULTI -source = goslim_goa::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_erecta -source = MEROPS::drosophila_erecta -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_simulans -[species drosophila_persimilis] -taxonomy_id = 7234 -aliases = dpersimilis, drosophila, drosophilapersimilis +[species drosophila_virilis] +taxonomy_id = 7244 +aliases = dvirilis, drosophila, drosophilavirilis source = EntrezGene::MULTI -source = GO::MULTI -source = goslim_goa::MULTI source = Interpro::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_persimilis -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_virilis -[species drosophila_mojavensis] -taxonomy_id = 7230 -aliases = dmojavensis, drosophila, drosophilamojavensis +[species drosophila_willistoni] +taxonomy_id = 7260 +aliases = dwillistoni, drosophila, drosophilawillistoni source = EntrezGene::MULTI source = Interpro::MULTI -source = GO::MULTI -source = goslim_goa::MULTI -source = InterproGO::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI source = RefSeq_dna::MULTI-invertebrate source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_willistoni + +[species drosophila_yakuba] +taxonomy_id = 7245 +aliases = dyakuba, drosophila, drosophilayakuba +source = EntrezGene::MULTI +source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_mojavensis -source = EPD::drosophila_mojavensis -source = ArrayExpress::EG +source = UniParc::MULTI +source = RefSeq_dna::MULTI-invertebrate +source = RefSeq_peptide::MULTI-invertebrate +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG +source = flybase_gene_id::drosophila_yakuba [species daphnia_pulex] @@ -5040,26 +5024,6 @@ source = RNAMMER::MULTI source = ArrayExpress::EG -[species drosophila_virilis] -taxonomy_id = 7244 -aliases = dvirilis, drosophila, drosophilavirilis -source = EntrezGene::MULTI -source = Interpro::MULTI -source = GO::MULTI -source = goslim_goa::MULTI -source = InterproGO::MULTI -source = RefSeq_dna::MULTI-invertebrate -source = RefSeq_peptide::MULTI-invertebrate -source = Uniprot/SPTREMBL::MULTI -source = Uniprot/SWISSPROT::MULTI -source = flybase_gene_id::drosophila_virilis -source = EPD::drosophila_virilis -source = MEROPS::drosophila_virilis -source = ArrayExpress::EG -#source = TF::drosophila_virilis -#source = GLEANR::drosophila_virilis -#source = GPCR::drosophila_virilis - [species echinops_telfairi] taxonomy_id = 9371 aliases = echinopstelfairi, etelfairi, tenrec @@ -7114,6 +7078,7 @@ source = RefSeq_peptide::tribolium_castaneum source = UniGene::tribolium_castaneum source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI source = ArrayExpress::EG [species gaeumannomyces_graminis] @@ -7157,3 +7122,62 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = ArrayExpress::EG +[species danaus_plexippus] +taxonomy_id = 13037 +aliases = dplexippus, danaus plexippus, monarch butterfly +source = EntrezGene::MULTI +source = Interpro::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG + +[species heliconius_melpomene] +taxonomy_id = 34740 +aliases = hmelpomene, heliconius melpomene, postman butterfly +source = EntrezGene::MULTI +source = Interpro::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = InterproGO::MULTI +source = ArrayExpress::EG + +[species strigamia_maritima] +taxonomy_id = 126957 +aliases = strigamiamaritima, smaritima, Strigamia maritima +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::EG +source = miRBase::MULTI +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = ArrayExpress::EG + +[species megaselia_scalaris] +taxonomy_id = 36166 +aliases = megaseliascalaris, mscalaris, Megaselia scalaris +source = EntrezGene::MULTI +source = GO::MULTI +source = goslim_goa::EG +source = Interpro::MULTI +source = InterproGO::MULTI +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = UniParc::MULTI +source = RFAM::EG +source = miRBase::MULTI +source = RNAMMER::MULTI +source = TRNASCAN_SE::MULTI +source = ArrayExpress::EG