diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 7f2f854f277c75522bfe6170ce3684eac7b632de..d52960fab4f9a5cd1bfa077687f8deaeaffacea5 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -1520,6 +1520,17 @@ parser = OTTTParser release_uri = data_uri = +[source Reactome::MULTI] +# Used by all species +name = Reactome +download = Y +order = 1 +priority = 1 +prio_descr = +parser = ReactomeParser +release_uri = http://www.reactome.org +data_uri = http://www.reactome.org/download/current/Ensembl2Reactome_All_Levels.txt + [source RGD::rattus_norvegicus] # Used by rattus_norvegicus name = RGD @@ -5091,6 +5102,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::ailuropoda_melanoleuca source = RefSeq_peptide::ailuropoda_melanoleuca source = RefSeq_import::otherfeatures @@ -5111,6 +5123,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::anas_platyrhynchos source = RefSeq_peptide::anas_platyrhynchos source = RefSeq_import::otherfeatures @@ -5130,6 +5143,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::anolis_carolinensis source = RefSeq_peptide::anolis_carolinensis source = RefSeq_import::otherfeatures @@ -5600,6 +5614,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::bos_taurus source = RefSeq_peptide::bos_taurus source = RefSeq_import::otherfeatures @@ -5620,6 +5635,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::callithrix_jacchus source = RefSeq_peptide::callithrix_jacchus source = RefSeq_import::otherfeatures @@ -5639,6 +5655,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::canis_familiaris source = RefSeq_peptide::canis_familiaris source = RefSeq_import::otherfeatures @@ -5659,6 +5676,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::cavia_porcellus source = RefSeq_peptide::cavia_porcellus source = RefSeq_import::otherfeatures @@ -5678,6 +5696,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -5697,6 +5716,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -5718,6 +5738,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::ciona_intestinalis source = RefSeq_peptide::ciona_intestinalis @@ -5741,6 +5762,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-invertebrate source = RefSeq_peptide::MULTI-vertebrate_other @@ -5781,6 +5803,7 @@ source = GO::danio_rerio source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::danio_rerio source = RefSeq_peptide::danio_rerio source = RefSeq_import::otherfeatures @@ -5805,6 +5828,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::dasypus_novemcinctus source = RefSeq_peptide::dasypus_novemcinctus source = RefSeq_import::otherfeatures @@ -5844,6 +5868,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6072,6 +6097,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::echinops_telfairi source = RefSeq_peptide::echinops_telfairi source = RefSeq_import::otherfeatures @@ -6091,6 +6117,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6111,6 +6138,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::equus_caballus source = RefSeq_peptide::equus_caballus source = RefSeq_import::otherfeatures @@ -6131,6 +6159,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::felis_catus source = RefSeq_peptide::felis_catus source = RefSeq_import::otherfeatures @@ -6150,6 +6179,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6169,6 +6199,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6190,6 +6221,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::gallus_gallus source = RefSeq_peptide::gallus_gallus source = RefSeq_import::otherfeatures @@ -6211,6 +6243,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6231,6 +6264,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::gorilla_gorilla source = RefSeq_peptide::gorilla_gorilla source = RefSeq_import::otherfeatures @@ -6246,34 +6280,36 @@ source = ArrayExpress::MULTI [species homo_sapiens] taxonomy_id = 9606 aliases = homosapiens, hsapiens, human -#source = CCDS::homo_sapiens -#source = DBASS3::homo_sapiens -#source = DBASS5::homo_sapiens -#source = EntrezGene::MULTI -#source = GO::homo_sapiens -#source = goslim_goa::MULTI -#source = HPA::homo_sapiens -#source = InterproGO::MULTI -#source = HGNC::homo_sapiens -#source = HGNC::homo_sapiens#01 -#source = HGNC::homo_sapiens#02 -#source = Interpro::MULTI -#source = MIM::homo_sapiens -#source = MIM2GENE::homo_sapiens -#source = RefSeq_dna::homo_sapiens -#source = RefSeq_dna::homo_sapiens#01 -#source = RefSeq_peptide::homo_sapiens +source = CCDS::homo_sapiens +source = DBASS3::homo_sapiens +source = DBASS5::homo_sapiens +source = EntrezGene::MULTI +source = GO::homo_sapiens +source = goslim_goa::MULTI +source = HPA::homo_sapiens +source = InterproGO::MULTI +source = HGNC::homo_sapiens +source = HGNC::homo_sapiens#01 +source = HGNC::homo_sapiens#02 +source = Interpro::MULTI +source = MIM::homo_sapiens +source = MIM2GENE::homo_sapiens +source = Reactome::MULTI +source = RefSeq_dna::homo_sapiens +source = RefSeq_dna::homo_sapiens#01 +source = RefSeq_peptide::homo_sapiens source = RefSeq_import::otherfeatures -#source = UniGene::homo_sapiens -#source = Uniprot/SPTREMBL::MULTI -#source = Uniprot/SWISSPROT::MULTI -#source = Uniprot/SWISSPROT::DIRECT -#source = UniParc::MULTI -#source = miRBase::MULTI -#source = RFAM::MULTI -#source = UCSC::homo_sapiens -#source = HGNC_curated_transcript::homo_sapiens -#source = ArrayExpress::MULTI +source = Reactome::MULTI +source = UniGene::homo_sapiens +source = Uniprot/SPTREMBL::MULTI +source = Uniprot/SWISSPROT::MULTI +source = Uniprot/SWISSPROT::DIRECT +source = UniParc::MULTI +source = miRBase::MULTI +source = RFAM::MULTI +source = UCSC::homo_sapiens +source = HGNC_curated_transcript::homo_sapiens +source = ArrayExpress::MULTI [species ictidomys_tridecemlineatus] taxonomy_id = 43179 @@ -6283,6 +6319,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::ictidomys_tridecemlineatus source = RefSeq_peptide::ictidomys_tridecemlineatus source = RefSeq_import::otherfeatures @@ -6319,6 +6356,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/SWISSPROT::DIRECT @@ -6338,6 +6376,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::lepisosteus_oculatus source = RefSeq_peptide::lepisosteus_oculatus source = Uniprot/SPTREMBL::MULTI @@ -6362,6 +6401,7 @@ source = Uniprot/SWISSPROT::DIRECT source = UniParc::MULTI source = RFAM::MULTI source = miRBase::MULTI +source = Reactome::MULTI source = RefSeq_dna::loxodonta_africana source = RefSeq_peptide::loxodonta_africana source = RefSeq_import::otherfeatures @@ -6375,6 +6415,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::macaca_mulatta source = RefSeq_peptide::macaca_mulatta source = RefSeq_import::otherfeatures @@ -6395,6 +6436,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6415,6 +6457,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::meleagris_gallopavo source = RefSeq_peptide::meleagris_gallopavo source = RefSeq_import::otherfeatures @@ -6435,6 +6478,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6455,6 +6499,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::monodelphis_domestica source = RefSeq_peptide::monodelphis_domestica source = RefSeq_import::otherfeatures @@ -6483,6 +6528,7 @@ source = MGI::mus_musculus#03 source = MGI::mus_musculus#05 source = MGI_curated_transcript::mus_musculus source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::mus_musculus source = RefSeq_dna::mus_musculus#01 source = RefSeq_peptide::mus_musculus @@ -6506,6 +6552,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::mustela_putorius_furo source = RefSeq_peptide::mustela_putorius_furo source = RefSeq_import::otherfeatures @@ -6526,6 +6573,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6546,6 +6594,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::ochotona_princeps source = RefSeq_peptide::ochotona_princeps source = RefSeq_import::otherfeatures @@ -6564,6 +6613,7 @@ source = EntrezGene::MULTI source = GO::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::oreochromis_niloticus source = RefSeq_peptide::oreochromis_niloticus source = RefSeq_import::otherfeatures @@ -6585,6 +6635,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::ornithorhynchus_anatinus source = RefSeq_peptide::ornithorhynchus_anatinus source = RefSeq_import::otherfeatures @@ -6608,6 +6659,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::oryctolagus_cuniculus source = RefSeq_peptide::oryctolagus_cuniculus source = RefSeq_import::otherfeatures @@ -6628,6 +6680,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::oryzias_latipes source = RefSeq_peptide::oryzias_latipes source = RefSeq_import::otherfeatures @@ -6648,6 +6701,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::otolemur_garnettii source = RefSeq_peptide::otolemur_garnettii source = RefSeq_import::otherfeatures @@ -6668,6 +6722,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::ovis_aries source = RefSeq_peptide::ovis_aries source = RefSeq_import::otherfeatures @@ -6688,6 +6743,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::pan_troglodytes source = RefSeq_peptide::pan_troglodytes source = RefSeq_import::otherfeatures @@ -6708,6 +6764,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::papio_anubis source = RefSeq_peptide::papio_anubis source = RefSeq_import::otherfeatures @@ -6742,6 +6799,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6761,6 +6819,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6800,6 +6859,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -6818,6 +6878,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::pongo_abelii source = RefSeq_peptide::pongo_abelii source = RefSeq_import::otherfeatures @@ -6838,6 +6899,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6857,6 +6919,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6876,6 +6939,7 @@ source = GO::rattus_norvegicus source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RGD::rattus_norvegicus source = RGD::rattus_norvegicus#01 source = RGD::rattus_norvegicus#02 @@ -6917,6 +6981,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -6952,6 +7017,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::sorex_araneus source = RefSeq_peptide::sorex_araneus source = RefSeq_import::otherfeatures @@ -7110,6 +7176,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::taeniopygia_guttata source = RefSeq_peptide::taeniopygia_guttata source = RefSeq_import::otherfeatures @@ -7130,6 +7197,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::takifugu_rubripes source = RefSeq_peptide::takifugu_rubripes source = RefSeq_import::otherfeatures @@ -7150,6 +7218,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -7169,6 +7238,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -7193,6 +7263,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -7213,6 +7284,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::tursiops_truncatus source = RefSeq_peptide::tursiops_truncatus source = RefSeq_import::otherfeatures @@ -7232,6 +7304,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = RefSeq_import::otherfeatures @@ -7251,6 +7324,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures @@ -7274,6 +7348,7 @@ source = GO::MULTI source = goslim_goa::MULTI source = InterproGO::MULTI source = Interpro::MULTI +source = Reactome::MULTI source = RefSeq_dna::MULTI-vertebrate_other source = RefSeq_peptide::MULTI-vertebrate_other source = RefSeq_import::otherfeatures