From 037576d9d0ed50dc5ac98988371f01d2528d1857 Mon Sep 17 00:00:00 2001 From: Ian Longden <ianl@sanger.ac.uk> Date: Tue, 18 Sep 2007 15:04:59 +0000 Subject: [PATCH] ncRNA now have a species sub directory so that all species can be done in one directory/database --- misc-scripts/xref_mapping/xref_config.ini | 326 ++++++++++++++++++++-- 1 file changed, 299 insertions(+), 27 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index 21743ba76c..0f47016649 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -1434,8 +1434,219 @@ release_uri = data_uri = -[source ncRNA::MULTI] -# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, erinaceus_europaeus, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, rattus_norvegicus, spermophilus_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus +[source ncRNA::bos_taurus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Bos_taurus/ncRNA/ncRNA.txt + +[source ncRNA::canis_familiaris] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Canis_familiaris/ncRNA/ncRNA.txt + + +[source ncRNA::ciona_intestinalis] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Ciona_intestinalis/ncRNA/ncRNA.txt + + +[source ncRNA::ciona_savignyi] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Ciona_savignyi/ncRNA/ncRNA.txt + + + +[source ncRNA::danio_rerio] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Danio_rerio/ncRNA/ncRNA.txt + + + +[source ncRNA::dasypus_novemcinctus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Dasypus_novemcinctus/ncRNA/ncRNA.txt + + + +[source ncRNA::erinaceus_europaeus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Erinaceus_europaeus/ncRNA/ncRNA.txt + + + +[source ncRNA::gallus_gallus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Gallus_gallus/ncRNA/ncRNA.txt + + + +[source ncRNA::gasterosteus_aculeatus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Gasterosteus_aculeatus/ncRNA/ncRNA.txt + + + +[source ncRNA::homo_sapiens] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Homo_sapiens/ncRNA/ncRNA.txt + + + +[source ncRNA::loxodonta_africana] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Loxodonta_africana/ncRNA/ncRNA.txt + + + +[source ncRNA::macaca_mulatta] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Macaca_mulatta/ncRNA/ncRNA.txt + + + +[source ncRNA::monodelphis_domestica] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Monodelphis_domestica/ncRNA/ncRNA.txt + + + +[source ncRNA::mus_musculus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Mus_musculus/ncRNA/ncRNA.txt + + + +[source ncRNA::myotis_lucifugus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Myotis_lucifugus/ncRNA/ncRNA.txt + + + +[source ncRNA::oryctolagus_cuniculus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Oryctolagus_cuniculus/ncRNA/ncRNA.txt + + + +[source ncRNA::oryzias_latipes] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Oryzias_latipes/ncRNA/ncRNA.txt + + + +[source ncRNA::pan_troglodytes] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Pan_troglodytes/ncRNA/ncRNA.txt + + + +[source ncRNA::rattus_norvegicus] name = ncRNA download = Y order = 70 @@ -1443,7 +1654,68 @@ priority = 1 prio_descr = parser = ncRNAParser release_uri = -data_uri = file:ncRNA/ncRNA.txt +data_uri = file:Rattus_norvegicus/ncRNA/ncRNA.txt + + + +[source ncRNA::spermophilus_tridecemlineatus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Spermophilus_tridecemlineatus/ncRNA/ncRNA.txt + + + +[source ncRNA::takifugu_rubripes] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Takifugu_rubripes/ncRNA/ncRNA.txt + + + +[source ncRNA::tupaia_belangeri] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Tupaia_belangeri/ncRNA/ncRNA.txt + + + +[source ncRNA::xenopus_tropicalis] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Xenopus_tropicalis/ncRNA/ncRNA.txt + + + +[source ncRNA::ornithorhynchus_anatinus] +name = ncRNA +download = Y +order = 70 +priority = 1 +prio_descr = +parser = ncRNAParser +release_uri = +data_uri = file:Ornithorhynchus_anatinus/ncRNA/ncRNA.txt + [source wormpep_id::caenorhabditis_elegans] # Used by caenorhabditis_elegans @@ -1614,7 +1886,7 @@ source = UniGene::bos_taurus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::bos_taurus [species caenorhabditis_elegans] taxonomy_id = 6239 @@ -1645,7 +1917,7 @@ source = UniGene::canis_familiaris source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::canis_familiaris [species ciona_intestinalis] taxonomy_id = 7719 @@ -1664,7 +1936,7 @@ source = cint_aniseed_jgi_v1::ciona_intestinalis source = cint_aniseed_jgi_v2::ciona_intestinalis source = cint_jgi_v1::ciona_intestinalis source = cint_jgi_v2::ciona_intestinalis -source = ncRNA::MULTI +source = ncRNA::ciona_intestinalis [species ciona_savignyi] taxonomy_id = 51511 @@ -1680,7 +1952,7 @@ source = UniGene::ciona_savignyi source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::ciona_savignyi [species danio_rerio] taxonomy_id = 7955 @@ -1698,7 +1970,7 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI source = ZFIN_ID::danio_rerio -source = ncRNA::MULTI +source = ncRNA::danio_rerio [species dasypus_novemcinctus] taxonomy_id = 9361 @@ -1710,7 +1982,7 @@ source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::dasypus_novemcinctus [species drosophila_melanogaster] taxonomy_id = 7227 @@ -1752,7 +2024,7 @@ source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::erinaceus_europaeus [species felis_catus] taxonomy_id = 9685 @@ -1779,7 +2051,7 @@ source = UniGene::gallus_gallus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::gallus_gallus [species gasterosteus_aculeatus] taxonomy_id = 69293 @@ -1794,7 +2066,7 @@ source = RefSeq_peptide::MULTI-vertebrate_other source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::gasterosteus_aculeatus [species homo_sapiens] taxonomy_id = 9606 @@ -1823,7 +2095,7 @@ source = UniGene::homo_sapiens source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::homo_sapiens [species loxodonta_africana] taxonomy_id = 9785 @@ -1835,7 +2107,7 @@ source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::loxodonta_africana [species macaca_mulatta] taxonomy_id = 9544 @@ -1848,7 +2120,7 @@ source = RefSeq_dna::MULTI-vertebrate_mammalian source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -source = ncRNA::MULTI +source = ncRNA::macaca_mulatta [species monodelphis_domestica] taxonomy_id = 13616 @@ -1862,7 +2134,7 @@ source = RefSeq_peptide::MULTI-vertebrate_mammalian source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::monodelphis_domestica [species mus_musculus] taxonomy_id = 10090 @@ -1887,7 +2159,7 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI source = Vega_mouse_transcript::mus_musculus -source = ncRNA::MULTI +source = ncRNA::mus_musculus [species myotis_lucifugus] taxonomy_id = 59463 @@ -1902,7 +2174,7 @@ source = UniGene::myotis_lucifugus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::myotis_lucifugus [species ornithorhynchus_anatinus] taxonomy_id = 9258 @@ -1918,7 +2190,7 @@ source = Uniprot/Varsplic::MULTI source = Oxford_FGU_Oa_tscript::ornithorhynchus_anatinus source = Oxford_FGU_Oa_gene::ornithorhynchus_anatinus source = Platypus_olfactory_receptor::ornithorhynchus_anatinus -source = ncRNA::MULTI +source = ncRNA::ornithorhynchus_anatinus [species oryctolagus_cuniculus] taxonomy_id = 9986 @@ -1930,7 +2202,7 @@ source = Interpro::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::oryctolagus_cuniculus [species oryzias_latipes] taxonomy_id = 8090 @@ -1947,7 +2219,7 @@ source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI source = UniProt::protein_id source = Uniprot::EMBL -source = ncRNA::MULTI +source = ncRNA::oryzias_latipes [species pan_troglodytes] taxonomy_id = 9598 @@ -1961,7 +2233,7 @@ source = RefSeq_peptide::pan_troglodytes source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::pan_troglodytes [species rattus_norvegicus] taxonomy_id = 10116 @@ -1980,7 +2252,7 @@ source = UniGene::rattus_norvegicus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::rattus_norvegicus [species saccharomyces_cerevisiae] taxonomy_id = 4932 @@ -2009,7 +2281,7 @@ source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::spermophilus_tridecemlineatus [species takifugu_rubripes] taxonomy_id = 31033 @@ -2024,7 +2296,7 @@ source = UniGene::takifugu_rubripes source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::takifugu_rubripes [species tupaia_belangeri] taxonomy_id = 37347 @@ -2039,7 +2311,7 @@ source = UniGene::MULTI source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI -source = ncRNA::MULTI +source = ncRNA::tupaia_belangeri [species xenopus_tropicalis] taxonomy_id = 8364 @@ -2055,5 +2327,5 @@ source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI source = Uniprot/Varsplic::MULTI source = Xenopus_Jamboree::xenopus_tropicalis -source = ncRNA::MULTI +source = ncRNA::xenopus_tropicalis -- GitLab