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Commit 037576d9 authored by Ian Longden's avatar Ian Longden
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ncRNA now have a species sub directory so that all species can be done in one directory/database

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misc-scripts/xref_mapping/xref_config.ini
+ 299
− 27
View file @ 037576d9
......@@ -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
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