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Commit 77e32653 authored by Magali Ruffier's avatar Magali Ruffier
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ENSCORESW-2805: tidy up dependent sources

parent 9bbb4715
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4 merge requests!342Feature/schema update 96,!293Feature/xref config,!342Feature/schema update 96,!293Feature/xref config
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misc-scripts/xref_mapping/xref_config.ini
+ 16
− 255
View file @ 77e32653
......@@ -27,6 +27,7 @@ name = EC_NUMBER
download = N
order = 50
priority = 70
parser = UniProtParser
[source BioGRID::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -35,17 +36,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source DEDb::drosophila_melanogaster]
# Used by drosophila_melanogaster
name = DEDb
download = N
order = 50
priority = 1
prio_descr = Drosophila melanogaster Exon DataBase
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source EPD::drosophila_melanogaster]
# Used by the 12 drosophila genomes
......@@ -54,70 +44,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source EPD::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
name = EPD
download = N
order = 50
priority = 1
parser = FlybaseParser
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
name = EPD
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.org/genomes/dsim/current/gff/dsim-all-r1.4.gff.gz
[source EPD::drosophila_sechellia]
# Used by the 12 drosophila genomes
name = EPD
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.org/releases/current/dsec_r1.3/gff/dsec-all-r1.3.gff.gz
[source EPD::drosophila_mojavensis]
# Used by the 12 drosophila genomes
name = EPD
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.org/releases/current/dmoj_r1.3/gff/dmoj-all-r1.3.gff.gz
[source EPD::drosophila_virilis]
# Used by the 12 drosophila genomes
name = EPD
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.org/releases/current/dvir_r1.2/gff/dvir-all-r1.2.gff.gz
[source FlyAtlas::drosophila_melanogaster]
# Used by drosophila_melanogaster
name = FlyAtlas
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyAtlas::drosophila_pseudoobscura]
# Used by drosophila_pseudoobscura
name = FlyAtlas
download = N
order = 50
priority = 1
parser = FlybaseParser
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
......@@ -126,7 +52,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyReactome::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -135,7 +60,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source GenomeRNAi::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -144,7 +68,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source InteractiveFly::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -153,34 +76,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source MEROPS::drosophila_melanogaster]
# Used by the 12 drosophila genomes
name = MEROPS
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source MEROPS::drosophila_grimshawi]
# Used by the 12 drosophila genomes
name = MEROPS
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_grimshawi/current/gff/dgri-all-*.gff.gz
[source MEROPS::drosophila_virilis]
# Used by the 12 drosophila genomes
name = MEROPS
download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.org/releases/current/dvir_1.2/gff/dvir-all-r1.2.gff.gz
[source miRBase::drosophila_melanogaster]
# Used by the 12 drosophila genomes
......@@ -189,16 +84,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source miRBase::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
name = miRBase
download = N
order = 50
priority = 1
parser = FlybaseParser
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
......@@ -207,7 +92,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source TransFac::drosophila_melanogaster]
# Used by the 12 drosophila genomes
......@@ -216,7 +100,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source TransFac::drosophila_pseudoobscura]
# Used by the 12 drosophila genomes
......@@ -225,7 +108,6 @@ download = N
order = 50
priority = 1
parser = FlybaseParser
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
......@@ -235,7 +117,6 @@ order = 50
priority = 1
prio_descr = Annotation ID assigned by FlyBase
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source flybase_gene_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -377,7 +258,6 @@ order = 50
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source flybase_translation_id::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -387,7 +267,6 @@ order = 50
priority = 1
prio_descr = ID assigned by FlyBase
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseCGID_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -397,7 +276,6 @@ order = 50
priority = 1
prio_descr = FlyBase_Annotation_IDs
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseCGID_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -407,7 +285,6 @@ order = 50
priority = 1
prio_descr = FlyBase_Annotation_IDs
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseCGID_translation::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -417,7 +294,6 @@ order = 50
priority = 1
prio_descr = FlyBase_Annotation_IDs
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseName_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -427,7 +303,6 @@ order = 50
priority = 1
prio_descr = Name assigned to gene in FlyBase gff
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseName_transcript::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -437,7 +312,6 @@ order = 50
priority = 1
prio_descr = Transcript name in FlyBase gff
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source FlyBaseName_translations::drosophila_melanogaster]
# Used by drosophila_melanogaster
......@@ -447,7 +321,6 @@ order = 50
priority = 1
prio_descr = Translation name in FlyBase gff
parser = FlybaseParser
data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.46_FB2012_04/gff/dmel-all-r5.46.gff.gz
[source PHIbase::MULTI]
name = PHIbase
......@@ -686,7 +559,6 @@ name = Interpro
download = Y
order = 70
priority = 1
prio_descr =
parser = InterproFromCoreParser
data_uri = script:project=>ensemblgenomes,
......@@ -1094,14 +966,6 @@ order = 10
priority = 1
parser = SGDParser
[source SGD_TRANSCRIPT::saccharomyces_cerevisiae]
# Used by saccharomyces_cerevisiae
name = SGD_TRANSCRIPT
download = N
order = 10
priority = 1
parser = SGDParser
[source SGD::saccharomyces_cerevisiae]
# Used by saccharomyces_cerevisiae
name = SGD
......@@ -1183,30 +1047,6 @@ parser = UCSC_mouse_parser
release_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/README.txt
data_uri = ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz
[source UniProt::protein_id-predicted]
# Special source used in UniProtParser. No species uses this source.
name = protein_id_predicted
download = N
order = 20
priority = 1
parser = UniProtParser
[source UniProt::protein_id]
# Special source used in UniProtParser. No species uses this source.
name = protein_id
download = N
order = 20
priority = 1
parser = UniProtParser
[source UniProt::PDB]
# Special source used in UniProtParser. No species uses this source.
name = PDB
download = N
order = 20
priority = 1
parser = UniProtParser
[source Uniprot/SPTREMBL::MULTI-invertebrate]
name = Uniprot/SPTREMBL
download = Y
......@@ -1240,15 +1080,6 @@ prio_descr = protein_evidence_gt_2
parser = UniProtParser
status = LOWEVIDENCE
[source Uniprot/SPTREMBL::MULTI-predicted]
# Special source used in UniProtParser. No species uses this source.
name = Uniprot/SPTREMBL_predicted
download = N
order = 20
priority = 1
parser = UniProtParser
[source Uniprot/SWISSPROT::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, drosophila_melanogaster, echinops_telfairi, erinaceus_europaeus, felis_catus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, 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/SWISSPROT
......@@ -1261,7 +1092,6 @@ dependent_on = MIM
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt
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
......@@ -1273,7 +1103,6 @@ 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
[source Uniprot/SWISSPROT::DIRECT]
# Special source used in UniProtParser for direct mappings from Uniprot
name = Uniprot/SWISSPROT
......@@ -1292,42 +1121,39 @@ priority = 1
prio_descr = direct
parser = UniProtParser
[source Uniprot/SWISSPROT::MULTI-predicted]
# Special source used in UniProtParser. No species uses this source.
name = Uniprot/SWISSPROT_predicted
[source Uniprot_gn]
# Special source used in UniProtParser foir gene names..
name = Uniprot_gn
download = N
order = 20
priority = 1
parser = UniProtParser
[source Uniprot_gn]
# Special source used in UniProtParser foir gene names..
name = Uniprot_gn
[source UniProt::protein_id]
# Special source used in UniProtParser. No species uses this source.
name = protein_id
download = N
order = 20
priority = 1
parser = UniProtParser
[source Uniprot/SPTREMBL::drosophila_melanogaster]
# Used by drosophila_melanogaster
name = Uniprot/SPTREMBL
download = Y
[source UniProt::PDB]
# Special source used in UniProtParser. No species uses this source.
name = PDB
download = N
order = 20
priority = 1
parser = UniProtParser_descriptions_only
release_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz
parser = UniProtParser
[source Uniprot::EMBL-predicted]
[source UniProt::MEROPS]
# Special source used in UniProtParser. No species uses this source.
name = EMBL_predicted
name = MEROPS
download = N
order = 20
priority = 1
parser = UniProtParser
[source Uniprot::EMBL]
[source UniProt::EMBL]
# Special source used in UniProtParser. No species uses this source.
name = EMBL
download = N
......@@ -1335,7 +1161,7 @@ order = 20
priority = 1
parser = UniProtParser
[source Uniprot::ChEMBL]
[source UniProt::ChEMBL]
# Special source used in UniProtParser. No species uses this source.
name = ChEMBL
download = N
......@@ -1343,7 +1169,6 @@ order = 20
priority = 1
parser = UniProtParser
[source UniParc::MULTI]
name = UniParc
download = Y
......@@ -1519,7 +1344,6 @@ order = 70
priority = 1
parser = comes via official naming
[source RNAMMER::MULTI]
# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
name = RNAMMER
......@@ -1529,7 +1353,6 @@ priority = 1
parser = CoreXrefParser
data_uri = script:biotype=>rRNA,object_type=>gene,project=>ensemblgenomes,copy_description_from_object=>1,
[source TRNASCAN_SE::MULTI]
# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
name = TRNASCAN_SE
......@@ -1593,13 +1416,6 @@ download = N
order = 70
priority = 1
[source GeneDB_Spombe::MULTI]
# Used by schizosaccharomyces_pombe
name = GeneDB_Spombe
download = N
order = 70
priority = 1
[source phatr_jgi_v2::MULTI]
# Used by Pt
name = phatr_jgi_v2
......@@ -1642,20 +1458,6 @@ download = N
order = 70
priority = 1
[source physo1_jgi_v1.1_transcript::MULTI]
# Used by Pt
name = physo1_jgi_v1.1_transcript
download = N
order = 70
priority = 1
[source phyra_jgi_v1.1_gene::MULTI]
# Used by Pt
name = phyra_jgi_v1.1_gene
download = N
order = 70
priority = 1
[source phyra_jgi_v1.1::MULTI]
# Used by Pt
name = phyra_jgi_v1.1
......@@ -1663,13 +1465,6 @@ download = N
order = 70
priority = 1
[source phyra_jgi_v1.1_transcript::MULTI]
# Used by Pt
name = phyra_jgi_v1.1_transcript
download = N
order = 70
priority = 1
[source BROAD_Magnaporthe_DB::MULTI]
# Used by magnaporthe_oryzae, magnaporthe_poae and gaeumannomyces_graminis
name = BROAD_Magnaporthe_DB
......@@ -1686,21 +1481,6 @@ download = N
order = 70
priority = 1
[source BROAD_P_infestans_GENE::MULTI]
# Used by phytophthora_infestans
name = BROAD_P_infestans_GENE
download = N
order = 70
priority = 1
[source BROAD_P_infestans_TRANSCRIPT::MULTI]
# Used by phytophthora_infestans
name = BROAD_P_infestans_TRANSCRIPT
download = N
order = 70
priority = 1
[source thaps_jgi_v2_bd::MULTI]
# Used by Tp
name = thaps_jgi_v2_bd
......@@ -2297,25 +2077,6 @@ source = Gramene_Pathway::zea_mays
taxonomy_id = 644352
source = BROAD_Magnaporthe_DB::MULTI
[species metazoa]
taxonomy_id = 33208
source = EntrezGene::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 = ArrayExpress::EG
source = ncRNA_EG::EG
source = goslim_goa::EG
source = GO::MULTI
source = Interpro::CORE
source = RNAMMER::MULTI
source = miRBase::MULTI
source = RFAM::EG
source = TRNASCAN_SE::MULTI
source = misc_EG::EG
[species caenorhabditis_elegans]
taxonomy_id = 6239
source = wormbase::celegans
......
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