Commit f8e91244 authored by Ian Longden's avatar Ian Longden
Browse files

addition of RFAM_transcript_name and RFAM_gene_name and the same for miRBASE....

addition of RFAM_transcript_name and RFAM_gene_name and the same for miRBASE. changing of priorities for HGNC and MGI source
parent 3b8268ac
......@@ -382,7 +382,7 @@ priority = 1
prio_descr =
parser = CCDSParser
release_uri =
data_uri = script:host=>ens-livemirror,dbname=>ccds_human,tran_name=>ENST,
data_uri = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,tran_name=>ENST,
[source CCDS::mus_musculus]
# Used by mus_musculus
......@@ -393,7 +393,7 @@ priority = 1
prio_descr =
parser = CCDSParser
release_uri =
data_uri = script:host=>ens-livemirror,dbname=>ccds_mouse,tran_name=>ENSMUST,
data_uri = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,tran_name=>ENSMUST,
[source Celera_Pep::anopheles_gambiae]
# Used by anopheles_gambiae
......@@ -559,28 +559,6 @@ release_uri =
data_uri = comes via EntrezGene
#[source Ens_Ag_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
#name = Ens_Ag_gene
#download = N
#order = 50
#priority = 1
#prio_descr = Ensembl mosquito gene predictions
#parser = Flybase_dmel_GFFv3_Parser
#release_uri =
#data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
#[source Ens_Am_gene::drosophila_melanogaster]
# Used by drosophila_melanogaster
#name = Ens_Am_gene
#download = N
#order = 50
#priority = 1
#prio_descr = Ensembl bee gene predictions
#parser = Flybase_dmel_GFFv3_Parser
#release_uri =
#data_uri = ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/dmel-all-*.gff.gz
[source Fantom::mus_musculus]
# Used by mus_muscullus
name = Fantom
......@@ -977,7 +955,8 @@ priority = 1
prio_descr = main
parser = GOSlimParser
release_uri =
data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_61,
data_uri = script:
#data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_61,
[source goslim_goa::EG]
# Used by Ensembl Genomes
......@@ -1059,7 +1038,7 @@ priority = 1
prio_descr = Human Protein Atlas (HPA) database
parser = HPAParser
release_uri =
data_uri = http://www.proteinatlas.org/data/xref.php
data_uri = http://www.proteinatlas.org/download/xref.php
#[source IMGT_HLA::homo_sapiens]
# Used by homo_sapiens
......@@ -1072,6 +1051,16 @@ data_uri = http://www.proteinatlas.org/data/xref.php
#release_uri =
#data_uri = http://hla.alleles.org/xrefs/embl.txt
[source LRG_HGNC_notransfer]
name = LRG_HGNC_notransfer
download = N
order = 30
priority = 5
prio_descr =
parser = HGNCParser
release_uri =
data_uri =
[source HGNC::homo_sapiens#01]
# Used by homo_sapiens
name = HGNC
......@@ -1082,7 +1071,7 @@ priority = 2
prio_descr = ccds
parser = HGNC_CCDSParser
release_uri =
data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,dbname=>ccds_human,host=>ens-livemirror,
data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=HGNC+output+data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_status&col=gd_ccds_ids&status=Approved&status_opt=2&level=pri&=on&where=&order_by=gd_app_sym_sort&limit=&format=text&submit=submit&.cgifields=&.cgifields=level&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag,host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,
[source HGNC::homo_sapiens#07]
......@@ -1090,7 +1079,7 @@ data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.c
name = HGNC
download = N
order = 30
priority = 3
priority = 1
prio_descr = ensembl_manual
parser = HGNCParser
release_uri =
......@@ -1101,12 +1090,12 @@ data_uri =
name = HGNC
download = Y
order = 30
priority = 1
prio_descr = havana
priority = 3
prio_descr = vega
parser = HGNC_ENSTParser
release_uri =
data_uri = script:
#data_uri = script:vhost=>ens-staging1,vdbname=>homo_sapiens_vega_58_37c,vport=>5306,vuser=>anonymous,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
#data_uri = script:vuser=>ensro,vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vport=>3306,cuser=>ensro,chost=>ens-staging1,cport=>3306,cdbname=>homo_sapiens_core_61_37f,
[source HGNC::homo_sapiens#02]
......@@ -1198,8 +1187,8 @@ parser = IKMCParser
release_uri =
data_uri = script:
[source IKMC_No_products_available_yet::mus_musculus]
name = IKMC_No_products_available_yet
[source IKMCs_No_products_available_yet::mus_musculus]
name = IKMCs_No_products_available_yet
download = N
order = 40
priority = 1
......@@ -1208,8 +1197,8 @@ parser = IKMCParser
release_uri =
data_uri =
[source IKMC_Vector_available::mus_musculus]
name = IKMC_Vector_available
[source IKMCs_Vector_available::mus_musculus]
name = IKMCs_Vector_available
download = N
order = 40
priority = 1
......@@ -1218,8 +1207,8 @@ parser = IKMCParser
release_uri =
data_uri =
[source IKMC_ES_cells_available::mus_musculus]
name = IKMC_ES_cells_available
[source IKMCs_ES_cells_available::mus_musculus]
name = IKMCs_ES_cells_available
download = N
order = 40
priority = 1
......@@ -1228,8 +1217,8 @@ parser = IKMCParser
release_uri =
data_uri =
[source IKMC_Mice_available::mus_musculus]
name = IKMC_Mice_available
[source IKMCs_Mice_available::mus_musculus]
name = IKMCs_Mice_available
download = N
order = 40
priority = 1
......@@ -1408,30 +1397,41 @@ parser = Mim2GeneParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene
[source MGI::mus_musculus#01]
[source MGI::mus_musculus#04]
# Used by mus_musculus
name = MGI
download = N
order = 30
priority = 3
priority = 4
prio_descr = uniprot
parser =
release_uri =
data_uri = taken from uniprot files
[source MGI::mus_musculus#01]
# Used by mus_musculus
name = MGI
download = Y
order = 30
priority = 1
prio_descr = official
parser = MGIParser
release_uri =
data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_ENSEMBL.rpt
[source MGI::mus_musculus#02]
# Used by mus_musculus
name = MGI
download = Y
order = 45
priority = 1
priority = 2
prio_descr = vega
parser = MGI_Vega_Parser
release_uri =
data_uri = script:
#data_uri = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
#data_uri = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n,
[source MGI::mus_musculus#03]
[source MGI::mus_musculus#05]
# Used by mus_musculus
name = MGI
download = Y
......@@ -1443,12 +1443,12 @@ release_uri =
data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.sql.rpt
data_uri = ftp://ftp.informatics.jax.org/pub/reports/MRK_Synonym.sql.rpt
[source MGI::mus_musculus#04]
[source MGI::mus_musculus#03]
# Used by mus_musculus
name = MGI
download = Y
order = 35
priority = 2
priority = 3
prio_descr = ccds
parser = MGI_CCDS_Parser
release_uri =
......@@ -1660,7 +1660,7 @@ priority = 1
prio_descr = ccds
parser = RefSeq_CCDSParser
release_uri =
data_uri = script:host=>ens-livemirror,dbname=>ccds_human,
data_uri = script:host=>genebuild7,dbname=>db8_human_cdsonly_22sept2010,
[source RefSeq_dna::homo_sapiens#01]
# Used by homo_sapiens
......@@ -1693,7 +1693,7 @@ priority = 1
prio_descr = ccds
parser = RefSeq_CCDSParser
release_uri =
data_uri = script:host=>ens-livemirror,dbname=>ccds_mouse,
data_uri = script:host=>genebuild7,dbname=>db8_mouse_cdsonly_22sept2010,
[source RefSeq_dna::pan_troglodytes]
......@@ -2428,19 +2428,19 @@ release_uri =
[source HGNC_curated_transcript::homo_sapiens]
name = HGNC_curated_transcript
name = HGNC_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr =
prio_descr = curated with transcript number postfix
parser = curated_transcriptParser
release_uri =
data_uri = script:
#data_uri = script:vhost=>ensembldb.ensembl.org,vport=>5306,vdbname=>homo_sapiens_vega_58_37c,vuser=>anonymous,vprot=>5306,chost=>ens-livemirror,cport=>3306,cdbname=>homo_sapiens_core_58_37c,
#data_uri = script:vhost=>ens-research,vdbname=>st3_homo_sapiens_vega_59_20100903,vuser=>ensro,vport=>3306,chost=>ens-staging,cport=>3306,cdbname=>homo_sapiens_core_61_37f,
[source HGNC_automatic_transcript::homo_sapiens]
name = HGNC_automatic_transcript
[source HGNC_transcript_name]
name = HGNC_transcript_name
download = N
order = 49
priority = 1
......@@ -2448,8 +2448,8 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source HGNC_curated_gene::homo_sapiens]
name = HGNC_curated_gene
[source HGNC_gene_name]
name = HGNC_gene_name
download = N
order = 49
priority = 1
......@@ -2457,17 +2457,9 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source HGNC_automatic_gene::homo_sapiens]
name = HGNC_automatic_gene
download = N
order = 49
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
[source MGI_curated_transcript::mus_musculus]
name = MGI_curated_transcript
name = MGI_curated_transcript_notransfer
download = Y
order = 49
priority = 1
......@@ -2475,10 +2467,11 @@ prio_descr =
parser = curated_transcriptParser
release_uri =
data_uri = script:
#data_uri = script:vhost=>ens-staging2,vport=>3306,vdbname=>mus_musculus_vega_58_37k,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_58_37k,
#data_uri = script:vhost=>ens-research,vport=>3306,vdbname=>st3_mus_musculus_vega_61_20100917,chost=>ens-staging2,cport=>3306,cdbname=>mus_musculus_core_61_37n,
[source MGI_curated_gene::mus_musculus]
name = MGI_curated_gene
[source MGI_automatic_transcript::mus_musculus]
name = MGI_automatic_transcript_notransfer
download = N
order = 49
priority = 1
......@@ -2486,25 +2479,27 @@ prio_descr =
parser = done_in_official_naming
release_uri =
[source MGI_automatic_gene::mus_musculus]
name = MGI_automatic_gene
[source MGI_gene_name]
# Used homo_sapiens,mus_musculus
name = MGI_gene_name
download = N
order = 49
order = 70
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
parser = comes via official naming
release_uri =
data_uri =
[source MGI_automatic_transcript::mus_musculus]
name = MGI_automatic_transcript
[source MGI_transcript_name]
# Used homo_sapiens,mus_musculus
name = MGI_transcript_name
download = N
order = 49
order = 70
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
parser = comes via official naming
release_uri =
data_uri =
[source Clone_based_vega_transcript::homo_sapiens]
name = Clone_based_vega_transcript
......@@ -2557,13 +2552,13 @@ parser = XenopusJamboreeParser
release_uri =
data_uri = ftp://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt
[source ZFIN_ID::danio_rerio]
[source ZFIN_ID::danio_rerio#01]
# Used by danio_rerio
name = ZFIN_ID
download = Y
order = 30
priority = 1
prio_descr =
priority = 2
prio_descr = uniprot/refseq
parser = ZFINParser
release_uri =
data_uri = http://zfin.org/data_transfer/Downloads/refseq.txt
......@@ -2571,6 +2566,57 @@ data_uri = http://zfin.org/data_transfer/Downloads/uniprot.txt
data_uri = http://zfin.org/data_transfer/Downloads/aliases.txt
data_uri = http://zfin.org/data_transfer/Downloads/gene_seq.txt
[source ZFIN_ID::danio_rerio#02]
# Used by danio_rerio
name = ZFIN_ID
download = Y
order = 30
priority = 1
prio_descr = vega
parser = ZFIN_DARTParser
release_uri =
data_uri = script:vuser=>ensro,vhost=>ens-staging,vdbname=>danio_rerio_vega_61_9a,vport=>3306,
[source ZFIN_ID::danio_rerio#03]
# Used by danio_rerio
name = ZFIN_ID
download = Y
order = 1
priority = 10
prio_descr = description_only
parser = ZFINDescParser
release_uri =
data_uri = http://zfin.org/data_transfer/Downloads/genetic_markers.txt
[source ZFIN_ID_curated_transcript::danio_rerio]
name = ZFIN_ID_curated_transcript_notransfer
download = Y
order = 49
priority = 1
prio_descr = curated with transcript number postfix
parser = curated_transcriptParser
release_uri =
data_uri = script:
[source ZFIN_ID_transcript_name]
name = ZFIN_ID_transcript_name
download = N
order = 49
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
[source ZFIN_ID_gene_name]
name = ZFIN_ID_gene_name
download = N
order = 49
priority = 1
prio_descr =
parser = done_in_official_naming
release_uri =
[source cint_aniseed_jgi_v1::ciona_intestinalis]
# Used by ciona_intestinalis
name = cint_aniseed_jgi_v1
......@@ -2638,6 +2684,29 @@ parser = comes via ncRNAParser
release_uri =
data_uri =
[source miRBase_gene_name]
# Used homo_sapiens,mus_musculus
name = miRBase_gene_name
download = N
order = 70
priority = 1
prio_descr =
parser = comes via official naming
release_uri =
data_uri =
[source miRBase_transcript_name]
# Used homo_sapiens,mus_musculus
name = miRBase_transcript_name
download = N
order = 70
priority = 1
prio_descr =
parser = comes via official naming
release_uri =
data_uri =
[source ncRNA::MULTI]
name = ncRNA
download = Y
......@@ -2646,7 +2715,7 @@ priority = 1
prio_descr =
parser = ncRNA_DBParser
release_uri =
data_uri = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs
data_uri = script:host=>genebuild7,port=>3306,dbname=>sw4_ncRNA_Xrefs,
[source ncRNA::culex_pipiens]
name = ncRNA_Culex
......@@ -2658,6 +2727,29 @@ parser = ncRNAParser
release_uri =
data_uri = file:/lustre/work1/ensembl/kmegy/Culex/Xrefs/culex_ncRNAxref_sw4.txt
[source RFAM_gene_name]
# Used homo_sapiens,mus_musculus
name = RFAM_gene_name
download = N
order = 70
priority = 1
prio_descr =
parser = comes via official naming
release_uri =
data_uri =
[source RFAM_transcript_name]
# Used homo_sapiens,mus_musculus
name = RFAM_transcript_name
download = N
order = 70
priority = 1
prio_descr =
parser = comes via official naming
release_uri =
data_uri =
[source RNAMMER::MULTI-asp]
# Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
name = RNAMMER
......@@ -3186,8 +3278,11 @@ source = RefSeq_peptide::danio_rerio
source = UniGene::danio_rerio
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = ZFIN_ID::danio_rerio
source = ZFIN_ID::danio_rerio#01
source = ZFIN_ID::danio_rerio#02
source = ZFIN_ID::danio_rerio#03
source = ncRNA::MULTI
#source = ZFIN_ID_curated_transcript::danio_rerio
[species dasypus_novemcinctus]
taxonomy_id = 9361
......@@ -3623,9 +3718,10 @@ source = InterproGO::MULTI
source = IMGT/GENE_DB::mus_musculus
source = IKMCs_KOs::mus_musculus
source = IPI::mus_musculus
source = MGI::mus_musculus#01
source = MGI::mus_musculus#02
source = MGI::mus_musculus#03
source = MGI::mus_musculus#04
source = MGI::mus_musculus#05
source = MGI_curated_transcript::mus_musculus
source = Interpro::MULTI
source = RefSeq_dna::mus_musculus
......@@ -3639,6 +3735,7 @@ source = ncRNA::MULTI
source = UCSC::mus_musculus
source = Fantom::mus_musculus
[species myotis_lucifugus]
taxonomy_id = 59463
aliases = little brown bat, microbat
......
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