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Commit d269e438 authored by Ian Longden's avatar Ian Longden
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config changes

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misc-scripts/xref_mapping/xref_config.ini
+ 111
− 32
View file @ d269e438
......@@ -245,7 +245,7 @@ priority = 1
prio_descr =
parser = CCDSParser
release_uri =
data_uri = script:host=>genebuild4,dbname=>jb16_human_patch_52,
data_uri = script:host=>ens-research,dbname=>ianl_human_ccds_oct08,tran_name=>ENST,
[source CCDS::mus_musculus]
# Used by mus_musculus
......@@ -256,7 +256,7 @@ priority = 1
prio_descr =
parser = CCDSParser
release_uri =
data_uri = script:host=>genebuildx,dbname=>xxx,
data_uri = script:host=>ens-research,dbname=>ianl_mouse_ccds_oct08,tran_name=>ENSMUST,
[source Celera_Pep::anopheles_gambiae]
# Used by anopheles_gambiae
......@@ -558,6 +558,7 @@ prio_descr = main
parser = GOParser
release_uri = http://www.ebi.ac.uk/GOA/uniprot_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source InterproGO::MULTI]
# Used by all
......@@ -591,6 +592,7 @@ prio_descr = main
parser = GOParser
release_uri =
data_uri = ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.zfin.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source GO::homo_sapiens]
# Used by homo_sapiens
......@@ -602,6 +604,7 @@ prio_descr = main
parser = GOParser
release_uri = http://www.ebi.ac.uk/GOA/HUMAN_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/gene_association.goa_human.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source GO::mus_musculus]
# Used by mus_musculus
......@@ -613,6 +616,7 @@ prio_descr = main
parser = GOParser
release_uri = http://www.ebi.ac.uk/GOA/MOUSE_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_association.goa_mouse.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source GO::mus_musculus#01]
# Used by mus_musculus
......@@ -624,6 +628,7 @@ data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_associatio
parser = GOParser
release_uri =
data_uri = http://www.geneontology.org/cgi-bin/downloadGOGA.pl/gene_association.mgi.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source GO::rattus_norvegicus]
# Used by rattus_norvegicus
......@@ -635,6 +640,7 @@ prio_descr = main
parser = GOParser
release_uri = http://www.ebi.ac.uk/GOA/RAT_release.html
data_uri = ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz
data_uri = http://archive.geneontology.org/lastest-termdb/go_daily-termdb.obo-xml.gz
[source HPA::homo_sapiens]
......@@ -654,11 +660,11 @@ name = HGNC
download = Y
order = 30
#order 51
priority = 2
priority = 1
prio_descr = ccds
parser = HGNC_CCDSParser
release_uri =
data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_pub_refseq_ids&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr,dbname=>steve_cdstrack_08may08,host=>genebuild7,
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=>ianl_human_ccds_oct08,host=>ens-research,
[source HGNC::homo_sapiens#07]
......@@ -666,11 +672,11 @@ data_uri = script:wget=>http://www.genenames.org/cgi-bin/hgnc_downloads.c
name = HGNC
download = N
order = 30
priority = 1
priority = 2
prio_descr = ensembl_mapped
parser = HGNCParser
release_uri =
data_uri = file:HGNC/HGNC_TO_ENSG
data_uri =
[source HGNC::homo_sapiens]
# Used by homo_sapiens
......@@ -681,7 +687,7 @@ priority = 3
prio_descr = havana
parser = HGNC_ENSTParser
release_uri =
data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m,
data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n,
......@@ -694,7 +700,7 @@ priority = 4
prio_descr = entrezgene_manual
parser = HGNCParser
release_uri =
data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=md_ensembl_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
data_uri = http://www.genenames.org/cgi-bin/hgnc_downloads.cgi?title=Genew+output+data&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_refseq_ids&col=md_eg_id&col=md_refseq_id&col=gd_pub_ensembl_id&status=Approved&status=Approved+Non-Human&status_opt=3&=on&where=&order_by=gd_hgnc_id&limit=&format=text&submit=submit&.cgifields=&.cgifields=status&.cgifields=chr
[source HGNC::homo_sapiens#03]
......@@ -943,38 +949,81 @@ parser = MIMParser
release_uri =
data_uri = ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z
[source MGI::mus_musculus]
[source MGI::mus_musculus#01]
# Used by mus_musculus
name = MGI
download = N
order = 30
priority = 1
prio_descr =
parser = MGDParser
priority = 3
prio_descr = uniprot
parser =
release_uri =
data_uri = taken from uniprot files
[source MGI::mus_musculus#02]
# Used by mus_musculus
name = MGI
download = Y
order = 45
priority = 2
prio_descr = vega
parser = MGI_Vega_Parser
release_uri =
data_uri = script:vhost=>ens-staging,vport=>3306,vdbname=>mus_musculus_vega_52_37e,cdbname=>mus_musculus_core_52_37e,chost=>ens-staging,
[source MGI::mus_musculus#03]
# Used by mus_musculus
name = MGI
download = Y
order = 1
priority = 10
prio_descr = descriptions
parser = MGI_Desc_Parser
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]
# Used by mus_musculus
name = MGI
download = Y
order = 35
priority = 1
prio_descr = ccds
parser = MGI_CCDS_Parser
release_uri =
data_uri = script:wget=>ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse/CCDS.20071128.txt,
[source OTTT::homo_sapiens]
#
# NOW taken when merging done with havana
#
# Used by homo_sapiens
name = OTTT
download = Y
download = N
order = 50
priority = 1
prio_descr =
parser = OTTTParser
release_uri =
data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m,
data_uri =
#data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n,
[source OTTT::mus_musculus]
#
# NOW taken when merging done with havana
#
# Used by mus_musculus
name = OTTT
download = Y
download = N
order = 50
priority = 1
prio_descr =
parser = OTTTParser
release_uri =
data_uri = script:host=>ensdb-1-11,port=>5317,dbname=>mus_musculus_vega_51_37d,
data_uri = script:host=>ens-staging,port=>5317,dbname=>mus_musculus_vega_52_37e,
[source RGD::rattus_norvegicus]
# Used by rattus_norvegicus
......@@ -1142,7 +1191,7 @@ parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz
[source RefSeq_dna::mus_musculus]
[source RefSeq_dna::mus_musculus#01]
# Used by mus_musculus
name = RefSeq_dna
download = Y
......@@ -1153,6 +1202,18 @@ parser = RefSeqParser
release_uri = ftp://ftp.ncbi.nih.gov/refseq/release/release-notes/RefSeq-release*.txt
data_uri = ftp://ftp.ncbi.nih.gov/refseq/M_musculus/mRNA_Prot/mouse.rna.fna.gz
[source RefSeq_dna::mus_musculus]
# Used by mus_musculus
name = RefSeq_dna
download = Y
order = 25
priority = 1
prio_descr = ccds
parser = RefSeq_CCDSParser
release_uri =
data_uri = script:host=>genebuild7,dbname=>steve_cdstrack_08may08,
[source RefSeq_dna::pan_troglodytes]
# Used by pan_troglodytes
name = RefSeq_dna
......@@ -1753,7 +1814,17 @@ priority = 1
prio_descr =
parser = HGNC_curated_transcriptParser
release_uri =
data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_51_36m,
data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_52_36n,
[source MGI_curated_transcript::mus_musculus]
name = MGI_curated_transcript
download = Y
order = 49
priority = 1
prio_descr =
parser = MGI_curated_transcriptParser
release_uri =
data_uri = script:cdbname=>mus_musculus_core_52_37e,chost=>ens-staging,vhost=>ens-staging,vdbname=>mus_musculus_vega_52_37e,
[source Clone_based_vega_transcript::homo_sapiens]
......@@ -1767,16 +1838,19 @@ release_uri =
data_uri = loaded as part of HGNC_curated_transcript
[source Vega_mouse_transcript::mus_musculus]
#[source Vega_mouse_transcript::mus_musculus]
# Used by mus_musculus
name = Vega_mouse_transcript
download = Y
order = 50
priority = 1
prio_descr =
parser = VegaParser
release_uri =
data_uri = ftp://ftp.sanger.ac.uk/pub/vega/mouse/cdna/Mus_musculus.VEGA.*.cdna.tot.fa.gz
#
# Vega_transcript now used and obtained during merge
#
#name = Vega_mouse_transcript
#download = Y
#order = 50
#priority = 1
#prio_descr =
#parser = VegaParser
#release_uri =
#data_uri = ftp://ftp.sanger.ac.uk/pub/vega/mouse/cdna/Mus_musculus.VEGA.*.cdna.tot.fa.gz
[source Xenopus_Jamboree::xenopus_tropicalis]
# Used by xenopus_tropicalis
......@@ -2596,9 +2670,9 @@ source = Illumina_V1::homo_sapiens
source = Illumina_V2::homo_sapiens
source = Interpro::MULTI
source = MIM::homo_sapiens
source = OTTT::homo_sapiens
#source = OTTT::homo_sapiens # got from merge
source = RefSeq_dna::homo_sapiens
source = RefSeq_dna::homo_sapiens#01
#source = RefSeq_dna::homo_sapiens#01
source = RefSeq_peptide::homo_sapiens
source = UniGene::homo_sapiens
source = Uniprot/SPTREMBL::MULTI
......@@ -2660,15 +2734,20 @@ source = IMGT/GENE_DB::mus_musculus
source = IPI::mus_musculus
source = Illumina_V1::mus_musculus
source = Illumina_V2::mus_musculus
source = MGI::mus_musculus#02
source = MGI::mus_musculus#03
source = MGI::mus_musculus#04
source = MGI_curated_transcript::mus_musculus
source = Interpro::MULTI
source = OTTT::mus_musculus
#source = OTTT::mus_musculus # data obtained form merge
source = RefSeq_dna::mus_musculus
#source = RefSeq_dna::mus_musculus#01
source = RefSeq_peptide::mus_musculus
source = UniGene::mus_musculus
source = Uniprot/SPTREMBL::MULTI
source = Uniprot/SWISSPROT::MULTI
source = Uniprot/Varsplic::MULTI
source = Vega_mouse_transcript::mus_musculus
#source = Uniprot/Varsplic::MULTI
#source = Vega_mouse_transcript::mus_musculus # removed use Vega_transcript
source = ncRNA::mus_musculus
source = UCSC::mus_musculus
......
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