From adf5748adf01cb68717caf24eff654df009285db Mon Sep 17 00:00:00 2001 From: Ian Longden <ianl@sanger.ac.uk> Date: Wed, 4 Nov 2009 10:12:45 +0000 Subject: [PATCH] update staging databases etc --- misc-scripts/xref_mapping/xref_config.ini | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/misc-scripts/xref_mapping/xref_config.ini b/misc-scripts/xref_mapping/xref_config.ini index bc5a3c924a..f5c4f1df7b 100644 --- a/misc-scripts/xref_mapping/xref_config.ini +++ b/misc-scripts/xref_mapping/xref_config.ini @@ -493,7 +493,7 @@ priority = 1 prio_descr = parser = CCDSParser release_uri = -data_uri = script:host=>ens-livemirror,dbname=>ccds_human_GRCh37_take2,tran_name=>ENST, +data_uri = script:host=>ens-livemirror,dbname=>ccds_human,tran_name=>ENST, [source CCDS::mus_musculus] # Used by mus_musculus @@ -1003,7 +1003,7 @@ priority = 1 prio_descr = main parser = GOSlimParser release_uri = -data_uri = script:host=>ens-staging,dbname=>ensembl_ontology_56, +data_uri = script:host=>ens-staging1,dbname=>ensembl_ontology_57, [source GO::homo_sapiens] @@ -1087,7 +1087,7 @@ 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=>ba1_human_cdsonly_20may09,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=>ccds_human,host=>ens-livemirror, [source HGNC::homo_sapiens#07] @@ -1121,7 +1121,7 @@ priority = 4 prio_descr = havana parser = HGNC_ENSTParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_56_37a, +data_uri = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b, @@ -1414,7 +1414,7 @@ priority = 1 prio_descr = vega parser = MGI_Vega_Parser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>mus_musculus_vega_56_37i, +data_uri = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j, [source MGI::mus_musculus#03] # Used by mus_musculus @@ -1623,7 +1623,7 @@ priority = 1 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = -data_uri = script:host=>genebuild7,dbname=>ba1_cdstrack_20may09, +data_uri = script:host=>ens-livemirror,dbname=>ccds_human, [source RefSeq_dna::homo_sapiens#01] # Used by homo_sapiens @@ -1656,7 +1656,7 @@ priority = 1 prio_descr = ccds parser = RefSeq_CCDSParser release_uri = -data_uri = script:host=>genebuild7,dbname=>ba1_cdstrack_20may09, +data_uri = script:host=>ens-livemirror,dbname=>ccds_mouse, [source RefSeq_dna::pan_troglodytes] @@ -2319,7 +2319,7 @@ priority = 1 prio_descr = parser = HGNC_curated_transcriptParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>homo_sapiens_vega_56_37a, +data_uri = script:host=>ens-staging1,port=>3306,dbname=>homo_sapiens_vega_57_37b, [source HGNC_automatic_transcript::homo_sapiens] @@ -2357,7 +2357,7 @@ priority = 1 prio_descr = parser = MGI_curated_transcriptParser release_uri = -data_uri = script:host=>ens-staging,port=>3306,dbname=>mus_musculus_vega_56_37i, +data_uri = script:host=>ens-staging2,port=>3306,dbname=>mus_musculus_vega_57_37j, [source MGI_curated_gene::mus_musculus] name = MGI_curated_gene @@ -3623,8 +3623,6 @@ source = ncRNA::MULTI [species rattus_norvegicus] taxonomy_id = 10116 aliases = rat, rattusnorvegicus, rnovegicus -#source = AgilentProbe::rattus_norvegicus # now dealt with by functional genomics team -#source = Codelink::rattus_norvegicus # now dealt with by functional genomics team source = EntrezGene::MULTI source = GO::rattus_norvegicus source = goslim_goa::MULTI @@ -3637,8 +3635,7 @@ source = RefSeq_peptide::rattus_norvegicus source = UniGene::rattus_norvegicus source = Uniprot/SPTREMBL::MULTI source = Uniprot/SWISSPROT::MULTI -#source = Uniprot/Varsplic::MULTI # not included anymore as users found it confusing -#source = ncRNA::MULTI # copied in separately after running Xrefs +source = ncRNA::MULTI [species saccharomyces_cerevisiae] -- GitLab