update staging databases etc

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]