src/hg/makeDb/schema/all.joiner 1.785

Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.784
retrieving revision 1.785
diff -b -B -U 4 -r1.784 -r1.785
--- src/hg/makeDb/schema/all.joiner	9 Apr 2010 16:31:19 -0000	1.784
+++ src/hg/makeDb/schema/all.joiner	9 Apr 2010 16:59:10 -0000	1.785
@@ -62,8 +62,11 @@
 
 # Define organism databases for which we build a xenoRefGene track:
 set xrg $panTro,$galGal,$ci,$canFam,$dp,$droYak,$droMult,$bosTau,$rn,$hg,$rheMac,$monDom,$felCat,$oryCun,$oryLat,$anoCar,$caePb,$caeRem,$caeJap,$cb,$mm,$priPac,$strPur,$ponAbe,$calJac,$petMar,$braFlo,$ce,$taeGut,danRer6,$aplCal,$ailMel,$loxAfr
 
+# Define organism databases for which we host the vegaGenes
+set vegaGeneDbs hg18,hg19,mm9
+
 # Define organism databases for which we build a SNP track:
 set snpDb130 hg18
 set snpDb129 hg18
 set snpDb128 hg18,mm9
@@ -111,9 +114,9 @@
 # Define databases that support family browser (gene sorter)
 set familyDb $hg,$mm,$rn,$ce,$sacCer,$dm
 
 # Define databases that support CCDS
-set ccdsDb hg18,hg17,mm8,mm9
+set ccdsDb hg19,hg18,hg17,mm8,mm9
 
 # Magic for tables split between chromosomes
 set split splitPrefix=chr%\_
 
@@ -647,21 +650,14 @@
 "Link together augustusAbinitio predicted gene structure and peptide"
    $gbd.augustusAbinitio.name
    $gbd.augustusAbinitioPep.name chopBefore=. full unique
 
-identifier vegaGeneIdHuman external=VegaGene
-"Link together various VEGA human curated gene annotation"
-    hg18.vegaGtp.transcript
-    hg18.vegaGene.name
-    hg18.vegaPseudoGene.name
-    hg18.vegaPep.name
-
-identifier vegaGeneIdMouse external=VegaGene
-"Link together various VEGA mouse curated gene annotation"
-    mm9.vegaGtp.transcript
-    mm9.vegaGene.name
-    mm9.vegaPseudoGene.name
-    mm9.vegaPep.name
+identifier vegaGeneId external=VegaGene
+"Link together various VEGA curated gene annotation"
+    $vegaGeneDbs.vegaGtp.transcript
+    $vegaGeneDbs.vegaGene.name
+    $vegaGeneDbs.vegaPseudoGene.name
+    $vegaGeneDbs.vegaPep.name
 
 identifier vegaName
 "Link together various VEGA human curated gene annotation"
     $gbd.vegaInfo.transcriptId
@@ -1276,8 +1272,9 @@
     $kgDb.knownToRefSeq.value dupeOk
     mm7.geneNetworkId.id minCheck=0.80
     mm8.geneNetworkId.id minCheck=0.80
     mm9.geneNetworkId.id minCheck=0.80
+    hg19.geneNetworkId.id
     rn3.geneNetworkId.id minCheck=0.40
 
 identifier knownGeneId dependency
 "Known Gene ID - the genbank accession of the representative mRNA"
@@ -1358,8 +1355,9 @@
     $kgDb.kg2ToKg3.newId minCheck=0.5 exclude=
     $kgDb.kg3ToKg4.oldId minCheck=0.5
     $kgDb.kg3ToKg4.newId exclude=
     $kgDb.kgTargetAli.qName full
+    hg19.kg4ToKg5.newId
 
 identifier knownGeneOld3Id dependency
 "Previous UCSC Gene build"
     $kgDb.knownGeneOld3.name