src/hg/makeDb/schema/all.joiner 1.808

Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.807
retrieving revision 1.808
diff -b -B -U 4 -r1.807 -r1.808
--- src/hg/makeDb/schema/all.joiner	1 Jun 2010 20:43:58 -0000	1.807
+++ src/hg/makeDb/schema/all.joiner	2 Jun 2010 23:04:24 -0000	1.808
@@ -180,8 +180,18 @@
      $gbd.spMrna.spID minCheck=0.80
      dm1.bdgpSwissProt.spSymbol minCheck=0.80
      dm1.flyBaseSwissProt.spSymbol minCheck=0.80
 
+identifier ProteomeTaxonId external=Proteome
+"Proteome Taxon ID"
+     proteome.taxonName.id
+     proteome.spXref3.division minCheck=.90
+
+identifier ProteomeAccession external=Proteome
+"Proteome  Accession"
+     proteome.spXref3.accession dupeOk
+     proteome.hgncXref.uniProt minCheck=.65
+
 identifier UniProtAccession external=UniProt
 "UniProt(Swiss-Prot/TrEMBL) Accession"
      uniProt.displayId.acc
      uniProt.accToKeyword.acc
@@ -759,8 +769,24 @@
     hgFixed.affyRatExonTissuesAllExps.id
     $rn.affyExonTissues.expIds comma full
     $rn.affyExonTissues.expScores comma indexOf full
 
+identifier affyExonTissuesGsId
+"UCSC Gene IDs for affyExonTissuesGs."
+    $hg.affyExonTissuesGs.name
+    $hg.knownGene.name minCheck=0.95
+
+identifier affyExonTissuesGsMedianId
+"UCSC Gene IDs for affyExonTissuesGsMedian."
+    $hg.affyExonTissuesGsMedian.name
+    $hg.knownGene.name minCheck=0.95
+
+identifier affyExonTissuesGsMedianDistId
+"UCSC Gene IDs for affyExonTissuesGsMedianDist."
+    $hg.affyExonTissuesGsMedianDist.query dupeOk
+    $hg.affyExonTissuesGsMedianDist.target
+    $hg.knownGene.name minCheck=0.95
+
 identifier gnfHumanAtlas2
 "Novartis GNF Human gene probe ID"
     hgFixed.gnfHumanAtlas2All.name
     hgFixed.gnfHumanAtlas2AllRatio.name unique
@@ -1292,11 +1318,19 @@
     mm9.geneNetworkId.id minCheck=0.80
     hg19.geneNetworkId.id
     rn3.geneNetworkId.id minCheck=0.40
 
+identifier kgOldId
+"Old Known Gene ID - the genbank accession of the representative mRNA"
+    hg17.kgOld.name dupeOk
+    hg17.kgXrefOld.kgId  minCheck=.95
+
 identifier knownGeneId dependency
 "Known Gene ID - the genbank accession of the representative mRNA"
     $kgDb.knownGene.name dupeOk
+    hg16.hg17Kg.name minCheck=.30
+    $kgDb2.knownExpDistance.query
+    $kgDb2.knownExpDistance.target
     $kgDb.bioCycPathway.kgID
     $kgDb.ceBlastTab.query
     $kgDb.hgBlastTab.query
     $kgDb.dmBlastTab.query
@@ -1383,8 +1417,10 @@
 identifier knownGeneOld2Id dependency
 "Old knownGene (KGII) and kgXref tables kept after KGIII implementation"
     $kgDb.knownGeneOld2.name dupeOk
     $kgDb.kgXrefOld2.kgID full
+    $kgDb.humanBlastTab.query
+    $kgDb.humanBlastTab.target
 
 identifier knownToHprdName
 "Dependencies on knownToHprd.name"
     $kgDb.knownToHprd.name dupeOk
@@ -1423,8 +1459,23 @@
     $ccdsDb.ccdsGene.name dupeOk
     $ccdsDb.ccdsInfo.ccds full
     $ccdsDb.ccdsKgMap.ccdsId
 
+identifier ctdGeneSymbol
+"CTD Gene Symbol"
+    hgFixed.ctdSorted.GeneSymbol dupeOk
+    $hg.kgXref.geneSymbol minCheck=0.30
+
+identifier gadId
+"GAD Gene ID"
+    $hg.kgXref.geneSymbol dupeOk
+    $hg.gad.name minCheck=0.95
+
+identifier gadAllId
+"GAD Gene Symbol in raw input"
+    $hg.kgXref.geneSymbol dupeOk
+    $hg.gadAll.geneSymbol minCheck=0.95
+
 identifier hugeId
 "HuGE Gene ID"
     $hg.kgXref.geneSymbol dupeOk
     $hg.huge.geneSymbol minCheck=0.89
@@ -1797,8 +1848,13 @@
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
 
+identifier sgdProtHomologId
+"sacCer protHomolog protein ID"
+    $sacCer.protHomolog.proteinID dupeOk
+    $sacCer.samSubdir.proteinId
+
 identifier sgdId external=SGD
 "Sacchromyces Genome Database ID - Coding or other"
 
 identifier sgdCodingId typeOf=sgdId dependency