Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.782
retrieving revision 1.783
diff -b -B -U 1000000 -r1.782 -r1.783
--- src/hg/makeDb/schema/all.joiner	7 Apr 2010 23:32:57 -0000	1.782
+++ src/hg/makeDb/schema/all.joiner	8 Apr 2010 17:47:50 -0000	1.783
@@ -1,3509 +1,3513 @@
 # This contains linkage information between various fields
 # in various databases.
 
 # Define databases used for various organisms
 set ailMel ailMel1
 set anoCar anoCar1
 set anoGam anoGam1
 set apiMel apiMel1,apiMel2
 set aplCal aplCal1
 set bosTau bosTau2,bosTau3,bosTau4
 set braFlo braFlo1
 set caeJap caeJap1
 set caePb caePb1,caePb2
 set caeRem caeRem2,caeRem3
 set calJac calJac1,calJac3
 set canFam canFam1,canFam2
 set cavPor cavPor3
 set cb cb1,cb3
 set ce ce2,ce4,ce6
 set ci ci1,ci2
 set cioSav cioSav1
 set danRer danRer3,danRer4,danRer5,danRer6
 set dm dm1,dm2,dm3
 set dp dp2,dp3
 set droEre droEre1
 set droMoj droMoj1,droMoj2
 set droMult droAna1,droAna2,droMoj1,droMoj2,droVir1,droVir2,droEre1,droSim1,droGri1,droPer1,droSec1,droWil1
 set droVir droVir1,droVir2
 set droYak droYak1,droYak2
 set equCab equCab1,equCab2
 set felCat felCat3,felCatV17e
 set fr fr1,fr2
 set galGal galGal2,galGal3
 set gasAcu gasAcu1
 set gorGor gorGor1
 set hg hg16,hg17,hg18,hg19
 set loxAfr loxAfr3
 set mm mm6,mm7,mm8,mm9
 set monDom monDom1,monDom4,monDom5
 set ornAna ornAna1
 set oryCun oryCun2
 set oryLat oryLat2
 set panTro panTro1,panTro2
 set petMar petMar1
 set ponAbe ponAbe2
 set priPac priPac1
 set rheMac rheMac2
 set rn rn3,rn4
 set sacCer sacCer1,sacCer2
 set susScr susScr2
 set strPur strPur1,strPur2
 set taeGut taeGut1
 set tetNig tetNig1,tetNig2
 set xenTro xenTro1,xenTro2
 
 # Define all organism/assembly-specific databases.
 set gbd $hg,$mm,$rn,$fr,$ce,$cb,$dm,$dp,$sacCer,$panTro,$galGal,$ci,$danRer,$canFam,$droYak,$droMult,$anoGam,$apiMel,$cioSav,$tetNig,$xenTro,$monDom,$bosTau,$rheMac,$strPur,$felCat,$gasAcu,$oryCun,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut,$gorGor,$aplCal,$loxAfr,$aplCal,$susScr,$ailMel
 
 # Define organism databases based on whole-genome shotgun projects
 # (Assembly based on WGS project contigs accessioned in Genbank)
 set wgs $rn,$panTro,$galGal,$canFam,$bosTau,$felCat,$monDom,$tetNig,$fr,$oryCun,$oryLat,$calJac,$cavPor,$taeGut,$aplCal,$susScr,$ailMel
 
 # 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 build a SNP track:
 set snpDb130 hg18
 set snpDb129 hg18
 set snpDb128 hg18,mm9
 set snpDb127 hg18,bosTau3
 set snpDb126 hg18,mm8
 set snpDb125 hg17,panTro1,canFam1,rn4
 
 # Only consider one of members of gbd at a time.
 exclusiveSet $gbd
 
 # Define other databases that we check
 set otherDb uniProt,go,hgFixed,proteome,visiGene
 
 # Define protein databases (currently not checked)
 set proteinDb proteins070202,proteins060115,proteins050415,proteins051015,proteins050415,proteins050315,proteins050201,proteins041115,proteins040515,proteins040315,proteins0111,proteins0305,proteins031112,proteins040115,proteins0405,proteins070403,proteins072003,proteins092903,proteins1129
 
 # Define zoo databases (currently not checked)
 set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
 
 # Define transMap databases
 # transMapDb not public: dasNov1,echTel1,loxAfr1,oryCun1,otoGar1,loxAfr3
 set transMapDb anoCar1,bosTau4,calJac1,calJac3,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryCun2,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2,loxAfr3
 
 # Set up list of databases we ignore and those we check.  Program
 # will complain about other databases.
 databasesChecked $gbd,$otherDb
 databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash
 
 # Define various non-self chains
 set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CalJac3,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr2,LoxAfr3,SusScr1,SusScr2,AilMel1,FelCatV17e,CanFamPoodle1,ChoHof1,DasNov2,DipOrd1,EchTel1,EriEur1,MacEug1,MyoLuc1,OchPri2,OryCun1,OryCun2,ProCap1,PteVam1,SorAra1,SpeTri1,TupBel1,TurTru1,VicPac1
 
 # Define databases that support known genes
 set kgDb $hg,$mm,$rn
 # Older format (KG 2)
 set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4
 # Newer format (KG 3 aka UCSC Genes)
 set kgDb3 hg18,hg19,mm9
 
 # Protein browser databases.
 set pbDb hg18,hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb1 hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb2 rn3
 set pbDb3 hg16,hg17,hg18
 
 # 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
 
 # Magic for tables split between chromosomes
 set split splitPrefix=chr%\_
 
 # Databases with the tRNAs track
 set tRNAsDbs hg18,hg19,mm9,rn4
 
 # Databases with the CGAP SAGE track
 set cgapSageDbs hg18,mm8
 
 # Define the shared identifiers and the fields they appear in.
 
 
 # GO - Gene Ontology Info
 
 identifier goAccession external=GO
 "Gene ontology term accessions.  Example - GO:0003574"
      go.term.acc
      go.goaPart.goId minCheck=0.999
 
 identifier goAccessionChopped
 "Gene ontology term accessions without the GO:"
      go.term.acc chopBefore=GO:
      dm1.bdgpGeneInfo.go comma minCheck=0.99
      dm1.bdgpNonCodingInfo.go comma minCheck=0.99
 
 identifier goId external=GO
 "Gene ontology term ID's.  Shouldn't be used outside of go database"
      go.term.id
      go.term2term.term1_id
      go.term2term.term2_id
      go.term_audit.term_id
      go.term_dbxref.term_id
      go.term_definition.term_id unique
      go.term_synonym.term_id
      go.graph_path.term1_id
      go.graph_path.term2_id
 
 identifier goDbXrefId external=GO
 "Gene ontology database cross-reference"
      go.dbxref.id
      go.term_dbxref.dbxref_id
 
 # UniProt Related Stuff
 
 identifier UniProtId external=UniProt
 "UniProt(Swiss-Prot/TrEMBL) display ID."
      uniProt.displayId.val
      proteome.uniProtAlias.alias minCheck=0.2
      proteome.spOldNew.newDisplayId minCheck=0.3
      proteome.spOldNew.oldDisplayId minCheck=0.3
      proteome.spDisease.displayID minCheck=0.9
      go.goaPart.dbObjectSymbol minCheck=0.95
      $gbd.dupSpMrna.proteinID minCheck=0.80
      $gbd.dupSpMrna.dupProteinID minCheck=0.50
      $kgDb2.kgProtAlias.displayID minCheck=0.80
      $kgDb2.kgSpAlias.alias minCheck=0.20
      $kgDb2.kgXref.spDisplayID minCheck=0.80
      $kgDb3.kgXref.spDisplayID minCheck=0.50
      $kgDb2.knownCanonical.protein minCheck=0.80
      $gbd.spMrna.spID minCheck=0.80
      dm1.bdgpSwissProt.spSymbol minCheck=0.80
      dm1.flyBaseSwissProt.spSymbol minCheck=0.80
 
 identifier UniProtAccession external=UniProt
 "UniProt(Swiss-Prot/TrEMBL) Accession"
      uniProt.displayId.acc
      uniProt.accToKeyword.acc
      uniProt.accToTaxon.acc
      uniProt.citation.acc
      uniProt.comment.acc
      uniProt.description.acc unique
      uniProt.extDbRef.acc
      uniProt.feature.acc
      uniProt.gene.acc
      uniProt.geneLogic.acc
      uniProt.info.acc unique
      uniProt.otherAcc.acc
      uniProt.protein.acc unique full
      proteome.spOldNew.acc minCheck=0.8
      proteome.uniProtAlias.acc minCheck=0.9
      proteome.spReactomeId.spID minCheck=0.9
      proteome.spReactomeEvent.spID minCheck=0.9
      $kgDb2.kgProtAlias.alias  minCheck=0.2
      $kgDb2.kgSpAlias.spID  minCheck=0.2
      $kgDb2.kgProtMap.qName minCheck=0.9
      $kgDb2.kgXref.spID minCheck=0.9
      $kgDb3.kgSpAlias.spID minCheck=0.50
      $kgDb3.kgXref.spID minCheck=0.50
      $gbd.pepMwAa.accession minCheck=0.9
      $gbd.pepPi.accession minCheck=0.9
      $ce.sangerCanonical.protein minCheck=0.8
      $ce.sangerGene.proteinID minCheck=0.8
      $ce.sangerLinks.protName minCheck=0.8
      dm1.bdgpCanonical.protein minCheck=0.9
      dm1.bdgpGene.proteinID minCheck=0.9
      dm1.bdgpSwissProt.swissProtId minCheck=0.9
      dm1.flyBaseSwissProt.swissProtId minCheck=0.9
      $sacCer.sgdGene.proteinID minCheck=0.9
      $sacCer.sgdCanonical.protein minCheck=0.9
      $sacCer.sgdToSwissProt.value minCheck=0.9
      go.goaPart.dbObjectId minCheck=0.99
      visiGene.gene.uniProt
 
 identifier UniProtAuthor
 "Author ID in UniProt (just use inside UCSC Relationalized UniProt)"
     uniProt.author.id
     uniProt.referenceAuthors.author full
 
 identifier UniProtReference
 "Reference (journal) ID in UniProt (just inside UCSC Relationalized)"
     uniProt.reference.id
     uniProt.citation.reference full
     uniProt.referenceAuthors.reference
 
 identifier UniProtCitation
 "Citation ID in UniProt (just use inside UCSC Relationalized UniProt)"
     uniProt.citation.id
     uniProt.citationRc.citation
 
 identifier UniProtCitationRp
 "Reference Position Line ID in UniProt (just inside UCSC Relationalized)"
     uniProt.citationRp.id
     uniProt.citation.rp full
 
 identifier UniProtRcType
 "Reference Comment Type in UniProt (just inside UCSC Relationalized)"
     uniProt.rcType.id
     uniProt.citationRc.rcType full
 
 identifier UniProtRcVal
 "Reference Comment Text in UniProt (just inside UCSC Relationalized)"
     uniProt.rcVal.id
     uniProt.citationRc.rcVal full
 
 identifier UniProtCommentType
 "Type of UniProt comment type (just inside UCSC Relationalized)"
     uniProt.commentType.id
     uniProt.comment.commentType full
 
 identifier UniProtCommentVal
 "Text of UniProt comment text (just inside UCSC Relationalized)"
      uniProt.commentVal.id
      uniProt.comment.commentVal full
 
 identifier UniProtExtDb
 "UniProt(Swiss-Prot/TrEMBL) external database ID (just inside UCSC Relationalized)"
      uniProt.extDb.id
      uniProt.extDbRef.extDb full
 
 identifier UniProtFeatureClass
 "Type of UniProt feature class (just inside UCSC Relationalized)"
      uniProt.featureClass.id
      uniProt.feature.featureClass full
 
 identifier UniProtFeatureType
 "Type of UniProt feature type (just inside UCSC Relationalized)"
      uniProt.featureType.id
      uniProt.feature.featureType full exclude=0
 
 identifier UniProtOrganelle
 "Type of UniProt organelle ID (just inside UCSC Relationalized)"
      uniProt.organelle.id
      uniProt.info.organelle full exclude=0
 
 identifier UniProtKeyword
 "UniProt(Swiss-Prot/TrEMBL) keyword ID (just inside UCSC Relationalized)"
      uniProt.keyword.id
      uniProt.accToKeyword.keyword full
 
 identifier ncbiTaxon
 "NCBI Taxon ID - number for a species.  Used by UniProt too"
      uniProt.taxon.id dupeOk
      uniProt.accToTaxon.taxon full
      uniProt.commonName.taxon
      visiGene.antibody.taxon
      visiGene.gene.taxon
      visiGene.genotype.taxon
      visiGene.specimen.taxon
      visiGene.lifeTime.taxon
      visiGene.lifeStageScheme.taxon
      visiGene.strain.taxon
 
 # tRNAs track Stuff
 
 identifier tRNAsId
 "ID of tRNAs"
     $tRNAsDbs.tRNAs.name dupeOk
 
 # CGAP SAGE track Stuff
 
 identifier cgapSageLibId external=CGAP
 "ID linking cgapSage and cgapSageLib tables"
     $cgapSageDbs.cgapSageLib.libId
     $cgapSageDbs.cgapSage.libIds comma
 
 # VisiGene Related Stuff
 
 identifier vgFileLocation
 "Where is that .jpg file? Usually a directory."
     visiGene.fileLocation.id
     visiGene.imageFile.fullLocation
     visiGene.imageFile.thumbLocation
 
 identifier vgStrain
 "Er, what type of mouse is that?"
     visiGene.strain.id
     visiGene.genotype.strain exclude=0
 
 identifier vgBodyPart
 "Brain, eye, cerebral cortex, etc."
     visiGene.bodyPart.id
     visiGene.specimen.bodyPart exclude=0
     visiGene.expressionLevel.bodyPart exclude=0
 
 identifier vgCellType
 "Neuron, glia, etc."
     visiGene.cellType.id
     visiGene.expressionLevel.cellType exclude=0
 
 identifier vgCellSubtype
 "More detailed splitting up of cell types.  What type of neuron, etc."
     visiGene.cellSubtype.id
     visiGene.expressionLevel.cellSubtype exclude=0
 
 identifier vgSliceType
 "Horizontal, coronal, wholeMount, etc."
     visiGene.sliceType.id
     visiGene.preparation.sliceType exclude=0
 
 identifier vgFixation
 "Fixation conditions - 3% formaldehyde or the like."
     visiGene.fixation.id
     visiGene.preparation.fixation exclude=0
 
 identifier vgEmbedding
 "Embedding media for slices - paraffin, etc."
     visiGene.embedding.id
     visiGene.preparation.embedding exclude=0
 
 identifier vgPermeablization
 "Permeablization conditions"
     visiGene.permeablization.id
     visiGene.preparation.permeablization exclude=0
 
 identifier vgContributor
 "Info on a contributor"
     visiGene.contributor.id
     visiGene.submissionContributor.contributor
 
 identifier vgJournal
 "Info on a journal"
     visiGene.journal.id
     visiGene.submissionSet.journal exclude=0
 
 identifier vgCopyright
 "Copyright information"
     visiGene.copyright.id
     visiGene.submissionSet.copyright exclude=0
 
 identifier vgSubmissionSource
 "Source of data - an external database, a contributor, etc."
     visiGene.submissionSource.id
     visiGene.submissionSet.submissionSource
     visiGene.antibodySource.submissionSource exclude=0
 
 identifier vgSubmissionSet
 "Info on a batch of images submitted at once"
     visiGene.submissionSet.id
     visiGene.submissionContributor.submissionSet
     visiGene.imageFile.submissionSet
     visiGene.image.submissionSet
 
 identifier vgSectionSet
 "Info on a bunch of sections through some specimen"
     visiGene.sectionSet.id
     visiGene.image.sectionSet exclude=0
 
 identifier vgAntibody
 "Info on an antibody"
     visiGene.antibody.id
     visiGene.probe.antibody exclude=0
     visiGene.antibodySource.antibody exclude=0
 
 identifier vgBac
 "Info on a BAC"
     visiGene.bac.id
     visiGene.probe.bac exclude=0
 
 identifier vgGene
 "Info on a gene"
     visiGene.gene.id
     visiGene.geneSynonym.gene
     visiGene.allele.gene
     visiGene.probe.gene
 
 identifier vgAllele
 "Name of a gene allele"
     visiGene.allele.id
     visiGene.genotypeAllele.allele
 
 identifier vgGenotype
 "How different genetically from wild type."
     visiGene.genotype.id
     visiGene.genotypeAllele.genotype
     visiGene.specimen.genotype
 
 identifier vgSex
 "Sex of a specimen"
     visiGene.sex.id
     visiGene.specimen.sex exclude=0
 
 identifier vgSpecimen
 "A biological specimen - something mounted, possibly sliced up"
     visiGene.specimen.id
     visiGene.image.specimen
 
 identifier vgPreparation
 "How a specimen is prepared."
     visiGene.preparation.id
     visiGene.image.preparation exclude=0
 
 identifier vgProbeType
 "Type of probe - RNA, antibody, etc."
     visiGene.probeType.id
     visiGene.probe.probeType
 
 identifier vgProbe
 "Information on a probe used to stain or hilight image"
     visiGene.probe.id
     visiGene.imageProbe.probe
     visiGene.vgPrbMap.probe
 
 identifier vgProbeColor
 "Color - what color probe is in"
     visiGene.probeColor.id
     visiGene.imageProbe.probeColor exclude=0
 
 identifier vgCaption
 "Caption for image.  Id corresponding to text."
     visiGene.caption.id
     visiGene.imageFile.caption exclude=0
 
 identifier vgImageFile
 "A biological image file"
     visiGene.imageFile.id
     visiGene.image.imageFile
     visiGene.imageFileFwd.fromIf
     visiGene.imageFileFwd.toIf
 
 identifier vgImage
 "Master identifier for a visiGene image.  May be just a pane in an image file."
     visiGene.image.id
     visiGene.imageProbe.image
     $kgDb.knownToVisiGene.value
 
 identifier vgImageProbe
 "Association between a probe and an image."
     visiGene.imageProbe.id
     visiGene.expressionLevel.imageProbe
 
 identifier vgExpressionPattern
 "Expression pattern - scattered, regional, etc."
     visiGene.expressionPattern.id
     visiGene.expressionLevel.expressionPattern exclude=0
 
 identifier vgLifeStageScheme
 "A scheme for describing stages of development for an organism"
     visiGene.lifeStageScheme.id
     visiGene.lifeStage.lifeStageScheme
 
 identifier vgPrb
 "Permanent ID/Probe Sequence table"
     visiGene.vgPrb.id
     visiGene.vgPrbMap.vgPrb
 
 # Various types of gene predictions in UCSC Genome Browser
 
 identifier gencodeGeneNameJun05 dependency
 "Link together Gencode gene model and class for June 05 Data Freeze"
     hg17.encodeGencodeGeneJun05.name
     hg17.gencodeGeneClassJun05.name full unique
 
 identifier gencodeGeneNameKnownOct05 dependency
 "Link together Gencode gene model (Known) and class for Oct 05 Data Freeze"
     $hg.encodeGencodeGeneKnownOct05.name
     $hg.gencodeGeneClassOct05.name minCheck=0.88 unique
 
 identifier gencodeGeneNamePutativeOct05 dependency
 "Link together Gencode gene model (Putative) and class for Oct 05 Data Freeze"
     $hg.encodeGencodeGenePutativeOct05.name
     $hg.gencodeGeneClassOct05.name minCheck=0.05 unique
 
 identifier gencodeGeneNamePseudoOct05 dependency
 "Link together Gencode gene model (Pseudo) and class for Oct 05 Data Freeze"
     $hg.encodeGencodeGenePseudoOct05.name
     $hg.gencodeGeneClassOct05.name minCheck=0.06 unique
 
 identifier gencodeGeneNameKnownMar07 dependency
 "Link together Gencode gene model (Known) and class for Mar 07 Data Version"
     $hg.encodeGencodeGeneKnownMar07.name
     $hg.gencodeGeneClassMar07.name minCheck=0.83 unique
 
 identifier gencodeGeneNamePutativeMar07 dependency
 "Link together Gencode gene model (Putative) and class for Mar 07 Data Version"
     $hg.encodeGencodeGenePutativeMar07.name
     $hg.gencodeGeneClassMar07.name minCheck=0.10 unique
 
 identifier gencodeGeneNamePolymorphicMar07 dependency
 "Link together Gencode gene model (Polymorphic) and class for Mar 07 Data Version"
     $hg.encodeGencodeGenePolymorphicMar07.name
     $hg.gencodeGeneClassMar07.name minCheck=0.006 unique
 
 identifier gencodeGeneNamePseudoMar07 dependency
 "Link together Gencode gene model (Pseudo) and class for Mar 07 Data Version"
     $hg.encodeGencodeGenePseudoMar07.name
     $hg.gencodeGeneClassMar07.name minCheck=0.05 unique
 
 identifier encodePseudogeneConsensus dependency
 "Link together Consensus Pseudogenes and class"
     $hg.encodePseudogeneConsensus.name
     $hg.encodePseudogeneClass.name minCheck=0.16 unique
 
 identifier encodePseudogeneGIS dependency
 "Link together GIS Pseudogenes and class"
     $hg.encodePseudogeneGIS.name
     $hg.encodePseudogeneClass.name minCheck=0.04 unique
 
 identifier encodePseudogeneHavana dependency
 "Link together Havana Pseudogenes and class"
     $hg.encodePseudogeneHavana.name
     $hg.encodePseudogeneClass.name minCheck=0.17 unique
 
 identifier encodePseudogeneUcsc dependency
 "Link together Ucsc Retrogenes and class"
     $hg.encodePseudogeneUcsc.name dupeOk
     $hg.encodePseudogeneClass.name minCheck=0.22 unique
 
 identifier encodePseudogeneUcsc2 dependency
 "Link together Ucsc Pseudogenes and class"
     $hg.encodePseudogeneUcsc2.name dupeOk
     $hg.encodePseudogeneClass.name minCheck=0.04 unique
 
 identifier encodePseudogeneYale dependency
 "Link together Yale Pseudogenes and class"
     $hg.encodePseudogeneYale.name
     $hg.encodePseudogeneClass.name minCheck=0.16 unique
 
 identifier wgEncodeNhgriBip
 "Link together Gencode gene model (Known) and class for Jan 2009 Data Version"
     hg18.wgEncodeNhgriBip.name dupeOk
     panTro2.wgEncodeNhgriBip.name
     rheMac2.wgEncodeNhgriBip.name
     mm9.wgEncodeNhgriBip.name
     rn4.wgEncodeNhgriBip.name
     canFam2.wgEncodeNhgriBip.name
     bosTau4.wgEncodeNhgriBip.name
 
 identifier wgEncodeGencodeClassesRel2
 "Link together Gencode gene model (Known) and class for Jan 2009 Data Version"
     hg18.wgEncodeGencodeClassesRel2.name
     hg18.wgEncodeGencodeAutoRel2.name unique
     hg18.wgEncodeGencodeManualRel2.name unique
     hg18.wgEncodeGencodePolyaRel2.name unique
 
 identifier wgEncodeGencodeClassesV3
 "Link together Gencode gene model (Known) and class for July 2009 Data Version"
     hg18.wgEncodeGencodeClassesV3.name
     hg18.wgEncodeGencodeAutoV3.name unique
     hg18.wgEncodeGencodeManualV3.name unique
     hg18.wgEncodeGencodePolyaV3.name unique
 
 identifier acemblyName dependency
 "Link together Acembly gene model structure and peptide."
     $hg,$mm.acembly.name
     $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90
     hg17.acemblyPep.name unique minCheck=0.63
     $hg,$mm.acemblyClass.name full unique
 
 identifier ECgeneName dependency
 "Link together EC gene predicted gene structure and peptide"
     $gbd.ECgene.name
     $gbd.ECgenePep.name unique
 
 identifier geneidName dependency
 "Link together geneid predicted gene structure and peptide"
     $gbd.geneid.name
     $gbd.geneidPep.name full unique
 
 identifier genscanName dependency
 "Link together genscan predicted gene structure and peptide"
     $gbd.genscan.name
     $gbd.genscanPep.name full unique
 
 identifier jgiName dependency
 "Link together jgi predicted gene structure and peptide"
     $gbd.jgiGene.name
     $gbd.jgiPep.name unique minCheck=0.9
 
 identifier softberryGeneName dependency
 "Link together Fshgene++ gene structure, pepdide, and homolog"
     $gbd.softberryGene.name
     $gbd.softberryPep.name full unique
     $gbd.softberryHom.name unique
 
 identifier twinscanName dependency
 "Link together twinscan predicted gene structure and peptide"
     $gbd.twinscan.name
     $gbd.twinscanPep.name full unique
 
 identifier nscanName dependency
 "Link together nscan predicted gene structure and peptide"
     $gbd.nscanGene.name
     $gbd.nscanPep.name unique
 
 identifier nscanPasaName dependency
 "Link together nscan predicted gene structure (PASA) and peptide"
     $gbd.nscanPasaGene.name
     $gbd.nscanPasaPep.name unique
 
 identifier augustusHintsName dependency
 "Link together augustusHints predicted gene structure and peptide"
    $gbd.augustusHints.name
    $gbd.augustusHintsPep.name chopBefore=. full unique
 
 identifier augustusXRAName dependency
 "Link together augustusXRA predicted gene structure and peptide"
    $gbd.augustusXRA.name
    $gbd.augustusXRAPep.name chopBefore=. full unique
 
 identifier augustusAbinitioName dependency
 "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 vegaName
 "Link together various VEGA human curated gene annotation"
     $gbd.vegaInfo.transcriptId
     $gbd.vegaGene.name
     $gbd.vegaPseudoGene.name
 
 identifier vegaGeneName typeOf=vegaName dependency
 "Link together VEGA predicted gene structure and peptide"
     $gbd.vegaGene.name
     danRer5.vegaPep.name unique minCheck=0.72
 
 identifier vegaZfishName
 "Link together various VEGA zebrafish curated gene annotation"
     $gbd.vegaInfoZfish.transcriptId
 
 identifier vegaGeneZfishName typeOf=vegaZfishName dependency
 "Link together Zebrafish VEGA predicted gene structure additional information"
     $danRer.vegaGene.name
     $danRer.vegaInfoZfish.transcriptId minCheck=0.99
     $danRer.vegaToCloneId.transcriptId minCheck=0.99
 
 identifier vegaPseudoZfishName typeOf=vegaZfishName
 "Link together VEGA pseudogene and other info."
     $danRer.vegaPseudoGene.name
 
 identifier vegaPseudoGeneZfishName typeOf=vegaPseudoZfishName dependency
 "Link together Zebrafish VEGA predicted gene structure additional information"
     $danRer.vegaPseudoGene.name
     $danRer.vegaInfoZfish.transcriptId minCheck=0.004
     $danRer.vegaToCloneId.transcriptId minCheck=0.004
 
 identifier vegaPseudogeneName typeOf=vegaName
 "Link together VEGA pseudogene and other info."
     $gbd.vegaPseudoGene.name
 
 #identifier pseudoGeneName
 #"Link together pseudo predicted gene structure and peptide"
 #	$hg.pseudoMrna.qName dupeOk
 #	hg16,hg17,hg18.pseudoGeneLink.name minCheck=0.99
 
 identifier mrnaBlastzName
 "Link together mrnaBlastz and pseudoMrna"
     $hg.mrnaBlastz.qName dupeOk
     $hg,!hg16.pseudoMrna.qName
     hg16.pseudoMrna.qName minCheck=0.76
 
 # Microarray stuff.
 
 identifier agilentHumanProbeId external=agilent fuzzy
 "Agilent Human CGH/CNV array probe ID"
     $hg.agilentCgh105a.name
     $hg.agilentCgh1x1m.name
     $hg.agilentCgh244a.name
     $hg.agilentCgh2x400k.name
     $hg.agilentCgh44k.name
     $hg.agilentCgh4x180k.name
     $hg.agilentCgh8x60k.name
     $hg.agilentCnv2x400k.name
     $hg.agilentCnv2x105k.name
     $hg.agilentHrd1x1m.name
 
 identifier agilentMouseProbeId external=agilent fuzzy
 "Agilent Mouse CGH/CNV array probe ID"
     $mm.agilentCgh105a.name
     $mm.agilentCgh244a.name
     $mm.agilentCgh44k.name
 
 identifier agilentRatProbeId external=agilent fuzzy
 "Agilent Rat CGH/CNV array probe ID"
     $rn.agilentCgh105a.name
     $rn.agilentCgh244a.name
 
 identifier sestanBrainAtlasId
 "Sample IDs for the Sestan brain atlas array."
     hgFixed.sestanBrainAtlasExps.id
     $hg.sestanBrainAtlas.expIds comma full
     $hg.sestanBrainAtlas.expScores comma indexOf full
 
 identifier affyMouseExonSampleId
 "Sample IDs for Affymetrix all mouse exon array."
     hgFixed.affyMouseExonTissuesAllExps.id
     $mm.affyExonTissues.expIds comma full
     $mm.affyExonTissues.expScores comma indexOf full
 
 identifier affyRatExonSampleId
 "Sample IDs for Affymetrix all rat exon array."
     hgFixed.affyRatExonTissuesAllExps.id
     $rn.affyExonTissues.expIds comma full
     $rn.affyExonTissues.expScores comma indexOf full
 
 identifier gnfHumanAtlas2
 "Novartis GNF Human gene probe ID"
     hgFixed.gnfHumanAtlas2All.name
     hgFixed.gnfHumanAtlas2AllRatio.name unique
     hgFixed.gnfHumanAtlas2Median.name full unique
     hgFixed.gnfHumanAtlas2MedianRatio.name unique
     hgFixed.gladHumESRatio.name unique
     hgFixed.gladHumES.name
     hgFixed.gladHumESOtherData.name
     $hg.knownToGnfAtlas2.value
     $hg.gnfAtlas2.name
     $hg.affyGnf1h.qName
 
 identifier gnfMouseAtlas2
 "Novartis GNF Mouse gene probe ID"
     hgFixed.gnfMouseAtlas2All.name
     hgFixed.gnfMouseAtlas2AllRatio.name unique
     hgFixed.gnfMouseAtlas2Median.name full unique
     hgFixed.gnfMouseAtlas2MedianRatio.name unique
     $mm.knownToGnf1m.value
     $mm.gnfAtlas2.name
     $mm.affyGnf1m.qName
 
 identifier gnfMOE430v2
 "Novartis GNF Mouse gene probe ID"
     hgFixed.gnfMOE430v2All.name
     hgFixed.gnfMOE430v2AllRatio.name unique
     hgFixed.gnfMOE430v2Median.name full unique
     hgFixed.gnfMOE430v2MedianRatio.name unique
     $mm.knownToGnfMOE430v2.value
     $mm.gnfMOE430v2.name
     $mm.affyMOE430v2.qName
 
 identifier gnfRatAtlas2
 "Novartis GNF Rat gene probe ID"
     hgFixed.gnfRatAtlas2All.name
     hgFixed.gnfRatAtlas2AllRatio.name unique
     hgFixed.gnfRatAtlas2Median.name full unique
     hgFixed.gnfRatAtlas2MedianRatio.name unique
     $rn.knownToU34A.value
     $rn.gnfAtlas2.name
     $rn.affyU34A.qName
 
 identifier affyZonWildType
 "Affymetrix Zebrafish chip Zon Lab data probe ID"
     hgFixed.zebrafishZonWTAll.name
     hgFixed.zebrafishZonWTAllRatio.name unique
     hgFixed.zebrafishZonWTMedian.name unique
     hgFixed.zebrafishZonWTMedianRatio.name. unique
     $danRer.ensToAffyZebrafish.name
     $danRer.ensToAffyZonWildType.name
     $danRer.affyZonWildType.name
     $danRer.affyZebrafish.qName
     danRer5.affyZebrafishConsensus.qName
 
 identifier affyZonWildTypeDanRer5
 "Affymetrix Zebrafish chip Zon Lab data probe ID Consensus"
     danRer5.affyZonWildType.name dupeOk
     danRer5.affyZebrafishConsensus.qName
 
 identifier affyTargetZonWildTypeDanRer5
 "Affymetrix Zebrafish chip Zon Lab data probe ID Target"
     danRer5.affyTargetZonWildType.name dupeOk
     danRer5.affyZebrafishTarget.qName
 
 identifier affyU95
 "Affymetrix Human U95 chip identifiers"
     $hg.affyU95.qName dupeOk
     $hg.affyRatio.name
     $hg.knownToU95.value
 
 identifier affyU133
 "Affymetrix Human U133 chip identifiers"
     $hg.affyU133.qName dupeOk chopBefore=U133A: chopBefore=U133B: chopAfter=;
     $hg.knownToU133.value
 
 identifier affyU133Plus2
 "Affymetrix Human U133 chip identifiers"
     $hg.affyU133Plus2.qName dupeOk
     $hg.knownToU133Plus2.value
 
 identifier affyU74
 "Affymetrix Mouse U74 chip identifiers"
     $mm.affyU74.qName dupeOk
     $mm.affyGnfU74A.name
     $mm.affyGnfU74B.name
     $mm.affyGnfU74C.name
     $mm.knownToU74.value
 
 identifier affyMOE430
 "Affymetrix Mouse MOE430 chip identifiers"
     $mm.affyMOE430.qName dupeOk
     $mm.knownToMOE430.value
     $mm.knownToMOE430A.value
     $mm.rinnSex.name
     hgFixed.mouseRinnSex.name minCheck=0.96
     hgFixed.mouseRinnSexMedian.name minCheck=0.96
     hgFixed.mouseRinnSexRatio.name minCheck=0.97
     hgFixed.mouseRinnSexMedianRatio.name minCheck=0.97
 
 identifier affyRAE230
 "Affymetrix Rat RAE230 chip identifiers"
     $rn.affyRAE230.qName dupeOk
     $rn.knownToRAE230.value
 
 identifier affyU34A
 "Affymetrix Rat U34A chip identifiers"
     $rn.affyU34A.qName dupeOk
     $rn.knownToU34A.value
 
 identifier illuminaWG6
 "Illumina WG-6 3.0 Probe set identifiers"
     $hg.illuminaProbes.name dupeOk
     $hg.illuminaProbesAlign.qName full
     $hg.illuminaProbesSeq.id minCheck=0.8
 
 identifier kimWormGeneId
 "Identifiers for Kim-lab worm genes"
     hgFixed.kimWormLifeAllRatio.name
     hgFixed.kimWormLifeMedianRatio.name full unique
     $ce.sangerToKim.value minCheck=0.6
 
 identifier nci60SampleId
 "Identifiers of NCI 60 Cell lines for expression experiments"
     hgFixed.nci60Exps.id
     $hg.nci60.expIds comma full
     $hg.nci60.expScores comma indexOf full
 
 identifier rosettaChr22SampleId
 "Identifiers for samples used in Rosetta chromosome 22 public experiments"
     hgFixed.rosettaExps.name
     hgFixed.rosChr22Dat.expName
 
 identifier gnfHumanAtlas2SampleId
 "Identifiers of RNA samples used in GNF Human Expression Atlas 2"
      hgFixed.gnfHumanAtlas2AllExps.id
      hgFixed.gnfHumanAtlas2All.expScores comma indexOf full
      hgFixed.gnfHumanAtlas2AllRatio.expScores comma indexOf full
 
 identifier gnfHumanAtlas2MedianSampleId
 "Identifiers of pooled RNA samples used in GNF Human Expression Atlas 2"
      hgFixed.gnfHumanAtlas2MedianExps.id
      hgFixed.gnfHumanAtlas2Median.expScores comma indexOf full
      hgFixed.gnfHumanAtlas2MedianRatio.expScores comma indexOf full
      $hg.gnfAtlas2.expScores comma indexOf full
 
 identifier gnfMouseAtlas2SampleId
 "Identifiers of RNA samples used in GNF Mouse Expression Atlas 2"
      hgFixed.gnfMouseAtlas2AllExps.id
      hgFixed.gnfMouseAtlas2All.expScores comma indexOf full
      hgFixed.gnfMouseAtlas2AllRatio.expScores comma indexOf full
 
 identifier gnfMouseAtlas2MedianSampleId
 "Identifiers of pooled RNA samples used in GNF Mouse Expression Atlas 2"
      hgFixed.gnfMouseAtlas2MedianExps.id
      hgFixed.gnfMouseAtlas2Median.expScores comma indexOf full
      hgFixed.gnfMouseAtlas2MedianRatio.expScores comma indexOf full
      $mm.gnfAtlas2.expScores comma indexOf full
 
 identifier gnfRatAtlas2SampleId
 "Identifiers of RNA samples used in GNF Rat Expression Atlas 2"
      hgFixed.gnfRatAtlas2AllExps.id
      hgFixed.gnfRatAtlas2All.expScores comma indexOf full
      hgFixed.gnfRatAtlas2AllRatio.expScores comma indexOf full
 
 identifier gnfRatAtlas2MedianSampleId
 "Identifiers of pooled RNA samples used in GNF Rat Expression Atlas 2"
      hgFixed.gnfRatAtlas2MedianExps.id
      hgFixed.gnfRatAtlas2Median.expScores comma indexOf full
      hgFixed.gnfRatAtlas2MedianRatio.expScores comma indexOf full
      $rn.gnfAtlas2.expScores comma indexOf full
 
 identifier gnfU95SampleIdV0
 "Identifiers of RNA samples used early version of GNF Human Expression Atlas 1"
      hgFixed.affyExps.id
      $hg.affyRatio.expIds comma
      $hg.affyRatio.expScores comma indexOf
 
 identifier gnfU95SampleIdV1
 "Identifiers of RNA samples used in GNF Human Expression Atlas 1"
      hgFixed.gnfHumanU95AllExps.id
      hgFixed.gnfHumanU95All.expScores comma indexOf full
      hgFixed.gnfHumanU95AllRatio.expScores comma indexOf full
 
 identifier gnfU95MedianSampleIdV1
 "Identifiers of pooled RNA samples used in GNF Human Expression Atlas 1"
      hgFixed.gnfHumanU95MedianExps.id
      hgFixed.gnfHumanU95Median.expScores comma indexOf full
      hgFixed.gnfHumanU95MedianRatio.expScores comma indexOf full
 
 identifier gnfU74aSampleId
 "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip"
      hgFixed.gnfMouseU74aAllExps.id
      hgFixed.gnfMouseU74aAll.expScores comma indexOf full
      hgFixed.gnfMouseU74aAllRatio.expScores comma indexOf full
      $mm.affyGnfU74A.expIds comma full
      $mm.affyGnfU74A.expScores comma indexOf full
 
 identifier gnfU74aMedianSampleId
 "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip"
      hgFixed.gnfMouseU74aMedianExps.id
      hgFixed.gnfMouseU74aMedian.expScores comma indexOf full
      hgFixed.gnfMouseU74aMedianRatio.expScores comma indexOf full
 
 identifier gnfU74bSampleId
 "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip"
      hgFixed.gnfMouseU74bAllExps.id
      hgFixed.gnfMouseU74bAll.expScores comma indexOf full
      hgFixed.gnfMouseU74bAllRatio.expScores comma indexOf full
      $mm.affyGnfU74B.expIds comma full
      $mm.affyGnfU74B.expScores comma indexOf full
 
 identifier gnfU74bMedianSampleId
 "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip"
      hgFixed.gnfMouseU74bMedianExps.id
      hgFixed.gnfMouseU74bMedian.expScores comma indexOf full
      hgFixed.gnfMouseU74bMedianRatio.expScores comma indexOf full
 
 identifier gnfU74cSampleId
 "Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip"
      hgFixed.gnfMouseU74cAllExps.id
      hgFixed.gnfMouseU74cAll.expScores comma indexOf full
      hgFixed.gnfMouseU74cAllRatio.expScores comma indexOf full
      $mm.affyGnfU74C.expIds comma full
      $mm.affyGnfU74C.expScores comma indexOf full
 
 identifier gnfU74cMedianSampleId
 "Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip"
      hgFixed.gnfMouseU74cMedianExps.id
      hgFixed.gnfMouseU74cMedian.expScores comma indexOf full
      hgFixed.gnfMouseU74cMedianRatio.expScores comma indexOf full
 
 identifier arbFlyLifeAllSampleId
 "Identifiers of RNA samples used in Arbeitman fly life cycle experiments"
      hgFixed.arbFlyLifeAllExps.id
      hgFixed.arbFlyLifeAll.expScores comma indexOf full
      hgFixed.arbFlyLifeAllRatio.expScores comma indexOf full
 
 identifier arbFlyLifeMedianSampleId
 "Identifiers of pooled RNA samples used in Arbeitman fly life cycle experiments"
      hgFixed.arbFlyLifeMedianExps.id
      hgFixed.arbFlyLifeMedian.expScores comma indexOf full
      hgFixed.arbFlyLifeMedianRatio.expScores comma indexOf full
 
 identifier kimWormLifeAllSampleId
 "Identifiers of RNA samples used in Kim worm life cycle experiments"
      hgFixed.kimWormLifeAllExps.id
      hgFixed.kimWormLifeAllRatio.expScores comma indexOf full
 
 identifier kimWormLifeMedianSampleId
 "Identifiers of pooled RNA samples used in Kim worm life cycle experiments"
      hgFixed.kimWormLifeMedianExps.id
      hgFixed.kimWormLifeMedianRatio.expScores comma indexOf full
 
 identifier yeastChoCellCycleSampleId
 "Identifiers of RNA samples used in Cho yeast cell cycle experiments"
      hgFixed.yeastChoCellCycleExps.id
      hgFixed.yeastChoCellCycle.expScores comma indexOf full
      hgFixed.yeastChoCellCycleRatio.expScores comma indexOf full
 
 identifier hgFixedSageExpId
 # I'd like to drop this table set. Check with Chuck.
 "Sage experiment (tissue type etc) ID in hgFixed"
     hgFixed.sageExp.num
     hgFixed.sage.exps comma full
     hgFixed.sageCounts.expCounts comma indexOf full
 
 identifier sageExpId
 "Sage experiment (tissue type etc) ID"
     $gbd.sageExp.num
     $gbd.sage.exps comma full
 
 identifier rinnSexSampleId
 "Identifiers of RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip"
      hgFixed.mouseRinnSexExps.id
      hgFixed.mouseRinnSex.expScores comma indexOf full
      hgFixed.mouseRinnSexRatio.expScores comma indexOf full
 
 identifier rinnSexMedianSampleId
 "Identifiers of median RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip"
      hgFixed.mouseRinnSexMedianExps.id
      hgFixed.mouseRinnSexMedian.expScores comma indexOf full
      hgFixed.mouseRinnSexMedianRatio.expScores comma indexOf full
 
 identifier stanfordPromotersCellId
 "Identifiers of cell lines for Stanford ENCODE project luciferase assays"
     hgFixed.encode_Stanford_PromotersExps.id
     $hg.encode_Stanford_Promoters.expIds comma full
     $hg.encode_Stanford_Promoters.expScores comma indexOf full
 
 identifier mouseLandscape
 "U. Toronto mouse gene probe ID"
     hgFixed.mouseLandscape.name
     $mm.knownToXM.value
 
 identifier mouseLandscapeSampleId
 "Identifiers of U. Toronto RNA samples"
      hgFixed.mouseLandscapeExps.id
      hgFixed.mouseLandscape.expScores comma indexOf full
 
 identifier gladHumESSampleId
 "Identifiers of RNA samples used in Gladstone Arrays"
      hgFixed.gladHumESExps.id
      hgFixed.gladHumES.expScores comma indexOf full
      hgFixed.gladHumESRatio.expScores comma indexOf full
 
 # Stuff to link together alignment chains and nets
 
 identifier chainSelf
 "Link together self chain info"
     $gbd.chainSelf.id $split
     $gbd.chainSelfLink.chainId $split full
     $gbd.netSelf.chainId exclude=0
 
 identifier chainSelfNonSplit
 "Link together self chain info"
     hg19.chainSelf.id
     hg19.chainSelfLink.chainId full
 
 identifier chain[${chainDest}]Id
 "Link together chain info"
     $gbd.chain[].id $split
     $gbd.chain[].id
     $gbd.chain[]Link.chainId $split full
     $gbd.chain[]Link.chainId full
     $gbd.net[].chainId exclude=0
     $gbd.netRxBest[].chainId exclude=0
     $gbd.net[]NonGap.chainId exclude=0
     $gbd.netSynteny[].chainId exclude=0
 
 identifier rBestChainPanTro1Id
 "Link together reciprocal best chain/net"
     hg16.rBestChainPanTro1.id $split
     hg16.rBestChainPanTro1Link.chainId $split full
     hg16.rBestNetPanTro1.chainId exclude=0
 
 # Genbank/trEMBL Accessions and meaningful subsets thereof
 identifier genbankAccession external=genbank
 "Generic Genbank Accession.  More specific Genbank accessions follow"
     $gbd.seq.acc
 
 identifier stsAccession external=genbank typeOf=genbankAccession
 "Genbank accession of a Sequence Tag Site (STS) sequence."
     $gbd.stsInfo2.genbank dupeOk
 
 identifier bacEndNames
 "Names for BAC end reads."
     $gbd.all_bacends.qName dupeOk
     $gbd.bacEndPairs.lfNames comma
     $danRer.bacEndSingles.lfNames comma
     $danRer.bacEndPairsBad.lfNames comma
     $danRer.bacEndAlias.alias minCheck=0.55
     $hg.fishClones.beNames comma minCheck=0.70
 
 identifier danRerBacExtName
 "External name for BAC clones."
     $danRer.bacCloneXRef.name dupeOk
     $danRer.bacEndPairs.name
     $danRer.bacEndSingles.name
 
 identifier bacAccession typeOf=genbankAccession external=genbank
 "Genbank accession of a sequenced BAC (~150kb of genomic sequence)."
 
 identifier humanBacAccession typeOf=bacAccession
 "Genbank accession of a sequenced $hg.BAC (~150kb of genomic sequence)."
     $hg.clonePos.name chopAfter=. dupeOk
     $hg,!hg18.gold.frag chopAfter=. $split
     hg18.gold.frag chopAfter=. $split minCheck=0.98
     hg16.certificate.accession1
     hg16.certificate.accession2
     $hg,!hg18.gl.frag chopAfter=. $split
     hg18.gl.frag chopAfter=. $split minCheck=0.95
     $hg.fishClones.accNames chopAfter=. comma minCheck=0.70
 
 identifier humanBacAccessionVersion typeOf=bacAccession
 "Genbank accession.version of sequence $hg.BAC"
     $hg.clonePos.name dupeOk
     $hg,!hg18.gl.frag $split chopAfter=_
     $hg,!hg18.gold.frag $split
     hg18.gl.frag $split chopAfter=_ minCheck=0.95
     hg18.gold.frag $split minCheck=0.90
 
 identifier wgsContigAccession typeOf=genbankAccession
 "Genbank accession.version of whole-genome shotgun contig"
     $wgs.contigAcc.acc
 
 identifier wgsContigName
 "Sequencing project name for whole-genome shotgun contigs."
     $wgs.contigAcc.contig
     $wgs,!panTro1.gold.frag $split full
 
 identifier proteinAccession typeOf=genbankAccession fuzzy
 "Genbank protein accession."
     $kgDb.kgProtAlias.alias
     $kgDb.kgSpAlias.alias minCheck=0.1
     $kgDb.kgXref.protAcc
     $gbd.refLink.protAcc
 
 identifier estOrMrnaAccession typeOf=genbankAccession
 "Genbank EST or mRNA accession."
     $gbd.gbSeq.acc
     $gbd.gbStatus.acc unique
     $gbd.gbCdnaInfo.acc unique
     $gbd.imageClone.acc
     $gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma
     ce2.altGraphX.mrnaRefs comma minCheck=0.97
     hg16.altGraphX.mrnaRefs comma minCheck=0.99
     hg17.altGraphX.mrnaRefs comma minCheck=0.97
     hg18.altGraphX.mrnaRefs comma minCheck=0.98
     mm7.altGraphX.mrnaRefs comma minCheck=0.99
 
 identifier estAccession typeOf=estOrMrnaAccession
 "Genbank EST accession"
 
 identifier nativeEstAccession typeOf=estAccession
 "Genbank Native (same organism as database) EST accession"
     $gbd.all_est.qName dupeOk
     $gbd,!sacCer2.est.qName $split full
     $gbd,!sacCer2,!caeJap1.intronEst.qName $split
     sacCer2.est.qName splitPrefix=%\_ full
     sacCer2.intronEst.qName splitPrefix=%\_
     caeJap1.intronEst.qName
     ailMel1.intronEst.qName
     $gbd.estOrientInfo.name full
 
 identifier nativeEstAccessionNonSplit typeOf=estAccession
 "Genbank Native (same organism as database) EST accession"
     hg19.all_est.qName dupeOk
     hg19.est.qName full
     hg19.intronEst.qName
     hg19.estOrientInfo.name full
 
 identifier xenoEstAccession typeOf=estAccession
 "Genbank xeno (different organism from database) EST accession"
     $gbd.xenoEst.qName dupeOk
 
 identifier mrnaAccession typeOf=estOrMrnaAccession fuzzy
 "Genbank mRNA accession"
 
 identifier xenoMrnaAccession typeOf=mrnaAccession
 "Genbank xeno (different organism from database) mRNA accession"
     $gbd.xenoMrna.qName dupeOk
 
 identifier nativeMrnaAccession typeOf=mrnaAccession
 "Genbank Native (same organism as database) mRNA accession"
     $gbd.all_mrna.qName dupeOk
     $gbd,!ce2.mrnaOrientInfo.name full minCheck=0.01
     ce2.mrnaOrientInfo.name minCheck=0.08
     $gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.mrnaID minCheck=0.80
     $gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.dupMrnaID minCheck=0.95
     $gbd,!mm7,!mm8,!mm9,!hg17,!rn3,!rn4.mrnaRefseq.mrna minCheck=0.25
     mm7.mrnaRefseq.mrna minCheck=0.30
     mm8.mrnaRefseq.mrna minCheck=0.30
     mm9.mrnaRefseq.mrna minCheck=0.30
     hg17.mrnaRefseq.mrna minCheck=0.80
     $rn.mrnaRefseq.mrna minCheck=0.03
     $gbd,!mm7,!mm8,!mm9,!hg17,!hg18,!rn4.spMrna.mrnaID minCheck=0.98
     $mm.spMrna.mrnaID minCheck=0.20
     $mm.dupSpMrna.mrnaID minCheck=0.10
     $mm.dupSpMrna.dupMrnaID minCheck=0.10
     hg17.spMrna.mrnaID minCheck=0.30
     hg17.dupSpMrna.mrnaID minCheck=0.20
     hg17.dupSpMrna.dupMrnaID minCheck=0.20
     hg18.dupSpMrna.mrnaID minCheck=0.20
     hg18.dupSpMrna.dupMrnaID minCheck=0.70
     rn4.dupSpMrna.mrnaID minCheck=0.15
     rn4.dupSpMrna.dupMrnaID minCheck=0.60
 
 identifier mgcAccession typeOf=nativeMrnaAccession
 "Mammalian Gene Collection Genbank mRNA accession."
     $gbd.mgcFullMrna.qName dupeOk
     $gbd.mgcGenes.name full
 
 identifier orfeomeAccession typeOf=nativeMrnaAccession
 "ORFeome collaboration Genbank mRNA accession."
     $gbd.orfeomeMrna.qName dupeOk
     $gbd.orfeomeGenes.name full
 
 identifier refSeqId typeOf=mrnaAccession
 "RefSeq mRNA accession"
     $gbd.refLink.mrnaAcc
     $gbd.refSeqStatus.mrnaAcc minCheck=0.10
     $kgDb.kgXref.refseq exclude= minCheck=0.50
     $kgDb,!hg16,!hg17,!hg18,!mm7,!mm8,!mm9.knownToRefSeq.value minCheck=0.98
     hg18,mm7,mm8,mm9.knownToRefSeq.value minCheck=0.96
     hg16,hg17.knownToRefSeq.value minCheck=0.94
     $kgDb.refSeqKg.refseq minCheck=0.60
     $ccdsDb,!hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.35
     $gbd,!rn3.mrnaRefseq.refseq minCheck=0.25
     rn3.mrnaRefseq.refseq minCheck=0.03
     $gbd,!bosTau2,!bosTau3,!canFam1,!canFam2,!droSim1,!droYak1,!droYak2,!panTro1,!rheMac2,!dp2,!dp3.mrnaOrientInfo.name minCheck=0.0
 # The rule above should only apply to mrnaOrientInfo entries from refSeq (not
 # the regular genBank mRNAs).  The minCheck=0.0 preserves table relationshps.
     $gbd.refFlat.name
     $gbd.refGene.name
     $gbd.refMrna.name
     $gbd.refSeqAli.qName
     $gbd.refSeqSummary.mrnaAcc minCheck=0.99
     dm1.bdgpToRefSeq.value minCheck=0.94
     $dm,!dm1.flyBaseToRefSeq.value minCheck=0.96
     $mm.mrnaRefseq.mrna minCheck=0.03
     $mm.spMrna.mrnaID minCheck=0.40
     $mm.dupSpMrna.mrnaID minCheck=0.60
     $mm,!mm8,!mm9.dupSpMrna.dupMrnaID minCheck=0.20
     mm9.dupSpMrna.dupMrnaID minCheck=0.19
     mm8.dupSpMrna.dupMrnaID minCheck=0.19
     hg17.mrnaRefseq.mrna minCheck=0.10
     hg17.spMrna.mrnaID minCheck=0.49
     hg17.dupSpMrna.mrnaID minCheck=0.40
     hg17.dupSpMrna.dupMrnaID minCheck=0.20
     hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.37
 
 identifier xenoRefSeqId typeOf=xenoMrnaAccession
 "Other Species RefSeq mRNA accession"
     $xrg.xenoRefGene.name dupeOk
     $xrg.xenoRefFlat.name full
     $xrg.xenoRefSeqAli.qName full
     $xrg.xenoRefFlat.name full
 
 identifier knownToRefSeqId typeOf=mrnaAccession
 "RefSeq mRNA accession in knownToRefSeq table"
     $kgDb.knownToRefSeq.value dupeOk
     mm7.geneNetworkId.id minCheck=0.80
     mm8.geneNetworkId.id minCheck=0.80
     mm9.geneNetworkId.id minCheck=0.80
     rn3.geneNetworkId.id minCheck=0.40
 
 identifier knownGeneId dependency
 "Known Gene ID - the genbank accession of the representative mRNA"
     $kgDb.knownGene.name dupeOk
     $kgDb.bioCycPathway.kgID
     $kgDb.ceBlastTab.query
     $kgDb.hgBlastTab.query
     $kgDb.dmBlastTab.query
     $kgDb.drBlastTab.query
     $kgDb.mmBlastTab.query
     $kgDb.rnBlastTab.query
     $kgDb.scBlastTab.query
     $kgDb,!rn3.dupSpMrna.mrnaID
     rn3.dupSpMrna.mrnaID minCheck=0.90
 #   $kgDb,!hg16,!hg17.pseudoGeneLink.kgName exclude=noKg
 #   hg16,hg17.pseudoGeneLink.kgName minCheck=0.18 exclude=noKg
     $kgDb.foldUtr3.name
     $kgDb.foldUtr5.name
     $hg.gnfU95Distance.query
     $hg.gnfU95Distance.target
     $kgDb.gnfAtlas2Distance.query
     $kgDb.gnfAtlas2Distance.target
     $kgDb.affyGnfU74ADistance.query
     $kgDb.affyGnfU74ADistance.target
     $kgDb.affyGnfU74BDistance.query
     $kgDb.affyGnfU74BDistance.target
     $kgDb.affyGnfU74CDistance.query
     $kgDb.affyGnfU74CDistance.target
     $kgDb.mouseLandscapeDistance.query minCheck=0.94
     $kgDb.mouseLandscapeDistance.target minCheck=0.94
     $hg.gladHumESDistance.query
     $hg.gladHumESDistance.target
     $kgDb.keggPathway.kgID
     $kgDb.kgAlias.kgID
     $kgDb.kgProtAlias.kgID
     $kgDb.kgSpAlias.kgID
     $kgDb.kgXref.kgID full
     $kgDb.kgTxInfo.name full
     $kgDb.knownBlastTab.query
     $kgDb.knownBlastTab.target
     $kgDb.knownCanonical.transcript
     $kgDb.knownGeneMrna.name full
     $kgDb,!hg18,!mm9.knownGeneLink.name
     $kgDb.knownIsoforms.transcript full
     $kgDb.knownToAllenBrain.name
     $kgDb.knownToCdsSnp.name
     $kgDb.knownToEnsembl.name
     $kgDb.knownToGnf1h.name
     $kgDb.knownToGnfAtlas2.name
     $kgDb.knownToHInv.name
     $kgDb.knownToHprd.name
     $kgDb.knownToLocusLink.name
     $kgDb.knownToPfam.name
     $kgDb.knownToRefSeq.name
     $kgDb.knownToSuper.gene
     $kgDb.knownToTreefam.name
     $kgDb.knownToU133.name
     $kgDb.knownToU133Plus2.name
     $kgDb.knownToU95.name
     $kgDb.knownToVisiGene.name
     $kgDb.refSeqKg.kgId minCheck=0.50
     $kgDb.rankProp.query
     $kgDb.rankProp.target
     $kgDb.pPsiBlast.kgId1
     $kgDb.pPsiBlast.kgId2
     $ccdsDb.ccdsKgMap.geneId
     $kgDb2.knownGenePep.name full
     $kgDb3.knownGenePep.name
     $kgDb3.knownCanonical.protein exclude=
     $kgDb3.kgProtMap2.qName
     $hg.humanHprdP2P.query
     $hg.humanHprdP2P.target
     $hg.humanVidalP2P.query
     $hg.humanVidalP2P.target
     $hg.humanWankerP2P.query
     $hg.humanWankerP2P.target
     $kgDb.kgColor.kgID full
     $kgDb.kg2ToKg3.newId minCheck=0.5 exclude=
     $kgDb.kg3ToKg4.oldId minCheck=0.5
     $kgDb.kg3ToKg4.newId exclude=
     $kgDb.kgTargetAli.qName full
 
 identifier knownGeneOld3Id dependency
 "Previous UCSC Gene build"
     $kgDb.knownGeneOld3.name
     $kgDb.kg3ToKg4.oldId full
 
 identifier knownGeneOld2Id dependency
 "Old knownGene (KGII) and kgXref tables kept after KGIII implementation"
     $kgDb.knownGeneOld2.name dupeOk
     $kgDb.kgXrefOld2.kgID full
 
 identifier knownToHprdName
 "Dependencies on knownToHprd.name"
     $kgDb.knownToHprd.name dupeOk
     $kgDb.humanHprdP2P.target
 
 identifier pfamDesc
 "pfam description for each accession"
     $kgDb.pfamDesc.pfamAC
     $kgDb.knownToPfam.value
 
 identifier scopName
 "scop Domain Names"
     $kgDb.ucscScop.domainName dupeOk
     $kgDb.scopDesc.name full minCheck=0.60
 
 identifier scopToUcscId
 "scop Domains to UCSC Id"
     $kgDb.kgProtMap2.qName
     $kgDb,!hg18.ucscScop.ucscId minCheck=0.99
     hg18.ucscScop.ucscId minCheck=0.70
 
 identifier knownIsoformCluster
 "ID of a cluster of overlapping known genes"
     $kgDb.knownCanonical.clusterId
     $kgDb.knownIsoforms.clusterId full
 
 # known relationship for both KG2 and KG3, but doesn't work across dbs.
 identifier knownXref
 "Swissprot IDs"
     $kgDb.kgXref.spID  dupeOk
     proteome.spXref2.accession
     proteome.hgnc.uniProt
 
 identifier ccdsGeneId
 "CCDS Gene ID"
     $ccdsDb.ccdsGene.name dupeOk
     $ccdsDb.ccdsInfo.ccds full
     $ccdsDb.ccdsKgMap.ccdsId
 
 identifier hugeId
 "HuGE Gene ID"
     $hg.kgXref.geneSymbol dupeOk
     $hg.huge.geneSymbol minCheck=0.89
 
 # Fields parsed out of a Genbank flat file, associated with mRNA records
 
 identifier gbCdnas
 "Connects gbCdnaInfo with mRNA/EST"
     $gbd.gbCdnaInfo.acc
     $gbd.all_mrna.qName
     $gbd.all_est.qName
     $gbd.refGene.name
     $gbd.xenoRefGene.name
     $gbd.gbMiscDiff.acc
     $gbd.refSeqAli.qName
     $gbd.xenoRefSeqAli.qName
     $gbd.xenoMrna.qName
     $gbd.xenoEst.qName
     $gbd.gbWarn.acc
 
 identifier genBankAuthor
 "Connects genBank mRNA/EST and its author"
     $gbd.author.id
     $gbd.gbCdnaInfo.author
 
 identifier genBankCds
 "Connects genBank mRNA/EST and its coding region (CDS)"
     $gbd.cds.id
     $gbd.gbCdnaInfo.cds
 
 identifier genBankCell
 "Connects genBank mRNA/EST and the cell type it came from"
     $gbd.cell.id
     $gbd.gbCdnaInfo.cell
 
 identifier genBankDevelopment
 "Connects genBank mRNA/EST and development stage of the organism it came from"
     $gbd.development.id
     $gbd.gbCdnaInfo.development
 
 identifier genBankDescription
 "Connects genBank mRNA/EST and descriptive text"
     $gbd.description.id
     $gbd.gbCdnaInfo.description
 
 identifier genBankGeneName
 "Connects genBank mRNA/EST and gene name"
     $gbd.geneName.id
     $gbd.gbCdnaInfo.geneName
     $gbd.refLink.geneName
 
 identifier genBankKeyword
 "Connects genBank mRNA/EST and keyword"
     $gbd.keyword.id
     $gbd.gbCdnaInfo.keyword
 
 identifier genBankLibrary
 "Connects genBank mRNA/EST and cDNA library"
     $gbd.library.id
     $gbd.gbCdnaInfo.library
     $gbd,!hg17.altGraphX.mrnaLibs comma
     hg17.altGraphX.mrnaLibs comma minCheck=0.99
 
 identifier genBankMrnaClone
 "Connects genBank mRNA/EST and cDNA clone name"
     $gbd.mrnaClone.id
     $gbd.gbCdnaInfo.mrnaClone
 
 identifier genBankOrganism
 "Connects genBank mRNA/EST and organism it came from"
     $gbd.organism.id
     $gbd.gbCdnaInfo.organism
 
 identifier genBankProductName
 "Connects genBank mRNA/EST and protein product name"
     $gbd.productName.id
     $gbd.gbCdnaInfo.productName
     $gbd.refLink.prodName
 
 identifier genBankSex
 "Connects genBank mRNA/EST and sex mRNA came from"
     $gbd.sex.id
     $gbd.gbCdnaInfo.sex
 
 identifier genBankSource
 "Connects genBank mRNA/EST and source of mRNA"
     $gbd.source.id
     $gbd.gbCdnaInfo.source
 
 identifier genBankTissue
 "Connects genBank mRNA/EST and tissue mRNA isolated from"
     $gbd.tissue.id
     $gbd.gbCdnaInfo.tissue
     $gbd.altGraphX.mrnaTissues comma
 
 # Some misc clone-oriented identifiers
 
 identifier bacCloneName fuzzy
 "A Roswell Park, Cal Tech or other clone ID"
     $gbd.fishClones.name
     $gbd.bacEndPairs.name
 
 identifier imageCloneId external=IMAGEConsortium fuzzy
 "An image cDNA clone ID"
     $gbd.imageClone.imageId
 
 identifier humanFosmidId
 "Human Fosmid (~50kb genomic sequence) clone"
     $hg.fosEndPairs.name dupeOk
 
 identifier humanFosmidEndId
 "Identifier of read from one end of human formid."
     $hg.all_fosends.qName dupeOk
     $hg.fosEndPairs.lfNames comma
 
 ## TYPED TO HERE %%%
 # Mapping Stuff, STS, etc.
 
 identifier dbStsId external=dbSts fuzzy
 "NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
     $hg.all_sts_primer.qName chopBefore=dbSTS_
     $gbd.all_sts_seq.qName
     $gbd.stsInfo2.dbSTSid
 
 identifier ucscStsId
 "UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $gbd.stsInfo2.identNo
     $gbd.stsAlias.identNo
     $gbd.stsMap.identNo
 
 identifier ucscMouseStsId
 "UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $mm.stsInfoMouseNew.identNo
     $mm.stsAlias.identNo
     $mm.all_sts_primer.qName chopAfter=_ minCheck=0.99
     $mm.stsMapMouseNew.identNo
 
 identifier stsName fuzzy
 "STS (Sequenced Tagged Site, aka mapping sequence) Name"
     $hg.fishClones.stsNames comma
     $gbd.stsInfo2.otherNames comma
     $mm.stsInfoMouseNew.alias separator=;
 
 identifier stsTrueName typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $gbd,!hg16.stsInfo2.name
     $gbd.stsAlias.trueName
     $gbd.stsMap.name
 
 identifier stsTrueNameHg16 typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16"
     hg16.stsInfo2.name dupeOk
     hg16.stsAlias.trueName
     hg16.stsMap.name
 
 identifier mouseStsTrueName typeOf=stsName
 "Mouse STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $mm.stsInfoMouseNew.name
     $mm.stsAlias.trueName minCheck=0.99
     $mm,!mm7,!mm8,!mm9.all_sts_primer.qName chopBefore=_ minCheck=0.99
     mm7,mm8,mm9.all_sts_primer.qName chopBefore=_ minCheck=0.98
     $mm.stsMapMouseNew.name
     $mm.jaxQTL3.marker exclude= minCheck=0.99
     $mm.jaxQTL3.flank1 exclude= minCheck=0.95
     $mm.jaxQTL3.flank2 exclude= minCheck=0.99
 
 identifier ratStsTrueName typeOf=stsName
 "Rat STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $rn.stsInfoRat.name dupeOk
     $rn,!rn3.stsMapRat.name
     rn3.stsMapRat.name minCheck=0.99
 
 identifier rhMapName
 "Zebrafish RH (Radiation Hybrid) Map Name"
     $danRer.rhMap.qName dupeOk
     $danRer.rhMapZfishInfo.name minCheck=0.90 unique
 
 identifier igtcName
 "IGTC (genetrap.org) sequence name"
     $mm.seq.acc
     $mm.igtc.qName
 
 identifier kompName
 "KOMP (knockoutmouse.org) gene name"
     $mm.komp.name dupeOk
     $mm.kompExtra.name
 
 identifier ikmcName
 "IKMC (knockoutmouse.org) gene name"
     $mm.ikmc.name dupeOk
     $mm.ikmcExtra.name
 
 
 # "Biological" Gene Names
 
 identifier hugoName external=HUGO fuzzy
 "International Human Gene Identifier"
     $hg.refLink.name
     $hg.atlasOncoGene.locusSymbol
     $hg.kgAlias.alias
     $hg.kgSpAlias.alias minCheck=0.1
     $hg.kgXref.geneSymbol
     $hg.refFlat.geneName
     $hg.jaxOrtholog.humanSymbol
     $hg.omimMorbidMap.geneSymbols
     visiGene.gene.name
 
 identifier kgGeneSymbol
 "UCSC Genes Gene Symbol"
     $hg.kgXref.geneSymbol dupeOk
     $hg.omimGeneMap.geneSymbol comma minCheck=0.40
     $hg.omimMorbidMap.geneSymbols comma minCheck=0.25
 
 identifier mouseGeneName fuzzy
 "Mouse gene name from Jackson Labs/RefSeq"
     $hg.jaxOrtholog.mouseSymbol
     $mm.refLink.name
     visiGene.gene.name
 
 # Model Organism Database Identifiers
 
 identifier jaxMgiId
 "Jackson Labs Mouse Gene Identifier"
     $hg.jaxOrtholog.mgiId
 
 identifier wormBaseIsoformCluster
 "Overlapping (after splicing) WormBase transcripts"
     $ce.sangerCanonical.clusterId
     $ce.sangerIsoforms.clusterId full
 
 identifier wormBaseId external=WormBase dependency
 "WormBase (C. elegans) ORF ID"
     $ce.sangerGene.name
     $gbd,!rn3.ceBlastTab.target minCheck=0.90
     $ce.kimExpDistance.query minCheck=0.68
     $ce.kimExpDistance.target minCheck=0.66
     $ce.orfToGene.name
     $ce.sangerBlastTab.query
     $ce.sangerBlastTab.target
     $ce.sangerCanonical.transcript
     $ce.sangerIsoforms.transcript
     $ce.sangerLinks.orfName minCheck=0.96
     $ce.sangerPep.name minCheck=0.96
     $ce.sangerToKim.name
     $ce.sangerToPfam.name
     $ce.sangerToRefSeq.name
     $ce.dmBlastTab.query
     $ce,!ce2.drBlastTab.query
     $ce.hgBlastTab.query
     $ce,!ce2.mmBlastTab.query
     $ce,!ce2.rnBlastTab.query
     $ce.scBlastTab.query
     $ce.sangerGeneToWBGeneID.sangerGene
 
 identifier wormBasePseudoGene external=WormBase dependency
 "WormBase (C. elegans) pseudo genes"
     $ce.sangerPseudoGene.name
 
 identifier wormBaseRnaGene external=WormBase dependency
 "WormBase (C. elegans) RNA genes"
     $ce.sangerRnaGene.name
 
 identifier flyBaseRefId
 "FlyBase (Drosophila) Reference (Literature)"
     $dm.fbRef.id
     $dm.fbPhenotype.fbRef
 
 identifier flyBaseAlleleId
 "FlyBase (Drosophila) Allele ID"
     $dm.fbAllele.id
     $dm.fbPhenotype.fbAllele exclude=0
 
 identifier flyBaseGeneId external=FlyBase
 "FlyBase (Drosophila) Gene ID"
     $dm.fbGene.geneId
     $dm.bdgpExprLink.flyBaseId minCheck=0.95
     dm1.bdgpGeneInfo.flyBaseId minCheck=0.95
     dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20
     dm1.bdgpSwissProt.flyBaseId minCheck=0.95
     $dm.fbAllele.geneId
     $dm.fbPhenotype.geneId
     $dm.fbSynonym.geneId
     $dm.fbTranscript.geneId minCheck=0.95
     dm1.flyBaseSwissProt.flyBaseId minCheck=0.95
     $dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90
     $dm,!dm1.pscreen.geneIds comma minCheck=0.95
     $gbd,!hg17,!hg18,!danRer3,!mm7,!mm8,!mm9,!rn3,!rn4,!ce2,!ce6,!sacCer1,!sacCer2.dmBlastTab.target minCheck=0.90
 
 identifier bdgpIsoformCluster
 "Overlapping (after splicing) BDGP Drosophila transcripts"
     dm1.bdgpCanonical.clusterId
     dm1.bdgpIsoforms.clusterId full
 
 identifier bdgpGeneId external=BDGP
 "Berkeley Drosophila Genome Project Gene ID"
     dm1.bdgpGeneInfo.bdgpName
     dm1.bdgpExprLink.bdgpName minCheck=0.85
     dm1.bdgpToCanonical.value
 
 identifier bdgpTranscriptId external=BDGP dependency
 "Berkeley Drosophila Genome Project Transcript ID"
     dm1.bdgpGene.name
     dm1.arbExpDistance.query
     dm1.arbExpDistance.target
     dm1.bdgpBlastTab.query
     dm1.bdgpBlastTab.target
     dm1.bdgpCanonical.transcript
     dm1.bdgpIsoforms.transcript
     dm1.bdgpGenePep.name
     dm1.bdgpSwissProt.bdgpName
     dm1.bdgpToCanonical.name
     dm1.bdgpToLocusLink.name minCheck=0.80
     dm1.bdgpToPfam.name
     dm1.bdgpToRefSeq.name minCheck=0.97
     dm1.ceBlastTab.query
     dm1.drBlastTab.query
     dm1.hgBlastTab.query
     dm1.mmBlastTab.query
     dm1.rnBlastTab.query
     dm1.scBlastTab.query
     dm1.fbTranscript.transcriptId minCheck=0.95
     dm1.hgBlastTab.query
     dm1.blastFBPep00.name
     dm1.pscreen.geneIds comma minCheck=0.90
 
 identifier bdgpNonCodingId external=BDGP
 "Berkeley Drosophila Genome Project Noncoding Gene ID"
     dm1.bdgpNonCoding.name chopAfter=- dupeOk
     dm1.bdgpNonCodingInfo.bdgpName minCheck=0.89
 
 identifier flyBase2004IdDm external=FlyBase
 "FlyBase Xref as of 2004 for dm"
     $dm.flyBase2004Xref.name
     $dm,!dm1.flyBaseGene.name minCheck=0.99
     $dm,!dm1.flyBasePep.name
     $dm,!dm1.flyBaseNoncoding.name minCheck=0.90
     $dm,!dm1.arbExpDistance.query
     $dm,!dm1.arbExpDistance.target
     $dm,!dm1.ceBlastTab.query
     $dm,!dm1.drBlastTab.query minCheck=0.97
     $dm,!dm1.hgBlastTab.query minCheck=0.96
     $dm,!dm1.mmBlastTab.query
     $dm,!dm1.rnBlastTab.query
     $dm,!dm1.scBlastTab.query
     $dm,!dm1.flyBaseBlastTab.query
     $dm,!dm1.flyBaseBlastTab.target
     $dm,!dm1.flyBaseCanonical.transcript
     $dm,!dm1.flyBaseIsoforms.transcript
     $dm,!dm1.flyBaseToRefSeq.name
     $dm,!dm1.flyBaseToUniProt.name
     $dm,!dm1.flyBaseToPfam.name
     $dm,!dm1.flyBaseToCG.name
     $dm,!dm1.flyBaseToDescription.name
     $dm,!dm1.flyP2P.query minCheck=0.98
     $dm,!dm1.flyP2P.target minCheck=0.98
     hg17,hg18,danRer3,mm7,mm8,mm9,rn3,rn4,ce2,sacCer1,sacCer2.dmBlastTab.target minCheck=0.90
 
 identifier flyBase2004IdDp external=FlyBase
 "FlyBase Xref as of 2004 for dp3"
     dp3.flyBase2004Xref.name
     dp3.flyBaseGene.name
 
 identifier sgdIsoformCluster
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
 
 identifier sgdId external=SGD
 "Sacchromyces Genome Database ID - Coding or other"
 
 identifier sgdCodingId typeOf=sgdId dependency
 "Sacchromyces Genome Database ID"
     $sacCer.sgdGene.name
     $gbd.scBlastTab.target minCheck=0.90
     $sacCer.sgdBlastTab.query
     $sacCer.sgdBlastTab.target
     $sacCer.ceBlastTab.query
     $sacCer.dmBlastTab.query
     $sacCer,!sacCer1.drBlastTab.query
     $sacCer.hgBlastTab.query minCheck=0.999
     $sacCer.mmBlastTab.query
     $sacCer.rnBlastTab.query
     sacCer2.knownBlastTab.query
     $sacCer.choExpDistance.target minCheck=0.60
     $sacCer.choExpDistance.query minCheck=0.60
     $sacCer.sgdCanonical.transcript
     $sacCer.sgdDescription.name
     $sacCer.sgdIsoforms.transcript
     $sacCer.sgdAbundance.name minCheck=0.95
     $sacCer.sgdLocalization.name minCheck=0.95
     $sacCer.sgdPep.name
     $sacCer.sgdToSwissProt.name minCheck=0.85
     $sacCer.sgdToName.name minCheck=0.86
     $sacCer.esRegGeneToModule.gene minCheck=0.94
     $sacCer.esRegGeneToMotif.gene minCheck=0.97
     $sacCer.esRegUpstreamRegion.name minCheck=0.96
     $sacCer.sgdToPfam.name minCheck=0.55
 
 identifier sgdNoncodingId typeOf=sgdId
 "Sacchromyces Genome Database Noncoding/Dubious feature ID"
     $sacCer.sgdOther.name dupeOk
     $sacCer.sgdOtherDescription.name
 
 # RGD Family Identifiers
 
 identifier rgdGeneId external=RGD
 "RGD gene ID"
     $rn.rgdGeneLink.refSeq
     $rn.rgdGene.name
 
 identifier rgdEstId external=RGD
 "RGD EST ID"
     $rn.rgdEstLink.name
     $rn.rgdEst.qName
 
 identifier rgdQtlId external=RGD
 "RGD QTL ID"
     $rn,$hg.rgdQtl.name
     $rn,$hg.rgdQtlLink.name minCheck=0.89
 
 identifier rgdRatQtlId external=RGD
 "RGD Rat QTL ID mapped to other organism"
     $hg.rgdRatQtl.name dupeOk
     $hg.rgdRatQtlLink.name minCheck=0.89
 
 identifier rgdSslpId external=RGD
 "RGD SSLP ID"
     $rn.rgdSslp.name
     $rn.rgdSslpLink.name
 
 
 # The Ensembl Gmish
 
 identifier ensemblGeneId external=Ensembl
 "Ensemble Gene ID"
     $gbd.ensTranscript.gene_name dupeOk
     $gbd.ensGtp.gene chopAfter=.
     $gbd.ensGeneXref.gene_name
 
 identifier ensemblGeneId3 external=Ensembl
 "Ensemble Gene ID"
     $gbd.ensemblXref3.gene dupeOk
 
 identifier ensemblProteinId external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensTranscript.translation_name dupeOk
     $gbd.ensGtp.protein chopAfter=.
     $gbd.sfAssign.seqID minCheck=0.01
 
 identifier ensemblProteinId3 external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensemblXref3.protein dupeOk
     $gbd.sfAssign.seqID minCheck=0.01
 
 identifier ensemblTranscriptId external=Ensembl dependency
 "Ensembl Transcript ID"
     $gbd,!ce6,!felCat3.ensGene.name chopAfter=.
     $gbd.ensGeneXref.transcript_name chopAfter=. minCheck=0.95
     $gbd.ensGtp.transcript chopAfter=. minCheck=0.94
     $gbd.ensPep.name chopAfter=. minCheck=0.96
     $gbd.ensTranscript.transcript_name chopAfter=. minCheck=0.20
     $gbd.ensInfo.name minCheck=0.9
     $kgDb.knownToEnsembl.value chopAfter=.
     $ccdsDb.ccdsInfo.mrnaAcc minCheck=0.30
     $danRer.ensZfishBlastTab.query
     $danRer.ensZfishBlastTab.target
     $danRer.ceBlastTab.query
     $danRer.dmBlastTab.query
     $danRer.hgBlastTab.query
     $danRer.mmBlastTab.query
     $danRer.rnBlastTab.query
     $danRer.scBlastTab.query
 
 identifier ensemblTranscriptIdCe external=Ensembl dependency
 "Ensembl Transcript ID for C. elegans"
     $ce.ensGene.name chopAfter=. dupeOk
     $ce.ensGtp.transcript chopAfter=. minCheck=0.98
     $ce.ensPep.name chopAfter=. minCheck=0.98
 
 identifier ensemblTranscriptIdFelCat external=Ensembl dependency
 "Ensembl Transcript ID for felCat"
     $felCat.ensGene.name dupeOk
     $felCat.ensGtp.transcript minCheck=0.99
     $felCat.ensPep.name minCheck=0.99
 
 # UCSC to Ensembl chrom name translation
 identifier ensemblLinkId external=Ensembl dependency
 "Ensembl Links from hgTracks"
     hg18,hg19.chromInfo.chrom
     hg18,hg19.ucscToEnsembl.ucsc
 
 identifier ucscToEnsembl external=Ensembl dependency
 "UCSC to Ensembl chrom name translation"
     hg18,hg19.ucscToEnsembl.ensembl
     hg18,hg19.ensemblLift.chrom
 
 # Ensembl EST
 
 identifier ensemblEstTranscriptId external=Ensembl dependency
 "Ensembl EST Transcript ID"
     $gbd.ensEstGene.name chopAfter=.
     $gbd.ensEstGtp.transcript chopAfter=.
     $gbd.ensEstPep.name chopAfter=.
 
 identifier gazeGeneId external=Genoscope
 "GAZE Gene ID"
     $gbd.gaze.name
     $gbd.gazePep.name
 
 # H-Invitational Database Identifiers
 
 identifier hinvTranscriptId external=H-INV dependency
 "H-Invitational Transcript ID"
     $hg.HInv.geneId
     $hg.knownToHInv.value
     $hg.HInvGeneMrna.qName
 
 # Protein Family Identifiers
 
 identifier pfamId external=Pfam fuzzy
 "Pfam (Protein Family) ID"
     $kgDb.knownToPfam.value
     dm1.bdgpToPfam.value
 
 identifier superfamilyId external=SCOP
 "Protein SCOP/Superfamily ID"
     hgFixed.scopDes.sunid
     $gbd.sfDes.id	# This table is redundant with hgFixed.scopDes
     $gbd.sfAssign.sfID
 
 # Pathway Identifiers
 
 identifier bioCycMapId external=BioCyc
 "BioCyc Pathway Map ID"
     $gbd.bioCycMapDesc.mapID
     $gbd.bioCycPathway.mapID minCheck=0.78
 
 identifier keggMapId external=KEGG
 "KEGG Pathway Map ID"
     $gbd.keggMapDesc.mapID dupeOk
     $gbd.keggPathway.mapID
 
 identifier cgapId
 "NCI Cancer Genome Annotation Project Gene ID"
     $gbd.cgapAlias.cgapID dupeOk
     $gbd.cgapBiocPathway.cgapID
 
 identifier cgapMapId
 "NCI Cancer Genome Annotation Project Map ID"
     $gbd.cgapBiocDesc.mapID
     $gbd.cgapBiocPathway.mapID
 
 identifier cgapAlias
 "NCI Cancer Genome Annotation Project Alias"
     $gbd.cgapAlias.alias dupeOk
     $gbd,!hg16,!hg18,!hg19.knownGene.name minCheck=0.50
     hg16.knownGene.name minCheck=0.05
     hg18,hg19.kgXref.geneSymbol minCheck=0.85
 
 # SNP (Simple Nucleotide Polymorphism) Stuff
 
 identifier affySnp10KId external=Affymetrix
 "Affymetrix 10K SNP Identifier"
     hgFixed.affy10KDetails.affyId
     $hg.affy10K.name
 
 identifier affySnp120KId external=Affymetrix
 "Affymetrix 120K SNP Identifier"
     hgFixed.affy120KDetails.affyId
     $hg.affy120K.name
 
 identifier dbSnpId external=dbSNP fuzzy
 "NCBI dbSNP ID"
     $kgDb.knownToCdsSnp.value
 
 identifier dbSnpHgId typeOf=dbSnpId
 "Human dbSNP ID"
     hgFixed.dbSnpRsHg.rsId
     $hg.snpMap.name minCheck=0.90
     hgFixed.affy10KDetails.rsId minCheck=0.94
     hgFixed.affy120KDetails.rsId minCheck=0.97
 
 identifier dbSnpMmId typeOf=dbSnpId
 "Mouse dbSNP ID"
     hgFixed.dbSnpRsMm.rsId
     $mm.snpMap.name
 
 identifier dbSnpRnId typeOf=dbSnpId
 "Rat dbSNP ID"
     hgFixed.dbSnpRsRn.rsId
     $rn.snpMap.name
 
 identifier hapmapSnpId
 "HapMap SNPs"
     $hg.hapmapAllelesSummary.name
     $hg.hapmapSnpsCEU.name
     $hg.hapmapSnpsCHB.name
     $hg.hapmapSnpsJPT.name
     $hg.hapmapSnpsYRI.name
     $hg.hapmapAllelesChimp.name
     $hg.hapmapAllelesMacaque.name
     $hg,!hg17.hapmapLdCeu.name unique
     $hg,!hg17.hapmapLdChb.name unique
     $hg,!hg17.hapmapLdChbJpt.name unique
     $hg,!hg17.hapmapLdJpt.name unique
     $hg,!hg17.hapmapLdYri.name unique
     $hg,!hg17.hapmapLdPhCeu.name unique
     $hg,!hg17.hapmapLdPhChbJpt.name unique
     $hg,!hg17.hapmapLdPhYri.name unique
 
 identifier snpAnnotations125
 "SNP annotations"
     $snpDb125.snp125.name dupeOk
     $snpDb125.snp125Exceptions.name
     $snpDb125.snpSeq.acc minCheck=.8
     hg17.snpArrayAffy10.rsId minCheck=0.98
     hg17.snpArrayAffy10v2.rsId minCheck=0.98
     hg17.snpArrayAffy250Nsp.rsId minCheck=0.98
     hg17.snpArrayAffy250Sty.rsId minCheck=0.98
     hg17.snpArrayAffy50HindIII.rsId minCheck=0.98
     hg17.snpArrayAffy50XbaI.rsId minCheck=0.98
     hg17.snpArrayIllumina300.name
 
 identifier snpAnnotations126
 "SNP annotations"
     $snpDb126.snp126.name dupeOk
     $snpDb126.snp126Exceptions.name
     $snpDb126.snpSeq.acc minCheck=.8
     hg18.snp126ortho.name
     hg18.snp126orthoPanTro2RheMac2.name
     hg18.snpArrayAffy5.rsId minCheck=0.98
     hg18.snpArrayAffy6.rsId minCheck=0.98
     hg18.snpArrayAffy250Nsp.rsId
     hg18.snpArrayAffy250Sty.rsId
     hg18.snpArrayIllumina300.name
     hg18.snpArrayIllumina550.name
     hg18.snpArrayIllumina650.name
 
 identifier snpAnnotations127
 "SNP annotations"
     $snpDb127.snp127.name dupeOk
     $snpDb127.snp127Exceptions.name
     $snpDb127.snpSeq.acc minCheck=.8
 
 identifier snpName128
 "dbSNP version 128 rs* identifiers"
     $gbd.snp128.name dupeOk
     $gbd.snp128Exceptions.name
     $gbd.snp128Seq.acc minCheck=.9
     hg18.snp128OrthoPanTro2RheMac2.name
 
 identifier snpExceptions128
 "Annotations of unusual conditions in dbSNP version 128"
     $gbd.snp128ExceptionDesc.exception
     $gbd.snp128Exceptions.exception
 
 identifier snpName129
 "dbSNP version 129 rs* identifiers"
     $gbd.snp129.name dupeOk
     $gbd.snp129Exceptions.name minCheck=.99
     $gbd.snp129Seq.acc minCheck=.99
     hg18.snp129OrthoPt2Pa2Rm2.name
     hg18.snpArrayIllumina1M.name minCheck=0.95
 
 identifier snpExceptions129
 "Annotations of unusual conditions in dbSNP version 129"
     $gbd.snp129ExceptionDesc.exception
     $gbd.snp129Exceptions.exception
 
 identifier snpName130
 "dbSNP version 130 rs* identifiers"
     $gbd.snp130.name dupeOk
     $gbd.snp130Exceptions.name minCheck=.999
     $gbd.snp130Seq.acc minCheck=.98
     $gbd.snp130CodingDbSnp.name minCheck=.99
     $hg.snp130OrthoPt2Pa2Rm2.name
     hg18.snpArrayIlluminaHuman660W_Quad.name minCheck=0.90
     hg18.snpArrayIlluminaHumanCytoSNP_12.name minCheck=0.95
     hg18.snpArrayIlluminaHumanOmni1_Quad.name minCheck=0.85
     # gwasCatalog SNPs were mapped to genome using snp130.  Move this and update trackDb
     # settings if we remap to new version:
     $hg.gwasCatalog.name
 
 identifier snpExceptions130
 "Annotations of unusual conditions in dbSNP version 130"
     $gbd.snp130ExceptionDesc.exception
     $gbd.snp130Exceptions.exception
 
 # Other NCBI Identifiers
 
 identifier locusLinkId external=LocusLink
 "NCBI LocusLink ID"
     $gbd.refLink.locusLinkId dupeOk
     $gbd.keggPathway.locusID minCheck=0.98
     $kgDb,!hg16,!mm8.knownToLocusLink.value minCheck=0.98
     hg16,mm8.knownToLocusLink.value minCheck=0.96
 
 identifier omimId external=OMIM
 "Online Mendelian Inheritance in Man (OMIM) ID"
     $gbd.refLink.omimId dupeOk exclude=0
 
 identifier omimGeneId
 "omimGene ID"
     $hg.omimGene.name dupeOk
     $hg.omimGeneMap.omimId minCheck=0.85
     $hg.refLink.omimId exclude=0 minCheck=0.98
     $hg.omimMorbidMap.omimId minCheck=0.75
     $hg.omimToKnownCanonical.omimId
 
 identifier unigeneId fuzzy
 "NCBI UniGene Cluster ID"
 #   hgFixed.sage.uni
     $hg.uniGene_2.name chopBefore=.
     $hg.sage.uni
 
 identifier unigeneId2 external=UniGene
 "NCBI UniGene Cluster ID for databases with UniGene seq table entry"
     $gbd.seq.acc
     $galGal.uniGene_gg.qName
     $danRer.uniGene_dr.qName
     $hg.uniGene_3.qName
 
 identifier kiddEichlerId external=EichlerLab
 "Clone accession used in Kidd..Eichler '08"
     $hg.kiddEichlerToNcbi.name
     $hg.kiddEichlerDiscAbc7.name chopAfter=, minCheck=0.80
     $hg.kiddEichlerDiscAbc8.name chopAfter=,
     $hg.kiddEichlerDiscAbc9.name chopAfter=,
     $hg.kiddEichlerDiscAbc10.name chopAfter=,
     $hg.kiddEichlerDiscAbc11.name chopAfter=,
     $hg.kiddEichlerDiscAbc12.name chopAfter=,
     $hg.kiddEichlerDiscAbc13.name chopAfter=,
     $hg.kiddEichlerDiscAbc14.name chopAfter=,
     hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.01
     $hg,!hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.005
 
 # BGI SNP Identifiers
 
 identifier bgiSnpId external=BGI
 "BGI SNP ID"
     $galGal.bgiSnp.name
     $galGal.bgiGeneSnp.snpName
 
 identifier bgiGeneId external=BGI
 "BGI Gene ID"
     $galGal.bgiGene.name
     $galGal.bgiGeneSnp.geneName minCheck=0.1
 
 # Other Identifiers
 
 identifier extFileId
 "External file ID"
     $gbd.extFile.id
     $gbd.seq.extFile
     rn3.multizHg15Mm3.extFile
     $sacCer.multizYeast.extFile
     $dm.a_gambiae_mypa.extFile
     $dm.d_pseudoobscura_mypa.extFile
     $dm.d_yakuba_mypa.extFile
     #$gbd.multiz4way.extFile
     #$gbd.multiz5way.extFile
     #$gbd.multiz6way.extFile
     #$gbd.multiz7way.extFile
     #$gbd.multiz8way.extFile
     #$gbd.multiz9way.extFile
     #$gbd.multiz10way.extFile
     #$gbd.multiz11way.extFile
     #$gbd.multiz12way.extFile
     #$gbd.multiz15way.extFile
     #$gbd.multiz17way.extFile
     #$gbd.multiz28way.extFile
 
 identifier gbExtFileId
 "External file ID for GenBank incremental update system"
     $gbd.gbExtFile.id
     $gbd.gbSeq.gbExtFile minCheck=0.85
 
 identifier encodeRegion
 "ENCODE (extensive analysis of 1% of genome) Region"
     hgFixed.encodeRegionInfo.name
     $hg.encodeRegions.name
 
 identifier blastDm1FBPepId
 "dm1 proteins"
      dm1.blastFBPep00.name
      $anoGam.blastDm1FB.qName
      $apiMel.blastDm1FB.qName
      $dp.blastDm1FB.qName
      $droYak.blastDm1FB.qName
      $droMult.blastDm1FB.qName
 
 identifier blastDm2FBPepId dependency
 "dm2 proteins"
      dm2.blastFBPep01.name
      $anoGam.blastDm2FB.qName
      $apiMel.blastDm2FB.qName
      $dp.blastDm2FB.qName
      $droYak.blastDm2FB.qName
      $droMult.blastDm2FB.qName
 
 identifier blastHg16KGPepId
 "hg16 proteins"
      hg16.blastKGPep00.name
      sacCer1.blastHg16KG.qName
      ce2.blastHg16KG.qName
      ci1.blastHg16KG.qName
      cioSav1.blastHg16KG.qName
      dm1.blastHg16KG.qName
      galGal2.blastHg16KG.qName
 
 identifier blastHg16KGRefId
 "hg16 ref 00"
      hg16.blastKGRef00.acc
      sacCer1.blastHg16KG.qName
      ce2.blastHg16KG.qName
      ci1.blastHg16KG.qName
      cioSav1.blastHg16KG.qName
      dm1.blastHg16KG.qName
      galGal2.blastHg16KG.qName
 
 # identifier blastHg17KGPep00Id  (knownGene upgraded)
 # "hg17 proteins 00"
 #      $hg.blastKGPep00.name
 #      $xenTro.blastHg17KG.qName
 
 identifier blastKG01
 "hg17 proteins 01"
      $gbd.blastHg17KG.qName dupeOk
      hg17.blastKGPep01.name
      hg17.blastKGRef01.acc
 
 identifier blastHg17KGPep01Id
 "hg17 peptides 01"
      hg17.blastKGPep01.name
      hg17.knownGene.name  minCheck=0.30
      hg17.blastKGRef01.acc full
      monDom1.blastHg17KG.qName
      fr1.blastHg17KG.qName
      tetNig1.blastHg17KG.qName
      xenTro1.blastHg17KG.qName
 
 identifier blastHg17KGRef01Id
 "hg17 ref 01"
      hg17.blastKGRef01.acc
      monDom1.blastHg17KG.qName
      fr1.blastHg17KG.qName
      tetNig1.blastHg17KG.qName
      xenTro1.blastHg17KG.qName
 
 identifier blastHg17KGPep02Id
 "hg17 peptides 02"
      hg17.blastKGPep02.name
      hg17.knownGene.name  minCheck=0.95
      hg17.blastKGRef02.acc full
      danRer3.blastHg17KG.qName
      bosTau2.blastHg17KG.qName
      canFam2.blastHg17KG.qName
      apiMel2.blastHg17KG.qName
      dm2.blastHg17KG.qName
 
 identifier blastHg17KGRef02Id
 "hg17 ref 02"
      hg17.blastKGRef02.acc
      danRer3.blastHg17KG.qName
      bosTau2.blastHg17KG.qName
      canFam2.blastHg17KG.qName
      apiMel2.blastHg17KG.qName
      dm2.blastHg17KG.qName
 
 identifier blastHg18KGPep04Id
 "hg18 peptides 04"
      hg18.blastKGPep04.name
      hg18.blastKGRef04.acc full
      hg18.knownGeneOld2.name  minCheck=0.95
      monDom4.blastHg18KG.qName
      galGal3.blastHg18KG.qName
      xenTro2.blastHg18KG.qName
      danRer4.blastHg18KG.qName
      danRer5.blastHg18KG.qName
      canFam2.blastHg18KG.qName
      felCat3.blastHg18KG.qName
      dm2.blastHg18KG.qName
      fr2.blastHg18KG.qName
      mm8.blastHg18KG.qName
      ce4.blastHg18KG.qName
      strPur1.blastHg18KG.qName
      strPur2.blastHg18KG.qName
      bosTau2.blastHg18KG.qName
      ornAna1.blastHg18KG.qName
      equCab1.blastHg18KG.qName
      equCab2.blastHg18KG.qName
      anoCar1.blastHg18KG.qName
      gasAcu1.blastHg18KG.qName
      bosTau3.blastHg18KG.qName
      bosTau4.blastHg18KG.qName
      tetNig1.blastHg18KG.qName
      tetNig2.blastHg18KG.qName
      taeGut1.blastHg18KG.qName
      oryLat2.blastHg18KG.qName
      sacCer2.blastHg18KG.qName
      mm9.blastHg18KG.qName
      aplCal1.blastHg18KG.qName
 
 identifier blastHg18KGRef04Id
 "hg18 ref 04"
      hg18.blastKGRef04.acc
      hg18.knownGeneOld2.name  minCheck=0.95
      monDom4.blastHg18KG.qName
      galGal3.blastHg18KG.qName
      xenTro2.blastHg18KG.qName
      danRer4.blastHg18KG.qName
      danRer5.blastHg18KG.qName
      canFam2.blastHg18KG.qName
      felCat3.blastHg18KG.qName
      dm2.blastHg18KG.qName
      fr2.blastHg18KG.qName
      mm8.blastHg18KG.qName
      ce4.blastHg18KG.qName
      strPur1.blastHg18KG.qName
      strPur2.blastHg18KG.qName
      bosTau2.blastHg18KG.qName
      ornAna1.blastHg18KG.qName
      equCab1.blastHg18KG.qName
      equCab2.blastHg18KG.qName
      anoCar1.blastHg18KG.qName
      gasAcu1.blastHg18KG.qName
      bosTau3.blastHg18KG.qName
      bosTau4.blastHg18KG.qName
      tetNig1.blastHg18KG.qName
      tetNig2.blastHg18KG.qName
      taeGut1.blastHg18KG.qName
      oryLat2.blastHg18KG.qName
      mm9.blastHg18KG.qName
      aplCal1.blastHg18KG.qName
 
 identifier blastHg17KGRef01SwissId
 "hg17 proteins swiss 01"
      $hg.blastKGRef01.extra1 dupeOk
      uniProt.displayId.acc
 
 identifier blastCe4SG01
 "ce4 proteins 01"
      $gbd.blastCe6SG.qName dupeOk
      ce4.blastSGPep01.name
      ce4.blastSGRef01.acc
 
 identifier blastCe6SG01
 "ce6 proteins 01"
      $gbd.blastCe6SG.qName dupeOk
      ce6.blastSGPep01.name
      ce6.blastSGRef01.acc
 
 identifier tfbsCons
 "transcription factor binding sites"
     $hg.tfbsConsSites.name dupeOk
     $hg.tfbsConsFactors.name
 
 identifier esRegModule
 "Eran Segal's collection of motifs that appear together in a regulatory module"
     $sacCer.esRegModuleToMotif.module dupeOk
     $sacCer.esRegGeneToModule.module full minCheck=0.99
 
 identifier esRegMotif
 "Eran Segal's motifs deduced from coregulated genes"
     $sacCer.esRegMotif.name
     $sacCer.esRegModuleToMotif.motif
     $sacCer.esRegGeneToMotif.name
 
 identifier yeastGrowthCondition
 "A growth condition for yeast cells"
     $sacCer.growthCondition.name
     $sacCer.transRegCodeCondition.growthCondition
 
 identifier transRegCode
 "Harbison, Gordon et al regulatory motifs and CHIP/CHIP data"
     $sacCer.transRegCodeCondition.name dupeOk
     $sacCer.transRegCodeMotif.name
     $sacCer.transRegCode.name
     $sacCer.transRegCodeProbe.tfList comma chopAfter=_
 
 identifier anoEstTclId
 "AnoEST TCL* ID -- joins track and aux. table of expressed IDs"
     $anoGam.anoEstTcl.name
     $anoGam.anoEstExpressed.name minCheck=0.30
 
 identifier allenBrainGene
 "KG link to Allen Brain Institute: Gene Expression in the Human Cortex"
     $gbd.kgXref.geneSymbol dupeOk
     $gbd.allenBrainGene.geneSymbol minCheck=0.95
 
 identifier allenBrainProbe
 "A probe used in the Allen Brain Atlas"
     $gbd.allenBrainUrl.name
     $gbd.allenBrainAli.qName
 
 identifier jaxRepTranscriptName external=MGI
 "Jackson Labs/MGI Allele name: representative transcript ID"
     $mm.jaxRepTranscript.name dupeOk
     $mm.jaxRepTranscriptAlias.name
 
 identifier jaxAlleleName external=MGI
 "Jackson Labs/MGI Allele name: concatenated representative transcript ID and allele ID"
     $mm.jaxAllele.name dupeOk
     $mm.jaxAlleleInfo.name
     $mm.jaxAllelePheno.allele
 
 identifier jaxPhenotypeName external=MGI
 "Jackson Labs/MGI Phenotype name: representative transcript ID"
     $mm.jaxPhenotype.name dupeOk
     $mm.jaxPhenotypeAlias.name
     mm8.jaxAllelePheno.transcript minCheck=0.9
 
 #links between the UniProt variants tables
 identifier protVarId
 "UniProt Variants track mutation identifier for attributes and links"
     hg18.protVar.id
     hg18.protVarAttr.id
     hg18.protVarLink.id
     hg18.protVarPos.name
 
 #links between UniProt and the variants tables
 identifier protVarIdUni
 "UniProt Variants track mutation identifier contains UniProt ID"
     uniProt.protein.acc
     hg18.protVar.name chopAfter=:
 
 #links between gv (the new Locus Variants) and related tables
 identifier gvId
 "Locus Variants track mutation identifier for attributes and links"
     hgFixed.gv.id
     hgFixed.gvLink.id minCheck=0.95
     hgFixed.gvAttr.id minCheck=0.98
     hgFixed.gvAttrLong.id
     hg17,hg18.gvPos.name
 
 identifier gvSrcId
 "Locus Variants track source ID"
     hgFixed.gvSrc.srcId
     hgFixed.gv.srcId
 
 #links between oreganno (regulatory annotation) and related tables
 identifier oregId
 "ORegAnno track identifier: links annotations to attributes and external links"
     $hg,$dm,$sacCer,$mm.oreganno.id
     $hg,$dm,$sacCer,$mm.oregannoAttr.id
     $hg,$dm,$sacCer,$mm.oregannoLink.id
 
 # retroposon track, dbRIP_* and polyGenotype table link
 identifier dbRIPNameAlu fuzzy
 "Retroposon, dbRIP database name id to polymorphism statistics link"
     hg17.dbRIPAlu.name unique
     hg17.polyGenotype.name
 
 identifier dbRIPNameL1 fuzzy
 "Retroposon, dbRIP database name id to polymorphism statistics link"
     hg17.dbRIPL1.name unique
     hg17.polyGenotype.name
 
 identifier dbRIPNameSVA fuzzy
 "Retroposon, dbRIP database name id to polymorphism statistics link"
     hg17.dbRIPSVA.name unique
     hg17.polyGenotype.name
 
 identifier jkgTranscriptId
 "Known genes 3 trancript identifier"
     $hg,$mm.jkgTxCdsRepick.name
     $hg,$mm.jkgTxInfo.name
     $hg,$mm.jkgTxCdsEvidence.name
 
 #links between omicia and links and attributes tables
 identifier omiciaHg18Id
 "Omicia track identifier: links annotations to attributes and external links"
     hg18.omicia.name
     hg18.omiciaAttr.id
     hg18.omiciaLink.id
 
 # transMap alignment (psl) tables and info tables; 1-to-1 mapping
 identifier transMapAlnInfoRefSeqId
 "transMap RefSeq per-genome alignments"
     $transMapDb.transMapAlnRefSeq.qName unique
     $transMapDb.transMapInfoRefSeq.mappedId unique full
 
 identifier transMapAlnInfoUcscGenesId
 "transMap UcscGenes per-genome alignments"
     $transMapDb.transMapAlnUcscGenes.qName unique
     $transMapDb.transMapInfoUcscGenes.mappedId unique full
 
 identifier transMapAlnInfoMRnaId
 "transMap MRna per-genome alignments"
     $transMapDb.transMapAlnMRna.qName unique
     $transMapDb.transMapInfoMRna.mappedId unique full
 
 identifier transMapAlnInfoSplicedEstId
 "transMap SplicedEst per-genome alignments"
     $transMapDb.transMapAlnSplicedEst.qName unique
     $transMapDb.transMapInfoSplicedEst.mappedId unique full
 
 # transMap info table and hgFixed src tables
 identifier transMapSrcInfoRefSeqId
 "transMap RefSeq pre-geneome alignment to source"
     hgFixed.transMapSrcRefSeq.id dupeOk
     $transMapDb.transMapInfoRefSeq.srcId
 
 identifier transMapSrcInfoUcscGenesId
 "transMap UcscGenes pre-geneome alignment to source"
     hgFixed.transMapSrcUcscGenes.id dupeOk
     $transMapDb.transMapInfoUcscGenes.srcId
 
 identifier transMapSrcInfoMRnaId
 "transMap MRna pre-geneome alignment to source"
     hgFixed.transMapSrcMRna.id dupeOk
     $transMapDb.transMapInfoMRna.srcId
 
 identifier transMapSrcInfoSplicedEstId
 "transMap SplicedEst pre-geneome alignment to source"
     hgFixed.transMapSrcSplicedEst.id dupeOk
     $transMapDb.transMapInfoSplicedEst.srcId
 
 # transMap aln table and hgFixed src tables
 identifier transMapSrcAlnUcscGenesId
 "transMap UcscGenes alignment to source"
     hgFixed.transMapSrcUcscGenes.id dupeOk chopAfter=-
     $transMapDb.transMapAlnUcscGenes.qName chopAfter=-
 
 identifier transMapSrcAlnMRnaId
 "transMap MRnas alignment to source"
     hgFixed.transMapSrcMRna.id dupeOk chopAfter=-
     $transMapDb.transMapAlnMRna.qName chopAfter=-
 
 identifier transMapSrcAlnRefSeqId
 "transMap RefSeqs alignment to source"
     hgFixed.transMapSrcRefSeq.id dupeOk chopAfter=-
     $transMapDb.transMapAlnRefSeq.qName chopAfter=-
 
 identifier transMapSrcAlnSplicedEstId
 "transMap SplicedEsts alignment to source"
     hgFixed.transMapSrcSplicedEst.id dupeOk chopAfter=-
     $transMapDb.transMapAlnSplicedEst.qName chopAfter=-
 
 # transMap source tables
 identifier transMapSrcRefSeqId
 "transMap RefSeq source gene and sequences "
     hgFixed.transMapSrcRefSeq.id dupeOk  chopAfter=-
     hgFixed.transMapSeqRefSeq.acc
     hgFixed.transMapGeneRefSeq.id
 
 identifier transMapSrcUcscGenesId
 "transMap UcscGenes source gene and sequences "
     hgFixed.transMapSrcUcscGenes.id dupeOk  chopAfter=-
     hgFixed.transMapSeqUcscGenes.acc
     hgFixed.transMapGeneUcscGenes.id
 
 identifier transMapSrcMRnaId
 "transMap MRna source gene and sequences "
     hgFixed.transMapSrcMRna.id dupeOk  chopAfter=-
     hgFixed.transMapSeqMRna.acc
     hgFixed.transMapGeneMRna.id
 
 identifier transMapSrcSplicedEstId
 "transMap SplicedEst source sequences "
     hgFixed.transMapSrcSplicedEst.id dupeOk  chopAfter=-
     hgFixed.transMapSeqSplicedEst.acc
 
 # transMap extFile tables
 identifier transMapExtFileRefSeqId
 "transMap RefSeq external file "
     hgFixed.transMapSeqRefSeq.extFile dupeOk
     hgFixed.transMapExtFileRefSeq.id unique
 
 identifier transMapExtFileUcscGenesId
 "transMap UcscGenes external file "
     hgFixed.transMapSeqUcscGenes.extFile dupeOk
     hgFixed.transMapExtFileUcscGenes.id unique
 
 identifier transMapExtFileMRnaId
 "transMap MRna external file "
     hgFixed.transMapSeqMRna.extFile dupeOk
     hgFixed.transMapExtFileMRna.id unique
 
 identifier transMapExtFileSplicedEstId
 "transMap SplicedEst external file "
     hgFixed.transMapSeqSplicedEst.extFile dupeOk
     hgFixed.transMapExtFileSplicedEst.id unique
 
 # transMap and knownGenes
 identifier transMapGeneUcscGenesId
 "UCSC Genes and transMapGene table"
     hgFixed.transMapGeneUcscGenes.id dupeOk
     $kgDb3.knownGene.name full
 
 identifier transMapAlnKnownGeneHgId
 "UCSC Genes and transMapAln table"
     mm9.knownGene.name
     hg18.transMapAlnUcscGenes.qName chopAfter=-
 
 identifier transMapAlnKnownGeneMmId
 "UCSC Genes and transMapAln table"
     hg19.knownGene.name
     mm9.transMapAlnUcscGenes.qName chopAfter=-
 
 # lsSnpPdb tables
 identifier lsSnpPdbProtId
 "lsSnpPdb table protId field"
     uniProt.extDbRef.acc dupeOk
     hg18.lsSnpPdb.protId
 
 identifier lsSnpPdbKgId
 "lsSnpPdb table protId field"
     hg18.kgXref.spID dupeOk
     hg18.lsSnpPdb.protId
 
 identifier lsSnpPdbPdbId
 "lsSnpPdb table pdbId field"
     uniProt.extDbRef.extAcc1 dupeOk
     hg18.lsSnpPdb.pdbId minCheck=0.99
 
 identifier lsSnpPdbSnpId
 "lsSnpPdb table snpId field"
     hg18.snp129.name dupeOk
     hg18.lsSnpPdb.snpId
 
 
 # Dependencies not already captured in identifiers
 
 dependency $hg.gladHumESDistance $hg.knownToGnfAtlas2 hgFixed.gladHumESRatio
 dependency $mm.mouseLandscapeDistance $mm.knownToXM hgFixed.mouseLandscape
 dependency $mm.affyGnfU74ADistance $mm.knownToU74  hgFixed.gnfMouseU74aMedianRatio
 dependency $mm.affyGnfU74BDistance $mm.knownToU74  hgFixed.gnfMouseU74bMedianRatio
 dependency $mm.affyGnfU74CDistance $mm.knownToU74  hgFixed.gnfMouseU74cMedianRatio
 dependency $hg.gnfU95Distance $hg.knownToU95 hgFixed.gnfHumanU95MedianRatio
 dependency $hg.gnfAtlas2Distance $hg.knownToGnfAtlas2 hgFixed.gnfHumanAtlas2MedianRatio
 dependency $ce.kimExpDistance hgFixed.kimWormLifeMedianRatio
 dependency dm1.arbExpDistance dm1.bdgpToCanonical hgFixed.arbFlyLifeMedianRatio
 dependency $dm,!dm1.arbExpDistance $dm,!dm1.flyBaseToCG hgFixed.arbFlyLifeMedianRatio
 dependency $sacCer.choExpDistance hgFixed.yeastChoCellCycle
 
 # FAN says: the following hg17 tables are an exception
 dependency $pbDb,!hg17.pbAnomLimit $pbDb.knownGenePep
 dependency $pbDb,!hg17.pbResAvgStd $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepCCntDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepExonCntDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepHydroDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepIPCntDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepMolWtDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepPi $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepPiDist $pbDb.knownGenePep
 dependency $pbDb,!hg17.pepResDist $pbDb.knownGenePep
 dependency $pbDb.pepMwAaDist $pbDb.knownGenePep
 dependency $pbDb.pbAaDistA $pbDb.knownGenePep
 dependency $pbDb.pbAaDistC $pbDb.knownGenePep
 dependency $pbDb.pbAaDistD $pbDb.knownGenePep
 dependency $pbDb.pbAaDistE $pbDb.knownGenePep
 dependency $pbDb.pbAaDistF $pbDb.knownGenePep
 dependency $pbDb.pbAaDistG $pbDb.knownGenePep
 dependency $pbDb.pbAaDistH $pbDb.knownGenePep
 dependency $pbDb.pbAaDistI $pbDb.knownGenePep
 dependency $pbDb.pbAaDistK $pbDb.knownGenePep
 dependency $pbDb.pbAaDistL $pbDb.knownGenePep
 dependency $pbDb.pbAaDistM $pbDb.knownGenePep
 dependency $pbDb.pbAaDistN $pbDb.knownGenePep
 dependency $pbDb.pbAaDistP $pbDb.knownGenePep
 dependency $pbDb.pbAaDistQ $pbDb.knownGenePep
 dependency $pbDb.pbAaDistR $pbDb.knownGenePep
 dependency $pbDb.pbAaDistS $pbDb.knownGenePep
 dependency $pbDb.pbAaDistT $pbDb.knownGenePep
 dependency $pbDb.pbAaDistV $pbDb.knownGenePep
 dependency $pbDb.pbAaDistW $pbDb.knownGenePep
 dependency $pbDb.pbAaDistY $pbDb.knownGenePep
 
 
 # Table types - only needed when the table does not have the same name .as file record.
 type genePred
     $hg.acembly
     $gbd.ECgene
     $gbd.geneid
     $gbd.genscan
     $gbd.sgpGene
     $gbd.softberryGene
     $gbd.twinscan
     $gbd.ensGene
     $gbd.vegaGene
     $gbd.refGene
     $gbd.xenoRefGene
     $gbd.jgiFilteredModels
     $gbd.geneMapper
 
 type pepPred
     $hg.acemblyPep
     $gbd.ECgenePep
     $gbd.geneidPep
     $gbd.genscanPep
     $gbd.sgpPep
     $gbd.softberryPep
     $gbd.twinscanPep
     $gbd.ensPep
     $gbd.vegaPep
     $gbd.knownGenePep
     $ce.sangerPep
     dm1.bdgpGenePep
     $dm.flyBasePep
 
 type psl
     $hg.affyU95
     $hg.affyU133
     $hg.affyU133Plus2
     $hg.HInvGeneMrna
     $mm.affyU74
     $danRer.affyZebrafish
     $gbd.all_bacends
     $gbd.all_fosends
     $gbd.all_est
     $gbd.est
     $gbd.intronEst
     $gbd.xenoEst
     $gbd.xenoMrna
     $gbd.all_mrna
     $gbd.refSeqAli
     $gbd.all_sts_primer
     $gbd.all_sts_seq
     $transMapDb.transMapAlnUcscGenes
     $transMapDb.transMapAlnRefSeq
     $transMapDb.transMapAlnMRna
     $transMapDb.transMapAlnSplicedEst
 
 type estOrientInfo
     $gbd.estOrientInfo
     $gbd.mrnaOrientInfo
 
 type expRecord
     hgFixed.nci60Exps
     hgFixed.rosettaExps
     hgFixed.affyExps.id
     hgFixed.gnfHumanU95AllExps
     hgFixed.gnfHumanU95MedianExps
     hgFixed.gnfMouseU74aAllExps
     hgFixed.gnfMouseU74aMedianExps
     hgFixed.gnfMouseU74bAllExps
     hgFixed.gnfMouseU74bMedianExps
     hgFixed.gnfMouseU74cAllExps
     hgFixed.gnfMouseU74cMedianExps
     hgFixed.arbFlyLifeAllExps
     hgFixed.arbFlyLifeMedianExps
     hgFixed.kimWormLifeAllExps
     hgFixed.kimWormLifeMedianExps
     hgFixed.yeastChoCellCycleExps
     hgFixed.gladHumESExps
 
 type expData
     hgFixed.kimWormLifeAllRatio
     hgFixed.kimWormLifeMedianRatio
     hgFixed.gnfHumanU95All
     hgFixed.gnfHumanU95AllRatio
     hgFixed.gnfHumanU95Median
     hgFixed.gnfHumanU95MedianRatio
     hgFixed.gnfMouseU74aAll
     hgFixed.gnfMouseU74aAllRatio
     hgFixed.gnfMouseU74aMedian
     hgFixed.gnfMouseU74aMedianRatio
     hgFixed.gnfMouseU74bAll
     hgFixed.gnfMouseU74bAllRatio
     hgFixed.gnfMouseU74bMedian
     hgFixed.gnfMouseU74bMedianRatio
     hgFixed.gnfMouseU74cAll
     hgFixed.gnfMouseU74cAllRatio
     hgFixed.gnfMouseU74cMedian
     hgFixed.gnfMouseU74cMedianRatio
     hgFixed.arbFlyLifeAll
     hgFixed.arbFlyLifeAllRatio
     hgFixed.arbFlyLifeMedian
     hgFixed.arbFlyLifeMedianRatio
     hgFixed.kimWormLifeAllRatio
     hgFixed.kimWormLifeMedianRatio
     hgFixed.yeastChoCellCycle
     hgFixed.yeastChoCellCycleRatio
     hgFixed.gladHumES
     hgFixed.gladHumESRatio
 
 type exprBed
     $hg.affyRatio
     $mm.affyGnfU74A
     $mm.affyGnfU74B
     $mm.affyGnfU74C
     $hg.nci60
     $rn.gnfAtlas2
     # hgFixed.rosChr22Dat
 
 type expDistance
     $hg.gnfAtlas2Distance
     $hg.gnfU95Distance
     $mm.affyGnfU74ADistance
     $mm.affyGnfU74BDistance
     $mm.affyGnfU74CDistance
     $mm.mouseLandscapeDistance
     $hg.knownGnfDistance
     $ce.kimExpDistance
     $dm.arbExpDistance
     $sacCer.choExpDistance
     $hg.gladHumESDistance
 
 type chain
     $gbd.chr%_chain%
     $gbd.chr%_chainSelf
 
 type agpFrag
     $gbd.chr%_gold
 
 type agpGap
     $gbd.chr%_gap
 
 type gl
     $gbd.chr%_gl
 
 type knownTo
     $gbd.knownToCdsSnp
     $gbd.knownToEnsembl
     $gbd.knownToLocusLink
     $gbd.knownToPfam
     $gbd.knownToRefSeq
     $gbd.knownToAllenBrain
     $hg.knownToU95
     $hg.knownToU133
     $hg.knownToU133Plus2
     $hg.knownToHInv
     $mm.knownToU74
     $mm.knownToXM
     $ce.sangerToKim
     $ce.sangerToPfam
     $ce.sangerToRefSeq
     dm1.bdgpToLocusLink
     dm1.bdgpToPfam
     dm1.bdgpToRefSeq
     $sacCer.sgdToSwissProt
     $sacCer.sgdToSgd
     $sacCer.sgdToName
 
 type idName
     $gbd.source
     $gbd.organism
     $gbd.library
     $gbd.mrnaClone
     $gbd.sex
     $gbd.tissue
     $gbd.development
     $gbd.cell
     $gbd.cds
     $gbd.description
     $gbd.author
     $gbd.geneName
     $gbd.productName
     $gbd.keyword
 
 type blastTab
     $gbd.ceBlastTab
     $gbd.hgBlastTab
     $gbd.dmBlastTab
     $gbd.drBlastTab
     $gbd.mmBlastTab
     $gbd.rnBlastTab
     $gbd.scBlastTab
     $gbd.knownBlastTab
     $ce.sangerBlastTab
     dm1.bdgpBlastTab
     sacCer1.sgdBlastTab
     sacCer2.knownBlastTab
 
 type knownCanonical
     $gbd.knownCanonical
     $ce.sangerCanonical
     dm1.bdgpCanonical
     $sacCer.sgdCanonical
 
 type knownIsoforms
     $gbd.knownIsoforms
     $ce.sangerIsoforms
     dm1.bdgpIsoforms
     $sacCer.sgdIsoforms
 
 type rnaFold
     $gbd.foldUtr3
     $gbd.foldUtr5
 
 type bed
     $gbd.vegaPseudoGene
     $sacCer.sgdOther
 
 type geneAndProt
     $kgDb.knownGene
     $ce.sangerGene
     dm1.bdgpGene
     $sacCer.sgdGene
 
 type transMapInfo
     $transMapDb.transMapInfoRefSeq
     $transMapDb.transMapInfoUcscGenes
     $transMapDb.transMapInfoMRna
     $transMapDb.transMapInfoSplicedEst
 
 type transMapInfo
     $transMapDb.transMapInfoRefSeq
     $transMapDb.transMapInfoUcscGenes
     $transMapDb.transMapInfoMRna
     $transMapDb.transMapInfoSplicedEst
 
 type transMapSrc
     hgFixed.transMapSrcRefSeq
     hgFixed.transMapSrcUcscGenes
     hgFixed.transMapSrcMRna
     hgFixed.transMapSrcSplicedEst
 
 type transMapGene
     hgFixed.transMapGeneRefSeq
     hgFixed.transMapGeneUcscGenes
     hgFixed.transMapGeneMRna
 
 
 # Ignored tables - no linkage here that we check at least.
 
 tablesIgnored go
     instance_data
     source_audit
 
 tablesIgnored visiGene
     vgPrbAli
     vgPrbAliAll
     tableDescriptions
 
 tablesIgnored hgFixed
     omimTitle
     cutters
     rebaseRefs
 
 tablesIgnored $gbd
     NIAGene
     ancientRepeat
     axtInfo
     blatFr1
     chromInfo
     cpgIsland
     cpgIslandExt
     ctgPos
     cytoBand
     cytoBandIdeo
     evofold
     exoniphy
     firstEF
     gbLoaded
     gbDelete_tmp
     gc5Base
     gcPercent
     genscanSubopt
     grp
     hgFindSpec%
     history
     knownAlt
     miRNA
     nestedRepeats
     nestedRepeatsRM327
     quality
     rnaCluster
     rnaGene
     regPotential%
     sangerGenefinder
     sangamoDnaseHs
     sangamoDnaseHsNeg
     sangamoDnaseHsPos
     simpleRepeat
     windowmaskerSdust
     sgpGene
     tableDescriptions
     tigrGeneIndex
     trackDb%
     chr%_mrna
     chr%_blastz%
     chr%_blat%
     chr%_gap
     chr%_rmsk
     chr%_rmskRM327
     gap
     rmsk
     axtNet%
     blat%
     blast%
     repeats
     multiz%way
     multiz%waySummary
     multiz%wayFrames
     phyloP%way%
     phastCons%way%
     phastConsElements%way%
     jaxQTL
     jaxQtl
     jaxQtlAsIs
     jaxQtlPadded
     uwNucOccA375
     uwNucOccDennis
     uwNucOccMec
 
 
 tablesIgnored $kgDb
     pbAaDist_
     pbAnomLimit
     pbResAvgStd
     pbStamp
     pep%Dist
 
 tablesIgnored hg19
     gold
     bacEndPairsBad
     multizMHCSummary
     netSyn_mann_hap4
     net_dbb_hap3
     net_apd_hap1
     net_ssto_hap7
     net_qbl_hap6
     net_mcf_hap5
     net_mann_hap4
     net_haplotypes
     net_cox_hap2
     net_chr4_ctg9_hap1
     net_chr17_ctg5_hap1
     netVenter1
     netSyn_ssto_hap7
     netSyn_qbl_hap
     netSyn_qbl_hap6
     netSyn_mcf_hap5
     netSyn_apd_hap1
     netSyn_cox_hap2
     netSyn_dbb_hap3
     chain_ssto_hap7
     chain_ssto_hap7Link
     hapRegions
     multizMHC
     chain_mcf_hap5Link
     chain_qbl_hap6
     chain_qbl_hap6Link
     chain_haplotypesLink
     chain_mann_hap4
     chain_mann_hap4Link
     chain_mcf_hap5
     chain_chr4_ctg9_hap1
     chain_chr4_ctg9_hap1Link
     chain_cox_hap2
     chain_cox_hap2Link
     chain_dbb_hap3
     chain_dbb_hap3Link
     chainVenter1
     chainVenter1Link
     chain_apd_hap1
     chain_apd_hap1Link
     chain_chr17_ctg5_hap1
     chain_chr17_ctg5_hap1Link
     chain_haplotypes
 
 tablesIgnored mm9
     crgMapability%
     rest
 
 tablesIgnored $calJac
     gold
 
 tablesIgnored $petMar
     %gold
     intronEst
 
 tablesIgnored $braFlo
     %gold
     intronEst
 
 tablesIgnored $cavPor
     gold
 
 tablesIgnored $cb
     chr%_gold
 
 tablesIgnored $ce
     chr%_gold
     chr%_wabaCbr
     wabaCbr
     nucleosomeControl
     nucleosomeFragmentsSense
     nucleosomeFragmentsAntisense
     nucleosomeStringency
     monoNucleosomesSense
     monoNucleosomesAntiSense
     nucleosomeControlSenseCoverage
     nucleosomeControlAntisenseCoverage
     nucleosomeAdjustedCoverage
     25mersRepeats
     mt%Forward
     mt%Reverse
     wt%Forward
     wt%Reverse
     algBind%
 
 tablesIgnored $ci
     snapGene
 
 tablesIgnored $dm
     anophelesEcores
     fbGo
     fbRole
     fbUniProt
     flyreg
     flyreg2
 
 tablesIgnored $loxAfr
     gold
 
 tablesIgnored $equCab
     chr%_gold
 
 tablesIgnored $fr
     chr%_gold
 
 tablesIgnored $galGal
     chr%_gold
     supercontig
     caCondor454
 
 tablesIgnored $danRer
     chr%_gold
     ctgPos2
     wz_ests
 
 tablesIgnored $caePb
     chr%_gold
     ctgPos2
 
 tablesIgnored $caeRem
     chr%_gold
     ctgPos2
 
 tablesIgnored $caeJap
     chr%_gold
     ctgPos2
 
 tablesIgnored $priPac
     chr%_gold
     ctgPos2
 
 tablesIgnored $canFam
     chr%_gold
     genomicSuperDups
 
 tablesIgnored $droYak
     chr%_gold
 
 tablesIgnored $droMult
     gold
     intronEst
 
 tablesIgnored $anoCar
     gold
 
 tablesIgnored $anoGam
     chr%_gold
     anoEstNcl
 
 tablesIgnored $bosTau
     gold
     intronEst
     contigOrient
 
 tablesIgnored $apiMel
     gold
     intronEst
     brhInparalog
     modelRefGene
     scaffolds
 
 tablesIgnored $snpDb125
     snp125ExceptionDesc
 
 tablesIgnored $snpDb126
     snp126ExceptionDesc
 
 tablesIgnored $snpDb127
     snp127ExceptionDesc
 
 tablesIgnored $hg
     acescan
     affyTranscriptome
     affyTxnPhase3FragsHDF
     affyTxnPhase3FragsHeLaCyto
     affyTxnPhase3FragsHeLaNuclear
     affyTxnPhase3FragsHepG2Cyto
     affyTxnPhase3FragsHepG2Nuclear
     affyTxnPhase3FragsJurkat
     affyTxnPhase3FragsNCCIT
     affyTxnPhase3FragsPC3
     affyTxnPhase3FragsSK_N_AS
     affyTxnPhase3FragsU87MG
     affyTxnPhase3FragsHeLaTopStrand
     affyTxnPhase3FragsHeLaBottomStrand
     affyTxnPhase3FragsHepG2TopStrand
     affyTxnPhase3FragsHepG2BottomStrand
     affyTxnPhase3HDF
     affyTxnPhase3HeLaCyto
     affyTxnPhase3HeLaNuclear
     affyTxnPhase3HepG2Cyto
     affyTxnPhase3HepG2Nuclear
     affyTxnPhase3Jurkat
     affyTxnPhase3NCCIT
     affyTxnPhase3PC3
     affyTxnPhase3SK_N_AS
     affyTxnPhase3U87MG
     affyTxnPhase3HeLabottom_strand
     affyTxnPhase3HeLatop_strand
     affyTxnPhase3HepG2bottom_strand
     affyTxnPhase3HepG2top_strand
     affyTxnPhase3HeLaBottomStrand
     affyTxnPhase3HeLaTopStrand
     affyTxnPhase3HepG2BottomStrand
     affyTxnPhase3HepG2TopStrand
     burgeRnaSeqGemMapper%
     chimpDels
     chimpParalogy
     chimpSimpleDiff
     celeraCoverage
     celeraDupPositive
     celeraOverlay
     cccTrendPvalBd
     cccTrendPvalCad
     cccTrendPvalCd
     cccTrendPvalHt
     cccTrendPvalRa
     cccTrendPvalT1d
     cccTrendPvalT2d
     cnpFosmid
     cnpIafrate
     cnpIafrate2
     cnpLocke
     cnpRedon
     cnpSebat
     cnpSebat2
     cnpSharp
     cnpSharp2
     cnpSharpSampleCount
     cnpSharpSamples
     cnpTuzun
     ctgPos
     delConrad
     delConrad2
     delHinds
     delHinds2
     delMccarroll
     dgv
     eponine
     exaptedRepeats
     fox2ClipClusters
     fox2ClipSeq
     fox2ClipSeqDensityForwardStrand
     fox2ClipSeqDensityReverseStrand
     geneTests
     genomicSuperDups
     haplotype
     hgdpGeo
     hgdpFst
     hgdpHzy%
     hgdpIhs%
     hgdpXpehh%
     laminB1
     laminB1Lads
     mammalPsg
     nimhBipolarUs
     nimhBipolarDe
     perlegen
     pga
     pgVenter
     pgWatson
     pgYoruban2
     pgYoruban3
     pgYh1
     pgNA%
     pgSjk
     promoterStanford
     pseudoYale
     recombRate
     slamMouse
     slamNonCodingMouse
     slamRat
     slamNonCodingRat
     snp
     snp125ExceptionDesc
     snp126ExceptionDesc
     switchDbTss
     syntenyMouse
     syntenyRat
     targetScanS
     vistaEnhancers
     wgRna
     zoom1_affyTranscriptome
     zoom2_affyTranscriptome
     encodeAffyChIpRnapHl60PvalHr00
     encodeAffyChIpRnapHl60PvalHr02
     encodeAffyChIpRnapHl60PvalHr08
     encodeAffyChIpRnapHl60PvalHr32
     encodeAffyChIpRnapHl60SitesHr00
     encodeAffyChIpRnapHl60SitesHr02
     encodeAffyChIpRnapHl60SitesHr08
     encodeAffyChIpRnapHl60SitesHr32
     encodeAffyRnaHl60SigHr00
     encodeAffyRnaHl60SigHr02
     encodeAffyRnaHl60SigHr08
     encodeAffyRnaHl60SigHr32
     encodeAffyRnaHl60SitesHr00
     encodeAffyRnaHl60SitesHr02
     encodeAffyRnaHl60SitesHr08
     encodeAffyRnaHl60SitesHr32
     encodeAffyEc1BrainCerebellumSites
     encodeAffyEc51BrainCerebellumSites
     encodeAffyEc1BrainFrontalLobeSites
     encodeAffyEc51BrainFrontalLobeSites
     encodeAffyEc1BrainHippocampusSites
     encodeAffyEc51BrainHippocampusSites
     encodeAffyEc1BrainHypothalamusSites
     encodeAffyEc51BrainHypothalamusSites
     encodeAffyEc1FetalKidneySites
     encodeAffyEc51FetalKidneySites
     encodeAffyEc1FetalSpleenSites
     encodeAffyEc51FetalSpleenSites
     encodeAffyEc1PlacentaSites
     encodeAffyEc51PlacentaSites
     encodeAffyEc1TestisSites
     encodeAffyEc51TestisSites
     encodeAffyEc1FetalTestisSites
     encodeAffyEc51FetalTestisSites
     encodeAffyEc1ProstateSites
     encodeAffyEc51ProstateSites
     encodeAffyEc1OvarySites
     encodeAffyEc51OvarySites
     encodeAffyEc1HeLaC1S3Sites
     encodeAffyEc51HeLaC1S3Sites
     encodeAffyEc1GM06990Sites
     encodeAffyEc51GM06990Sites
     encodeAffyEc1HepG2Sites
     encodeAffyEc51HepG2Sites
     encodeAffyEc1K562Sites
     encodeAffyEc51K562Sites
     encodeAffyEc1TertBJSites
     encodeAffyEc51TertBJSites
     encodeAffyEc1BrainCerebellumSignal
     encodeAffyEc51BrainCerebellumSignal
     encodeAffyEc1BrainFrontalLobeSignal
     encodeAffyEc51BrainFrontalLobeSignal
     encodeAffyEc1BrainHippocampusSignal
     encodeAffyEc51BrainHippocampusSignal
     encodeAffyEc1BrainHypothalamusSignal
     encodeAffyEc51BrainHypothalamusSignal
     encodeAffyEc1FetalKidneySignal
     encodeAffyEc51FetalKidneySignal
     encodeAffyEc1FetalSpleenSignal
     encodeAffyEc51FetalSpleenSignal
     encodeAffyEc1PlacentaSignal
     encodeAffyEc51PlacentaSignal
     encodeAffyEc1TestisSignal
     encodeAffyEc51TestisSignal
     encodeAffyEc1FetalTestisSignal
     encodeAffyEc51FetalTestisSignal
     encodeAffyEc1ProstateSignal
     encodeAffyEc51ProstateSignal
     encodeAffyEc1OvarySignal
     encodeAffyEc51OvarySignal
     encodeAffyEc1HeLaC1S3Signal
     encodeAffyEc51HeLaC1S3Signal
     encodeAffyEc1GM06990Signal
     encodeAffyEc51GM06990Signal
     encodeAffyEc1HepG2Signal
     encodeAffyEc51HepG2Signal
     encodeAffyEc1K562Signal
     encodeAffyEc51K562Signal
     encodeAffyEc1TertBJSignal
     encodeAffyEc51TertBJSignal
     encodeEvoFold
     encodeGisChip%
     encodeGencodeGenePolyA%
     enocdeGencodeRaceFrags%
     encodeNhgriDnaseHs%
     encodeRegulomeDnaseGM06990%
     encodeSangerChip%
     encodeStanfordPromoters%
     encodeUcsdChipAch3Imr90
     encodeUcsdChipMeh3k4Imr90
     encodeUcsdChipRnapHct116
     encodeUcsdChipRnapHela
     encodeUcsdChipRnapImr90
     encodeUcsdChipRnapThp1
     encodeUcsdChipTaf250Hct116
     encodeUcsdChipTaf250Hela
     encodeUcsdChipTaf250Imr90
     encodeUcsdChipTaf250Thp1
     encodeUcsdNgChipKnownSites
     encodeUcsdNgChipNovelSites
     encodeUcsdNgChipSignal
     encodeUcsdNgHeLaH3K4me3_p0
     encodeUcsdNgHeLaH3K4me3_p30
     encodeUcsdNgHeLaRnap_p0
     encodeUcsdNgHeLaRnap_p30
     encodeUcsdNgValChipH3K4me
     encodeUcsdNgValChipH3ac
     encodeUcsdNgValChipRnap
     encodeUcsdNgValChipTaf
     encodeUncFaireSignal
     encodeUncFairePeaks
     encodeUncFairePeaksChipotle
     encodeUvaDnaRep%
     encodeYaleChipPval%
     encodeYaleChipSignal%
     encodeYaleChipSites%
     encodeTba%
     kiddEichlerValidAbc7
     kiddEichlerValidAbc8
     kiddEichlerValidAbc9
     kiddEichlerValidAbc10
     kiddEichlerValidAbc11
     kiddEichlerValidAbc12
     kiddEichlerValidAbc13
     kiddEichlerValidAbc14
     kiddEichlerValidG248
     wgEncode%
 
 tablesIgnored $mm
     chr%_gold
     syntenyRat
     syntenyHuman
     ctgPos
     rikenCageCtssMinus
     rikenCageCtssPlus
     rikenCageTc
 
 tablesIgnored $panTro
     chr%_gold
     humanDels
 
 tablesIgnored $rn
     chr%_gold
     all_sts_primer
     bactigPos
     recombRateRat
     syntenyMouse
     syntenyHuman
 
 tablesIgnored $sacCer
     chr%_gold
     chr%_gap
     2micron_mrna
     2micron_intronEst
     2micron_est
     2micron_gold
     2micron_gap
     sgdClone
     yeastP2P
     uwFootprintsMappability
     uwFootprintsPrints
     uwFootprintsTagCounts
 
 tablesIgnored $tetNig
     gold
     ecoresHg17
     cytokines
     hoxGenes
 
 tablesIgnored $felCat
     gold
     intronEst
     microsat
 
 tablesIgnored hg16
     chicken_hmrg
     rat_hmrg
     mouse_hmrg
     syntenyMm4
 
 tablesIgnored hg17
     ecoresTetNig1
 
 tablesIgnored canFam2
     uncertified
 
 tablesIgnored equCab2
     ctgPos2
 
 tablesIgnored oryLat2
     microsat
 
 tablesIgnored oryCun2
     ctgPos2
     gold
     intronEst
 
 tablesIgnored susScr2
     bosTau4ChainPileUp
     gold
     ctgPos2
 
 tablesIgnored ailMel1
     gold
+
+tablesIgnored aplCal1
+    gold
+    intronEst

