# This contains linkage information between various fields
# in various databases.

# Define databases used for various organisms
set ailMel ailMel1
set anoCar anoCar1,anoCar2
set anoGam anoGam1
set apiMel apiMel1,apiMel2
set aplCal aplCal1
set bosTau bosTau2,bosTau3,bosTau4,bosTau5,bosTau6,bosTau7
set braFlo braFlo1,braFlo2
set bruMal bruMal1
set caeAng caeAng1
set caeJap caeJap1,caeJap3,caeJap4
set caePb caePb1,caePb2,caePb3
set caeRem caeRem2,caeRem3,caeRem4
set caeSp11 caeSp111
set calJac calJac1,calJac3
set canFam canFam1,canFam2,canFam3
set cavPor cavPor3
set cb cb1,cb3,cb4
set ce ce2,ce4,ce6,ce9,ce10
set cerSim cerSim1
set choHof choHof1
set chrPic chrPic1
set ci ci1,ci2
set cioSav cioSav1,cioSav2
set danRer danRer3,danRer4,danRer5,danRer6,danRer7
set dasNov dasNov2,dasNov3
set dipOrd dipOrd1
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
set droVir droVir1,droVir2
set droYak droYak1,droYak2
set echTel echTel1,echTel2
set equCab equCab1,equCab2
set eriEur eriEur1
set felCat felCat3,felCat4,felCat5
set fr fr1,fr2,fr3
set gadMor gadMor1
set galGal galGal2,galGal3,galGal4
set geoFor geoFor1
set melGal melGal1
set gasAcu gasAcu1
set gorGor gorGor1,gorGor3
set haeCon haeCon1
set hetGla hetGla1,hetGla2
set hg hg16,hg17,hg18,hg19
set latCha latCha1
set loxAfr loxAfr3
set macEug macEug1,macEug2
set melInc melInc1
set melHap melHap1
set melUnd melUnd1
set micMur micMur1
set mm mm7,mm8,mm9,mm10
set monDom monDom1,monDom4,monDom5
set musFur musFur1
set myoLuc myoLuc1,myoLuc2
set nomLeu nomLeu1,nomLeu2,nomLeu3
set ochPri ochPri2
set oreNil oreNil1,oreNil2
set ornAna ornAna1
set oryCun oryCun2
set oryLat oryLat2
set otoGar otoGar1,otoGar3
set oviAri oviAri1
set panTro panTro1,panTro2,panTro3,panTro4
set papAnu papAnu2
set papHam papHam1
set petMar petMar1,petMar2
set ponAbe ponAbe2
set priPac priPac1,priPac2
set proCap proCap1
set pteVam pteVam1
set rheMac rheMac2,rheMac3
set rn rn3,rn4,rn5
set sacCer sacCer1,sacCer2,sacCer3
set saiBol saiBol1
set sarHar sarHar1
set sorAra sorAra1,sorAra2
set speTri speTri1,speTri2
set susScr susScr1,susScr2,susScr3
set strPur strPur1,strPur2
set tarSyr tarSyr1
set taeGut taeGut1
set tetNig tetNig1,tetNig2
set triMan triMan1
set tupBel tupBel1
set turTru turTru1,turTru2
set vicPac vicPac1
set xenTro xenTro1,xenTro2,xenTro3

# Define all organism/assembly-specific databases.
set gbd $ailMel,$anoCar,$anoGam,$apiMel,$aplCal,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$canFam,$calJac,$cavPor,$cb,$ce,$cerSim,$choHof,$chrPic,$ci,$cioSav,$danRer,$dasNov,$dipOrd,$dm,$dp,$droMult,$droYak,$echTel,$equCab,$eriEur,$felCat,$fr,$gadMor,$galGal,$gasAcu,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$latCha,$loxAfr,$macEug,$melGal,$melHap,$melInc,$melUnd,$micMur,$mm,$monDom,$musFur,$myoLuc,$nomLeu,$ochPri,$oreNil,$ornAna,$oryCun,$oryLat,$otoGar,$oviAri,$panTro,$papAnu,$papHam,$petMar,$ponAbe,$priPac,$proCap,$pteVam,$rheMac,$rn,$sacCer,$saiBol,$sarHar,$sorAra,$speTri,$strPur,$susScr,$taeGut,$tarSyr,$tetNig,$triMan,$tupBel,$turTru,$vicPac,$xenTro

# Define organism databases based on whole-genome shotgun projects
# (Assembly based on WGS project contigs accessioned in Genbank)
set wgs $ailMel,$aplCal,$bosTau,$bruMal,$calJac,$canFam,$cavPor,$choHof,$chrPic,$cioSav,$dasNov,$dipOrd,$echTel,$eriEur,$felCat,$fr,$galGal,$haeCon,$hetGla,$macEug,$melGal,$melHap,$melInc,$micMur,$monDom,$musFur,$myoLuc,$nomLeu,$ochPri,$otoGar,$oryCun,$oryLat,$oviAri,$panTro,$proCap,$pteVam,$rn,$sarHar,$sorAra,$speTri,$susScr,$taeGut,$tarSyr,$tetNig,$tupBel,$turTru,$vicPac

# Define organism databases for which we build a xenoRefGene track:
set xrg $ailMel,$anoCar,$aplCal,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$calJac,$canFam,$cb,$ce,$cerSim,$choHof,$chrPic,$ci,danRer6,danRer7,$dasNov,$dipOrd,$dp,$droMult,$droYak,$echTel,$eriEur,$felCat,$gadMor,$galGal,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$latCha,$loxAfr,$macEug,$melGal,$melHap,$melInc,$melUnd,$micMur,$mm,$monDom,$musFur,$myoLuc,$nomLeu,$ochPri,$oreNil,$oryCun,$oryLat,$otoGar,$oviAri,$panTro,$papAnu,$papHam,$petMar,$ponAbe,$priPac,$proCap,$pteVam,$rheMac,$rn,$saiBol,$sarHar,$sorAra,$speTri,$strPur,$susScr,$taeGut,$tarSyr,$triMan,$tupBel,$turTru,$vicPac

# Ensembl gene track lists constructed from update procedure
set ensGeneDb ailMel1,anoCar2,bosTau6,calJac3,canFam2,canFam3,cavPor3,ce10,choHof1,ci2,cioSav2,danRer7,dasNov2,dipOrd1,dm3,echTel1,echTel2,eriEur1,equCab2,felCat3,felCat5,fr2,fr3,galGal3,galGal4,gasAcu1,gorGor3,hg19,latCha1,loxAfr3,macEug1,melGal1,micMur1,mm9,mm10,monDom5,musFur1,myoLuc2,nomLeu1,ochPri2,oreNil1,ornAna1,oryCun2,oryLat2,otoGar3,panTro2,panTro4,petMar2,ponAbe2,proCap1,pteVam1,rheMac2,rn4,rn5,sacCer3,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,xenTro3

set ensGeneWgs choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,felCat3,macEug1,micMur1,myoLuc2,ochPri2,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1

set ensGeneScaffold choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,felCat3,macEug1,micMur1,ochPri2,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1

# Define organism databases for which we host the vegaGenes
set vegaGeneDbs hg18,hg19,mm9,mm10

# Define organism databases for which we build a SNP track:
set snpDb127 hg18,bosTau3
set snpDb126 hg18,mm8
set snpDb125 hg17,panTro1,canFam1,rn4

# LS/SNP databases
set lsSnpDb hg18,hg19

# 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,echTel2,loxAfr1,oryCun1,otoGar1,loxAfr3
set transMapDb anoCar1,anoCar2,bosTau4,calJac1,calJac3,canFam2,cavPor3,choHof1,danRer5,danRer6,equCab2,felCat3,fr2,fr3,galGal3,gasAcu1,hg18,hg19,mm9,mm10,monDom4,monDom5,ornAna1,oryCun2,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2,xenTro3,loxAfr3,papAnu2,papHam1,micMur1,echTel1,echTel2,speTri2,saiBol1,gadMor1,melUnd1,eriEur1,proCap1,pteVam1,sorAra1,sorAra2,tarSyr1,tupBel1,ochPri2,oreNil2,turTru2,vicPac1,panTro4

# Define ucscRetro databases
set ucscRetroDb hg19,mm9,mm10

# 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,10Kgenomes,BRfoo,abc,andy,bioCyc070327,bioCyc090623,bioCyc100514,bosTau3Old,ccds,ccds20080404,ccdsNew,ccds_before,ctd,ctd021508,ctdOld,dark,elegansWS176,encpipeline_aamp,encpipeline_beta,encpipeline_galt,encpipeline_kate,encpipeline_prod,encpipeline_test,entrez,euaGli13,eutHer13,fakeDataE0,fanKgTemp,fanKgTemp2,fanTest,fanTest2,gencode,germlineVar_hg18,go040501,go041115,go050521,go050726,go060211,go061219,go080130,goJill,hg15test,hg18kg11,hg18snp130,hg18test,hg19Haps,hg19Patch10,hg19Patch9,hg19Patch5,hg19Patch2,hg19Patch2i,hg19snp131,hg19snp132,hg19snp134,hg19snp135,hg19snp137,hgcentralgsid,hgcentralrhead,hgcentraltest2,hgcentraltestangie,hiv1,hivgne8,homIni13,homIni14,homIni20,homNea0,homPan20,influenza,information_schema,ismb2004,jkFoo,jorgetest,kgHg17FTemp,kgHg18ATemp,kgMm8ATemp,kgRn3DTemp,markd,markdCcds,markdMGC,membership,metaData_vsmalladi,metadata_krish,mikep,mm9Temp,mm10snp137,mmtv,nonAfr13,oldChoHof1,panTro2snp127,pathway,petMar0,pongo,proteins080707,proteins090821,qa,rah,reactome,rn4UCGenes,rn4snp130,snpCompare,snpFixed,sp100331,sp101005,t18,testMePrivl,tmpBioCychg18,tmpFoo12,tmpUcscGeneshg19,treeFam,uf,ug,vega33,vega40,visiGeneOld,visiGeneXml

# Define various non-self chains
set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Rn3,Rn4,Rn5,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,PanTro3,PanTro4,GalGal2,GalGal3,GalGal4,Fr1,Fr2,Fr3,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,CanFam1,CanFam2,CanFam3,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,ApiMel3,TetNig1,TetNig2,XenTro1,XenTro2,XenTro3,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,RheMac3,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,FelCat4,FelCat5,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar2,AnoCar1,Ce2,Ce4,Ce6,Ce9,Ce10,OrnAna1,CaeAng1,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeJap3,CaeJap4,CaeJap1,Cb1,Cb3,Cb4,CaeSp111,PriPac2,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CalJac3,CavPor3,PetMar1,BraFlo1,BraFlo2,TaeGut1,GorGor1,GorGor2,GorGor3,AplCal1,PapHam1,TarSyr1,OtoGar1,OtoGar3,MicMur1,LoxAfr2,LoxAfr3,SusScr1,SusScr2,SusScr3,AilMel1,CanFamPoodle1,ChoHof1,DasNov2,DasNov3,DipOrd1,EchTel1,EriEur1,MacEug1,MyoLuc1,OchPri2,OryCun1,OryCun2,ProCap1,PteVam1,SorAra1,SpeTri1,SpeTri2,TupBel1,TurTru1,TurTru2,VicPac1,BruMal1,HaeCon1,MelHap1,MelInc1,MelUnd1,Hg19Patch10,Hg19Patch9,Hg19Patch5,Hg19Patch2,OviAri1,MelGal1,BosTau6,BosTau7,MyoLuc2,TurTle1,NomLeu1,NomLeu2,NomLeu3,MacEug2,GadMor1,LatCha1,OreNil1,OreNil2,HetGla1,HetGla2,SaiBol1,TriMan1,GeoFor1,Mm10Patch1

# Define databases that support known genes
set kgDb $hg,$mm,rn3
# Older format (KG 2)
set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4
# Newer format (KG 3 aka UCSC Genes)
set kgDb3 hg18,hg19,mm9,mm10

# 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 hg19,hg18,hg17,mm8,mm9,mm10

# Magic for tables split between chromosomes
set split splitPrefix=chr%\_

# Databases with the tRNAs track
set tRNAsDbs hg18,hg19,mm9,mm10,rn4,ailMel1,caePb1,canFam2,danRer5,felCat3,gorGor3,ornAna1,panTro3,susScr2,anoCar2,caePb2,cavPor3,danRer6,felCat4,loxAfr3,oryCun2,petMar1,taeGut1,bosTau4,caeRem2,cb3,danRer7,fr2,fr3,melGal1,oryLat2,ponAbe2,tetNig2,bosTau6,caeRem3,ce4,equCab1,galGal3,monDom5,oviAri1,priPac1,xenTro3,caeJap1,calJac3,ce6,equCab2,gasAcu1,nomLeu1,panTro2,rheMac2,sarHar1

# Databases with the CGAP SAGE track
set cgapSageDbs hg18,hg19,mm8

# Define the shared identifiers and the fields they appear in.

identifier cosmicId
"COSMIC entry ID"
     $hg.cosmic.name
     $hg.cosmicRaw.cosmic_mutation_id

# 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 exclude=
     $kgDb2.knownCanonical.protein minCheck=0.80
     $gbd.spMrna.spID minCheck=0.80 exclude=
     dm1.bdgpSwissProt.spSymbol minCheck=0.80
     dm1.flyBaseSwissProt.spSymbol minCheck=0.80

identifier ProteomeTaxonId external=Proteome
"Proteome Taxon ID"
     proteome.taxonName.id
     proteome.spXref3.division minCheck=.90

identifier ProteomeAccession external=Proteome
"Proteome  Accession"
     proteome.spXref3.accession dupeOk
     proteome.hgncXref.uniProt minCheck=.65

identifier UniProtAccession external=UniProt
"UniProt(Swiss-Prot/TrEMBL) Accession"
     uniProt.displayId.acc
     uniProt.accToKeyword.acc
     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 exclude=
     $kgDb3.kgXref.spID minCheck=0.50 exclude=
     $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
     $rn.rgdGene2ToUniProt.value minCheck=0.8

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"
    hg19.tRNAs.name 
    hg19.kgXref.tRnaName exclude= minCheck=0.50

# 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 refGeneRetro dependency
"Link refGene to ucscRetroInfo"
    $ucscRetroDb.refGene.name dupeOk
    hg19.ucscRetroInfo4.refSeq minCheck=0.96 exclude=noRefSeq
    hg19.ucscRetroInfo5.refSeq minCheck=0.96 exclude=noRefSeq
    mm9.ucscRetroInfo1.refSeq minCheck=0.96 exclude=noRefSeq
    mm10.ucscRetroInfo2.refSeq minCheck=0.96 exclude=noRefSeq

identifier knownGeneRetro dependency
"Link knownGene to ucscRetroInfo"
    $ucscRetroDb.knownGene.name dupeOk chopAfter=.
    hg19.ucscRetroInfo4.kgName minCheck=0.96 exclude=noKg chopAfter=.
    hg19.ucscRetroInfo5.kgName minCheck=0.96 exclude=noKg chopAfter=.
    mm9.ucscRetroInfo1.kgName minCheck=0.94 exclude=noKg chopAfter=.
    mm10.ucscRetroInfo2.kgName minCheck=0.96 exclude=noKg chopAfter=.

identifier ucscRetroInfo[1,2,4,5] dependency
"Link together Ucsc Retrogenes and ucsc retroGene alignments"
    $ucscRetroDb.ucscRetroInfo[].name unique
    $ucscRetroDb.ucscRetroAli[].qName 

identifier ucscRetroOrtho[1,2,4,5] dependency
"Link together Ucsc Retrogenes and ucsc retro orthlogy"
    $ucscRetroDb.ucscRetroAli[].qName dupeOk
    $ucscRetroDb.ucscRetroOrtho[].name

identifier ucscRetroExtFileId[1,2,4,5]
"External file ID for parent sequences for UCSC Retrogenes"
    $ucscRetroDb.ucscRetroExtFile[].id
    $ucscRetroDb.ucscRetroSeq[].extFile

identifier ucscRetroSeq4
"Sequences for GenBank sequences used as retrogene parents for version 4"
    hg19.ucscRetroSeq4.acc unique 
    hg19.ucscRetroCds4.id
    hg19.ucscRetroAli4.qName chopAfter=-
    hg19.ucscRetroInfo4.name chopAfter=-

identifier ucscRetroSeq5
"Sequences for GenBank sequences used as retrogene parents for version 5"
    hg19.ucscRetroSeq5.acc unique 
    hg19.ucscRetroCds5.id
    hg19.ucscRetroAli5.qName chopAfter=-
    hg19.ucscRetroInfo5.name chopAfter=-

identifier ucscRetroSeq1
"Sequences for GenBank sequences used as retrogene parents for version 1"
    mm9.ucscRetroSeq1.acc unique 
    mm9.ucscRetroCds1.id
    mm9.ucscRetroAli1.qName chopAfter=-
    mm9.ucscRetroInfo1.name chopAfter=-

identifier ucscRetroSeq2
"Sequences for GenBank sequences used as retrogene parents for version 2"
    mm10.ucscRetroSeq2.acc unique 
    mm10.ucscRetroCds2.id
    mm10.ucscRetroAli2.qName chopAfter=-
    mm10.ucscRetroInfo2.name chopAfter=-

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

# begin Gencode V7

#  = gencode genepreds with joining through wgEncodeGencodeAttrsV7
# wgEncodeGencodeBasicV7
# wgEncodeGencodeCompV7
# wgEncodeGencodePseudoGeneV7

#  = gencode genepreds with no associations
# wgEncodeGencodePolyaV7
# wgEncodeGencode2wayConsPseudoV7

# gencode association tables (joined through wgEncodeGencodeAttrsV7)
#wgEncodeGencodeAttrsV7
#wgEncodeGencodeExonSupportV7
#wgEncodeGencodeGeneSourceV7
#wgEncodeGencodePdbV7
#wgEncodeGencodePubMedV7
#wgEncodeGencodeRefSeqV7
#wgEncodeGencodeTagV7
#wgEncodeGencodeTranscriptSourceV7
#wgEncodeGencodeTranscriptSupportV7
#wgEncodeGencodeUniProtV7

identifier wgEncodeGencodeBasicAttrsV7
"Link together Gencode Basic Table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeAttrsV7.transcriptId
    hg19.wgEncodeGencodeBasicV7.name

identifier wgEncodeGencodeCompAttrsV7
"Link together Gencode Comprehensive Table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeAttrsV7.transcriptId
    hg19.wgEncodeGencodeCompV7.name

identifier wgEncodeGencodePseudoGeneAttrsV7
"Link together Gencode PseudoGene Table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeAttrsV7.transcriptId
    hg19.wgEncodeGencodePseudoGeneV7.name

identifier wgEncodeGencodeExonSupportV7
"Link together Gencode Exon Support table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeExonSupportV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV7
"Link together Gencode Gene Source table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeGeneSourceV7.geneId
    hg19.wgEncodeGencodeAttrsV7.geneId

identifier wgEncodeGencodePdbV7
"Link together Gencode Pdb table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodePdbV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.0397575

identifier wgEncodeGencodePubMedV7
"Link together Gencode Pubmed table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodePubMedV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV7
"Link together Gencode RefSeq table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeRefSeqV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.185827

identifier wgEncodeGencodeTagV7
"Link together Gencode Tag table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeTagV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV7
"Link together Gencode Transcript Source table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeTranscriptSourceV7.transcriptId
    hg19.wgEncodeGencodeAttrsV7.transcriptId

identifier wgEncodeGencodeTranscriptSupportV7
"Link together Gencode Transcript Support table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeTranscriptSupportV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.333503

identifier wgEncodeGencodeUniProtV7
"Link together Gencode UniProt Support table with Attributes table for May 2011 Data Version"
    hg19.wgEncodeGencodeUniProtV7.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV7.transcriptId minCheck=0.358209

# end Gencode V7

# begin Gencode V10

# gencode genepreds with no associations
# wgEncodeGencodePolyaV10
# wgEncodeGencode2wayConsPseudoV10

# gencode genepreds with joining through wgEncodeGencodeAttrsV10
identifier wgEncodeGencodeBasicAttrsV10
"Link together Gencode Basic Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV10.transcriptId
    hg19.wgEncodeGencodeBasicV10.name

identifier wgEncodeGencodeCompAttrsV10
"Link together Gencode Comprehensive Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV10.transcriptId
    hg19.wgEncodeGencodeCompV10.name

identifier wgEncodeGencodePseudoGeneAttrsV10
"Link together Gencode PseudoGene Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV10.transcriptId
    hg19.wgEncodeGencodePseudoGeneV10.name

# gencode association tables (joined through wgEncodeGencodeAttrsV10)
identifier wgEncodeGencodeExonSupportV10
"Link together Gencode Exon Support table with Attributes table"
    hg19.wgEncodeGencodeExonSupportV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV10
"Link together Gencode Gene Source table with Attributes table"
    hg19.wgEncodeGencodeGeneSourceV10.geneId
    hg19.wgEncodeGencodeAttrsV10.geneId

identifier wgEncodeGencodePdbV10
"Link together Gencode Pdb table with Attributes table"
    hg19.wgEncodeGencodePdbV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.02

identifier wgEncodeGencodePubMedV10
"Link together Gencode Pubmed table with Attributes table"
    hg19.wgEncodeGencodePubMedV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV10
"Link together Gencode RefSeq table with Attributes table"
    hg19.wgEncodeGencodeRefSeqV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.185827

identifier wgEncodeGencodeTagV10
"Link together Gencode Tag table with Attributes table"
    hg19.wgEncodeGencodeTagV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV10
"Link together Gencode Transcript Source table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSourceV10.transcriptId
    hg19.wgEncodeGencodeAttrsV10.transcriptId

identifier wgEncodeGencodeTranscriptSupportV10
"Link together Gencode Transcript Support table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSupportV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.30

identifier wgEncodeGencodeTranscriptionSupportLevelV10
"Link together Gencode Transcription Support Level table with Attributes table"
    hg19.wgEncodeGencodeTranscriptionSupportLevelV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.30

identifier wgEncodeGencodeUniProtV10
"Link together Gencode UniProt Support table with Attributes table"
    hg19.wgEncodeGencodeUniProtV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.358209

identifier wgEncodeGencodeAnnotationRemarkV10
"Link together Gencode Annotation Remark table with Attributes table"
    hg19.wgEncodeGencodeAnnotationRemarkV10.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV10.transcriptId minCheck=0.10 

# end Gencode V10

# begin Gencode V11

# gencode genepreds with no associations
# wgEncodeGencodePolyaV11
# wgEncodeGencode2wayConsPseudoV11

# gencode genepreds with joining through wgEncodeGencodeAttrsV11
identifier wgEncodeGencodeBasicAttrsV11
"Link together Gencode Basic Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV11.transcriptId
    hg19.wgEncodeGencodeBasicV11.name

identifier wgEncodeGencodeCompAttrsV11
"Link together Gencode Comprehensive Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV11.transcriptId
    hg19.wgEncodeGencodeCompV11.name

identifier wgEncodeGencodePseudoGeneAttrsV11
"Link together Gencode PseudoGene Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV11.transcriptId
    hg19.wgEncodeGencodePseudoGeneV11.name

# gencode association tables (joined through wgEncodeGencodeAttrsV11)
identifier wgEncodeGencodeExonSupportV11
"Link together Gencode Exon Support table with Attributes table"
    hg19.wgEncodeGencodeExonSupportV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV11
"Link together Gencode Gene Source table with Attributes table"
    hg19.wgEncodeGencodeGeneSourceV11.geneId
    hg19.wgEncodeGencodeAttrsV11.geneId

identifier wgEncodeGencodePdbV11
"Link together Gencode Pdb table with Attributes table"
    hg19.wgEncodeGencodePdbV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.02

identifier wgEncodeGencodePubMedV11
"Link together Gencode Pubmed table with Attributes table"
    hg19.wgEncodeGencodePubMedV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV11
"Link together Gencode RefSeq table with Attributes table"
    hg19.wgEncodeGencodeRefSeqV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.185827

identifier wgEncodeGencodeTagV11
"Link together Gencode Tag table with Attributes table"
    hg19.wgEncodeGencodeTagV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV11
"Link together Gencode Transcript Source table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSourceV11.transcriptId
    hg19.wgEncodeGencodeAttrsV11.transcriptId

identifier wgEncodeGencodeTranscriptSupportV11
"Link together Gencode Transcript Support table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSupportV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.29

identifier wgEncodeGencodeTranscriptionSupportLevelV11
"Link together Gencode Transcription Support Level table with Attributes table"
    hg19.wgEncodeGencodeTranscriptionSupportLevelV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.30

identifier wgEncodeGencodeUniProtV11
"Link together Gencode UniProt Support table with Attributes table"
    hg19.wgEncodeGencodeUniProtV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.358209

identifier wgEncodeGencodeAnnotationRemarkV11
"Link together Gencode Annotation Remark table with Attributes table"
    hg19.wgEncodeGencodeAnnotationRemarkV11.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV11.transcriptId minCheck=0.10 

# end Gencode V11

# begin Gencode V12

# gencode genepreds with no associations
# wgEncodeGencodePolyaV12
# wgEncodeGencode2wayConsPseudoV12

# gencode genepreds with joining through wgEncodeGencodeAttrsV12
identifier wgEncodeGencodeBasicAttrsV12
"Link together Gencode Basic Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV12.transcriptId
    hg19.wgEncodeGencodeBasicV12.name

identifier wgEncodeGencodeCompAttrsV12
"Link together Gencode Comprehensive Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV12.transcriptId
    hg19.wgEncodeGencodeCompV12.name

identifier wgEncodeGencodePseudoGeneAttrsV12
"Link together Gencode PseudoGene Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV12.transcriptId
    hg19.wgEncodeGencodePseudoGeneV12.name

# gencode association tables (joined through wgEncodeGencodeAttrsV12)
identifier wgEncodeGencodeExonSupportV12
"Link together Gencode Exon Support table with Attributes table"
    hg19.wgEncodeGencodeExonSupportV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV12
"Link together Gencode Gene Source table with Attributes table"
    hg19.wgEncodeGencodeGeneSourceV12.geneId
    hg19.wgEncodeGencodeAttrsV12.geneId

identifier wgEncodeGencodePdbV12
"Link together Gencode Pdb table with Attributes table"
    hg19.wgEncodeGencodePdbV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.02

identifier wgEncodeGencodePubMedV12
"Link together Gencode Pubmed table with Attributes table"
    hg19.wgEncodeGencodePubMedV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV12
"Link together Gencode RefSeq table with Attributes table"
    hg19.wgEncodeGencodeRefSeqV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.185827

identifier wgEncodeGencodeTagV12
"Link together Gencode Tag table with Attributes table"
    hg19.wgEncodeGencodeTagV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV12
"Link together Gencode Transcript Source table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSourceV12.transcriptId
    hg19.wgEncodeGencodeAttrsV12.transcriptId

identifier wgEncodeGencodeTranscriptSupportV12
"Link together Gencode Transcript Support table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSupportV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.29

identifier wgEncodeGencodeTranscriptionSupportLevelV12
"Link together Gencode Transcription Support Level table with Attributes table"
    hg19.wgEncodeGencodeTranscriptionSupportLevelV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.30

identifier wgEncodeGencodeUniProtV12
"Link together Gencode UniProt Support table with Attributes table"
    hg19.wgEncodeGencodeUniProtV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.358209

identifier wgEncodeGencodeAnnotationRemarkV12
"Link together Gencode Annotation Remark table with Attributes table"
    hg19.wgEncodeGencodeAnnotationRemarkV12.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV12.transcriptId minCheck=0.10 

# end Gencode V12

# begin Gencode V14

# gencode genepreds with no associations
# wgEncodeGencodePolyaV14
# wgEncodeGencode2wayConsPseudoV14

# gencode genepreds with joining through wgEncodeGencodeAttrsV14
identifier wgEncodeGencodeBasicAttrsV14
"Link together Gencode Basic Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV14.transcriptId
    hg19.wgEncodeGencodeBasicV14.name

identifier wgEncodeGencodeCompAttrsV14
"Link together Gencode Comprehensive Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV14.transcriptId
    hg19.wgEncodeGencodeCompV14.name

identifier wgEncodeGencodePseudoGeneAttrsV14
"Link together Gencode PseudoGene Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV14.transcriptId
    hg19.wgEncodeGencodePseudoGeneV14.name

# gencode association tables (joined through wgEncodeGencodeAttrsV14)
identifier wgEncodeGencodeExonSupportV14
"Link together Gencode Exon Support table with Attributes table"
    hg19.wgEncodeGencodeExonSupportV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV14
"Link together Gencode Gene Source table with Attributes table"
    hg19.wgEncodeGencodeGeneSourceV14.geneId
    hg19.wgEncodeGencodeAttrsV14.geneId

identifier wgEncodeGencodePdbV14
"Link together Gencode Pdb table with Attributes table"
    hg19.wgEncodeGencodePdbV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.02

identifier wgEncodeGencodePubMedV14
"Link together Gencode Pubmed table with Attributes table"
    hg19.wgEncodeGencodePubMedV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV14
"Link together Gencode RefSeq table with Attributes table"
    hg19.wgEncodeGencodeRefSeqV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.18

identifier wgEncodeGencodeTagV14
"Link together Gencode Tag table with Attributes table"
    hg19.wgEncodeGencodeTagV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV14
"Link together Gencode Transcript Source table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSourceV14.transcriptId
    hg19.wgEncodeGencodeAttrsV14.transcriptId

identifier wgEncodeGencodeTranscriptSupportV14
"Link together Gencode Transcript Support table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSupportV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.25

identifier wgEncodeGencodeTranscriptionSupportLevelV14
"Link together Gencode Transcription Support Level table with Attributes table"
    hg19.wgEncodeGencodeTranscriptionSupportLevelV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.30

identifier wgEncodeGencodeUniProtV14
"Link together Gencode UniProt Support table with Attributes table"
    hg19.wgEncodeGencodeUniProtV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.358209

identifier wgEncodeGencodeAnnotationRemarkV14
"Link together Gencode Annotation Remark table with Attributes table"
    hg19.wgEncodeGencodeAnnotationRemarkV14.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV14.transcriptId minCheck=0.10 

# end Gencode V14

# begin Gencode V16

# gencode genepreds with no associations
# wgEncodeGencodePolyaV16
# wgEncodeGencode2wayConsPseudoV16

# gencode genepreds with joining through wgEncodeGencodeAttrsV16
identifier wgEncodeGencodeBasicAttrsV16
"Link together Gencode Basic Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV16.transcriptId
    hg19.wgEncodeGencodeBasicV16.name

identifier wgEncodeGencodeCompAttrsV16
"Link together Gencode Comprehensive Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV16.transcriptId
    hg19.wgEncodeGencodeCompV16.name

identifier wgEncodeGencodePseudoGeneAttrsV16
"Link together Gencode PseudoGene Table with Attributes table"
    hg19.wgEncodeGencodeAttrsV16.transcriptId
    hg19.wgEncodeGencodePseudoGeneV16.name

# gencode association tables (joined through wgEncodeGencodeAttrsV16)
identifier wgEncodeGencodeExonSupportV16
"Link together Gencode Exon Support table with Attributes table"
    hg19.wgEncodeGencodeExonSupportV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.98202

identifier wgEncodeGencodeGeneSourceV16
"Link together Gencode Gene Source table with Attributes table"
    hg19.wgEncodeGencodeGeneSourceV16.geneId
    hg19.wgEncodeGencodeAttrsV16.geneId

identifier wgEncodeGencodePdbV16
"Link together Gencode Pdb table with Attributes table"
    hg19.wgEncodeGencodePdbV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.02

identifier wgEncodeGencodePubMedV16
"Link together Gencode Pubmed table with Attributes table"
    hg19.wgEncodeGencodePubMedV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId  minCheck=0.635488

identifier wgEncodeGencodeRefSeqV16
"Link together Gencode RefSeq table with Attributes table"
    hg19.wgEncodeGencodeRefSeqV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.05

identifier wgEncodeGencodeTagV16
"Link together Gencode Tag table with Attributes table"
    hg19.wgEncodeGencodeTagV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.373378

identifier wgEncodeGencodeTranscriptSourceV16
"Link together Gencode Transcript Source table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSourceV16.transcriptId
    hg19.wgEncodeGencodeAttrsV16.transcriptId

identifier wgEncodeGencodeTranscriptSupportV16
"Link together Gencode Transcript Support table with Attributes table"
    hg19.wgEncodeGencodeTranscriptSupportV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.25

identifier wgEncodeGencodeTranscriptionSupportLevelV16
"Link together Gencode Transcription Support Level table with Attributes table"
    hg19.wgEncodeGencodeTranscriptionSupportLevelV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.30

identifier wgEncodeGencodeUniProtV16
"Link together Gencode UniProt Support table with Attributes table"
    hg19.wgEncodeGencodeUniProtV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.358209

identifier wgEncodeGencodeAnnotationRemarkV16
"Link together Gencode Annotation Remark table with Attributes table"
    hg19.wgEncodeGencodeAnnotationRemarkV16.transcriptId dupeOk
    hg19.wgEncodeGencodeAttrsV16.transcriptId minCheck=0.10 

# end Gencode V16

identifier wgEncodeGencodeClassesV3Hg19
"Link together Gencode gene model (Known) and class for July 2009 Data Version"
    hg19.wgEncodeGencodeClassesV3.name
    hg19.wgEncodeGencodeAutoV3.name unique
    hg19.wgEncodeGencodeManualV3.name unique
    hg19.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 vegaGeneId external=VegaGene
"Link together various VEGA curated gene annotation"
    $vegaGeneDbs.vegaGtp.transcript
    $vegaGeneDbs.vegaGene.name
    $vegaGeneDbs.vegaPseudoGene.name
    $vegaGeneDbs.vegaPep.name

identifier vegaName
"Link together various VEGA human curated gene annotation"
    $gbd.vegaInfo.transcriptId
    $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

identifier decipherId
"DECIPHER ID"
$hg.decipher.name dupeOk
$hg.decipherRaw.id
$hg.knownToDecipher.value
$hg.knownCanonToDecipher.value

# Microarray stuff.

identifier agilentHumanProbeId external=agilent fuzzy
"Agilent Human CGH/CNV array probe ID"
    $hg.agilentCgh1x1m.name
    $hg.agilentHrd1x1m.name
    $hg.agilentCghSnp2x400k.name
    $hg.agilentCgh2x400k.name
    $hg.agilentCghSnpCancer4x180k.name
    $hg.agilentCghSnp4x180k.name
    $hg.agilentCgh4x180k.name
    $hg.agilentCgh8x60k.name
    $hg.agilentCgh244a.name
    $hg.agilentCgh105a.name
    $hg.agilentCgh44k.name

identifier agilentMouseProbeId external=agilent fuzzy
"Agilent Mouse CGH/CNV array probe ID"
    $mm.agilentCgh1x1m.name
    $mm.agilentCgh4x180k.name
    $mm.agilentCgh244a.name
    $mm.agilentCgh105a.name

identifier agilentRatProbeId external=agilent fuzzy
"Agilent Rat CGH/CNV array probe ID"
    $rn.agilentCgh1x1m.name
    $rn.agilentCgh4x180k.name
    $rn.agilentCgh244a.name
    $rn.agilentCgh105a.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 affyExonTissuesGsId
"UCSC Gene IDs for affyExonTissuesGs."
    $hg.affyExonTissuesGs.name
    $hg.knownGene.name minCheck=0.95

identifier affyExonTissuesGsMedianId
"UCSC Gene IDs for affyExonTissuesGsMedian."
    $hg.affyExonTissuesGsMedian.name
    $hg.knownGene.name minCheck=0.95

identifier affyExonTissuesGsMedianDistId
"UCSC Gene IDs for affyExonTissuesGsMedianDist."
    $hg.affyExonTissuesGsMedianDist.query dupeOk
    $hg.affyExonTissuesGsMedianDist.target
    $hg.knownGene.name minCheck=0.95

identifier gnfHumanAtlas2
"Novartis GNF Human gene probe ID"
    hgFixed.gnfHumanAtlas2All.name
    hgFixed.gnfHumanAtlas2AllRatio.name unique
    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.knownToGnfRatAtlas2.value
    $rn.rgdGene2ToGnfRatAtlas2.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 affyU133WithChop
# chopBefore and chopAfter needed for hg16, 17 and 18.
"Affymetrix Human U133 chip identifiers"
     hg16,hg17,hg18.affyU133.qName dupeOk chopBefore=U133A: chopBefore=U133B: chopAfter=;
     hg16,hg17,hg18.knownToU133.value

identifier affyU133
"Affymetrix Human U133 chip identifiers"
     $hg,!hg16,!hg17,!hg18.affyU133.qName dupeOk
     $hg,!hg16,!hg17,!hg18.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
    $rn.rgdGene2ToRAE230.value

identifier affyU34A
"Affymetrix Rat U34A chip identifiers"
    $rn.affyU34A.qName dupeOk
    $rn.knownToU34A.value
    $rn.rgdGene2ToU34A.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"
    $gbd.chainSelf.id
    $gbd.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 danRerBacSangerName
"Sanger's identifiers for BAC Clones"
    danRer3,danRer4.bacCloneXRef.sangerName dupeOk
    danRer3,danRer4.bacCloneAlias.sangerName minCheck=0.97

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

set notProteinAccession !echTel2,!cerSim1,!braFlo2,!petMar2,!dm3,!sorAra2

identifier proteinAccession typeOf=genbankAccession fuzzy
"Genbank protein accession."
    $kgDb.kgProtAlias.alias
    $kgDb.kgSpAlias.alias minCheck=0.1
    $kgDb.kgXref.protAcc
    $gbd,$notProteinAccession.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,!sacCer3.est.qName $split full
    $gbd,!sacCer2,!sacCer3,!caeJap1.intronEst.qName $split
    sacCer2,sacCer3.est.qName splitPrefix=%\_ full
    sacCer2,sacCer3.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,!mm10,!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
    mm10.mrnaRefseq.mrna minCheck=0.30
    hg17.mrnaRefseq.mrna minCheck=0.80
    $rn.mrnaRefseq.mrna minCheck=0.03
    $gbd,!hg17,!hg18,!hg19,!mm7,!mm8,!mm9,!mm10,!rn4.spMrna.mrnaID minCheck=0.98
    $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,!mm10.knownToRefSeq.value minCheck=0.98
    hg18,mm7,mm8,mm9,mm10.knownToRefSeq.value minCheck=0.96
    hg16,hg17.knownToRefSeq.value minCheck=0.93
    $kgDb.refSeqKg.refseq minCheck=0.60
    $ccdsDb,!hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.32
    $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=0.91
    $dm,!dm1.flyBaseToRefSeq.value minCheck=0.94
    $mm.mrnaRefseq.mrna minCheck=0.03
    $mm.dupSpMrna.mrnaID minCheck=0.60
    $mm,!mm8,!mm9,!mm10.dupSpMrna.dupMrnaID minCheck=0.20
    mm10.dupSpMrna.dupMrnaID minCheck=0.19
    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
    $rn.rgdGene2ToRefSeq.value minCheck=0.95

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=0.40
    mm10.geneNetworkId.id minCheck=0.40
    hg19.geneNetworkId.id minCheck=0.40
    rn3.geneNetworkId.id minCheck=0.40

identifier rgdGene2ToRefSeqId typeOf=mrnaAccession
"RefSeq mRNA accession in rgdGene2ToRefSeq table"
    $kgDb.rgdGene2ToRefSeq.value dupeOk
    rn4.geneNetworkId.id minCheck=0.30

identifier kgOldId
"Old Known Gene ID - the genbank accession of the representative mRNA"
    hg17.kgOld.name dupeOk
    hg17.kgXrefOld.kgId  minCheck=.95

identifier rn4KgPrevious
"rn4 knownGenePrevious was knownGene"
    rn4.knownGenePrevious.name dupeOk
    rn4.kgXrefPrevious.kgId

identifier knownGeneId dependency
"Known Gene ID - the genbank accession of the representative mRNA"
    $kgDb.knownGene.name dupeOk
    $kgDb.knownCanonToDecipher.name
    $kgDb.knownToDecipher.name
    $kgDb.knownToKeggEntrez.name
    hg16.hg17Kg.name minCheck=.30
    $kgDb2.knownExpDistance.query
    $kgDb2.knownExpDistance.target
    $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.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,!mm10.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.knownToWikipedia.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 exclude=
    $kgDb.kg3ToKg4.newId minCheck=0.5 exclude=
    $kgDb,!hg19.kg4ToKg5.newId minCheck=0.5 exclude=
    $kgDb.kg5ToKg6.newId exclude=
    $kgDb.kg6ToKg7.newId exclude=
    $kgDb,!hg16.kgTargetAli.qName full
    hg19.knownGeneTxMrna.name
    hg19.knownGeneTxPep.name

identifier knownGeneOld5Id dependency
"Previous UCSC Gene build"
    $kgDb.knownGeneOld5.name
    $kgDb.kg5ToKg6.oldId full
    $kgDb.kgXrefOld5.kgID full

identifier knownGeneOldId dependency
"Still-previous UCSC Genes build"
    $kgDb,!hg19.knownGeneOld4.name
    $kgDb.kg4ToKg5.oldId full

identifier knownGeneOld3Id dependency
"Still-still previous UCSC Genes build"
    $kgDb.knownGeneOld3.name
    $kgDb.kg3ToKg4.oldId full

identifier knownGeneOld2Id dependency
"Old knownGene (KGII) and kgXref tables kept after KGIII implementation - still needed?"
    $kgDb.knownGeneOld2.name dupeOk
    $kgDb.kgXrefOld2.kgID full
    $kgDb.humanBlastTab.query
    $kgDb.humanBlastTab.target

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

identifier rgdGene2IsoformCluster
"ID of a cluster of overlapping rgdGene2 genes"
    $kgDb.rgdGene2Canonical.clusterId
    $kgDb.rgdGene2Isoforms.clusterId full

# known relationship for both KG2 and KG3, but doesn't work across dbs.
identifier knownXref
"Swissprot IDs"
    $hg.kgXref.spID  dupeOk
    proteome.spXref2.accession
    proteome.hgncXref.uniProt

identifier tRNAName
"tRNA track name"
    hg19.kgXref.tRnaName exclude=
    hg19.tRNAs.name minCheck=0.50

identifier ccdsGeneId
"CCDS Gene ID"
    $ccdsDb.ccdsGene.name dupeOk
    $ccdsDb.ccdsInfo.ccds full
    $ccdsDb.ccdsKgMap.ccdsId
    $ccdsDb.ccdsNotes.ccds

identifier ctdGeneSymbol
"CTD Gene Symbol"
    hgFixed.ctdSorted.GeneSymbol dupeOk
    $hg.kgXref.geneSymbol minCheck=0.30

identifier rdmrGene
"R-DMR Gene"
    $hg.rdmr.name dupeOk
    $hg.rdmrRaw.gene minCheck=0.95

identifier gadId
"GAD Gene ID"
    $hg.kgXref.geneSymbol dupeOk
    $hg.gad.name minCheck=0.94

identifier gadAllId
"GAD Gene Symbol in raw input"
    $hg.kgXref.geneSymbol dupeOk
    $hg.gadAll.geneSymbol minCheck=0.95

identifier hugeId
"HuGE Gene ID"
    $hg.kgXref.geneSymbol dupeOk
    $hg.huge.geneSymbol minCheck=0.89

# 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.

set notDbStsId !sacCer3,!cerSim1,!petMar2,!braFlo2,!echTel2,!sorAra2

identifier dbStsId external=dbSts fuzzy
"NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
    $hg.all_sts_primer.qName chopBefore=dbSTS_
    $gbd,$notDbStsId.all_sts_seq.qName
    $gbd,$notDbStsId.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

set notStsName !sacCer3,!cerSim1,!petMar2,!braFlo2,!echTel2,!sorAra2

identifier stsName fuzzy
"STS (Sequenced Tagged Site, aka mapping sequence) Name"
    $hg.fishClones.stsNames comma
    $gbd,$notStsName.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,!mm10.all_sts_primer.qName chopBefore=_ minCheck=0.99
    mm7,mm8,mm9,mm10.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 minCheck=0.99

identifier hgIkmcName
"IKMC (knockoutmouse.org) mapped gene name"
    $hg.hgIkmc.name dupeOk
    $hg.hgIkmcExtra.name minCheck=0.99

# "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
    $rn.rgdGeneXref3.geneSymbol

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

set notWormBaseId !rn3,!cerSim1,!petMar2,!braFlo2,!echTel2,!sorAra2

identifier wormBaseId external=WormBase dependency
"WormBase (C. elegans) ORF ID"
    $ce.sangerGene.name
    $gbd,$notWormBaseId.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

set notFlyBaseGeneId !cerSim1,!hg17,!hg18,!danRer3,!mm7,!mm8,!mm9,!mm10,!rn3,!rn4,!ce2,!ce6,!ce9,!ce10,!sacCer1,!sacCer2,!sacCer3,!petMar2,!braFlo2,!echTel2,!sorAra2

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
    $gbd,$notFlyBaseGeneId.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,sacCer3.dmBlastTab.target minCheck=0.90

identifier flyBase2004IdDp external=FlyBase
"FlyBase Xref as of 2004 for dp3"
    dp3.flyBase2004Xref.name
    dp3.flyBaseGene.name

identifier flyregId external=FlyReg
"FlyReg motif name"
    $dm.flyregMotif.name
    $dm.flyreg.name minCheck=0.8
    $dm.flyreg2.name minCheck=0.8

identifier sgdIsoformCluster
"Overlapping (after splicing) SGD (Yeast) transcripts"
    $sacCer.sgdCanonical.clusterId
    $sacCer.sgdIsoforms.clusterId full

identifier sgdProtHomologId
"sacCer protHomolog protein ID"
    $sacCer.protHomolog.proteinID dupeOk
    $sacCer.samSubdir.proteinId

identifier sgdId external=SGD
"Sacchromyces Genome Database ID - Coding or other"

set notSgdCodingId !cerSim1,!petMar2,!braFlo2,!echTel2,!sorAra2

identifier sgdCodingId typeOf=sgdId dependency
"Sacchromyces Genome Database ID"
    $sacCer.sgdGene.name
    $gbd,$notSgdCodingId.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=0.88

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


# New RGD Genes Family Identifiers

identifier rgdGene2IdRaw external=RGD
"Raw RGD Genes ID"
    $rn.rgdGene2.name chopBefore=RGD:
    $rn.genes_rat.gene_rgd_id minCheck=0.40 

identifier rgdGene2Id external=RGD
"RGD Genes ID"
    $rn.rgdGene2.name
    $rn.rgdGenePathway.geneId minCheck=0.75
    $rn.rgdGene2BlastTab.query minCheck=0.75
    $rn.rgdGene2BlastTab.target minCheck=0.75
# disable for now    $rn.scBlastTab.query minCheck=0.75
    $rn.mmBlastTab.query minCheck=0.75
    $rn.hgBlastTab.query minCheck=0.75
    $rn.dmBlastTab.query minCheck=0.75
# disable for now    $rn.drBlastTab.query minCheck=0.75
    $rn.ceBlastTab.query minCheck=0.75
    $rn.rgdGene2ToDisplayId.name minCheck=0.75
    $rn.rgdGene2ToUniProt.name minCheck=0.75
    $rn.rgdGene2ToPDB.name minCheck=0.75
    $rn.rgdGene2ToPfam.name minCheck=0.75
    $rn.rgdGene2Xref.rgdGeneId minCheck=0.75
    $rn.rgdGene2Pep.name minCheck=0.75
    $rn.rgdGene2ToDescription.name minCheck=0.65
    $rn.rgdGene2Pep.name minCheck=0.75
    $rn.rgdGene2ToSymbol.rgdId minCheck=.75
    $rn.rgdGene2ToU34A.name minCheck=.75
    $rn.rgdGene2ToSuper.name minCheck=.75
    $rn.rgdGene2ToRAE230.name minCheck=.75
    $rn.rgdGene2ToRefSeq.name minCheck=.75
    $rn.rgdGene2ToLocusLink.name minCheck=.75
    $rn.rgdGene2ToGnfAtlas2.name minCheck=.75
    $rn.rgdGene2ToKeggEntrez.name minCheck=.75
    $rn.rgdGene2ToGenbankAll.name minCheck=.75
    $rn.rgdGene2ToGenbank.name minCheck=.75
    $rn.rgdGene2ToEnsembl.name minCheck=.75
    $rn.rgdGene2ToCdsSnp.name minCheck=.75
    $rn.affyExonTissuesGsMedianDistRgdGene2.query minCheck=.75
    $rn.affyExonTissuesGsMedianDistRgdGene2.target minCheck=.75
    $rn.affyExonTissuesGsMedianRgdGene2.name minCheck=.75
    $rn.affyExonTissuesGsRgdGene2.name minCheck=.75
    $rn.gnfAtlas2RgdGene2Distance.query minCheck=.75
    $rn.gnfAtlas2RgdGene2Distance.target minCheck=.75
    $rn.rgdGene2Canonical.transcript minCheck=.75
    $rn.rgdGene2Isoforms.transcript minCheck=.75
    $rn.rgdGene2KeggPathway.rgdId minCheck=.75

identifier rgdPathwayId external=RGD
"RGD Pathway ID"
    $rn.rgdPathway.pathwayId
    $rn.rgdGenePathway.pathwayId minCheck=.90

# 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

set notEnsemblTranscriptId !braFlo2,!ce10,!cerSim1,!felCat3

identifier ensemblTranscriptId external=Ensembl dependency
"Ensembl Transcript ID"
    $ensGeneDb,$notEnsemblTranscriptId.ensGene.name chopAfter=. dupeOk
    $gbd,$notEnsemblTranscriptId.ensGeneXref.transcript_name chopAfter=. minCheck=0.95
    $ensGeneDb,$notEnsemblTranscriptId.ensGtp.transcript chopAfter=. minCheck=0.94
    $ensGeneDb,$notEnsemblTranscriptId.ensPep.name chopAfter=. minCheck=0.93
    $gbd,$notEnsemblTranscriptId.ensTranscript.transcript_name chopAfter=. minCheck=0.20
    $gbd,$notEnsemblTranscriptId.ensInfo.name minCheck=0.9
    $ensGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.96
    $ensGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96
    $kgDb.knownToEnsembl.value chopAfter=.
    $kgDb.rgdGene2ToEnsembl.value chopAfter=.
    $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 ensemblTranscriptWGS external=Ensembl dependency
"Ensembl Transcript ID for WGS assemblies"
    $ensGeneWgs.ensGene.name dupeOk
    $ensGeneWgs.ensGtp.transcript minCheck=0.99
    $ensGeneWgs.ensPep.name minCheck=0.99
    $ensGeneWgs.ensInfo.name minCheck=0.99
    $ensGeneWgs.ensemblToGeneName.name minCheck=0.99
    $ensGeneWgs.ensemblSource.name minCheck=0.99

identifier ensemblGeneScaffold external=Ensembl dependency
"Ensembl gene scaffold table chrom names"
    $ensGeneScaffold.chromInfo.chrom
    $ensGeneScaffold.ensemblGeneScaffold.chrom

# to avoid the error on assemblies with Ensembl Gene scaffolds:
# Error: 7771 duplicates in vicPac1.ensGene.name including 'ENSVPAT00000000004'
# list on this avoid list:
set notEnsemblTranscriptId2 !ce6,!ce9,!ce10,!choHof1,!dipOrd1,!echTel1,!echTel2,!eriEur1,!felCat3,!micMur1,!ochPri2,!proCap1,!pteVam1,!sorAra1,!sorAra2,!tarSyr1,!tupBel1,!vicPac1

#pulled this line into its own rule to reflect lack of dependency
identifier ensemblTranscriptId2 external=Ensembl
"Ensembl Transcript ID"
    $gbd,$notEnsemblTranscriptId2.ensGene.name chopAfter=.
    $ccdsDb.ccdsInfo.mrnaAcc minCheck=0.30 

identifier ensemblTranscriptIdCe external=Ensembl dependency
"Ensembl Transcript ID for C. elegans"
    $ce.ensGene.name dupeOk
    $ce.ensGtp.transcript minCheck=0.98
    $ce.ensPep.name minCheck=0.98
    $ce.ensemblToGeneName.name
    $ce.ensemblSource.name

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
    felCat3.ensemblToGeneName.name minCheck=0.99
    felCat3.ensemblSource.name minCheck=0.99

# UCSC to Ensembl chrom name translation
identifier ensemblLinkId external=Ensembl dependency
"Ensembl Links from hgTracks"
    hg18,hg19,anoCar2,bosTau6,calJac3,oryCun2,panTro4,xenTro3,mm10,musFur1.chromInfo.chrom
    hg18,hg19,anoCar2,bosTau6,calJac3,oryCun2,panTro4,xenTro3,mm10,musFur1.ucscToEnsembl.ucsc

identifier ucscToEnsembl external=Ensembl dependency
"UCSC to Ensembl chrom name translation"
    hg18,hg19,panTro4.ucscToEnsembl.ensembl
    hg18,hg19,panTro4.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
    $gbd.knownToKeggEntrez.value
    $gbd.rgdGene2ToKeggEntrez.value

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,!mm9,!mm10.knownGene.name minCheck=0.50
    hg16.knownGene.name minCheck=0.05
    hg18,hg19,mm9,mm10.kgXref.geneSymbol minCheck=0.84

# 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 hg18 using snp130:
    hg18.gwasCatalog.name

identifier snpExceptions130
"Annotations of unusual conditions in dbSNP version 130"
    $gbd.snp130ExceptionDesc.exception
    $gbd.snp130Exceptions.exception

identifier snpName131
"dbSNP version 131 rs* identifiers"
    $gbd.snp131.name dupeOk
    $gbd.snp131Exceptions.name minCheck=.999
    $gbd.snp131Seq.acc minCheck=.93
    $gbd.snp131CodingDbSnp.name minCheck=.90
    $hg.snp131OrthoPt2Pa2Rm2.name
    hg18.snpArrayIlluminaHuman660W_Quad.name minCheck=0.90
    hg18.snpArrayIlluminaHumanCytoSNP_12.name minCheck=0.95
    hg18.snpArrayIlluminaHumanOmni1_Quad.name minCheck=0.85

identifier snpExceptions131
"Annotations of unusual conditions in dbSNP version 131"
    $gbd.snp131ExceptionDesc.exception
    $gbd.snp131Exceptions.exception

identifier snpName132
"dbSNP version 132 rs* identifiers"
    $gbd.snp132.name dupeOk
    $gbd.snp132Common.name
    $gbd.snp132Flagged.name
    $gbd.snp132Mult.name
    $gbd.snp132Seq.acc minCheck=.98
    $gbd.snp132CodingDbSnp.name minCheck=.90
    $hg.snp132OrthoPt2Pa2Rm2.name

identifier snpName135
"dbSNP version 135 rs* identifiers"
    $gbd.snp135.name dupeOk
    $gbd.snp135Common.name
    $gbd.snp135Flagged.name
    $gbd.snp135Mult.name
    $gbd.snp135Seq.acc minCheck=.98
    $gbd.snp135CodingDbSnp.name minCheck=.90
    $hg.snp135OrthoPt3Pa2Rm2.name

identifier snpName137
"dbSNP version 137 rs* identifiers"
    $gbd.snp137.name dupeOk
    $gbd.snp137Common.name
    $gbd.snp137Flagged.name
    $gbd.snp137Mult.name
    $gbd.snp137Seq.acc minCheck=.98
    $gbd.snp137CodingDbSnp.name minCheck=.90
    $hg.snp137OrthoPt3Pa2Rm2.name
    # gwasCatalog SNPs were mapped to hg19 using snp137.  Move this down to snp138
    # and update trackDb settings if we remap to new dbSNP version:
    hg19.gwasCatalog.name minCheck=0.99

# 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
    $hg.omim2gene.geneId minCheck=0.60
    $rn.rgdGene2ToLocusLink.value minCheck=0.70

identifier omimLocationId external=OMIM
"Online Mendelian Inheritance in Man (OMIM) Location ID"
    $hg.omimLocation.name dupeOk exclude=0
    $hg.omimGeneMap.omimId full minCheck=0.08 

identifier omimAvSnpId external=OMIM
"Online Mendelian Inheritance in Man (OMIM) AV SNP ID"
    $hg.omimAvSnp.name dupeOk exclude=0

identifier omimId external=OMIM
"Online Mendelian Inheritance in Man (OMIM) ID"
    $gbd.refLink.omimId dupeOk exclude=0
    $hg.omimGene2.name minCheck=0.90
    $hg.omimPhenotype.omimId minCheck=0.75
    $hg.omimGeneMap.omimId minCheck=0.85
    $hg.omim2gene.omimId minCheck=0.60

identifier omimAvId external=OMIM
"Online Mendelian Inheritance in Man (OMIM) AV ID"
    $hg.omimAv.avId dupeOk exclude=0
    $hg.omimAvRepl.avId minCheck=0.90
    $hg.omimAvSnp.name minCheck=0.90

identifier omimGene2Id
"omimGene2 ID"
    $hg.omimGene2.name dupeOk
    $hg.omimGeneSymbol.omimId minCheck=0.90
    $hg.omimAv.omimId minCheck=0.90
    $hg.omimAvRepl.omimId minCheck=0.90
    $hg.omimPhenotype.omimId minCheck=0.75
    $hg.refLink.omimId exclude=0 minCheck=0.98
    $hg.omim2gene.omimId minCheck=0.60

identifier omimPhenotypeId
"OMIM Phenotype ID"
    $hg.omimPhenotype.phenotypeId dupeOk

identifier evoCpgId
"Evo Cpg ID"
    $hg.evoCpg.name dupeOk

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.bgiGeneInfo.name minCheck=0.1
    $galGal.bgiGenePep.name minCheck=0.95
    $galGal.bgiGeneSnp.geneName minCheck=0.1

# Other Identifiers

identifier mm10Patch1ExtFileId
"External file ID for mm10 patch1 sequences"
    mm10.extMm10Patch1.id
    mm10.seqMm10Patch1.extFile

identifier hg19Patch10ExtFileId
"External file ID for hg19 patch10 sequences"
    hg19.extHg19Patch10.id
    hg19.seqHg19Patch10.extFile

identifier hg19Patch9ExtFileId
"External file ID for hg19 patch9 sequences"
    hg19.extHg19Patch9.id
    hg19.seqHg19Patch9.extFile

identifier hg19Patch5ExtFileId
"External file ID for hg19 patch5 sequences"
    hg19.extHg19Patch5.id
    hg19.seqHg19Patch5.extFile

identifier hg19Patch2ExtFileId
"External file ID for hg19 patch2 sequences"
    hg19.extHg19Patch2.id
    hg19.seqHg19Patch2.extFile

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
     felCat4.blastHg18KG.qName
     dm2.blastHg18KG.qName
     fr2.blastHg18KG.qName
     mm8.blastHg18KG.qName
     ce4.blastHg18KG.qName
     ce10.blastHg18KG.qName
     dm3.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
     ailMel1.blastHg18KG.qName
     oryCun2.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
     felCat4.blastHg18KG.qName
     dm2.blastHg18KG.qName
     fr2.blastHg18KG.qName
     mm8.blastHg18KG.qName
     ce4.blastHg18KG.qName
     ce10.blastHg18KG.qName
     dm3.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
     ailMel1.blastHg18KG.qName
     oryCun2.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 blastCe9SG01
"ce9 proteins 01"
     $gbd.blastCe9SG.qName dupeOk
     ce9.blastSGPep01.name
     ce9.blastSGRef01.acc

identifier tfbsCons
"transcription factor binding sites"
    $hg.tfbsConsSites.name dupeOk
    $hg.tfbsConsFactors.name

identifier cosmic
"Catalogue Of Somatic Mutations In Cancer"
    $hg.cosmic.name
    $hg.cosmicRaw.cosmic_mutation_id

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"
    # Using dupeOk here because there are some case-sensitive allele name diffs (ugh)
    $mm.jaxAllelePheno.allele dupeOk
    $mm.jaxAlleleInfo.name minCheck=0.89
    $mm.jaxAllele.name minCheck=0.89

identifier jaxPhenotypeName external=MGI
"Jackson Labs/MGI Phenotype name: representative transcript ID"
    $mm.jaxPhenotype.name dupeOk
    $mm.jaxPhenotypeAlias.name
    mm8,mm9,mm10.jaxAllelePheno.transcript minCheck=0.9

identifier jaxGeneTrapName external=MGI
"Jackson Labs/MGI GeneTrap name: concatenated representative transcript ID and allele ID"
    $mm.jaxGeneTrap.name dupeOk
    $mm.jaxGeneTrapInfo.name

#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 fuzzy
"UCSC Genes and transMapGene table"
    hgFixed.transMapGeneUcscGenes.id 
    $kgDb3.knownGene.name

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=-

identifier hg18ContigDiff
"contig difference track"
    hg18.gold.frag dupeOk $split
    hg18.hg18ContigDiff.name

identifier hg19ContigDiff
"contig difference track"
    hg19.gold.frag dupeOk
    hg19.hg19ContigDiff.name

# lsSnpPdb tables
identifier lsSnpPdbProtId
"lsSnpPdb table protId field"
    uniProt.extDbRef.acc dupeOk
    $lsSnpDb.lsSnpPdb.protId

identifier lsSnpPdbKgId
"lsSnpPdb table protId field"
    $lsSnpDb.kgXref.spID dupeOk
    $lsSnpDb.lsSnpPdb.protId

identifier lsSnpPdbPdbId
"lsSnpPdb table pdbId field"
    uniProt.extDbRef.extAcc1 dupeOk
    $lsSnpDb.lsSnpPdb.pdbId minCheck=0.99

identifier lsSnpPdbSnpHg18
"lsSnpPdb table snpId field"
    hg18.snp129.name dupeOk
    hg18.lsSnpPdb.snpId

identifier lsSnpPdbSnpHg19
"lsSnpPdb table snpId field"
    hg19.snp131.name dupeOk
    hg19.lsSnpPdb.snpId

identifier consIndelsId
"consIndels tables name field"
    hg17,hg18,hg19.consIndelsHgMmCanFam.name
    hg17,hg18,hg19.consIndelsHgMmCanFamConf.id

# publication track info 

identifier pubsArticleId external=pubTools
"internal ID of article, this is different from pubmed, doi or piis, generated during download "
    $gbd.pubsBlat.name dupeOk
    $gbd.pubsBlatPsl.articleId
    hgFixed.pubsArticle.articleId
    hgFixed.pubsSequenceAnnot.articleId
    hgFixed.pubsArticle.articleId

identifier pubsSequenceId external=pubTools
"ID of sequence found in article "
    hgFixed.pubsSequence.annotId dupeOk
    $gbd.pubsBlat.seqIds comma
    $gbd.pubsBlatPsl.qName

identifier pubsMarkerId
"keyword ('marker') found in an article, like a SNP/band/gene/etc"
    hgFixed.pubsMarkerAnnot.markerId dupeOk
    $gbd.pubsMarkerBand.name 
    $gbd.pubsMarkerSnp.name 
    $gbd.pubsMarkerGene.name 

identifier ceuBcellRNASeqId
"ID of ceuBcellRNASeq"
    $hg.ceuBcellRNASeq.name dupeOk

identifier geneReviewsId
"GeneReviews article ID"
    hg18,hg19.kgXref.geneSymbol dupeOk 
    hg18,hg19.geneReviews.name minCheck=0.85

identifier geneReviewsRefGeneId
"ID of GeneReviewsRefGene"
    hg18,hg19.kgXref.geneSymbol dupeOk
    hg18,hg19.geneReviewsRefGene.geneSymbol minCheck=0.85

identifier mouseStrains
"chrom names in the mouse alternate strains"
    mm10.chromInfo.chrom
    mm10.altSeqLiftOverPslStrains1.tName

# 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.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 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
    assemblyFrags
    affyDrosDev%
    ancientRepeat
    axtInfo
    bam%
    blatFr1
    chromInfo
    contamination
    cpgIsland%
    ctgPos
    ctgPos2
    cytoBand
    cytoBandIdeo
    evofold
    evofoldV2
    exoniphy
    firstEF
    gbLoaded
    gbDelete_tmp
    gc5Base
    gc5BaseBw
    gcPercent
    genscanSubopt
    %gold
    grp
    hgFindSpec%
    history
    intronEst
    knownAlt
    metaDb%
    microsat
    miRNA
    nestedRepeats
    nestedRepeatsRM327
    numtSAssembled
    numtS
    numtSMitochondrion
    numtSMitochondrionChrPlacement
    qPcrPrimers
    quality
    qualityBw
    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
    ucscGenePfam
    uwNucOccA375
    uwNucOccDennis
    uwNucOccMec
    ws210Gene
    snp132ExceptionDesc
    snp135ExceptionDesc
    snp137ExceptionDesc

tablesIgnored $kgDb
    pbAaDist_
    pbAnomLimit
    pbResAvgStd
    pbStamp
    pep%Dist

tablesIgnored hg19
    affyCytoScan
    affyExonProbe%
    allHg19RS_BW
    altSeqHaplotypes
    altSeqHaplotypesP9
    altSeqLiftOverPsl
    altSeqLiftOverPslP9
    altSeqPatches
    altSeqPatchesP9
    altSeqPatchesP10
    bacEndPairsBad
    bamAllNumtSSorted
    coriellDelDup
    lincRNAsCTAdipose
    lincRNAsCTAdrenal
    lincRNAsCTBrain
    lincRNAsCTBrain_R
    lincRNAsCTBreast
    lincRNAsCTColon
    lincRNAsCTForeskin_R
    lincRNAsCTHeart
    lincRNAsCTKidney
    lincRNAsCTLiver
    lincRNAsCTLung
    lincRNAsCTLymphNode
    lincRNAsCTOvary
    lincRNAsCTPlacenta_R
    lincRNAsCTProstate
    lincRNAsCTSkeletalMuscle
    lincRNAsCTTestes
    lincRNAsCTTestes_R
    lincRNAsCTThyroid
    lincRNAsCTWhiteBloodCell
    lincRNAsCThLF_r1
    lincRNAsCThLF_r2
    lincRNAsTranscripts
    xlincRNAs
    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
    hinv70Coding
    hinv70NonCoding
    hinv70PseudoGene
    uMassBrainHistone%
    dhcBamDenisova
    dhcHumDerDenAncAllFixed
    dhcHumDerDenAncAllFixedDbSnp
    dhcHumDerDenAncAllHighFreq
    dhcHumDerDenAncCcdsFrameshiftCodingFixed
    dhcHumDerDenAncCcdsFrameshiftCodingFixedDbSnp
    dhcHumDerDenAncCcdsFrameshiftCodingHighFreq
    dhcHumDerDenAncCcdsInFrameNonsynFixed
    dhcHumDerDenAncCcdsNonsynFixed
    dhcHumDerDenAncCcdsNonsynFixedDbSnp
    dhcHumDerDenAncCcdsNonsynHighFreq
    dhcHumDerDenAncCcdsSpliceFixed
    dhcHumDerDenAncCcdsSpliceFixedDbSnp
    dhcHumDerDenAncCcdsSpliceHighFreq
    dhcHumDerDenAncCcdsSynFixed
    dhcHumDerDenAncCcdsSynFixedDbSnp
    dhcHumDerDenAncCcdsSynHighFreq
    dhcHumDerDenAncCcdsUtr3Fixed
    dhcHumDerDenAncCcdsUtr3FixedDbSnp
    dhcHumDerDenAncCcdsUtr3HighFreq
    dhcHumDerDenAncCcdsUtr5Fixed
    dhcHumDerDenAncCcdsUtr5FixedDbSnp
    dhcHumDerDenAncCcdsUtr5HighFreq
    dhcHumDerDenAncFrameshiftCodingFixed
    dhcHumDerDenAncFrameshiftCodingFixedDbSnp
    dhcHumDerDenAncFrameshiftCodingHighFreq
    dhcHumDerDenAncInFrameNonsynFixed
    dhcHumDerDenAncNonsynFixed
    dhcHumDerDenAncNonsynFixedDbSnp
    dhcHumDerDenAncNonsynHighFreq
    dhcHumDerDenAncRegFixed
    dhcHumDerDenAncRegFixedDbSnp
    dhcHumDerDenAncRegHighFreq
    dhcHumDerDenAncRegMotifFixed
    dhcHumDerDenAncRegMotifFixedDbSnp
    dhcHumDerDenAncRegMotifHighFreq
    dhcHumDerDenAncRegMotifHighInfoFixed
    dhcHumDerDenAncRegMotifHighInfoFixedDbSnp
    dhcHumDerDenAncRegMotifHighInfoHighFreq
    dhcHumDerDenAncSpliceFixed
    dhcHumDerDenAncSpliceFixedDbSnp
    dhcHumDerDenAncSpliceHighFreq
    dhcHumDerDenAncSynFixed
    dhcHumDerDenAncSynFixedDbSnp
    dhcHumDerDenAncSynHighFreq
    dhcHumDerDenAncUtr3Fixed
    dhcHumDerDenAncUtr3FixedDbSnp
    dhcHumDerDenAncUtr3HighFreq
    dhcHumDerDenAncUtr5Fixed
    dhcHumDerDenAncUtr5FixedDbSnp
    dhcHumDerDenAncUtr5HighFreq
    dhcVcfDenisovaPinky
    dhcVcfDNK02
    dhcVcfHGDP00456
    dhcVcfHGDP00521
    dhcVcfHGDP00542
    dhcVcfHGDP00665
    dhcVcfHGDP00778
    dhcVcfHGDP00927
    dhcVcfHGDP00998
    dhcVcfHGDP01029
    dhcVcfHGDP01284
    dhcVcfHGDP01307


tablesIgnored mm9
    allMm9RS_BW
    bamMmsNumtSSorted
    crgMapability%
    rest

tablesIgnored mm10
    mm10Haplotypes
    altSeqLiftOverPslP1
    altSeqPatchesP1

tablesIgnored $ce
    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
    %_myp2a
    anophelesEcores
    bdtnpDnase%
    bdtnp%Fdr%
    fbGenscan
    fbGo
    fbRole
    fbUniProt
    mzD%

tablesIgnored $galGal
    bgiCov
    ecoresTetraodon
    supercontig
    caCondor454

tablesIgnored $danRer
    grcIncidentDb
    phastConsElements
    wz_ests
    UMassInput 
    UMassME1 
    UMassME1Hotspot 
    UMassME1Peak 
    UMassME3 
    UMassME3Hotspot 
    UMassME3Peak

tablesIgnored $canFam
    polyASeqSitesBrainFwd
    polyASeqSitesBrainRev
    polyASeqSitesKidneyFwd
    polyASeqSitesKidneyRev
    polyASeqSitesTestisFwd
    polyASeqSitesTestisRev
    genomicSuperDups
    mzH%

tablesIgnored $anoGam
    anoEstNcl

tablesIgnored $bosTau
    contigOrient

tablesIgnored $apiMel
    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
    ceuBcellRNASeqBW
    cnpFosmid
    cnpIafrate
    cnpIafrate2
    cnpLocke
    cnpRedon
    cnpSebat
    cnpSebat2
    cnpSharp
    cnpSharp2
    cnpSharpSampleCount
    cnpSharpSamples
    cnpTuzun
    darned
    decodeFemale
    decodeFemaleCarrier
    decodeFemaleNonCarrier
    decodeHotSpotFemale
    decodeHotSpotMale
    decodeMale
    decodeMaleCarrier
    decodeMaleFemaleDifference
    decodeMaleNonCarrier
    decodeSexAveraged
    decodeSexAveragedCarrier
    decodeSexAveragedNonCarrier
    delConrad
    delConrad2
    delHinds
    delHinds2
    delMccarroll
    dgv
    ecoresTetNig1
    encode%
    eponine
    exaptedRepeats
    fox2ClipClusters
    fox2ClipSeq
    fox2ClipSeqDensityForwardStrand
    fox2ClipSeqDensityReverseStrand
    geneTests
    genomicSuperDups
    grcIncidentDb
    haplotype
    hapMapRelease24CEURecombMap
    hapMapRelease24CombinedRecombMap
    hapMapRelease24YRIRecombMap
    hgdpGeo
    hgdpFst
    hgdpHzy%
    hgdpIhs%
    hgdpXpehh%
    hiSeqDepthTop%
    isca%
    laminB1
    laminB1Lads
    mammalPsg
    nimhBipolarUs
    nimhBipolarDe
    ntHumChimpCodingDiff
    ntMito
    ntOoaHaplo
    ntSss%
    perlegen
    pga
    pgVenter
    pgWatson
    pgYoruban2
    pgYoruban3
    pgYh1
    pgNA%
    pgSjk
    polyaDb
    polyaPredict
    polyASeqSitesBrainFwd
    polyASeqSitesBrainRev
    polyASeqSitesKidneyFwd
    polyASeqSitesKidneyRev
    polyASeqSitesLiverFwd
    polyASeqSitesLiverRev
    polyASeqSitesMaqcBrain1Fwd
    polyASeqSitesMaqcBrain1Rev
    polyASeqSitesMaqcBrain2Fwd
    polyASeqSitesMaqcBrain2Rev
    polyASeqSitesMaqcUhr1Fwd
    polyASeqSitesMaqcUhr1Rev
    polyASeqSitesMaqcUhr2Fwd
    polyASeqSitesMaqcUhr2Rev
    polyASeqSitesMuscleFwd
    polyASeqSitesMuscleRev
    polyASeqSitesTestisFwd
    polyASeqSitesTestisRev
    promoterStanford
    pseudoYale
    recombRate
    sibGene
    sibTxGraph
    slamMouse
    slamNonCodingMouse
    slamRat
    slamNonCodingRat
    snp
    snp125ExceptionDesc
    snp126ExceptionDesc
    switchDbTss
    syntenyMouse
    syntenyRat
    tajd%
    targetScanS
    tgpPhase1
    tgpPhase1AccessibilityPilotCriteria
    tgpPhase1AccessibilityStrictCriteria
    vistaEnhancers
    wgRna
    zoom1_affyTranscriptome
    zoom2_affyTranscriptome
    kiddEichlerValidAbc7
    kiddEichlerValidAbc8
    kiddEichlerValidAbc9
    kiddEichlerValidAbc10
    kiddEichlerValidAbc11
    kiddEichlerValidAbc12
    kiddEichlerValidAbc13
    kiddEichlerValidAbc14
    kiddEichlerValidG248
    wgEncode%

tablesIgnored $mm
    grcIncidentDb
    sibGene
    sibTxGraph
    syntenyRat
    syntenyHuman
    rikenCageCtssMinus
    rikenCageCtssPlus
    rikenCageTc
    broadStemChip%
    laminB1_AC
    laminB1_EF
    laminB1_ES
    laminB1_NP
    polyASeqSitesBrainFwd
    polyASeqSitesBrainRev
    polyASeqSitesKidneyFwd
    polyASeqSitesKidneyRev
    polyASeqSitesLiverFwd
    polyASeqSitesLiverRev
    polyASeqSitesMuscleFwd
    polyASeqSitesMuscleRev
    polyASeqSitesTestisFwd
    polyASeqSitesTestisRev


tablesIgnored $panTro
    humanDels

tablesIgnored $rheMac
    polyASeqSitesBrainFwd
    polyASeqSitesBrainRev
    polyASeqSitesIleumFwd
    polyASeqSitesIleumRev
    polyASeqSitesKidneyFwd
    polyASeqSitesKidneyRev
    polyASeqSitesLiverFwd
    polyASeqSitesLiverRev
    polyASeqSitesTestisFwd
    polyASeqSitesTestisRev

tablesIgnored $rn
    all_sts_primer
    bactigPos
    ecores%
    polyASeqSitesBrainFwd
    polyASeqSitesBrainRev
    polyASeqSitesTestisFwd
    polyASeqSitesTestisRev
    recombRateRat
    syntenyMouse
    syntenyHuman

tablesIgnored $sacCer
    2micron_mrna
    2micron_intronEst
    2micron_est
    2micron_gap
    sgdClone
    yeastP2P
    uwFootprintsMappability
    uwFootprintsPrints
    uwFootprintsTagCounts

tablesIgnored $tetNig
    ecoresHg17
    cytokines
    hoxGenes

tablesIgnored $fr
    ecoresHg16
    ecoresRn3

tablesIgnored hg16
    chicken_hmrg
    rat_hmrg
    mouse_hmrg
    syntenyMm4

tablesIgnored canFam2
    uncertified

tablesIgnored susScr2
    bosTau4ChainPileUp

tablesIgnored calJac3
    bacEnds
    bacEndCalJac3Singles

tablesIgnored rheMac2
    refSeqAnno

tablesIgnored choHof1
    tableList

tablesIgnored dipOrd1
    tableList

tablesIgnored echTel2
    tableList

tablesIgnored echTel1
    tableList

tablesIgnored eriEur1
    tableList

tablesIgnored micMur1
    tableList

tablesIgnored ochPri2
    tableList

tablesIgnored papAnu2
    tableList

tablesIgnored papHam1
    tableList

tablesIgnored proCap1
    tableList

tablesIgnored pteVam1
    tableList

tablesIgnored sorAra2
    tableList

tablesIgnored sorAra1
    tableList

tablesIgnored tarSyr1
    tableList

tablesIgnored tupBel1
    tableList

tablesIgnored vicPac1
    tableList