src/hg/makeDb/schema/all.joiner 1.768
1.768 2010/02/09 19:13:59 hartera
Added crgMapability subtracks to list of tables to be ignored for mm9.
Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.767
retrieving revision 1.768
diff -b -B -U 1000000 -r1.767 -r1.768
--- src/hg/makeDb/schema/all.joiner 26 Jan 2010 22:24:56 -0000 1.767
+++ src/hg/makeDb/schema/all.joiner 9 Feb 2010 19:13:59 -0000 1.768
@@ -1,3505 +1,3506 @@
# This contains linkage information between various fields
# in various databases.
# Define databases used for various organisms
set anoCar anoCar1
set anoGam anoGam1
set apiMel apiMel1,apiMel2
set aplCal aplCal1
set bosTau bosTau2,bosTau3,bosTau4
set braFlo braFlo1
set caeJap caeJap1
set caePb caePb1,caePb2
set caeRem caeRem2,caeRem3
set calJac calJac1
set canFam canFam1,canFam2
set cavPor cavPor3
set cb cb1,cb3
set ce ce2,ce4,ce6
set ci ci1,ci2
set cioSav cioSav1
set danRer danRer3,danRer4,danRer5,danRer6
set dm dm1,dm2,dm3
set dp dp2,dp3
set droEre droEre1
set droMoj droMoj1,droMoj2
set droMult droAna1,droAna2,droMoj1,droMoj2,droVir1,droVir2,droEre1,droSim1,droGri1,droPer1,droSec1,droWil1
set droVir droVir1,droVir2
set droYak droYak1,droYak2
set equCab equCab1,equCab2
set felCat felCat3
set fr fr1,fr2
set galGal galGal2,galGal3
set gasAcu gasAcu1
set gorGor gorGor1
set hg hg16,hg17,hg18,hg19
set loxAfr loxAfr3
set mm mm6,mm7,mm8,mm9
set monDom monDom1,monDom4,monDom5
set ornAna ornAna1
set oryCun oryCun2
set oryLat oryLat2
set panTro panTro1,panTro2
set petMar petMar1
set ponAbe ponAbe2
set priPac priPac1
set rheMac rheMac2
set rn rn3,rn4
set sacCer sacCer1,sacCer2
set strPur strPur1,strPur2
set taeGut taeGut1
set tetNig tetNig1,tetNig2
set xenTro xenTro1,xenTro2
# Define all organism/assembly-specific databases.
set gbd $hg,$mm,$rn,$fr,$ce,$cb,$dm,$dp,$sacCer,$panTro,$galGal,$ci,$danRer,$canFam,$droYak,$droMult,$anoGam,$apiMel,$cioSav,$tetNig,$xenTro,$monDom,$bosTau,$rheMac,$strPur,$felCat,$gasAcu,$oryCun,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut,$gorGor,$aplCal,$loxAfr,$aplCal
# Define organism databases based on whole-genome shotgun projects
# (Assembly based on WGS project contigs accessioned in Genbank)
set wgs $rn,$panTro,$galGal,$canFam,$bosTau,$felCat,$monDom,$tetNig,$fr,$oryCun,$oryLat,$calJac,$cavPor,$taeGut,$aplCal
# Define organism databases for which we build a xenoRefGene track:
set xrg $panTro,$galGal,$ci,$canFam,$dp,$droYak,$droMult,$bosTau,$rn,$hg,$rheMac,$monDom,$felCat,$oryCun,$oryLat,$anoCar,$caePb,$caeRem,$caeJap,$cb,$mm,$priPac,$strPur,$ponAbe,$calJac,$petMar,$braFlo,$ce,$taeGut,danRer6,$aplCal
# Define organism databases for which we build a SNP track:
set snpDb130 hg18
set snpDb129 hg18
set snpDb128 hg18,mm9
set snpDb127 hg18,bosTau3
set snpDb126 hg18,mm8
set snpDb125 hg17,panTro1,canFam1,rn4
# Only consider one of members of gbd at a time.
exclusiveSet $gbd
# Define other databases that we check
set otherDb uniProt,go,hgFixed,proteome,visiGene
# Define protein databases (currently not checked)
set proteinDb proteins070202,proteins060115,proteins050415,proteins051015,proteins050415,proteins050315,proteins050201,proteins041115,proteins040515,proteins040315,proteins0111,proteins0305,proteins031112,proteins040115,proteins0405,proteins070403,proteins072003,proteins092903,proteins1129
# Define zoo databases (currently not checked)
set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
# Define transMap databases
# transMapDb not public: dasNov1,echTel1,loxAfr1,oryCun1,otoGar1,loxAfr3
set transMapDb anoCar1,bosTau4,calJac1,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryCun2,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2
# Set up list of databases we ignore and those we check. Program
# will complain about other databases.
databasesChecked $gbd,$otherDb
databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash
# Define various non-self chains
set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr3
set nonSplitChains hg19,$tetNig,oryCun2
# Define databases that support known genes
set kgDb $hg,$mm,$rn
# Older format (KG 2)
set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4
# Newer format (KG 3 aka UCSC Genes)
set kgDb3 hg18,hg19,mm9
# Protein browser databases.
set pbDb hg18,hg17,hg16,mm7,mm8,mm9,rn3
set pbDb1 hg17,hg16,mm7,mm8,mm9,rn3
set pbDb2 rn3
set pbDb3 hg16,hg17,hg18
# Define databases that support family browser (gene sorter)
set familyDb $hg,$mm,$rn,$ce,$sacCer,$dm
# Define databases that support CCDS
set ccdsDb hg18,hg17,mm8,mm9
# Magic for tables split between chromosomes
set split splitPrefix=chr%\_
# Define the shared identifiers and the fields they appear in.
# GO - Gene Ontology Info
identifier goAccession external=GO
"Gene ontology term accessions. Example - GO:0003574"
go.term.acc
go.goaPart.goId minCheck=0.999
identifier goAccessionChopped
"Gene ontology term accessions without the GO:"
go.term.acc chopBefore=GO:
dm1.bdgpGeneInfo.go comma minCheck=0.99
dm1.bdgpNonCodingInfo.go comma minCheck=0.99
identifier goId external=GO
"Gene ontology term ID's. Shouldn't be used outside of go database"
go.term.id
go.term2term.term1_id
go.term2term.term2_id
go.term_audit.term_id
go.term_dbxref.term_id
go.term_definition.term_id unique
go.term_synonym.term_id
go.graph_path.term1_id
go.graph_path.term2_id
identifier goDbXrefId external=GO
"Gene ontology database cross-reference"
go.dbxref.id
go.term_dbxref.dbxref_id
# UniProt Related Stuff
identifier UniProtId external=UniProt
"UniProt(Swiss-Prot/TrEMBL) display ID."
uniProt.displayId.val
proteome.uniProtAlias.alias minCheck=0.2
proteome.spOldNew.newDisplayId minCheck=0.3
proteome.spOldNew.oldDisplayId minCheck=0.3
proteome.spDisease.displayID minCheck=0.9
go.goaPart.dbObjectSymbol minCheck=0.95
$gbd.dupSpMrna.proteinID minCheck=0.80
$gbd.dupSpMrna.dupProteinID minCheck=0.50
$kgDb2.kgProtAlias.displayID minCheck=0.80
$kgDb2.kgSpAlias.alias minCheck=0.20
$kgDb2.kgXref.spDisplayID minCheck=0.80
$kgDb3.kgXref.spDisplayID minCheck=0.50
$kgDb2.knownCanonical.protein minCheck=0.80
$gbd.spMrna.spID minCheck=0.80
dm1.bdgpSwissProt.spSymbol minCheck=0.80
dm1.flyBaseSwissProt.spSymbol minCheck=0.80
identifier UniProtAccession external=UniProt
"UniProt(Swiss-Prot/TrEMBL) Accession"
uniProt.displayId.acc
uniProt.accToKeyword.acc
uniProt.accToTaxon.acc
uniProt.citation.acc
uniProt.comment.acc
uniProt.description.acc unique
uniProt.extDbRef.acc
uniProt.feature.acc
uniProt.gene.acc
uniProt.geneLogic.acc
uniProt.info.acc unique
uniProt.otherAcc.acc
uniProt.protein.acc unique full
proteome.spOldNew.acc minCheck=0.8
proteome.uniProtAlias.acc minCheck=0.9
proteome.spReactomeId.spID minCheck=0.9
proteome.spReactomeEvent.spID minCheck=0.9
$kgDb2.kgProtAlias.alias minCheck=0.2
$kgDb2.kgSpAlias.spID minCheck=0.2
$kgDb2.kgProtMap.qName minCheck=0.9
$kgDb2.kgXref.spID minCheck=0.9
$kgDb3.kgSpAlias.spID minCheck=0.50
$kgDb3.kgXref.spID minCheck=0.50
$gbd.pepMwAa.accession minCheck=0.9
$gbd.pepPi.accession minCheck=0.9
$ce.sangerCanonical.protein minCheck=0.8
$ce.sangerGene.proteinID minCheck=0.8
$ce.sangerLinks.protName minCheck=0.8
dm1.bdgpCanonical.protein minCheck=0.9
dm1.bdgpGene.proteinID minCheck=0.9
dm1.bdgpSwissProt.swissProtId minCheck=0.9
dm1.flyBaseSwissProt.swissProtId minCheck=0.9
$sacCer.sgdGene.proteinID minCheck=0.9
$sacCer.sgdCanonical.protein minCheck=0.9
$sacCer.sgdToSwissProt.value minCheck=0.9
go.goaPart.dbObjectId minCheck=0.99
visiGene.gene.uniProt
identifier UniProtAuthor
"Author ID in UniProt (just use inside UCSC Relationalized UniProt)"
uniProt.author.id
uniProt.referenceAuthors.author full
identifier UniProtReference
"Reference (journal) ID in UniProt (just inside UCSC Relationalized)"
uniProt.reference.id
uniProt.citation.reference full
uniProt.referenceAuthors.reference
identifier UniProtCitation
"Citation ID in UniProt (just use inside UCSC Relationalized UniProt)"
uniProt.citation.id
uniProt.citationRc.citation
identifier UniProtCitationRp
"Reference Position Line ID in UniProt (just inside UCSC Relationalized)"
uniProt.citationRp.id
uniProt.citation.rp full
identifier UniProtRcType
"Reference Comment Type in UniProt (just inside UCSC Relationalized)"
uniProt.rcType.id
uniProt.citationRc.rcType full
identifier UniProtRcVal
"Reference Comment Text in UniProt (just inside UCSC Relationalized)"
uniProt.rcVal.id
uniProt.citationRc.rcVal full
identifier UniProtCommentType
"Type of UniProt comment type (just inside UCSC Relationalized)"
uniProt.commentType.id
uniProt.comment.commentType full
identifier UniProtCommentVal
"Text of UniProt comment text (just inside UCSC Relationalized)"
uniProt.commentVal.id
uniProt.comment.commentVal full
identifier UniProtExtDb
"UniProt(Swiss-Prot/TrEMBL) external database ID (just inside UCSC Relationalized)"
uniProt.extDb.id
uniProt.extDbRef.extDb full
identifier UniProtFeatureClass
"Type of UniProt feature class (just inside UCSC Relationalized)"
uniProt.featureClass.id
uniProt.feature.featureClass full
identifier UniProtFeatureType
"Type of UniProt feature type (just inside UCSC Relationalized)"
uniProt.featureType.id
uniProt.feature.featureType full exclude=0
identifier UniProtOrganelle
"Type of UniProt organelle ID (just inside UCSC Relationalized)"
uniProt.organelle.id
uniProt.info.organelle full exclude=0
identifier UniProtKeyword
"UniProt(Swiss-Prot/TrEMBL) keyword ID (just inside UCSC Relationalized)"
uniProt.keyword.id
uniProt.accToKeyword.keyword full
identifier ncbiTaxon
"NCBI Taxon ID - number for a species. Used by UniProt too"
uniProt.taxon.id dupeOk
uniProt.accToTaxon.taxon full
uniProt.commonName.taxon
visiGene.antibody.taxon
visiGene.gene.taxon
visiGene.genotype.taxon
visiGene.specimen.taxon
visiGene.lifeTime.taxon
visiGene.lifeStageScheme.taxon
visiGene.strain.taxon
# CGAP SAGE track Stuff
# Databases with the CGAP SAGE track
set cgapSageDbs hg18,mm8
identifier cgapSageLibId external=CGAP
"ID linking cgapSage and cgapSageLib tables"
$cgapSageDbs.cgapSageLib.libId
$cgapSageDbs.cgapSage.libIds comma
# VisiGene Related Stuff
identifier vgFileLocation
"Where is that .jpg file? Usually a directory."
visiGene.fileLocation.id
visiGene.imageFile.fullLocation
visiGene.imageFile.thumbLocation
identifier vgStrain
"Er, what type of mouse is that?"
visiGene.strain.id
visiGene.genotype.strain exclude=0
identifier vgBodyPart
"Brain, eye, cerebral cortex, etc."
visiGene.bodyPart.id
visiGene.specimen.bodyPart exclude=0
visiGene.expressionLevel.bodyPart exclude=0
identifier vgCellType
"Neuron, glia, etc."
visiGene.cellType.id
visiGene.expressionLevel.cellType exclude=0
identifier vgCellSubtype
"More detailed splitting up of cell types. What type of neuron, etc."
visiGene.cellSubtype.id
visiGene.expressionLevel.cellSubtype exclude=0
identifier vgSliceType
"Horizontal, coronal, wholeMount, etc."
visiGene.sliceType.id
visiGene.preparation.sliceType exclude=0
identifier vgFixation
"Fixation conditions - 3% formaldehyde or the like."
visiGene.fixation.id
visiGene.preparation.fixation exclude=0
identifier vgEmbedding
"Embedding media for slices - paraffin, etc."
visiGene.embedding.id
visiGene.preparation.embedding exclude=0
identifier vgPermeablization
"Permeablization conditions"
visiGene.permeablization.id
visiGene.preparation.permeablization exclude=0
identifier vgContributor
"Info on a contributor"
visiGene.contributor.id
visiGene.submissionContributor.contributor
identifier vgJournal
"Info on a journal"
visiGene.journal.id
visiGene.submissionSet.journal exclude=0
identifier vgCopyright
"Copyright information"
visiGene.copyright.id
visiGene.submissionSet.copyright exclude=0
identifier vgSubmissionSource
"Source of data - an external database, a contributor, etc."
visiGene.submissionSource.id
visiGene.submissionSet.submissionSource
visiGene.antibodySource.submissionSource exclude=0
identifier vgSubmissionSet
"Info on a batch of images submitted at once"
visiGene.submissionSet.id
visiGene.submissionContributor.submissionSet
visiGene.imageFile.submissionSet
visiGene.image.submissionSet
identifier vgSectionSet
"Info on a bunch of sections through some specimen"
visiGene.sectionSet.id
visiGene.image.sectionSet exclude=0
identifier vgAntibody
"Info on an antibody"
visiGene.antibody.id
visiGene.probe.antibody exclude=0
visiGene.antibodySource.antibody exclude=0
identifier vgBac
"Info on a BAC"
visiGene.bac.id
visiGene.probe.bac exclude=0
identifier vgGene
"Info on a gene"
visiGene.gene.id
visiGene.geneSynonym.gene
visiGene.allele.gene
visiGene.probe.gene
identifier vgAllele
"Name of a gene allele"
visiGene.allele.id
visiGene.genotypeAllele.allele
identifier vgGenotype
"How different genetically from wild type."
visiGene.genotype.id
visiGene.genotypeAllele.genotype
visiGene.specimen.genotype
identifier vgSex
"Sex of a specimen"
visiGene.sex.id
visiGene.specimen.sex exclude=0
identifier vgSpecimen
"A biological specimen - something mounted, possibly sliced up"
visiGene.specimen.id
visiGene.image.specimen
identifier vgPreparation
"How a specimen is prepared."
visiGene.preparation.id
visiGene.image.preparation exclude=0
identifier vgProbeType
"Type of probe - RNA, antibody, etc."
visiGene.probeType.id
visiGene.probe.probeType
identifier vgProbe
"Information on a probe used to stain or hilight image"
visiGene.probe.id
visiGene.imageProbe.probe
visiGene.vgPrbMap.probe
identifier vgProbeColor
"Color - what color probe is in"
visiGene.probeColor.id
visiGene.imageProbe.probeColor exclude=0
identifier vgCaption
"Caption for image. Id corresponding to text."
visiGene.caption.id
visiGene.imageFile.caption exclude=0
identifier vgImageFile
"A biological image file"
visiGene.imageFile.id
visiGene.image.imageFile
visiGene.imageFileFwd.fromIf
visiGene.imageFileFwd.toIf
identifier vgImage
"Master identifier for a visiGene image. May be just a pane in an image file."
visiGene.image.id
visiGene.imageProbe.image
$kgDb.knownToVisiGene.value
identifier vgImageProbe
"Association between a probe and an image."
visiGene.imageProbe.id
visiGene.expressionLevel.imageProbe
identifier vgExpressionPattern
"Expression pattern - scattered, regional, etc."
visiGene.expressionPattern.id
visiGene.expressionLevel.expressionPattern exclude=0
identifier vgLifeStageScheme
"A scheme for describing stages of development for an organism"
visiGene.lifeStageScheme.id
visiGene.lifeStage.lifeStageScheme
identifier vgPrb
"Permanent ID/Probe Sequence table"
visiGene.vgPrb.id
visiGene.vgPrbMap.vgPrb
# Various types of gene predictions in UCSC Genome Browser
identifier gencodeGeneNameJun05 dependency
"Link together Gencode gene model and class for June 05 Data Freeze"
hg17.encodeGencodeGeneJun05.name
hg17.gencodeGeneClassJun05.name full unique
identifier gencodeGeneNameKnownOct05 dependency
"Link together Gencode gene model (Known) and class for Oct 05 Data Freeze"
$hg.encodeGencodeGeneKnownOct05.name
$hg.gencodeGeneClassOct05.name minCheck=0.88 unique
identifier gencodeGeneNamePutativeOct05 dependency
"Link together Gencode gene model (Putative) and class for Oct 05 Data Freeze"
$hg.encodeGencodeGenePutativeOct05.name
$hg.gencodeGeneClassOct05.name minCheck=0.05 unique
identifier gencodeGeneNamePseudoOct05 dependency
"Link together Gencode gene model (Pseudo) and class for Oct 05 Data Freeze"
$hg.encodeGencodeGenePseudoOct05.name
$hg.gencodeGeneClassOct05.name minCheck=0.06 unique
identifier gencodeGeneNameKnownMar07 dependency
"Link together Gencode gene model (Known) and class for Mar 07 Data Version"
$hg.encodeGencodeGeneKnownMar07.name
$hg.gencodeGeneClassMar07.name minCheck=0.83 unique
identifier gencodeGeneNamePutativeMar07 dependency
"Link together Gencode gene model (Putative) and class for Mar 07 Data Version"
$hg.encodeGencodeGenePutativeMar07.name
$hg.gencodeGeneClassMar07.name minCheck=0.10 unique
identifier gencodeGeneNamePolymorphicMar07 dependency
"Link together Gencode gene model (Polymorphic) and class for Mar 07 Data Version"
$hg.encodeGencodeGenePolymorphicMar07.name
$hg.gencodeGeneClassMar07.name minCheck=0.006 unique
identifier gencodeGeneNamePseudoMar07 dependency
"Link together Gencode gene model (Pseudo) and class for Mar 07 Data Version"
$hg.encodeGencodeGenePseudoMar07.name
$hg.gencodeGeneClassMar07.name minCheck=0.05 unique
identifier encodePseudogeneConsensus dependency
"Link together Consensus Pseudogenes and class"
$hg.encodePseudogeneConsensus.name
$hg.encodePseudogeneClass.name minCheck=0.16 unique
identifier encodePseudogeneGIS dependency
"Link together GIS Pseudogenes and class"
$hg.encodePseudogeneGIS.name
$hg.encodePseudogeneClass.name minCheck=0.04 unique
identifier encodePseudogeneHavana dependency
"Link together Havana Pseudogenes and class"
$hg.encodePseudogeneHavana.name
$hg.encodePseudogeneClass.name minCheck=0.17 unique
identifier encodePseudogeneUcsc dependency
"Link together Ucsc Retrogenes and class"
$hg.encodePseudogeneUcsc.name dupeOk
$hg.encodePseudogeneClass.name minCheck=0.22 unique
identifier encodePseudogeneUcsc2 dependency
"Link together Ucsc Pseudogenes and class"
$hg.encodePseudogeneUcsc2.name dupeOk
$hg.encodePseudogeneClass.name minCheck=0.04 unique
identifier encodePseudogeneYale dependency
"Link together Yale Pseudogenes and class"
$hg.encodePseudogeneYale.name
$hg.encodePseudogeneClass.name minCheck=0.16 unique
identifier wgEncodeNhgriBip
"Link together Gencode gene model (Known) and class for Jan 2009 Data Version"
hg18.wgEncodeNhgriBip.name dupeOk
panTro2.wgEncodeNhgriBip.name
rheMac2.wgEncodeNhgriBip.name
mm9.wgEncodeNhgriBip.name
rn4.wgEncodeNhgriBip.name
canFam2.wgEncodeNhgriBip.name
bosTau4.wgEncodeNhgriBip.name
identifier wgEncodeGencodeClassesRel2
"Link together Gencode gene model (Known) and class for Jan 2009 Data Version"
hg18.wgEncodeGencodeClassesRel2.name
hg18.wgEncodeGencodeAutoRel2.name unique
hg18.wgEncodeGencodeManualRel2.name unique
hg18.wgEncodeGencodePolyaRel2.name unique
identifier wgEncodeGencodeClassesV3
"Link together Gencode gene model (Known) and class for July 2009 Data Version"
hg18.wgEncodeGencodeClassesV3.name
hg18.wgEncodeGencodeAutoV3.name unique
hg18.wgEncodeGencodeManualV3.name unique
hg18.wgEncodeGencodePolyaV3.name unique
identifier acemblyName dependency
"Link together Acembly gene model structure and peptide."
$hg,$mm.acembly.name
$hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90
hg17.acemblyPep.name unique minCheck=0.63
$hg,$mm.acemblyClass.name full unique
identifier ECgeneName dependency
"Link together EC gene predicted gene structure and peptide"
$gbd.ECgene.name
$gbd.ECgenePep.name unique
identifier geneidName dependency
"Link together geneid predicted gene structure and peptide"
$gbd.geneid.name
$gbd.geneidPep.name full unique
identifier genscanName dependency
"Link together genscan predicted gene structure and peptide"
$gbd.genscan.name
$gbd.genscanPep.name full unique
identifier jgiName dependency
"Link together jgi predicted gene structure and peptide"
$gbd.jgiGene.name
$gbd.jgiPep.name unique minCheck=0.9
identifier softberryGeneName dependency
"Link together Fshgene++ gene structure, pepdide, and homolog"
$gbd.softberryGene.name
$gbd.softberryPep.name full unique
$gbd.softberryHom.name unique
identifier twinscanName dependency
"Link together twinscan predicted gene structure and peptide"
$gbd.twinscan.name
$gbd.twinscanPep.name full unique
identifier nscanName dependency
"Link together nscan predicted gene structure and peptide"
$gbd.nscanGene.name
$gbd.nscanPep.name unique
identifier nscanPasaName dependency
"Link together nscan predicted gene structure (PASA) and peptide"
$gbd.nscanPasaGene.name
$gbd.nscanPasaPep.name unique
identifier augustusHintsName dependency
"Link together augustusHints predicted gene structure and peptide"
$gbd.augustusHints.name
$gbd.augustusHintsPep.name chopBefore=. full unique
identifier augustusXRAName dependency
"Link together augustusXRA predicted gene structure and peptide"
$gbd.augustusXRA.name
$gbd.augustusXRAPep.name chopBefore=. full unique
identifier augustusAbinitioName dependency
"Link together augustusAbinitio predicted gene structure and peptide"
$gbd.augustusAbinitio.name
$gbd.augustusAbinitioPep.name chopBefore=. full unique
identifier vegaGeneIdHuman external=VegaGene
"Link together various VEGA human curated gene annotation"
hg18.vegaGtp.transcript
hg18.vegaGene.name
hg18.vegaPseudoGene.name
hg18.vegaPep.name
identifier vegaGeneIdMouse external=VegaGene
"Link together various VEGA mouse curated gene annotation"
mm9.vegaGtp.transcript
mm9.vegaGene.name
mm9.vegaPseudoGene.name
mm9.vegaPep.name
identifier vegaName
"Link together various VEGA human curated gene annotation"
$gbd.vegaInfo.transcriptId
$gbd.vegaGene.name
$gbd.vegaPseudoGene.name
identifier vegaGeneName typeOf=vegaName dependency
"Link together VEGA predicted gene structure and peptide"
$gbd.vegaGene.name
danRer5.vegaPep.name unique minCheck=0.72
identifier vegaZfishName
"Link together various VEGA zebrafish curated gene annotation"
$gbd.vegaInfoZfish.transcriptId
identifier vegaGeneZfishName typeOf=vegaZfishName dependency
"Link together Zebrafish VEGA predicted gene structure additional information"
$danRer.vegaGene.name
$danRer.vegaInfoZfish.transcriptId minCheck=0.99
$danRer.vegaToCloneId.transcriptId minCheck=0.99
identifier vegaPseudoZfishName typeOf=vegaZfishName
"Link together VEGA pseudogene and other info."
$danRer.vegaPseudoGene.name
identifier vegaPseudoGeneZfishName typeOf=vegaPseudoZfishName dependency
"Link together Zebrafish VEGA predicted gene structure additional information"
$danRer.vegaPseudoGene.name
$danRer.vegaInfoZfish.transcriptId minCheck=0.004
$danRer.vegaToCloneId.transcriptId minCheck=0.004
identifier vegaPseudogeneName typeOf=vegaName
"Link together VEGA pseudogene and other info."
$gbd.vegaPseudoGene.name
#identifier pseudoGeneName
#"Link together pseudo predicted gene structure and peptide"
# $hg.pseudoMrna.qName dupeOk
# hg16,hg17,hg18.pseudoGeneLink.name minCheck=0.99
identifier mrnaBlastzName
"Link together mrnaBlastz and pseudoMrna"
$hg.mrnaBlastz.qName dupeOk
$hg,!hg16.pseudoMrna.qName
hg16.pseudoMrna.qName minCheck=0.76
# Microarray stuff.
identifier agilentHumanProbeId external=agilent fuzzy
"Agilent Human CGH/CNV array probe ID"
$hg.agilentCgh105a.name
$hg.agilentCgh1x1m.name
$hg.agilentCgh244a.name
$hg.agilentCgh2x400k.name
$hg.agilentCgh44k.name
$hg.agilentCgh4x180k.name
$hg.agilentCgh8x60k.name
$hg.agilentCnv2x400k.name
$hg.agilentCnv2x105k.name
$hg.agilentHrd1x1m.name
identifier agilentMouseProbeId external=agilent fuzzy
"Agilent Mouse CGH/CNV array probe ID"
$mm.agilentCgh105a.name
$mm.agilentCgh244a.name
$mm.agilentCgh44k.name
identifier agilentRatProbeId external=agilent fuzzy
"Agilent Rat CGH/CNV array probe ID"
$rn.agilentCgh105a.name
$rn.agilentCgh244a.name
identifier sestanBrainAtlasId
"Sample IDs for the Sestan brain atlas array."
hgFixed.sestanBrainAtlasExps.id
$hg.sestanBrainAtlas.expIds comma full
$hg.sestanBrainAtlas.expScores comma indexOf full
identifier affyMouseExonSampleId
"Sample IDs for Affymetrix all mouse exon array."
hgFixed.affyMouseExonTissuesAllExps.id
$mm.affyExonTissues.expIds comma full
$mm.affyExonTissues.expScores comma indexOf full
identifier affyRatExonSampleId
"Sample IDs for Affymetrix all rat exon array."
hgFixed.affyRatExonTissuesAllExps.id
$rn.affyExonTissues.expIds comma full
$rn.affyExonTissues.expScores comma indexOf full
identifier gnfHumanAtlas2
"Novartis GNF Human gene probe ID"
hgFixed.gnfHumanAtlas2All.name
hgFixed.gnfHumanAtlas2AllRatio.name unique
hgFixed.gnfHumanAtlas2Median.name full unique
hgFixed.gnfHumanAtlas2MedianRatio.name unique
hgFixed.gladHumESRatio.name unique
hgFixed.gladHumES.name
hgFixed.gladHumESOtherData.name
$hg.knownToGnfAtlas2.value
$hg.gnfAtlas2.name
$hg.affyGnf1h.qName
identifier gnfMouseAtlas2
"Novartis GNF Mouse gene probe ID"
hgFixed.gnfMouseAtlas2All.name
hgFixed.gnfMouseAtlas2AllRatio.name unique
hgFixed.gnfMouseAtlas2Median.name full unique
hgFixed.gnfMouseAtlas2MedianRatio.name unique
$mm.knownToGnf1m.value
$mm.gnfAtlas2.name
$mm.affyGnf1m.qName
identifier gnfMOE430v2
"Novartis GNF Mouse gene probe ID"
hgFixed.gnfMOE430v2All.name
hgFixed.gnfMOE430v2AllRatio.name unique
hgFixed.gnfMOE430v2Median.name full unique
hgFixed.gnfMOE430v2MedianRatio.name unique
$mm.knownToGnfMOE430v2.value
$mm.gnfMOE430v2.name
$mm.affyMOE430v2.qName
identifier gnfRatAtlas2
"Novartis GNF Rat gene probe ID"
hgFixed.gnfRatAtlas2All.name
hgFixed.gnfRatAtlas2AllRatio.name unique
hgFixed.gnfRatAtlas2Median.name full unique
hgFixed.gnfRatAtlas2MedianRatio.name unique
$rn.knownToU34A.value
$rn.gnfAtlas2.name
$rn.affyU34A.qName
identifier affyZonWildType
"Affymetrix Zebrafish chip Zon Lab data probe ID"
hgFixed.zebrafishZonWTAll.name
hgFixed.zebrafishZonWTAllRatio.name unique
hgFixed.zebrafishZonWTMedian.name unique
hgFixed.zebrafishZonWTMedianRatio.name. unique
$danRer.ensToAffyZebrafish.name
$danRer.ensToAffyZonWildType.name
$danRer.affyZonWildType.name
$danRer.affyZebrafish.qName
danRer5.affyZebrafishConsensus.qName
identifier affyZonWildTypeDanRer5
"Affymetrix Zebrafish chip Zon Lab data probe ID Consensus"
danRer5.affyZonWildType.name dupeOk
danRer5.affyZebrafishConsensus.qName
identifier affyTargetZonWildTypeDanRer5
"Affymetrix Zebrafish chip Zon Lab data probe ID Target"
danRer5.affyTargetZonWildType.name dupeOk
danRer5.affyZebrafishTarget.qName
identifier affyU95
"Affymetrix Human U95 chip identifiers"
$hg.affyU95.qName dupeOk
$hg.affyRatio.name
$hg.knownToU95.value
identifier affyU133
"Affymetrix Human U133 chip identifiers"
$hg.affyU133.qName dupeOk chopBefore=U133A: chopBefore=U133B: chopAfter=;
$hg.knownToU133.value
identifier affyU133Plus2
"Affymetrix Human U133 chip identifiers"
$hg.affyU133Plus2.qName dupeOk
$hg.knownToU133Plus2.value
identifier affyU74
"Affymetrix Mouse U74 chip identifiers"
$mm.affyU74.qName dupeOk
$mm.affyGnfU74A.name
$mm.affyGnfU74B.name
$mm.affyGnfU74C.name
$mm.knownToU74.value
identifier affyMOE430
"Affymetrix Mouse MOE430 chip identifiers"
$mm.affyMOE430.qName dupeOk
$mm.knownToMOE430.value
$mm.knownToMOE430A.value
$mm.rinnSex.name
hgFixed.mouseRinnSex.name minCheck=0.96
hgFixed.mouseRinnSexMedian.name minCheck=0.96
hgFixed.mouseRinnSexRatio.name minCheck=0.97
hgFixed.mouseRinnSexMedianRatio.name minCheck=0.97
identifier affyRAE230
"Affymetrix Rat RAE230 chip identifiers"
$rn.affyRAE230.qName dupeOk
$rn.knownToRAE230.value
identifier affyU34A
"Affymetrix Rat U34A chip identifiers"
$rn.affyU34A.qName dupeOk
$rn.knownToU34A.value
identifier illuminaWG6
"Illumina WG-6 3.0 Probe set identifiers"
$hg.illuminaProbes.name dupeOk
$hg.illuminaProbesAlign.qName full
$hg.illuminaProbesSeq.id minCheck=0.8
identifier kimWormGeneId
"Identifiers for Kim-lab worm genes"
hgFixed.kimWormLifeAllRatio.name
hgFixed.kimWormLifeMedianRatio.name full unique
$ce.sangerToKim.value minCheck=0.6
identifier nci60SampleId
"Identifiers of NCI 60 Cell lines for expression experiments"
hgFixed.nci60Exps.id
$hg.nci60.expIds comma full
$hg.nci60.expScores comma indexOf full
identifier rosettaChr22SampleId
"Identifiers for samples used in Rosetta chromosome 22 public experiments"
hgFixed.rosettaExps.name
hgFixed.rosChr22Dat.expName
identifier gnfHumanAtlas2SampleId
"Identifiers of RNA samples used in GNF Human Expression Atlas 2"
hgFixed.gnfHumanAtlas2AllExps.id
hgFixed.gnfHumanAtlas2All.expScores comma indexOf full
hgFixed.gnfHumanAtlas2AllRatio.expScores comma indexOf full
identifier gnfHumanAtlas2MedianSampleId
"Identifiers of pooled RNA samples used in GNF Human Expression Atlas 2"
hgFixed.gnfHumanAtlas2MedianExps.id
hgFixed.gnfHumanAtlas2Median.expScores comma indexOf full
hgFixed.gnfHumanAtlas2MedianRatio.expScores comma indexOf full
$hg.gnfAtlas2.expScores comma indexOf full
identifier gnfMouseAtlas2SampleId
"Identifiers of RNA samples used in GNF Mouse Expression Atlas 2"
hgFixed.gnfMouseAtlas2AllExps.id
hgFixed.gnfMouseAtlas2All.expScores comma indexOf full
hgFixed.gnfMouseAtlas2AllRatio.expScores comma indexOf full
identifier gnfMouseAtlas2MedianSampleId
"Identifiers of pooled RNA samples used in GNF Mouse Expression Atlas 2"
hgFixed.gnfMouseAtlas2MedianExps.id
hgFixed.gnfMouseAtlas2Median.expScores comma indexOf full
hgFixed.gnfMouseAtlas2MedianRatio.expScores comma indexOf full
$mm.gnfAtlas2.expScores comma indexOf full
identifier gnfRatAtlas2SampleId
"Identifiers of RNA samples used in GNF Rat Expression Atlas 2"
hgFixed.gnfRatAtlas2AllExps.id
hgFixed.gnfRatAtlas2All.expScores comma indexOf full
hgFixed.gnfRatAtlas2AllRatio.expScores comma indexOf full
identifier gnfRatAtlas2MedianSampleId
"Identifiers of pooled RNA samples used in GNF Rat Expression Atlas 2"
hgFixed.gnfRatAtlas2MedianExps.id
hgFixed.gnfRatAtlas2Median.expScores comma indexOf full
hgFixed.gnfRatAtlas2MedianRatio.expScores comma indexOf full
$rn.gnfAtlas2.expScores comma indexOf full
identifier gnfU95SampleIdV0
"Identifiers of RNA samples used early version of GNF Human Expression Atlas 1"
hgFixed.affyExps.id
$hg.affyRatio.expIds comma
$hg.affyRatio.expScores comma indexOf
identifier gnfU95SampleIdV1
"Identifiers of RNA samples used in GNF Human Expression Atlas 1"
hgFixed.gnfHumanU95AllExps.id
hgFixed.gnfHumanU95All.expScores comma indexOf full
hgFixed.gnfHumanU95AllRatio.expScores comma indexOf full
identifier gnfU95MedianSampleIdV1
"Identifiers of pooled RNA samples used in GNF Human Expression Atlas 1"
hgFixed.gnfHumanU95MedianExps.id
hgFixed.gnfHumanU95Median.expScores comma indexOf full
hgFixed.gnfHumanU95MedianRatio.expScores comma indexOf full
identifier gnfU74aSampleId
"Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip"
hgFixed.gnfMouseU74aAllExps.id
hgFixed.gnfMouseU74aAll.expScores comma indexOf full
hgFixed.gnfMouseU74aAllRatio.expScores comma indexOf full
$mm.affyGnfU74A.expIds comma full
$mm.affyGnfU74A.expScores comma indexOf full
identifier gnfU74aMedianSampleId
"Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74A Chip"
hgFixed.gnfMouseU74aMedianExps.id
hgFixed.gnfMouseU74aMedian.expScores comma indexOf full
hgFixed.gnfMouseU74aMedianRatio.expScores comma indexOf full
identifier gnfU74bSampleId
"Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip"
hgFixed.gnfMouseU74bAllExps.id
hgFixed.gnfMouseU74bAll.expScores comma indexOf full
hgFixed.gnfMouseU74bAllRatio.expScores comma indexOf full
$mm.affyGnfU74B.expIds comma full
$mm.affyGnfU74B.expScores comma indexOf full
identifier gnfU74bMedianSampleId
"Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74B Chip"
hgFixed.gnfMouseU74bMedianExps.id
hgFixed.gnfMouseU74bMedian.expScores comma indexOf full
hgFixed.gnfMouseU74bMedianRatio.expScores comma indexOf full
identifier gnfU74cSampleId
"Identifiers of RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip"
hgFixed.gnfMouseU74cAllExps.id
hgFixed.gnfMouseU74cAll.expScores comma indexOf full
hgFixed.gnfMouseU74cAllRatio.expScores comma indexOf full
$mm.affyGnfU74C.expIds comma full
$mm.affyGnfU74C.expScores comma indexOf full
identifier gnfU74cMedianSampleId
"Pooled RNA samples used in GNF Mouse Expression Atlas 1 on U74C Chip"
hgFixed.gnfMouseU74cMedianExps.id
hgFixed.gnfMouseU74cMedian.expScores comma indexOf full
hgFixed.gnfMouseU74cMedianRatio.expScores comma indexOf full
identifier arbFlyLifeAllSampleId
"Identifiers of RNA samples used in Arbeitman fly life cycle experiments"
hgFixed.arbFlyLifeAllExps.id
hgFixed.arbFlyLifeAll.expScores comma indexOf full
hgFixed.arbFlyLifeAllRatio.expScores comma indexOf full
identifier arbFlyLifeMedianSampleId
"Identifiers of pooled RNA samples used in Arbeitman fly life cycle experiments"
hgFixed.arbFlyLifeMedianExps.id
hgFixed.arbFlyLifeMedian.expScores comma indexOf full
hgFixed.arbFlyLifeMedianRatio.expScores comma indexOf full
identifier kimWormLifeAllSampleId
"Identifiers of RNA samples used in Kim worm life cycle experiments"
hgFixed.kimWormLifeAllExps.id
hgFixed.kimWormLifeAllRatio.expScores comma indexOf full
identifier kimWormLifeMedianSampleId
"Identifiers of pooled RNA samples used in Kim worm life cycle experiments"
hgFixed.kimWormLifeMedianExps.id
hgFixed.kimWormLifeMedianRatio.expScores comma indexOf full
identifier yeastChoCellCycleSampleId
"Identifiers of RNA samples used in Cho yeast cell cycle experiments"
hgFixed.yeastChoCellCycleExps.id
hgFixed.yeastChoCellCycle.expScores comma indexOf full
hgFixed.yeastChoCellCycleRatio.expScores comma indexOf full
identifier hgFixedSageExpId
# I'd like to drop this table set. Check with Chuck.
"Sage experiment (tissue type etc) ID in hgFixed"
hgFixed.sageExp.num
hgFixed.sage.exps comma full
hgFixed.sageCounts.expCounts comma indexOf full
identifier sageExpId
"Sage experiment (tissue type etc) ID"
$gbd.sageExp.num
$gbd.sage.exps comma full
identifier rinnSexSampleId
"Identifiers of RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip"
hgFixed.mouseRinnSexExps.id
hgFixed.mouseRinnSex.expScores comma indexOf full
hgFixed.mouseRinnSexRatio.expScores comma indexOf full
identifier rinnSexMedianSampleId
"Identifiers of median RNA samples used in Rinn Sex Experiments on mouse Affy MOE430 Chip"
hgFixed.mouseRinnSexMedianExps.id
hgFixed.mouseRinnSexMedian.expScores comma indexOf full
hgFixed.mouseRinnSexMedianRatio.expScores comma indexOf full
identifier stanfordPromotersCellId
"Identifiers of cell lines for Stanford ENCODE project luciferase assays"
hgFixed.encode_Stanford_PromotersExps.id
$hg.encode_Stanford_Promoters.expIds comma full
$hg.encode_Stanford_Promoters.expScores comma indexOf full
identifier mouseLandscape
"U. Toronto mouse gene probe ID"
hgFixed.mouseLandscape.name
$mm.knownToXM.value
identifier mouseLandscapeSampleId
"Identifiers of U. Toronto RNA samples"
hgFixed.mouseLandscapeExps.id
hgFixed.mouseLandscape.expScores comma indexOf full
identifier gladHumESSampleId
"Identifiers of RNA samples used in Gladstone Arrays"
hgFixed.gladHumESExps.id
hgFixed.gladHumES.expScores comma indexOf full
hgFixed.gladHumESRatio.expScores comma indexOf full
# Stuff to link together alignment chains and nets
identifier chainSelf
"Link together self chain info"
$gbd.chainSelf.id $split
$gbd.chainSelfLink.chainId $split full
$gbd.netSelf.chainId exclude=0
identifier chainSelfNonSplit
"Link together self chain info"
hg19.chainSelf.id
hg19.chainSelfLink.chainId full
identifier chain[${chainDest}]Id
"Link together chain info"
$gbd.chain[].id $split
$gbd.chain[]Link.chainId $split full
$gbd.net[].chainId exclude=0
$gbd.netRxBest[].chainId exclude=0
$gbd.net[]NonGap.chainId exclude=0
$gbd.netSynteny[].chainId exclude=0
identifier chain[${chainDest}]IdNonSplit
"Link together chain info for chain tables that are not split"
$nonSplitChains.chain[].id
$nonSplitChains.chain[]Link.chainId full
$nonSplitChains.net[].chainId exclude=0
$nonSplitChains.netSynteny[].chainId exclude=0
identifier rBestChainPanTro1Id
"Link together reciprocal best chain/net"
hg16.rBestChainPanTro1.id $split
hg16.rBestChainPanTro1Link.chainId $split full
hg16.rBestNetPanTro1.chainId exclude=0
# Genbank/trEMBL Accessions and meaningful subsets thereof
identifier genbankAccession external=genbank
"Generic Genbank Accession. More specific Genbank accessions follow"
$gbd.seq.acc
identifier stsAccession external=genbank typeOf=genbankAccession
"Genbank accession of a Sequence Tag Site (STS) sequence."
$gbd.stsInfo2.genbank dupeOk
identifier bacEndNames
"Names for BAC end reads."
$gbd.all_bacends.qName dupeOk
$gbd.bacEndPairs.lfNames comma
$danRer.bacEndSingles.lfNames comma
$danRer.bacEndPairsBad.lfNames comma
$danRer.bacEndAlias.alias minCheck=0.55
$hg.fishClones.beNames comma minCheck=0.70
identifier danRerBacExtName
"External name for BAC clones."
$danRer.bacCloneXRef.name dupeOk
$danRer.bacEndPairs.name
$danRer.bacEndSingles.name
identifier bacAccession typeOf=genbankAccession external=genbank
"Genbank accession of a sequenced BAC (~150kb of genomic sequence)."
identifier humanBacAccession typeOf=bacAccession
"Genbank accession of a sequenced $hg.BAC (~150kb of genomic sequence)."
$hg.clonePos.name chopAfter=. dupeOk
$hg,!hg18.gold.frag chopAfter=. $split
hg18.gold.frag chopAfter=. $split minCheck=0.98
hg16.certificate.accession1
hg16.certificate.accession2
$hg,!hg18.gl.frag chopAfter=. $split
hg18.gl.frag chopAfter=. $split minCheck=0.95
$hg.fishClones.accNames chopAfter=. comma minCheck=0.70
identifier humanBacAccessionVersion typeOf=bacAccession
"Genbank accession.version of sequence $hg.BAC"
$hg.clonePos.name dupeOk
$hg,!hg18.gl.frag $split chopAfter=_
$hg,!hg18.gold.frag $split
hg18.gl.frag $split chopAfter=_ minCheck=0.95
hg18.gold.frag $split minCheck=0.90
identifier wgsContigAccession typeOf=genbankAccession
"Genbank accession.version of whole-genome shotgun contig"
$wgs.contigAcc.acc
identifier wgsContigName
"Sequencing project name for whole-genome shotgun contigs."
$wgs.contigAcc.contig
$wgs,!panTro1.gold.frag $split full
identifier proteinAccession typeOf=genbankAccession fuzzy
"Genbank protein accession."
$kgDb.kgProtAlias.alias
$kgDb.kgSpAlias.alias minCheck=0.1
$kgDb.kgXref.protAcc
$gbd.refLink.protAcc
identifier estOrMrnaAccession typeOf=genbankAccession
"Genbank EST or mRNA accession."
$gbd.gbSeq.acc
$gbd.gbStatus.acc unique
$gbd.gbCdnaInfo.acc unique
$gbd.imageClone.acc
$gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma
ce2.altGraphX.mrnaRefs comma minCheck=0.97
hg16.altGraphX.mrnaRefs comma minCheck=0.99
hg17.altGraphX.mrnaRefs comma minCheck=0.97
hg18.altGraphX.mrnaRefs comma minCheck=0.98
mm7.altGraphX.mrnaRefs comma minCheck=0.99
identifier estAccession typeOf=estOrMrnaAccession
"Genbank EST accession"
identifier nativeEstAccession typeOf=estAccession
"Genbank Native (same organism as database) EST accession"
$gbd.all_est.qName dupeOk
$gbd,!sacCer2.est.qName $split full
$gbd,!sacCer2,!caeJap1.intronEst.qName $split
sacCer2.est.qName splitPrefix=%\_ full
sacCer2.intronEst.qName splitPrefix=%\_
caeJap1.intronEst.qName
$gbd.estOrientInfo.name full
identifier nativeEstAccessionNonSplit typeOf=estAccession
"Genbank Native (same organism as database) EST accession"
hg19.all_est.qName dupeOk
hg19.est.qName full
hg19.intronEst.qName
hg19.estOrientInfo.name full
identifier xenoEstAccession typeOf=estAccession
"Genbank xeno (different organism from database) EST accession"
$gbd.xenoEst.qName dupeOk
identifier mrnaAccession typeOf=estOrMrnaAccession fuzzy
"Genbank mRNA accession"
identifier xenoMrnaAccession typeOf=mrnaAccession
"Genbank xeno (different organism from database) mRNA accession"
$gbd.xenoMrna.qName dupeOk
identifier nativeMrnaAccession typeOf=mrnaAccession
"Genbank Native (same organism as database) mRNA accession"
$gbd.all_mrna.qName dupeOk
$gbd,!ce2.mrnaOrientInfo.name full minCheck=0.01
ce2.mrnaOrientInfo.name minCheck=0.08
$gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.mrnaID minCheck=0.80
$gbd,!mm7,!mm8,!hg17,!hg18,!rn4.dupSpMrna.dupMrnaID minCheck=0.95
$gbd,!mm7,!mm8,!mm9,!hg17,!rn3,!rn4.mrnaRefseq.mrna minCheck=0.25
mm7.mrnaRefseq.mrna minCheck=0.30
mm8.mrnaRefseq.mrna minCheck=0.30
mm9.mrnaRefseq.mrna minCheck=0.30
hg17.mrnaRefseq.mrna minCheck=0.80
$rn.mrnaRefseq.mrna minCheck=0.03
$gbd,!mm7,!mm8,!mm9,!hg17,!hg18,!rn4.spMrna.mrnaID minCheck=0.98
$mm.spMrna.mrnaID minCheck=0.20
$mm.dupSpMrna.mrnaID minCheck=0.10
$mm.dupSpMrna.dupMrnaID minCheck=0.10
hg17.spMrna.mrnaID minCheck=0.30
hg17.dupSpMrna.mrnaID minCheck=0.20
hg17.dupSpMrna.dupMrnaID minCheck=0.20
hg18.dupSpMrna.mrnaID minCheck=0.20
hg18.dupSpMrna.dupMrnaID minCheck=0.70
rn4.dupSpMrna.mrnaID minCheck=0.15
rn4.dupSpMrna.dupMrnaID minCheck=0.60
identifier mgcAccession typeOf=nativeMrnaAccession
"Mammalian Gene Collection Genbank mRNA accession."
$gbd.mgcFullMrna.qName dupeOk
$gbd.mgcGenes.name full
identifier orfeomeAccession typeOf=nativeMrnaAccession
"ORFeome collaboration Genbank mRNA accession."
$gbd.orfeomeMrna.qName dupeOk
$gbd.orfeomeGenes.name full
identifier refSeqId typeOf=mrnaAccession
"RefSeq mRNA accession"
$gbd.refLink.mrnaAcc
$gbd.refSeqStatus.mrnaAcc minCheck=0.10
$kgDb.kgXref.refseq exclude= minCheck=0.50
$kgDb,!hg16,!hg17,!hg18,!mm7,!mm8,!mm9.knownToRefSeq.value minCheck=0.98
hg18,mm7,mm8,mm9.knownToRefSeq.value minCheck=0.96
hg16,hg17.knownToRefSeq.value minCheck=0.94
$kgDb.refSeqKg.refseq minCheck=0.60
$ccdsDb,!hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.35
$gbd,!rn3.mrnaRefseq.refseq minCheck=0.25
rn3.mrnaRefseq.refseq minCheck=0.03
$gbd,!bosTau2,!bosTau3,!canFam1,!canFam2,!droSim1,!droYak1,!droYak2,!panTro1,!rheMac2,!dp2,!dp3.mrnaOrientInfo.name minCheck=0.0
# The rule above should only apply to mrnaOrientInfo entries from refSeq (not
# the regular genBank mRNAs). The minCheck=0.0 preserves table relationshps.
$gbd.refFlat.name
$gbd.refGene.name
$gbd.refMrna.name
$gbd.refSeqAli.qName
$gbd.refSeqSummary.mrnaAcc minCheck=0.99
dm1.bdgpToRefSeq.value minCheck=0.94
$dm,!dm1.flyBaseToRefSeq.value minCheck=0.96
$mm.mrnaRefseq.mrna minCheck=0.03
$mm.spMrna.mrnaID minCheck=0.40
$mm.dupSpMrna.mrnaID minCheck=0.60
$mm,!mm8,!mm9.dupSpMrna.dupMrnaID minCheck=0.20
mm9.dupSpMrna.dupMrnaID minCheck=0.19
mm8.dupSpMrna.dupMrnaID minCheck=0.19
hg17.mrnaRefseq.mrna minCheck=0.10
hg17.spMrna.mrnaID minCheck=0.50
hg17.dupSpMrna.mrnaID minCheck=0.40
hg17.dupSpMrna.dupMrnaID minCheck=0.20
hg18.ccdsInfo.mrnaAcc chopAfter=. minCheck=0.37
identifier xenoRefSeqId typeOf=xenoMrnaAccession
"Other Species RefSeq mRNA accession"
$xrg.xenoRefGene.name dupeOk
$xrg.xenoRefFlat.name full
$xrg.xenoRefSeqAli.qName full
$xrg.xenoRefFlat.name full
identifier knownToRefSeqId typeOf=mrnaAccession
"RefSeq mRNA accession in knownToRefSeq table"
$kgDb.knownToRefSeq.value dupeOk
mm7.geneNetworkId.id minCheck=0.80
mm8.geneNetworkId.id minCheck=0.80
mm9.geneNetworkId.id minCheck=0.80
rn3.geneNetworkId.id minCheck=0.40
identifier knownGeneId dependency
"Known Gene ID - the genbank accession of the representative mRNA"
$kgDb.knownGene.name dupeOk
$kgDb.bioCycPathway.kgID
$kgDb.ceBlastTab.query
$kgDb.hgBlastTab.query
$kgDb.dmBlastTab.query
$kgDb.drBlastTab.query
$kgDb.mmBlastTab.query
$kgDb.rnBlastTab.query
$kgDb.scBlastTab.query
$kgDb,!rn3.dupSpMrna.mrnaID
rn3.dupSpMrna.mrnaID minCheck=0.90
# $kgDb,!hg16,!hg17.pseudoGeneLink.kgName exclude=noKg
# hg16,hg17.pseudoGeneLink.kgName minCheck=0.18 exclude=noKg
$kgDb.foldUtr3.name
$kgDb.foldUtr5.name
$hg.gnfU95Distance.query
$hg.gnfU95Distance.target
$kgDb.gnfAtlas2Distance.query
$kgDb.gnfAtlas2Distance.target
$kgDb.affyGnfU74ADistance.query
$kgDb.affyGnfU74ADistance.target
$kgDb.affyGnfU74BDistance.query
$kgDb.affyGnfU74BDistance.target
$kgDb.affyGnfU74CDistance.query
$kgDb.affyGnfU74CDistance.target
$kgDb.mouseLandscapeDistance.query minCheck=0.94
$kgDb.mouseLandscapeDistance.target minCheck=0.94
$hg.gladHumESDistance.query
$hg.gladHumESDistance.target
$kgDb.keggPathway.kgID
$kgDb.kgAlias.kgID
$kgDb.kgProtAlias.kgID
$kgDb.kgSpAlias.kgID
$kgDb.kgXref.kgID full
$kgDb.kgTxInfo.name full
$kgDb.knownBlastTab.query
$kgDb.knownBlastTab.target
$kgDb.knownCanonical.transcript
$kgDb.knownGeneMrna.name full
$kgDb,!hg18,!mm9.knownGeneLink.name
$kgDb.knownIsoforms.transcript full
$kgDb.knownToAllenBrain.name
$kgDb.knownToCdsSnp.name
$kgDb.knownToEnsembl.name
$kgDb.knownToGnf1h.name
$kgDb.knownToGnfAtlas2.name
$kgDb.knownToHInv.name
$kgDb.knownToHprd.name
$kgDb.knownToLocusLink.name
$kgDb.knownToPfam.name
$kgDb.knownToRefSeq.name
$kgDb.knownToSuper.gene
$kgDb.knownToTreefam.name
$kgDb.knownToU133.name
$kgDb.knownToU133Plus2.name
$kgDb.knownToU95.name
$kgDb.knownToVisiGene.name
$kgDb.refSeqKg.kgId minCheck=0.50
$kgDb.rankProp.query
$kgDb.rankProp.target
$kgDb.pPsiBlast.kgId1
$kgDb.pPsiBlast.kgId2
$ccdsDb.ccdsKgMap.geneId
$kgDb2.knownGenePep.name full
$kgDb3.knownGenePep.name
$kgDb3.knownCanonical.protein exclude=
$kgDb3.kgProtMap2.qName
$hg.humanHprdP2P.query
$hg.humanHprdP2P.target
$hg.humanVidalP2P.query
$hg.humanVidalP2P.target
$hg.humanWankerP2P.query
$hg.humanWankerP2P.target
$kgDb.kgColor.kgID full
$kgDb.kg2ToKg3.newId minCheck=0.5 exclude=
$kgDb.kg3ToKg4.oldId minCheck=0.5
$kgDb.kg3ToKg4.newId exclude=
identifier knownGeneOld3Id dependency
"Previous UCSC Gene build"
$kgDb.knownGeneOld3.name
$kgDb.kg3ToKg4.oldId full
identifier knownGeneOld2Id dependency
"Old knownGene (KGII) and kgXref tables kept after KGIII implementation"
$kgDb.knownGeneOld2.name dupeOk
$kgDb.kgXrefOld2.kgID full
identifier knownToHprdName
"Dependencies on knownToHprd.name"
$kgDb.knownToHprd.name dupeOk
$kgDb.humanHprdP2P.target
identifier pfamDesc
"pfam description for each accession"
$kgDb.pfamDesc.pfamAC
$kgDb.knownToPfam.value
identifier scopName
"scop Domain Names"
$kgDb.ucscScop.domainName dupeOk
$kgDb.scopDesc.name full minCheck=0.60
identifier scopToUcscId
"scop Domains to UCSC Id"
$kgDb.kgProtMap2.qName
$kgDb,!hg18.ucscScop.ucscId minCheck=0.99
hg18.ucscScop.ucscId minCheck=0.70
identifier knownIsoformCluster
"ID of a cluster of overlapping known genes"
$kgDb.knownCanonical.clusterId
$kgDb.knownIsoforms.clusterId full
# known relationship for both KG2 and KG3, but doesn't work across dbs.
identifier knownXref
"Swissprot IDs"
$kgDb.kgXref.spID dupeOk
proteome.spXref2.accession
proteome.hgnc.uniProt
identifier ccdsGeneId
"CCDS Gene ID"
$ccdsDb.ccdsGene.name dupeOk
$ccdsDb.ccdsInfo.ccds full
$ccdsDb.ccdsKgMap.ccdsId
identifier hugeId
"HuGE Gene ID"
$hg.kgXref.geneSymbol dupeOk
$hg.huge.geneSymbol minCheck=0.89
# Fields parsed out of a Genbank flat file, associated with mRNA records
identifier gbCdnas
"Connects gbCdnaInfo with mRNA/EST"
$gbd.gbCdnaInfo.acc
$gbd.all_mrna.qName
$gbd.all_est.qName
$gbd.refGene.name
$gbd.xenoRefGene.name
$gbd.gbMiscDiff.acc
$gbd.refSeqAli.qName
$gbd.xenoRefSeqAli.qName
$gbd.xenoMrna.qName
$gbd.xenoEst.qName
$gbd.gbWarn.acc
identifier genBankAuthor
"Connects genBank mRNA/EST and its author"
$gbd.author.id
$gbd.gbCdnaInfo.author
identifier genBankCds
"Connects genBank mRNA/EST and its coding region (CDS)"
$gbd.cds.id
$gbd.gbCdnaInfo.cds
identifier genBankCell
"Connects genBank mRNA/EST and the cell type it came from"
$gbd.cell.id
$gbd.gbCdnaInfo.cell
identifier genBankDevelopment
"Connects genBank mRNA/EST and development stage of the organism it came from"
$gbd.development.id
$gbd.gbCdnaInfo.development
identifier genBankDescription
"Connects genBank mRNA/EST and descriptive text"
$gbd.description.id
$gbd.gbCdnaInfo.description
identifier genBankGeneName
"Connects genBank mRNA/EST and gene name"
$gbd.geneName.id
$gbd.gbCdnaInfo.geneName
$gbd.refLink.geneName
identifier genBankKeyword
"Connects genBank mRNA/EST and keyword"
$gbd.keyword.id
$gbd.gbCdnaInfo.keyword
identifier genBankLibrary
"Connects genBank mRNA/EST and cDNA library"
$gbd.library.id
$gbd.gbCdnaInfo.library
$gbd,!hg17.altGraphX.mrnaLibs comma
hg17.altGraphX.mrnaLibs comma minCheck=0.99
identifier genBankMrnaClone
"Connects genBank mRNA/EST and cDNA clone name"
$gbd.mrnaClone.id
$gbd.gbCdnaInfo.mrnaClone
identifier genBankOrganism
"Connects genBank mRNA/EST and organism it came from"
$gbd.organism.id
$gbd.gbCdnaInfo.organism
identifier genBankProductName
"Connects genBank mRNA/EST and protein product name"
$gbd.productName.id
$gbd.gbCdnaInfo.productName
$gbd.refLink.prodName
identifier genBankSex
"Connects genBank mRNA/EST and sex mRNA came from"
$gbd.sex.id
$gbd.gbCdnaInfo.sex
identifier genBankSource
"Connects genBank mRNA/EST and source of mRNA"
$gbd.source.id
$gbd.gbCdnaInfo.source
identifier genBankTissue
"Connects genBank mRNA/EST and tissue mRNA isolated from"
$gbd.tissue.id
$gbd.gbCdnaInfo.tissue
$gbd.altGraphX.mrnaTissues comma
# Some misc clone-oriented identifiers
identifier bacCloneName fuzzy
"A Roswell Park, Cal Tech or other clone ID"
$gbd.fishClones.name
$gbd.bacEndPairs.name
identifier imageCloneId external=IMAGEConsortium fuzzy
"An image cDNA clone ID"
$gbd.imageClone.imageId
identifier humanFosmidId
"Human Fosmid (~50kb genomic sequence) clone"
$hg.fosEndPairs.name dupeOk
identifier humanFosmidEndId
"Identifier of read from one end of human formid."
$hg.all_fosends.qName dupeOk
$hg.fosEndPairs.lfNames comma
## TYPED TO HERE %%%
# Mapping Stuff, STS, etc.
identifier dbStsId external=dbSts fuzzy
"NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
$hg.all_sts_primer.qName chopBefore=dbSTS_
$gbd.all_sts_seq.qName
$gbd.stsInfo2.dbSTSid
identifier ucscStsId
"UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID"
$gbd.stsInfo2.identNo
$gbd.stsAlias.identNo
$gbd.stsMap.identNo
identifier ucscMouseStsId
"UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID"
$mm.stsInfoMouseNew.identNo
$mm.stsAlias.identNo
$mm.all_sts_primer.qName chopAfter=_ minCheck=0.99
$mm.stsMapMouseNew.identNo
identifier stsName fuzzy
"STS (Sequenced Tagged Site, aka mapping sequence) Name"
$hg.fishClones.stsNames comma
$gbd.stsInfo2.otherNames comma
$mm.stsInfoMouseNew.alias separator=;
identifier stsTrueName typeOf=stsName
"STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
$gbd,!hg16.stsInfo2.name
$gbd.stsAlias.trueName
$gbd.stsMap.name
identifier stsTrueNameHg16 typeOf=stsName
"STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16"
hg16.stsInfo2.name dupeOk
hg16.stsAlias.trueName
hg16.stsMap.name
identifier mouseStsTrueName typeOf=stsName
"Mouse STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
$mm.stsInfoMouseNew.name
$mm.stsAlias.trueName minCheck=0.99
$mm,!mm7,!mm8,!mm9.all_sts_primer.qName chopBefore=_ minCheck=0.99
mm7,mm8,mm9.all_sts_primer.qName chopBefore=_ minCheck=0.98
$mm.stsMapMouseNew.name
$mm.jaxQTL3.marker exclude= minCheck=0.99
$mm.jaxQTL3.flank1 exclude= minCheck=0.95
$mm.jaxQTL3.flank2 exclude= minCheck=0.99
identifier ratStsTrueName typeOf=stsName
"Rat STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
$rn.stsInfoRat.name dupeOk
$rn,!rn3.stsMapRat.name
rn3.stsMapRat.name minCheck=0.99
identifier rhMapName
"Zebrafish RH (Radiation Hybrid) Map Name"
$danRer.rhMap.qName dupeOk
$danRer.rhMapZfishInfo.name minCheck=0.90 unique
identifier igtcName
"IGTC (genetrap.org) sequence name"
$mm.seq.acc
$mm.igtc.qName
identifier kompName
"KOMP (knockoutmouse.org) gene name"
$mm.komp.name dupeOk
$mm.kompExtra.name
# "Biological" Gene Names
identifier hugoName external=HUGO fuzzy
"International Human Gene Identifier"
$hg.refLink.name
$hg.atlasOncoGene.locusSymbol
$hg.kgAlias.alias
$hg.kgSpAlias.alias minCheck=0.1
$hg.kgXref.geneSymbol
$hg.refFlat.geneName
$hg.jaxOrtholog.humanSymbol
$hg.omimMorbidMap.geneSymbols
visiGene.gene.name
identifier kgGeneSymbol
"UCSC Genes Gene Symbol"
$hg.kgXref.geneSymbol dupeOk
$hg.omimGeneMap.geneSymbol comma minCheck=0.40
$hg.omimMorbidMap.geneSymbols comma minCheck=0.25
identifier mouseGeneName fuzzy
"Mouse gene name from Jackson Labs/RefSeq"
$hg.jaxOrtholog.mouseSymbol
$mm.refLink.name
visiGene.gene.name
# Model Organism Database Identifiers
identifier jaxMgiId
"Jackson Labs Mouse Gene Identifier"
$hg.jaxOrtholog.mgiId
identifier wormBaseIsoformCluster
"Overlapping (after splicing) WormBase transcripts"
$ce.sangerCanonical.clusterId
$ce.sangerIsoforms.clusterId full
identifier wormBaseId external=WormBase dependency
"WormBase (C. elegans) ORF ID"
$ce.sangerGene.name
$gbd,!rn3.ceBlastTab.target minCheck=0.90
$ce.kimExpDistance.query minCheck=0.68
$ce.kimExpDistance.target minCheck=0.66
$ce.orfToGene.name
$ce.sangerBlastTab.query
$ce.sangerBlastTab.target
$ce.sangerCanonical.transcript
$ce.sangerIsoforms.transcript
$ce.sangerLinks.orfName minCheck=0.96
$ce.sangerPep.name minCheck=0.96
$ce.sangerToKim.name
$ce.sangerToPfam.name
$ce.sangerToRefSeq.name
$ce.dmBlastTab.query
$ce,!ce2.drBlastTab.query
$ce.hgBlastTab.query
$ce,!ce2.mmBlastTab.query
$ce,!ce2.rnBlastTab.query
$ce.scBlastTab.query
$ce.sangerGeneToWBGeneID.sangerGene
identifier wormBasePseudoGene external=WormBase dependency
"WormBase (C. elegans) pseudo genes"
$ce.sangerPseudoGene.name
identifier wormBaseRnaGene external=WormBase dependency
"WormBase (C. elegans) RNA genes"
$ce.sangerRnaGene.name
identifier flyBaseRefId
"FlyBase (Drosophila) Reference (Literature)"
$dm.fbRef.id
$dm.fbPhenotype.fbRef
identifier flyBaseAlleleId
"FlyBase (Drosophila) Allele ID"
$dm.fbAllele.id
$dm.fbPhenotype.fbAllele exclude=0
identifier flyBaseGeneId external=FlyBase
"FlyBase (Drosophila) Gene ID"
$dm.fbGene.geneId
$dm.bdgpExprLink.flyBaseId minCheck=0.95
dm1.bdgpGeneInfo.flyBaseId minCheck=0.95
dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20
dm1.bdgpSwissProt.flyBaseId minCheck=0.95
$dm.fbAllele.geneId
$dm.fbPhenotype.geneId
$dm.fbSynonym.geneId
$dm.fbTranscript.geneId minCheck=0.95
dm1.flyBaseSwissProt.flyBaseId minCheck=0.95
$dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90
$dm,!dm1.pscreen.geneIds comma minCheck=0.95
$gbd,!hg17,!hg18,!danRer3,!mm7,!mm8,!mm9,!rn3,!rn4,!ce2,!ce6,!sacCer1,!sacCer2.dmBlastTab.target minCheck=0.90
identifier bdgpIsoformCluster
"Overlapping (after splicing) BDGP Drosophila transcripts"
dm1.bdgpCanonical.clusterId
dm1.bdgpIsoforms.clusterId full
identifier bdgpGeneId external=BDGP
"Berkeley Drosophila Genome Project Gene ID"
dm1.bdgpGeneInfo.bdgpName
dm1.bdgpExprLink.bdgpName minCheck=0.85
dm1.bdgpToCanonical.value
identifier bdgpTranscriptId external=BDGP dependency
"Berkeley Drosophila Genome Project Transcript ID"
dm1.bdgpGene.name
dm1.arbExpDistance.query
dm1.arbExpDistance.target
dm1.bdgpBlastTab.query
dm1.bdgpBlastTab.target
dm1.bdgpCanonical.transcript
dm1.bdgpIsoforms.transcript
dm1.bdgpGenePep.name
dm1.bdgpSwissProt.bdgpName
dm1.bdgpToCanonical.name
dm1.bdgpToLocusLink.name minCheck=0.80
dm1.bdgpToPfam.name
dm1.bdgpToRefSeq.name minCheck=0.97
dm1.ceBlastTab.query
dm1.drBlastTab.query
dm1.hgBlastTab.query
dm1.mmBlastTab.query
dm1.rnBlastTab.query
dm1.scBlastTab.query
dm1.fbTranscript.transcriptId minCheck=0.95
dm1.hgBlastTab.query
dm1.blastFBPep00.name
dm1.pscreen.geneIds comma minCheck=0.90
identifier bdgpNonCodingId external=BDGP
"Berkeley Drosophila Genome Project Noncoding Gene ID"
dm1.bdgpNonCoding.name chopAfter=- dupeOk
dm1.bdgpNonCodingInfo.bdgpName minCheck=0.89
identifier flyBase2004IdDm external=FlyBase
"FlyBase Xref as of 2004 for dm"
$dm.flyBase2004Xref.name
$dm,!dm1.flyBaseGene.name minCheck=0.99
$dm,!dm1.flyBasePep.name
$dm,!dm1.flyBaseNoncoding.name minCheck=0.90
$dm,!dm1.arbExpDistance.query
$dm,!dm1.arbExpDistance.target
$dm,!dm1.ceBlastTab.query
$dm,!dm1.drBlastTab.query minCheck=0.97
$dm,!dm1.hgBlastTab.query minCheck=0.99
$dm,!dm1.mmBlastTab.query
$dm,!dm1.rnBlastTab.query
$dm,!dm1.scBlastTab.query
$dm,!dm1.flyBaseBlastTab.query
$dm,!dm1.flyBaseBlastTab.target
$dm,!dm1.flyBaseCanonical.transcript
$dm,!dm1.flyBaseIsoforms.transcript
$dm,!dm1.flyBaseToRefSeq.name
$dm,!dm1.flyBaseToUniProt.name
$dm,!dm1.flyBaseToPfam.name
$dm,!dm1.flyBaseToCG.name
$dm,!dm1.flyBaseToDescription.name
$dm,!dm1.flyP2P.query minCheck=0.98
$dm,!dm1.flyP2P.target minCheck=0.98
hg17,hg18,danRer3,mm7,mm8,mm9,rn3,rn4,ce2,sacCer1,sacCer2.dmBlastTab.target minCheck=0.90
identifier flyBase2004IdDp external=FlyBase
"FlyBase Xref as of 2004 for dp3"
dp3.flyBase2004Xref.name
dp3.flyBaseGene.name
identifier sgdIsoformCluster
"Overlapping (after splicing) SGD (Yeast) transcripts"
$sacCer.sgdCanonical.clusterId
$sacCer.sgdIsoforms.clusterId full
identifier sgdId external=SGD
"Sacchromyces Genome Database ID - Coding or other"
identifier sgdCodingId typeOf=sgdId dependency
"Sacchromyces Genome Database ID"
$sacCer.sgdGene.name
$gbd.scBlastTab.target minCheck=0.90
$sacCer.sgdBlastTab.query
$sacCer.sgdBlastTab.target
$sacCer.ceBlastTab.query
$sacCer.dmBlastTab.query
$sacCer,!sacCer1.drBlastTab.query
$sacCer.hgBlastTab.query minCheck=0.999
$sacCer.mmBlastTab.query
$sacCer.rnBlastTab.query
sacCer2.knownBlastTab.query
$sacCer.choExpDistance.target minCheck=0.60
$sacCer.choExpDistance.query minCheck=0.60
$sacCer.sgdCanonical.transcript
$sacCer.sgdDescription.name
$sacCer.sgdIsoforms.transcript
$sacCer.sgdAbundance.name minCheck=0.95
$sacCer.sgdLocalization.name minCheck=0.95
$sacCer.sgdPep.name
$sacCer.sgdToSwissProt.name minCheck=0.85
$sacCer.sgdToName.name minCheck=0.86
$sacCer.esRegGeneToModule.gene minCheck=0.94
$sacCer.esRegGeneToMotif.gene minCheck=0.97
$sacCer.esRegUpstreamRegion.name minCheck=0.96
$sacCer.sgdToPfam.name minCheck=0.55
identifier sgdNoncodingId typeOf=sgdId
"Sacchromyces Genome Database Noncoding/Dubious feature ID"
$sacCer.sgdOther.name dupeOk
$sacCer.sgdOtherDescription.name
# RGD Family Identifiers
identifier rgdGeneId external=RGD
"RGD gene ID"
$rn.rgdGeneLink.refSeq
$rn.rgdGene.name
identifier rgdEstId external=RGD
"RGD EST ID"
$rn.rgdEstLink.name
$rn.rgdEst.qName
identifier rgdQtlId external=RGD
"RGD QTL ID"
$rn,$hg.rgdQtl.name
$rn,$hg.rgdQtlLink.name minCheck=0.89
identifier rgdRatQtlId external=RGD
"RGD Rat QTL ID mapped to other organism"
$hg.rgdRatQtl.name dupeOk
$hg.rgdRatQtlLink.name minCheck=0.89
identifier rgdSslpId external=RGD
"RGD SSLP ID"
$rn.rgdSslp.name
$rn.rgdSslpLink.name
# The Ensembl Gmish
identifier ensemblGeneId external=Ensembl
"Ensemble Gene ID"
$gbd.ensTranscript.gene_name dupeOk
$gbd.ensGtp.gene chopAfter=.
$gbd.ensGeneXref.gene_name
identifier ensemblGeneId3 external=Ensembl
"Ensemble Gene ID"
$gbd.ensemblXref3.gene dupeOk
identifier ensemblProteinId external=Ensembl
"Ensemble Translated Protein ID"
$gbd.ensTranscript.translation_name dupeOk
$gbd.ensGtp.protein chopAfter=.
$gbd.sfAssign.seqID minCheck=0.01
identifier ensemblProteinId3 external=Ensembl
"Ensemble Translated Protein ID"
$gbd.ensemblXref3.protein dupeOk
$gbd.sfAssign.seqID minCheck=0.01
identifier ensemblTranscriptId external=Ensembl dependency
"Ensembl Transcript ID"
$gbd,!ce6,!felCat3.ensGene.name chopAfter=.
$gbd.ensGeneXref.transcript_name chopAfter=. minCheck=0.95
$gbd.ensGtp.transcript chopAfter=. minCheck=0.94
$gbd.ensPep.name chopAfter=. minCheck=0.96
$gbd.ensTranscript.transcript_name chopAfter=. minCheck=0.20
$gbd.ensInfo.name minCheck=0.9
$kgDb.knownToEnsembl.value chopAfter=.
$ccdsDb.ccdsInfo.mrnaAcc minCheck=0.30
$danRer.ensZfishBlastTab.query
$danRer.ensZfishBlastTab.target
$danRer.ceBlastTab.query
$danRer.dmBlastTab.query
$danRer.hgBlastTab.query
$danRer.mmBlastTab.query
$danRer.rnBlastTab.query
$danRer.scBlastTab.query
identifier ensemblTranscriptIdCe external=Ensembl dependency
"Ensembl Transcript ID for C. elegans"
$ce.ensGene.name chopAfter=. dupeOk
$ce.ensGtp.transcript chopAfter=. minCheck=0.98
$ce.ensPep.name chopAfter=. minCheck=0.98
identifier ensemblTranscriptIdFelCat external=Ensembl dependency
"Ensembl Transcript ID for felCat"
$felCat.ensGene.name dupeOk
$felCat.ensGtp.transcript minCheck=0.99
$felCat.ensPep.name minCheck=0.99
# UCSC to Ensembl chrom name translation
identifier ensemblLinkId external=Ensembl dependency
"Ensembl Links from hgTracks"
hg18,hg19.chromInfo.chrom
hg18,hg19.ucscToEnsembl.ucsc
identifier ucscToEnsembl external=Ensembl dependency
"UCSC to Ensembl chrom name translation"
hg18,hg19.ucscToEnsembl.ensembl
hg18,hg19.ensemblLift.chrom
# Ensembl EST
identifier ensemblEstTranscriptId external=Ensembl dependency
"Ensembl EST Transcript ID"
$gbd.ensEstGene.name chopAfter=.
$gbd.ensEstGtp.transcript chopAfter=.
$gbd.ensEstPep.name chopAfter=.
identifier gazeGeneId external=Genoscope
"GAZE Gene ID"
$gbd.gaze.name
$gbd.gazePep.name
# H-Invitational Database Identifiers
identifier hinvTranscriptId external=H-INV dependency
"H-Invitational Transcript ID"
$hg.HInv.geneId
$hg.knownToHInv.value
$hg.HInvGeneMrna.qName
# Protein Family Identifiers
identifier pfamId external=Pfam fuzzy
"Pfam (Protein Family) ID"
$kgDb.knownToPfam.value
dm1.bdgpToPfam.value
identifier superfamilyId external=SCOP
"Protein SCOP/Superfamily ID"
hgFixed.scopDes.sunid
$gbd.sfDes.id # This table is redundant with hgFixed.scopDes
$gbd.sfAssign.sfID
# Pathway Identifiers
identifier bioCycMapId external=BioCyc
"BioCyc Pathway Map ID"
$gbd.bioCycMapDesc.mapID
$gbd.bioCycPathway.mapID minCheck=0.78
identifier keggMapId external=KEGG
"KEGG Pathway Map ID"
$gbd.keggMapDesc.mapID dupeOk
$gbd.keggPathway.mapID
identifier cgapId
"NCI Cancer Genome Annotation Project Gene ID"
$gbd.cgapAlias.cgapID dupeOk
$gbd.cgapBiocPathway.cgapID
identifier cgapMapId
"NCI Cancer Genome Annotation Project Map ID"
$gbd.cgapBiocDesc.mapID
$gbd.cgapBiocPathway.mapID
identifier cgapAlias
"NCI Cancer Genome Annotation Project Alias"
$gbd.cgapAlias.alias dupeOk
$gbd,!hg16,!hg18,!hg19.knownGene.name minCheck=0.50
hg16.knownGene.name minCheck=0.05
hg18,hg19.kgXref.geneSymbol minCheck=0.85
# SNP (Simple Nucleotide Polymorphism) Stuff
identifier affySnp10KId external=Affymetrix
"Affymetrix 10K SNP Identifier"
hgFixed.affy10KDetails.affyId
$hg.affy10K.name
identifier affySnp120KId external=Affymetrix
"Affymetrix 120K SNP Identifier"
hgFixed.affy120KDetails.affyId
$hg.affy120K.name
identifier dbSnpId external=dbSNP fuzzy
"NCBI dbSNP ID"
$kgDb.knownToCdsSnp.value
identifier dbSnpHgId typeOf=dbSnpId
"Human dbSNP ID"
hgFixed.dbSnpRsHg.rsId
$hg.snpMap.name minCheck=0.90
hgFixed.affy10KDetails.rsId minCheck=0.94
hgFixed.affy120KDetails.rsId minCheck=0.97
identifier dbSnpMmId typeOf=dbSnpId
"Mouse dbSNP ID"
hgFixed.dbSnpRsMm.rsId
$mm.snpMap.name
identifier dbSnpRnId typeOf=dbSnpId
"Rat dbSNP ID"
hgFixed.dbSnpRsRn.rsId
$rn.snpMap.name
identifier hapmapSnpId
"HapMap SNPs"
$hg.hapmapAllelesSummary.name
$hg.hapmapSnpsCEU.name
$hg.hapmapSnpsCHB.name
$hg.hapmapSnpsJPT.name
$hg.hapmapSnpsYRI.name
$hg.hapmapAllelesChimp.name
$hg.hapmapAllelesMacaque.name
$hg,!hg17.hapmapLdCeu.name unique
$hg,!hg17.hapmapLdChb.name unique
$hg,!hg17.hapmapLdChbJpt.name unique
$hg,!hg17.hapmapLdJpt.name unique
$hg,!hg17.hapmapLdYri.name unique
$hg,!hg17.hapmapLdPhCeu.name unique
$hg,!hg17.hapmapLdPhChbJpt.name unique
$hg,!hg17.hapmapLdPhYri.name unique
identifier snpAnnotations125
"SNP annotations"
$snpDb125.snp125.name dupeOk
$snpDb125.snp125Exceptions.name
$snpDb125.snpSeq.acc minCheck=.8
hg17.snpArrayAffy10.rsId minCheck=0.98
hg17.snpArrayAffy10v2.rsId minCheck=0.98
hg17.snpArrayAffy250Nsp.rsId minCheck=0.98
hg17.snpArrayAffy250Sty.rsId minCheck=0.98
hg17.snpArrayAffy50HindIII.rsId minCheck=0.98
hg17.snpArrayAffy50XbaI.rsId minCheck=0.98
hg17.snpArrayIllumina300.name
identifier snpAnnotations126
"SNP annotations"
$snpDb126.snp126.name dupeOk
$snpDb126.snp126Exceptions.name
$snpDb126.snpSeq.acc minCheck=.8
hg18.snp126ortho.name
hg18.snp126orthoPanTro2RheMac2.name
hg18.snpArrayAffy5.rsId minCheck=0.98
hg18.snpArrayAffy6.rsId minCheck=0.98
hg18.snpArrayAffy250Nsp.rsId
hg18.snpArrayAffy250Sty.rsId
hg18.snpArrayIllumina300.name
hg18.snpArrayIllumina550.name
hg18.snpArrayIllumina650.name
identifier snpAnnotations127
"SNP annotations"
$snpDb127.snp127.name dupeOk
$snpDb127.snp127Exceptions.name
$snpDb127.snpSeq.acc minCheck=.8
identifier snpName128
"dbSNP version 128 rs* identifiers"
$gbd.snp128.name dupeOk
$gbd.snp128Exceptions.name
$gbd.snp128Seq.acc minCheck=.9
hg18.snp128OrthoPanTro2RheMac2.name
identifier snpExceptions128
"Annotations of unusual conditions in dbSNP version 128"
$gbd.snp128ExceptionDesc.exception
$gbd.snp128Exceptions.exception
identifier snpName129
"dbSNP version 129 rs* identifiers"
$gbd.snp129.name dupeOk
$gbd.snp129Exceptions.name minCheck=.99
$gbd.snp129Seq.acc minCheck=.99
hg18.snp129OrthoPt2Pa2Rm2.name
hg18.snpArrayIllumina1M.name minCheck=0.95
identifier snpExceptions129
"Annotations of unusual conditions in dbSNP version 129"
$gbd.snp129ExceptionDesc.exception
$gbd.snp129Exceptions.exception
identifier snpName130
"dbSNP version 130 rs* identifiers"
$gbd.snp130.name dupeOk
$gbd.snp130Exceptions.name minCheck=.999
$gbd.snp130Seq.acc minCheck=.98
$gbd.snp130CodingDbSnp.name minCheck=.99
$hg.snp130OrthoPt2Pa2Rm2.name
hg18.snpArrayIlluminaHuman660W_Quad.name minCheck=0.90
hg18.snpArrayIlluminaHumanCytoSNP_12.name minCheck=0.95
hg18.snpArrayIlluminaHumanOmni1_Quad.name minCheck=0.85
# gwasCatalog SNPs were mapped to genome using snp130. Move this and update trackDb
# settings if we remap to new version:
$hg.gwasCatalog.name
identifier snpExceptions130
"Annotations of unusual conditions in dbSNP version 130"
$gbd.snp130ExceptionDesc.exception
$gbd.snp130Exceptions.exception
# Other NCBI Identifiers
identifier locusLinkId external=LocusLink
"NCBI LocusLink ID"
$gbd.refLink.locusLinkId dupeOk
$gbd.keggPathway.locusID minCheck=0.98
$kgDb,!hg16,!mm8.knownToLocusLink.value minCheck=0.98
hg16,mm8.knownToLocusLink.value minCheck=0.96
identifier omimId external=OMIM
"Online Mendelian Inheritance in Man (OMIM) ID"
$gbd.refLink.omimId dupeOk exclude=0
identifier omimGeneId
"omimGene ID"
$hg.omimGene.name dupeOk
$hg.omimGeneMap.omimId minCheck=0.85
$hg.refLink.omimId exclude=0 minCheck=0.98
$hg.omimMorbidMap.omimId minCheck=0.75
$hg.omimToKnownCanonical.omimId
identifier unigeneId fuzzy
"NCBI UniGene Cluster ID"
# hgFixed.sage.uni
$hg.uniGene_2.name chopBefore=.
$hg.sage.uni
identifier unigeneId2 external=UniGene
"NCBI UniGene Cluster ID for databases with UniGene seq table entry"
$gbd.seq.acc
$galGal.uniGene_gg.qName
$danRer.uniGene_dr.qName
$hg.uniGene_3.qName
identifier kiddEichlerId external=EichlerLab
"Clone accession used in Kidd..Eichler '08"
$hg.kiddEichlerToNcbi.name
$hg.kiddEichlerDiscAbc7.name chopAfter=, minCheck=0.80
$hg.kiddEichlerDiscAbc8.name chopAfter=,
$hg.kiddEichlerDiscAbc9.name chopAfter=,
$hg.kiddEichlerDiscAbc10.name chopAfter=,
$hg.kiddEichlerDiscAbc11.name chopAfter=,
$hg.kiddEichlerDiscAbc12.name chopAfter=,
$hg.kiddEichlerDiscAbc13.name chopAfter=,
$hg.kiddEichlerDiscAbc14.name chopAfter=,
hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.01
$hg,!hg17.kiddEichlerDiscG248.name chopAfter=, chopBefore=_ minCheck=0.005
# BGI SNP Identifiers
identifier bgiSnpId external=BGI
"BGI SNP ID"
$galGal.bgiSnp.name
$galGal.bgiGeneSnp.snpName
identifier bgiGeneId external=BGI
"BGI Gene ID"
$galGal.bgiGene.name
$galGal.bgiGeneSnp.geneName minCheck=0.1
# Other Identifiers
identifier extFileId
"External file ID"
$gbd.extFile.id
$gbd.seq.extFile
rn3.multizHg15Mm3.extFile
$sacCer.multizYeast.extFile
$dm.a_gambiae_mypa.extFile
$dm.d_pseudoobscura_mypa.extFile
$dm.d_yakuba_mypa.extFile
#$gbd.multiz4way.extFile
#$gbd.multiz5way.extFile
#$gbd.multiz6way.extFile
#$gbd.multiz7way.extFile
#$gbd.multiz8way.extFile
#$gbd.multiz9way.extFile
#$gbd.multiz10way.extFile
#$gbd.multiz11way.extFile
#$gbd.multiz12way.extFile
#$gbd.multiz15way.extFile
#$gbd.multiz17way.extFile
#$gbd.multiz28way.extFile
identifier gbExtFileId
"External file ID for GenBank incremental update system"
$gbd.gbExtFile.id
$gbd.gbSeq.gbExtFile minCheck=0.85
identifier encodeRegion
"ENCODE (extensive analysis of 1% of genome) Region"
hgFixed.encodeRegionInfo.name
$hg.encodeRegions.name
identifier blastDm1FBPepId
"dm1 proteins"
dm1.blastFBPep00.name
$anoGam.blastDm1FB.qName
$apiMel.blastDm1FB.qName
$dp.blastDm1FB.qName
$droYak.blastDm1FB.qName
$droMult.blastDm1FB.qName
identifier blastDm2FBPepId dependency
"dm2 proteins"
dm2.blastFBPep01.name
$anoGam.blastDm2FB.qName
$apiMel.blastDm2FB.qName
$dp.blastDm2FB.qName
$droYak.blastDm2FB.qName
$droMult.blastDm2FB.qName
identifier blastHg16KGPepId
"hg16 proteins"
hg16.blastKGPep00.name
sacCer1.blastHg16KG.qName
ce2.blastHg16KG.qName
ci1.blastHg16KG.qName
cioSav1.blastHg16KG.qName
dm1.blastHg16KG.qName
galGal2.blastHg16KG.qName
identifier blastHg16KGRefId
"hg16 ref 00"
hg16.blastKGRef00.acc
sacCer1.blastHg16KG.qName
ce2.blastHg16KG.qName
ci1.blastHg16KG.qName
cioSav1.blastHg16KG.qName
dm1.blastHg16KG.qName
galGal2.blastHg16KG.qName
# identifier blastHg17KGPep00Id (knownGene upgraded)
# "hg17 proteins 00"
# $hg.blastKGPep00.name
# $xenTro.blastHg17KG.qName
identifier blastKG01
"hg17 proteins 01"
$gbd.blastHg17KG.qName dupeOk
hg17.blastKGPep01.name
hg17.blastKGRef01.acc
identifier blastHg17KGPep01Id
"hg17 peptides 01"
hg17.blastKGPep01.name
hg17.knownGene.name minCheck=0.30
hg17.blastKGRef01.acc full
monDom1.blastHg17KG.qName
fr1.blastHg17KG.qName
tetNig1.blastHg17KG.qName
xenTro1.blastHg17KG.qName
identifier blastHg17KGRef01Id
"hg17 ref 01"
hg17.blastKGRef01.acc
monDom1.blastHg17KG.qName
fr1.blastHg17KG.qName
tetNig1.blastHg17KG.qName
xenTro1.blastHg17KG.qName
identifier blastHg17KGPep02Id
"hg17 peptides 02"
hg17.blastKGPep02.name
hg17.knownGene.name minCheck=0.95
hg17.blastKGRef02.acc full
danRer3.blastHg17KG.qName
bosTau2.blastHg17KG.qName
canFam2.blastHg17KG.qName
apiMel2.blastHg17KG.qName
dm2.blastHg17KG.qName
identifier blastHg17KGRef02Id
"hg17 ref 02"
hg17.blastKGRef02.acc
danRer3.blastHg17KG.qName
bosTau2.blastHg17KG.qName
canFam2.blastHg17KG.qName
apiMel2.blastHg17KG.qName
dm2.blastHg17KG.qName
identifier blastHg18KGPep04Id
"hg18 peptides 04"
hg18.blastKGPep04.name
hg18.blastKGRef04.acc full
hg18.knownGeneOld2.name minCheck=0.95
monDom4.blastHg18KG.qName
galGal3.blastHg18KG.qName
xenTro2.blastHg18KG.qName
danRer4.blastHg18KG.qName
danRer5.blastHg18KG.qName
canFam2.blastHg18KG.qName
felCat3.blastHg18KG.qName
dm2.blastHg18KG.qName
fr2.blastHg18KG.qName
mm8.blastHg18KG.qName
ce4.blastHg18KG.qName
strPur1.blastHg18KG.qName
strPur2.blastHg18KG.qName
bosTau2.blastHg18KG.qName
ornAna1.blastHg18KG.qName
equCab1.blastHg18KG.qName
equCab2.blastHg18KG.qName
anoCar1.blastHg18KG.qName
gasAcu1.blastHg18KG.qName
bosTau3.blastHg18KG.qName
bosTau4.blastHg18KG.qName
tetNig1.blastHg18KG.qName
tetNig2.blastHg18KG.qName
taeGut1.blastHg18KG.qName
oryLat2.blastHg18KG.qName
sacCer2.blastHg18KG.qName
mm9.blastHg18KG.qName
aplCal1.blastHg18KG.qName
identifier blastHg18KGRef04Id
"hg18 ref 04"
hg18.blastKGRef04.acc
hg18.knownGeneOld2.name minCheck=0.95
monDom4.blastHg18KG.qName
galGal3.blastHg18KG.qName
xenTro2.blastHg18KG.qName
danRer4.blastHg18KG.qName
danRer5.blastHg18KG.qName
canFam2.blastHg18KG.qName
felCat3.blastHg18KG.qName
dm2.blastHg18KG.qName
fr2.blastHg18KG.qName
mm8.blastHg18KG.qName
ce4.blastHg18KG.qName
strPur1.blastHg18KG.qName
strPur2.blastHg18KG.qName
bosTau2.blastHg18KG.qName
ornAna1.blastHg18KG.qName
equCab1.blastHg18KG.qName
equCab2.blastHg18KG.qName
anoCar1.blastHg18KG.qName
gasAcu1.blastHg18KG.qName
bosTau3.blastHg18KG.qName
bosTau4.blastHg18KG.qName
tetNig1.blastHg18KG.qName
tetNig2.blastHg18KG.qName
taeGut1.blastHg18KG.qName
oryLat2.blastHg18KG.qName
mm9.blastHg18KG.qName
aplCal1.blastHg18KG.qName
identifier blastHg17KGRef01SwissId
"hg17 proteins swiss 01"
$hg.blastKGRef01.extra1 dupeOk
uniProt.displayId.acc
identifier blastCe4SG01
"ce4 proteins 01"
$gbd.blastCe6SG.qName dupeOk
ce4.blastSGPep01.name
ce4.blastSGRef01.acc
identifier blastCe6SG01
"ce6 proteins 01"
$gbd.blastCe6SG.qName dupeOk
ce6.blastSGPep01.name
ce6.blastSGRef01.acc
identifier tfbsCons
"transcription factor binding sites"
$hg.tfbsConsSites.name dupeOk
$hg.tfbsConsFactors.name
identifier esRegModule
"Eran Segal's collection of motifs that appear together in a regulatory module"
$sacCer.esRegModuleToMotif.module dupeOk
$sacCer.esRegGeneToModule.module full minCheck=0.99
identifier esRegMotif
"Eran Segal's motifs deduced from coregulated genes"
$sacCer.esRegMotif.name
$sacCer.esRegModuleToMotif.motif
$sacCer.esRegGeneToMotif.name
identifier yeastGrowthCondition
"A growth condition for yeast cells"
$sacCer.growthCondition.name
$sacCer.transRegCodeCondition.growthCondition
identifier transRegCode
"Harbison, Gordon et al regulatory motifs and CHIP/CHIP data"
$sacCer.transRegCodeCondition.name dupeOk
$sacCer.transRegCodeMotif.name
$sacCer.transRegCode.name
$sacCer.transRegCodeProbe.tfList comma chopAfter=_
identifier anoEstTclId
"AnoEST TCL* ID -- joins track and aux. table of expressed IDs"
$anoGam.anoEstTcl.name
$anoGam.anoEstExpressed.name minCheck=0.30
identifier allenBrainGene
"KG link to Allen Brain Institute: Gene Expression in the Human Cortex"
$gbd.kgXref.geneSymbol dupeOk
$gbd.allenBrainGene.geneSymbol minCheck=0.95
identifier allenBrainProbe
"A probe used in the Allen Brain Atlas"
$gbd.allenBrainUrl.name
$gbd.allenBrainAli.qName
identifier jaxRepTranscriptName external=MGI
"Jackson Labs/MGI Allele name: representative transcript ID"
$mm.jaxRepTranscript.name dupeOk
$mm.jaxRepTranscriptAlias.name
identifier jaxAlleleName external=MGI
"Jackson Labs/MGI Allele name: concatenated representative transcript ID and allele ID"
$mm.jaxAllele.name dupeOk
$mm.jaxAlleleInfo.name
$mm.jaxAllelePheno.allele
identifier jaxPhenotypeName external=MGI
"Jackson Labs/MGI Phenotype name: representative transcript ID"
$mm.jaxPhenotype.name dupeOk
$mm.jaxPhenotypeAlias.name
mm8.jaxAllelePheno.transcript minCheck=0.9
#links between the UniProt variants tables
identifier protVarId
"UniProt Variants track mutation identifier for attributes and links"
hg18.protVar.id
hg18.protVarAttr.id
hg18.protVarLink.id
hg18.protVarPos.name
#links between UniProt and the variants tables
identifier protVarIdUni
"UniProt Variants track mutation identifier contains UniProt ID"
uniProt.protein.acc
hg18.protVar.name chopAfter=:
#links between gv (the new Locus Variants) and related tables
identifier gvId
"Locus Variants track mutation identifier for attributes and links"
hgFixed.gv.id
hgFixed.gvLink.id minCheck=0.95
hgFixed.gvAttr.id minCheck=0.98
hgFixed.gvAttrLong.id
hg17,hg18.gvPos.name
identifier gvSrcId
"Locus Variants track source ID"
hgFixed.gvSrc.srcId
hgFixed.gv.srcId
#links between oreganno (regulatory annotation) and related tables
identifier oregId
"ORegAnno track identifier: links annotations to attributes and external links"
$hg,$dm,$sacCer,$mm.oreganno.id
$hg,$dm,$sacCer,$mm.oregannoAttr.id
$hg,$dm,$sacCer,$mm.oregannoLink.id
# retroposon track, dbRIP_* and polyGenotype table link
identifier dbRIPNameAlu fuzzy
"Retroposon, dbRIP database name id to polymorphism statistics link"
hg17.dbRIPAlu.name unique
hg17.polyGenotype.name
identifier dbRIPNameL1 fuzzy
"Retroposon, dbRIP database name id to polymorphism statistics link"
hg17.dbRIPL1.name unique
hg17.polyGenotype.name
identifier dbRIPNameSVA fuzzy
"Retroposon, dbRIP database name id to polymorphism statistics link"
hg17.dbRIPSVA.name unique
hg17.polyGenotype.name
identifier jkgTranscriptId
"Known genes 3 trancript identifier"
$hg,$mm.jkgTxCdsRepick.name
$hg,$mm.jkgTxInfo.name
$hg,$mm.jkgTxCdsEvidence.name
#links between omicia and links and attributes tables
identifier omiciaHg18Id
"Omicia track identifier: links annotations to attributes and external links"
hg18.omicia.name
hg18.omiciaAttr.id
hg18.omiciaLink.id
# transMap alignment (psl) tables and info tables; 1-to-1 mapping
identifier transMapAlnInfoRefSeqId
"transMap RefSeq per-genome alignments"
$transMapDb.transMapAlnRefSeq.qName unique
$transMapDb.transMapInfoRefSeq.mappedId unique full
identifier transMapAlnInfoUcscGenesId
"transMap UcscGenes per-genome alignments"
$transMapDb.transMapAlnUcscGenes.qName unique
$transMapDb.transMapInfoUcscGenes.mappedId unique full
identifier transMapAlnInfoMRnaId
"transMap MRna per-genome alignments"
$transMapDb.transMapAlnMRna.qName unique
$transMapDb.transMapInfoMRna.mappedId unique full
identifier transMapAlnInfoSplicedEstId
"transMap SplicedEst per-genome alignments"
$transMapDb.transMapAlnSplicedEst.qName unique
$transMapDb.transMapInfoSplicedEst.mappedId unique full
# transMap info table and hgFixed src tables
identifier transMapSrcInfoRefSeqId
"transMap RefSeq pre-geneome alignment to source"
hgFixed.transMapSrcRefSeq.id dupeOk
$transMapDb.transMapInfoRefSeq.srcId
identifier transMapSrcInfoUcscGenesId
"transMap UcscGenes pre-geneome alignment to source"
hgFixed.transMapSrcUcscGenes.id dupeOk
$transMapDb.transMapInfoUcscGenes.srcId
identifier transMapSrcInfoMRnaId
"transMap MRna pre-geneome alignment to source"
hgFixed.transMapSrcMRna.id dupeOk
$transMapDb.transMapInfoMRna.srcId
identifier transMapSrcInfoSplicedEstId
"transMap SplicedEst pre-geneome alignment to source"
hgFixed.transMapSrcSplicedEst.id dupeOk
$transMapDb.transMapInfoSplicedEst.srcId
# transMap aln table and hgFixed src tables
identifier transMapSrcAlnUcscGenesId
"transMap UcscGenes alignment to source"
hgFixed.transMapSrcUcscGenes.id dupeOk chopAfter=-
$transMapDb.transMapAlnUcscGenes.qName chopAfter=-
identifier transMapSrcAlnMRnaId
"transMap MRnas alignment to source"
hgFixed.transMapSrcMRna.id dupeOk chopAfter=-
$transMapDb.transMapAlnMRna.qName chopAfter=-
identifier transMapSrcAlnRefSeqId
"transMap RefSeqs alignment to source"
hgFixed.transMapSrcRefSeq.id dupeOk chopAfter=-
$transMapDb.transMapAlnRefSeq.qName chopAfter=-
identifier transMapSrcAlnSplicedEstId
"transMap SplicedEsts alignment to source"
hgFixed.transMapSrcSplicedEst.id dupeOk chopAfter=-
$transMapDb.transMapAlnSplicedEst.qName chopAfter=-
# transMap source tables
identifier transMapSrcRefSeqId
"transMap RefSeq source gene and sequences "
hgFixed.transMapSrcRefSeq.id dupeOk chopAfter=-
hgFixed.transMapSeqRefSeq.acc
hgFixed.transMapGeneRefSeq.id
identifier transMapSrcUcscGenesId
"transMap UcscGenes source gene and sequences "
hgFixed.transMapSrcUcscGenes.id dupeOk chopAfter=-
hgFixed.transMapSeqUcscGenes.acc
hgFixed.transMapGeneUcscGenes.id
identifier transMapSrcMRnaId
"transMap MRna source gene and sequences "
hgFixed.transMapSrcMRna.id dupeOk chopAfter=-
hgFixed.transMapSeqMRna.acc
hgFixed.transMapGeneMRna.id
identifier transMapSrcSplicedEstId
"transMap SplicedEst source sequences "
hgFixed.transMapSrcSplicedEst.id dupeOk chopAfter=-
hgFixed.transMapSeqSplicedEst.acc
# transMap extFile tables
identifier transMapExtFileRefSeqId
"transMap RefSeq external file "
hgFixed.transMapSeqRefSeq.extFile dupeOk
hgFixed.transMapExtFileRefSeq.id unique
identifier transMapExtFileUcscGenesId
"transMap UcscGenes external file "
hgFixed.transMapSeqUcscGenes.extFile dupeOk
hgFixed.transMapExtFileUcscGenes.id unique
identifier transMapExtFileMRnaId
"transMap MRna external file "
hgFixed.transMapSeqMRna.extFile dupeOk
hgFixed.transMapExtFileMRna.id unique
identifier transMapExtFileSplicedEstId
"transMap SplicedEst external file "
hgFixed.transMapSeqSplicedEst.extFile dupeOk
hgFixed.transMapExtFileSplicedEst.id unique
# transMap and knownGenes
identifier transMapGeneUcscGenesId
"UCSC Genes and transMapGene table"
hgFixed.transMapGeneUcscGenes.id dupeOk
$kgDb3.knownGene.name full
identifier transMapAlnKnownGeneHgId
"UCSC Genes and transMapAln table"
mm9.knownGene.name
hg18.transMapAlnUcscGenes.qName chopAfter=-
identifier transMapAlnKnownGeneMmId
"UCSC Genes and transMapAln table"
hg19.knownGene.name
mm9.transMapAlnUcscGenes.qName chopAfter=-
# lsSnpPdb tables
identifier lsSnpPdbProtId
"lsSnpPdb table protId field"
uniProt.extDbRef.acc dupeOk
hg18.lsSnpPdb.protId
identifier lsSnpPdbKgId
"lsSnpPdb table protId field"
hg18.kgXref.spID dupeOk
hg18.lsSnpPdb.protId
identifier lsSnpPdbPdbId
"lsSnpPdb table pdbId field"
uniProt.extDbRef.extAcc1 dupeOk
hg18.lsSnpPdb.pdbId minCheck=0.99
identifier lsSnpPdbSnpId
"lsSnpPdb table snpId field"
hg18.snp129.name dupeOk
hg18.lsSnpPdb.snpId
# Dependencies not already captured in identifiers
dependency $hg.gladHumESDistance $hg.knownToGnfAtlas2 hgFixed.gladHumESRatio
dependency $mm.mouseLandscapeDistance $mm.knownToXM hgFixed.mouseLandscape
dependency $mm.affyGnfU74ADistance $mm.knownToU74 hgFixed.gnfMouseU74aMedianRatio
dependency $mm.affyGnfU74BDistance $mm.knownToU74 hgFixed.gnfMouseU74bMedianRatio
dependency $mm.affyGnfU74CDistance $mm.knownToU74 hgFixed.gnfMouseU74cMedianRatio
dependency $hg.gnfU95Distance $hg.knownToU95 hgFixed.gnfHumanU95MedianRatio
dependency $hg.gnfAtlas2Distance $hg.knownToGnfAtlas2 hgFixed.gnfHumanAtlas2MedianRatio
dependency $ce.kimExpDistance hgFixed.kimWormLifeMedianRatio
dependency dm1.arbExpDistance dm1.bdgpToCanonical hgFixed.arbFlyLifeMedianRatio
dependency $dm,!dm1.arbExpDistance $dm,!dm1.flyBaseToCG hgFixed.arbFlyLifeMedianRatio
dependency $sacCer.choExpDistance hgFixed.yeastChoCellCycle
# FAN says: the following hg17 tables are an exception
dependency $pbDb,!hg17.pbAnomLimit $pbDb.knownGenePep
dependency $pbDb,!hg17.pbResAvgStd $pbDb.knownGenePep
dependency $pbDb,!hg17.pepCCntDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepExonCntDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepHydroDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepIPCntDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepMolWtDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepPi $pbDb.knownGenePep
dependency $pbDb,!hg17.pepPiDist $pbDb.knownGenePep
dependency $pbDb,!hg17.pepResDist $pbDb.knownGenePep
dependency $pbDb.pepMwAaDist $pbDb.knownGenePep
dependency $pbDb.pbAaDistA $pbDb.knownGenePep
dependency $pbDb.pbAaDistC $pbDb.knownGenePep
dependency $pbDb.pbAaDistD $pbDb.knownGenePep
dependency $pbDb.pbAaDistE $pbDb.knownGenePep
dependency $pbDb.pbAaDistF $pbDb.knownGenePep
dependency $pbDb.pbAaDistG $pbDb.knownGenePep
dependency $pbDb.pbAaDistH $pbDb.knownGenePep
dependency $pbDb.pbAaDistI $pbDb.knownGenePep
dependency $pbDb.pbAaDistK $pbDb.knownGenePep
dependency $pbDb.pbAaDistL $pbDb.knownGenePep
dependency $pbDb.pbAaDistM $pbDb.knownGenePep
dependency $pbDb.pbAaDistN $pbDb.knownGenePep
dependency $pbDb.pbAaDistP $pbDb.knownGenePep
dependency $pbDb.pbAaDistQ $pbDb.knownGenePep
dependency $pbDb.pbAaDistR $pbDb.knownGenePep
dependency $pbDb.pbAaDistS $pbDb.knownGenePep
dependency $pbDb.pbAaDistT $pbDb.knownGenePep
dependency $pbDb.pbAaDistV $pbDb.knownGenePep
dependency $pbDb.pbAaDistW $pbDb.knownGenePep
dependency $pbDb.pbAaDistY $pbDb.knownGenePep
# Table types - only needed when the table does not have the same name .as file record.
type genePred
$hg.acembly
$gbd.ECgene
$gbd.geneid
$gbd.genscan
$gbd.sgpGene
$gbd.softberryGene
$gbd.twinscan
$gbd.ensGene
$gbd.vegaGene
$gbd.refGene
$gbd.xenoRefGene
$gbd.jgiFilteredModels
$gbd.geneMapper
type pepPred
$hg.acemblyPep
$gbd.ECgenePep
$gbd.geneidPep
$gbd.genscanPep
$gbd.sgpPep
$gbd.softberryPep
$gbd.twinscanPep
$gbd.ensPep
$gbd.vegaPep
$gbd.knownGenePep
$ce.sangerPep
dm1.bdgpGenePep
$dm.flyBasePep
type psl
$hg.affyU95
$hg.affyU133
$hg.affyU133Plus2
$hg.HInvGeneMrna
$mm.affyU74
$danRer.affyZebrafish
$gbd.all_bacends
$gbd.all_fosends
$gbd.all_est
$gbd.est
$gbd.intronEst
$gbd.xenoEst
$gbd.xenoMrna
$gbd.all_mrna
$gbd.refSeqAli
$gbd.all_sts_primer
$gbd.all_sts_seq
$transMapDb.transMapAlnUcscGenes
$transMapDb.transMapAlnRefSeq
$transMapDb.transMapAlnMRna
$transMapDb.transMapAlnSplicedEst
type estOrientInfo
$gbd.estOrientInfo
$gbd.mrnaOrientInfo
type expRecord
hgFixed.nci60Exps
hgFixed.rosettaExps
hgFixed.affyExps.id
hgFixed.gnfHumanU95AllExps
hgFixed.gnfHumanU95MedianExps
hgFixed.gnfMouseU74aAllExps
hgFixed.gnfMouseU74aMedianExps
hgFixed.gnfMouseU74bAllExps
hgFixed.gnfMouseU74bMedianExps
hgFixed.gnfMouseU74cAllExps
hgFixed.gnfMouseU74cMedianExps
hgFixed.arbFlyLifeAllExps
hgFixed.arbFlyLifeMedianExps
hgFixed.kimWormLifeAllExps
hgFixed.kimWormLifeMedianExps
hgFixed.yeastChoCellCycleExps
hgFixed.gladHumESExps
type expData
hgFixed.kimWormLifeAllRatio
hgFixed.kimWormLifeMedianRatio
hgFixed.gnfHumanU95All
hgFixed.gnfHumanU95AllRatio
hgFixed.gnfHumanU95Median
hgFixed.gnfHumanU95MedianRatio
hgFixed.gnfMouseU74aAll
hgFixed.gnfMouseU74aAllRatio
hgFixed.gnfMouseU74aMedian
hgFixed.gnfMouseU74aMedianRatio
hgFixed.gnfMouseU74bAll
hgFixed.gnfMouseU74bAllRatio
hgFixed.gnfMouseU74bMedian
hgFixed.gnfMouseU74bMedianRatio
hgFixed.gnfMouseU74cAll
hgFixed.gnfMouseU74cAllRatio
hgFixed.gnfMouseU74cMedian
hgFixed.gnfMouseU74cMedianRatio
hgFixed.arbFlyLifeAll
hgFixed.arbFlyLifeAllRatio
hgFixed.arbFlyLifeMedian
hgFixed.arbFlyLifeMedianRatio
hgFixed.kimWormLifeAllRatio
hgFixed.kimWormLifeMedianRatio
hgFixed.yeastChoCellCycle
hgFixed.yeastChoCellCycleRatio
hgFixed.gladHumES
hgFixed.gladHumESRatio
type exprBed
$hg.affyRatio
$mm.affyGnfU74A
$mm.affyGnfU74B
$mm.affyGnfU74C
$hg.nci60
$rn.gnfAtlas2
# hgFixed.rosChr22Dat
type expDistance
$hg.gnfAtlas2Distance
$hg.gnfU95Distance
$mm.affyGnfU74ADistance
$mm.affyGnfU74BDistance
$mm.affyGnfU74CDistance
$mm.mouseLandscapeDistance
$hg.knownGnfDistance
$ce.kimExpDistance
$dm.arbExpDistance
$sacCer.choExpDistance
$hg.gladHumESDistance
type chain
$gbd.chr%_chain%
$gbd.chr%_chainSelf
type agpFrag
$gbd.chr%_gold
type agpGap
$gbd.chr%_gap
type gl
$gbd.chr%_gl
type knownTo
$gbd.knownToCdsSnp
$gbd.knownToEnsembl
$gbd.knownToLocusLink
$gbd.knownToPfam
$gbd.knownToRefSeq
$gbd.knownToAllenBrain
$hg.knownToU95
$hg.knownToU133
$hg.knownToU133Plus2
$hg.knownToHInv
$mm.knownToU74
$mm.knownToXM
$ce.sangerToKim
$ce.sangerToPfam
$ce.sangerToRefSeq
dm1.bdgpToLocusLink
dm1.bdgpToPfam
dm1.bdgpToRefSeq
$sacCer.sgdToSwissProt
$sacCer.sgdToSgd
$sacCer.sgdToName
type idName
$gbd.source
$gbd.organism
$gbd.library
$gbd.mrnaClone
$gbd.sex
$gbd.tissue
$gbd.development
$gbd.cell
$gbd.cds
$gbd.description
$gbd.author
$gbd.geneName
$gbd.productName
$gbd.keyword
type blastTab
$gbd.ceBlastTab
$gbd.hgBlastTab
$gbd.dmBlastTab
$gbd.drBlastTab
$gbd.mmBlastTab
$gbd.rnBlastTab
$gbd.scBlastTab
$gbd.knownBlastTab
$ce.sangerBlastTab
dm1.bdgpBlastTab
sacCer1.sgdBlastTab
sacCer2.knownBlastTab
type knownCanonical
$gbd.knownCanonical
$ce.sangerCanonical
dm1.bdgpCanonical
$sacCer.sgdCanonical
type knownIsoforms
$gbd.knownIsoforms
$ce.sangerIsoforms
dm1.bdgpIsoforms
$sacCer.sgdIsoforms
type rnaFold
$gbd.foldUtr3
$gbd.foldUtr5
type bed
$gbd.vegaPseudoGene
$sacCer.sgdOther
type geneAndProt
$kgDb.knownGene
$ce.sangerGene
dm1.bdgpGene
$sacCer.sgdGene
type transMapInfo
$transMapDb.transMapInfoRefSeq
$transMapDb.transMapInfoUcscGenes
$transMapDb.transMapInfoMRna
$transMapDb.transMapInfoSplicedEst
type transMapInfo
$transMapDb.transMapInfoRefSeq
$transMapDb.transMapInfoUcscGenes
$transMapDb.transMapInfoMRna
$transMapDb.transMapInfoSplicedEst
type transMapSrc
hgFixed.transMapSrcRefSeq
hgFixed.transMapSrcUcscGenes
hgFixed.transMapSrcMRna
hgFixed.transMapSrcSplicedEst
type transMapGene
hgFixed.transMapGeneRefSeq
hgFixed.transMapGeneUcscGenes
hgFixed.transMapGeneMRna
# Ignored tables - no linkage here that we check at least.
tablesIgnored go
instance_data
source_audit
tablesIgnored visiGene
vgPrbAli
vgPrbAliAll
tableDescriptions
tablesIgnored hgFixed
omimTitle
cutters
rebaseRefs
tablesIgnored $gbd
NIAGene
ancientRepeat
axtInfo
blatFr1
chromInfo
cpgIsland
cpgIslandExt
ctgPos
cytoBand
cytoBandIdeo
evofold
exoniphy
firstEF
gbLoaded
gbDelete_tmp
gc5Base
gcPercent
genscanSubopt
grp
hgFindSpec%
history
knownAlt
miRNA
nestedRepeats
nestedRepeatsRM327
quality
rnaCluster
rnaGene
regPotential%
sangerGenefinder
sangamoDnaseHs
sangamoDnaseHsNeg
sangamoDnaseHsPos
simpleRepeat
windowmaskerSdust
sgpGene
tableDescriptions
tigrGeneIndex
trackDb%
chr%_mrna
chr%_blastz%
chr%_blat%
chr%_gap
chr%_rmsk
chr%_rmskRM327
gap
rmsk
axtNet%
blat%
blast%
repeats
multiz%way
multiz%waySummary
multiz%wayFrames
phyloP%way%
phastCons%way%
phastConsElements%way%
jaxQTL
jaxQtl
jaxQtlAsIs
jaxQtlPadded
uwNucOccA375
uwNucOccDennis
uwNucOccMec
tablesIgnored $kgDb
pbAaDist_
pbAnomLimit
pbResAvgStd
pbStamp
pep%Dist
tablesIgnored hg19
gold
bacEndPairsBad
multizMHCSummary
netSyn_mann_hap4
net_dbb_hap3
net_apd_hap1
net_ssto_hap7
net_qbl_hap6
net_mcf_hap5
net_mann_hap4
net_haplotypes
net_cox_hap2
net_chr4_ctg9_hap1
net_chr17_ctg5_hap1
netVenter1
netSyn_ssto_hap7
netSyn_qbl_hap
netSyn_qbl_hap6
netSyn_mcf_hap5
netSyn_apd_hap1
netSyn_cox_hap2
netSyn_dbb_hap3
chain_ssto_hap7
chain_ssto_hap7Link
hapRegions
multizMHC
chain_mcf_hap5Link
chain_qbl_hap6
chain_qbl_hap6Link
chain_haplotypesLink
chain_mann_hap4
chain_mann_hap4Link
chain_mcf_hap5
chain_chr4_ctg9_hap1
chain_chr4_ctg9_hap1Link
chain_cox_hap2
chain_cox_hap2Link
chain_dbb_hap3
chain_dbb_hap3Link
chainVenter1
chainVenter1Link
chain_apd_hap1
chain_apd_hap1Link
chain_chr17_ctg5_hap1
chain_chr17_ctg5_hap1Link
chain_haplotypes
tablesIgnored mm9
+ crgMapability%
rest
tablesIgnored $calJac
gold
tablesIgnored $petMar
%gold
intronEst
tablesIgnored $braFlo
%gold
intronEst
tablesIgnored $cavPor
gold
tablesIgnored $cb
chr%_gold
tablesIgnored $ce
chr%_gold
chr%_wabaCbr
wabaCbr
nucleosomeControl
nucleosomeFragmentsSense
nucleosomeFragmentsAntisense
nucleosomeStringency
monoNucleosomesSense
monoNucleosomesAntiSense
nucleosomeControlSenseCoverage
nucleosomeControlAntisenseCoverage
nucleosomeAdjustedCoverage
25mersRepeats
mt%Forward
mt%Reverse
wt%Forward
wt%Reverse
algBind%
tablesIgnored $ci
snapGene
tablesIgnored $dm
anophelesEcores
fbGo
fbRole
fbUniProt
flyreg
flyreg2
tablesIgnored $loxAfr
gold
chainHg19
chainHg19Link
xenoRefFlat
tablesIgnored $equCab
chr%_gold
tablesIgnored $fr
chr%_gold
tablesIgnored $galGal
chr%_gold
supercontig
caCondor454
tablesIgnored $danRer
chr%_gold
ctgPos2
wz_ests
tablesIgnored $caePb
chr%_gold
ctgPos2
tablesIgnored $caeRem
chr%_gold
ctgPos2
tablesIgnored $caeJap
chr%_gold
ctgPos2
tablesIgnored $priPac
chr%_gold
ctgPos2
tablesIgnored $canFam
chr%_gold
genomicSuperDups
tablesIgnored $droYak
chr%_gold
tablesIgnored $droMult
gold
intronEst
tablesIgnored $anoCar
gold
tablesIgnored $anoGam
chr%_gold
anoEstNcl
tablesIgnored $bosTau
gold
intronEst
contigOrient
tablesIgnored $apiMel
gold
intronEst
brhInparalog
modelRefGene
scaffolds
tablesIgnored $snpDb125
snp125ExceptionDesc
tablesIgnored $snpDb126
snp126ExceptionDesc
tablesIgnored $snpDb127
snp127ExceptionDesc
tablesIgnored $hg
acescan
affyTranscriptome
affyTxnPhase3FragsHDF
affyTxnPhase3FragsHeLaCyto
affyTxnPhase3FragsHeLaNuclear
affyTxnPhase3FragsHepG2Cyto
affyTxnPhase3FragsHepG2Nuclear
affyTxnPhase3FragsJurkat
affyTxnPhase3FragsNCCIT
affyTxnPhase3FragsPC3
affyTxnPhase3FragsSK_N_AS
affyTxnPhase3FragsU87MG
affyTxnPhase3FragsHeLaTopStrand
affyTxnPhase3FragsHeLaBottomStrand
affyTxnPhase3FragsHepG2TopStrand
affyTxnPhase3FragsHepG2BottomStrand
affyTxnPhase3HDF
affyTxnPhase3HeLaCyto
affyTxnPhase3HeLaNuclear
affyTxnPhase3HepG2Cyto
affyTxnPhase3HepG2Nuclear
affyTxnPhase3Jurkat
affyTxnPhase3NCCIT
affyTxnPhase3PC3
affyTxnPhase3SK_N_AS
affyTxnPhase3U87MG
affyTxnPhase3HeLabottom_strand
affyTxnPhase3HeLatop_strand
affyTxnPhase3HepG2bottom_strand
affyTxnPhase3HepG2top_strand
affyTxnPhase3HeLaBottomStrand
affyTxnPhase3HeLaTopStrand
affyTxnPhase3HepG2BottomStrand
affyTxnPhase3HepG2TopStrand
burgeRnaSeqGemMapperAlignBrain
burgeRnaSeqGemMapperAlignLiver
burgeRnaSeqGemMapperAlignHeart
burgeRnaSeqGemMapperAlignSkelMuscle
burgeRnaSeqGemMapperAlignColon
burgeRnaSeqGemMapperAlignAdipose
burgeRnaSeqGemMapperAlignTestes
burgeRnaSeqGemMapperAlignLymphNode
burgeRnaSeqGemMapperAlignBreast
burgeRnaSeqGemMapperAlignBT474
burgeRnaSeqGemMapperAlignHME
burgeRnaSeqGemMapperAlignMCF7
burgeRnaSeqGemMapperAlignMB435
burgeRnaSeqGemMapperAlignT47D
chimpDels
chimpParalogy
chimpSimpleDiff
celeraCoverage
celeraDupPositive
celeraOverlay
cccTrendPvalBd
cccTrendPvalCad
cccTrendPvalCd
cccTrendPvalHt
cccTrendPvalRa
cccTrendPvalT1d
cccTrendPvalT2d
cnpFosmid
cnpIafrate
cnpIafrate2
cnpLocke
cnpRedon
cnpSebat
cnpSebat2
cnpSharp
cnpSharp2
cnpSharpSampleCount
cnpSharpSamples
cnpTuzun
ctgPos
delConrad
delConrad2
delHinds
delHinds2
delMccarroll
dgv
eponine
exaptedRepeats
fox2ClipClusters
fox2ClipSeq
fox2ClipSeqDensityForwardStrand
fox2ClipSeqDensityReverseStrand
geneTests
genomicSuperDups
haplotype
hgdpGeo
hgdpFst
hgdpHzy%
hgdpIhs%
hgdpXpehh%
laminB1
laminB1Lads
mammalPsg
nimhBipolarUs
nimhBipolarDe
perlegen
pga
pgVenter
pgWatson
pgYoruban2
pgYoruban3
pgYh1
pgNA%
pgSjk
promoterStanford
pseudoYale
recombRate
slamMouse
slamNonCodingMouse
slamRat
slamNonCodingRat
snp
snp125ExceptionDesc
snp126ExceptionDesc
switchDbTss
syntenyMouse
syntenyRat
targetScanS
vistaEnhancers
wgRna
zoom1_affyTranscriptome
zoom2_affyTranscriptome
encodeAffyChIpRnapHl60PvalHr00
encodeAffyChIpRnapHl60PvalHr02
encodeAffyChIpRnapHl60PvalHr08
encodeAffyChIpRnapHl60PvalHr32
encodeAffyChIpRnapHl60SitesHr00
encodeAffyChIpRnapHl60SitesHr02
encodeAffyChIpRnapHl60SitesHr08
encodeAffyChIpRnapHl60SitesHr32
encodeAffyRnaHl60SigHr00
encodeAffyRnaHl60SigHr02
encodeAffyRnaHl60SigHr08
encodeAffyRnaHl60SigHr32
encodeAffyRnaHl60SitesHr00
encodeAffyRnaHl60SitesHr02
encodeAffyRnaHl60SitesHr08
encodeAffyRnaHl60SitesHr32
encodeAffyEc1BrainCerebellumSites
encodeAffyEc51BrainCerebellumSites
encodeAffyEc1BrainFrontalLobeSites
encodeAffyEc51BrainFrontalLobeSites
encodeAffyEc1BrainHippocampusSites
encodeAffyEc51BrainHippocampusSites
encodeAffyEc1BrainHypothalamusSites
encodeAffyEc51BrainHypothalamusSites
encodeAffyEc1FetalKidneySites
encodeAffyEc51FetalKidneySites
encodeAffyEc1FetalSpleenSites
encodeAffyEc51FetalSpleenSites
encodeAffyEc1PlacentaSites
encodeAffyEc51PlacentaSites
encodeAffyEc1TestisSites
encodeAffyEc51TestisSites
encodeAffyEc1FetalTestisSites
encodeAffyEc51FetalTestisSites
encodeAffyEc1ProstateSites
encodeAffyEc51ProstateSites
encodeAffyEc1OvarySites
encodeAffyEc51OvarySites
encodeAffyEc1HeLaC1S3Sites
encodeAffyEc51HeLaC1S3Sites
encodeAffyEc1GM06990Sites
encodeAffyEc51GM06990Sites
encodeAffyEc1HepG2Sites
encodeAffyEc51HepG2Sites
encodeAffyEc1K562Sites
encodeAffyEc51K562Sites
encodeAffyEc1TertBJSites
encodeAffyEc51TertBJSites
encodeAffyEc1BrainCerebellumSignal
encodeAffyEc51BrainCerebellumSignal
encodeAffyEc1BrainFrontalLobeSignal
encodeAffyEc51BrainFrontalLobeSignal
encodeAffyEc1BrainHippocampusSignal
encodeAffyEc51BrainHippocampusSignal
encodeAffyEc1BrainHypothalamusSignal
encodeAffyEc51BrainHypothalamusSignal
encodeAffyEc1FetalKidneySignal
encodeAffyEc51FetalKidneySignal
encodeAffyEc1FetalSpleenSignal
encodeAffyEc51FetalSpleenSignal
encodeAffyEc1PlacentaSignal
encodeAffyEc51PlacentaSignal
encodeAffyEc1TestisSignal
encodeAffyEc51TestisSignal
encodeAffyEc1FetalTestisSignal
encodeAffyEc51FetalTestisSignal
encodeAffyEc1ProstateSignal
encodeAffyEc51ProstateSignal
encodeAffyEc1OvarySignal
encodeAffyEc51OvarySignal
encodeAffyEc1HeLaC1S3Signal
encodeAffyEc51HeLaC1S3Signal
encodeAffyEc1GM06990Signal
encodeAffyEc51GM06990Signal
encodeAffyEc1HepG2Signal
encodeAffyEc51HepG2Signal
encodeAffyEc1K562Signal
encodeAffyEc51K562Signal
encodeAffyEc1TertBJSignal
encodeAffyEc51TertBJSignal
encodeEvoFold
encodeGisChip%
encodeGencodeGenePolyA%
enocdeGencodeRaceFrags%
encodeNhgriDnaseHs%
encodeRegulomeDnaseGM06990%
encodeSangerChip%
encodeStanfordPromoters%
encodeUcsdChipAch3Imr90
encodeUcsdChipMeh3k4Imr90
encodeUcsdChipRnapHct116
encodeUcsdChipRnapHela
encodeUcsdChipRnapImr90
encodeUcsdChipRnapThp1
encodeUcsdChipTaf250Hct116
encodeUcsdChipTaf250Hela
encodeUcsdChipTaf250Imr90
encodeUcsdChipTaf250Thp1
encodeUcsdNgChipKnownSites
encodeUcsdNgChipNovelSites
encodeUcsdNgChipSignal
encodeUcsdNgHeLaH3K4me3_p0
encodeUcsdNgHeLaH3K4me3_p30
encodeUcsdNgHeLaRnap_p0
encodeUcsdNgHeLaRnap_p30
encodeUcsdNgValChipH3K4me
encodeUcsdNgValChipH3ac
encodeUcsdNgValChipRnap
encodeUcsdNgValChipTaf
encodeUncFaireSignal
encodeUncFairePeaks
encodeUncFairePeaksChipotle
encodeUvaDnaRep%
encodeYaleChipPval%
encodeYaleChipSignal%
encodeYaleChipSites%
encodeTba%
kiddEichlerValidAbc7
kiddEichlerValidAbc8
kiddEichlerValidAbc9
kiddEichlerValidAbc10
kiddEichlerValidAbc11
kiddEichlerValidAbc12
kiddEichlerValidAbc13
kiddEichlerValidAbc14
kiddEichlerValidG248
wgEncode%
tablesIgnored $mm
chr%_gold
syntenyRat
syntenyHuman
ctgPos
rikenCageCtssMinus
rikenCageCtssPlus
rikenCageTc
tablesIgnored $panTro
chr%_gold
humanDels
tablesIgnored $rn
chr%_gold
all_sts_primer
bactigPos
recombRateRat
syntenyMouse
syntenyHuman
tablesIgnored $sacCer
chr%_gold
chr%_gap
2micron_mrna
2micron_intronEst
2micron_est
2micron_gold
2micron_gap
sgdClone
yeastP2P
uwFootprintsMappability
uwFootprintsPrints
uwFootprintsTagCounts
tablesIgnored $tetNig
gold
ecoresHg17
cytokines
hoxGenes
tablesIgnored $felCat
gold
intronEst
microsat
tablesIgnored hg16
chicken_hmrg
rat_hmrg
mouse_hmrg
syntenyMm4
tablesIgnored hg17
ecoresTetNig1
tablesIgnored canFam2
uncertified
tablesIgnored equCab2
ctgPos2
tablesIgnored oryLat2
microsat
tablesIgnored oryCun2
ctgPos2
gold
intronEst