dbgg – database for genetical genomics update

/ 1groningen bioinformatics center

Morris Swertz

Morris Swertz ([email protected]) Braunschweig CASIMIR meeeting

July 2, 2008

dbgg – database for genetical genomicsupdate

mailto:[email protected]


Morris Swertz

Objective› Share genotype/phenotype data and

tools:


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers

expressions preprocess

probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

Main work flow

Data dependency

Biomaterial/result

Lab/analysis process

Scale of information

Associated data files

process

material

10,000

Complicated experiments


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

Collaborator 1

Collaborator 2

Collaborator 3

Barriers to sharing data

Incomplete data!

Incompatible data!


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

Investigation 1

Investigation 2

Investigation 3

Barriers to sharing data

Incomplete and/or

incompatible data!


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

Barriers to sharing software tools


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map



Morris Swertz

10,000

QTL profiles

10,000

QTL profiles

10,000

QTL profiles


Hard to find and reuse tools


Morris Swertz

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers


probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

10.000

map

Use a standard tool?


Morris Swertz

Main work flow

Data dependency

Biomaterial/result

Lab/analysis process

Scale of information

Associated data files

process

material

10,000

arab 220903

100 200 300 400 500 600 700 800 900 1000m/z0

100

%

Koornneef0007 526 (11.117) AM (Top,4, Ar,10000.0,556.28,0.70,LS 10); Sm (Mn, 2x1.00); Sb (1,40.00 )1.40e3171.1702

1396

649.3804551

526.3066248172.1795

162

650.3882224

809.4496;80

inbreed

100

100.000

10,000,000

1000

10,000

10

1000

genotypeindividuals

mass peaks

genotypes QTL profiles

strains

network

SNP arrays

correlate

LC/MS

genome

map

preprocess aligned peaks

More biotechnologies, more protocols

Yes, if it could be easily adapted!(and they can’t)


Morris Swertz

Objectives› Share genotype/phenotype data and tools:

1. Interoperable software• Simple flat file exchange format• Database server• R/web-service interfaces• A procedure to extend the software

2. Build on extensible data model• Data• Annotations• Investigations• Integration references

› Next steps


Morris Swertz

The software› Share genotype/phenotype data and tools:



› Next steps


Morris Swertz

Software: flat file exchange format› Raw and processed data in matrix form

BxD1 BxD2 BxD3 BxD4 BxD5 BxD6 BxD71415670_at 0,293493 0,687197 0,137687 0,5992 0,691055 0,644053 0,9387541415671_at 0,124305 0,261548 0,771756 0,022287 0,374063 0,711998 0,5262771415672_at 0,592037 0,334535 0,173969 0,516279 0,21625 0,970534 0,1927341415673_at 0,555223 0,992222 0,17998 0,79899 0,505028 0,776323 0,7361551415674_a_at 0,585366 0,61328 0,448061 0,977578 0,746478 0,937131 0,7829041415675_at 0,938431 0,272201 0,477756 0,374765 0,840321 0,187776 0,540691415676_a_at 0,700227 0,971044 0,486389 0,236767 0,717116 0,714643 0,4434471415677_at 0,716683 0,380579 0,592676 0,224927 0,304563 0,285177 0,6874261415678_at 0,086303 0,069413 0,601634 0,289336 0,197956 0,820493 0,0721611415679_at 0,669657 0,578992 0,373976 0,581597 0,561598 0,051069 0,0701441415680_at 0,277747 0,716174 0,73642 0,428784 0,614857 0,763586 0,7042631415681_at 0,208313 0,279458 0,063052 0,077388 0,577486 0,087832 0,0638261415682_at 0,94562 0,077064 0,735568 0,081915 0,109705 0,278815 0,350941415683_at 0,308529 0,008908 0,793956 0,304491 0,613119 0,055048 0,698222E.g. microarray data.

Rows = individuals, cols = affy probes.


Morris Swertz

Software: flat file exchange format› Annotation info in tabular formname gene chr bplocal bpglobal1415670_at Copg 6 87875328 9245716701415671_at Atp6v0d1 8 108413750 12349086131415672_at Golga7 8 24706942 11512018051415673_at Psph 5 130080298 8201576541415674_a_at Trappc4 9 44155401 12989088981415675_at Dpm2 2 32395013 2274438781415676_a_at Psmb5 14 53568499 19128940201415677_at Dhrs1 14 54693657 19140191781415678_at Ppm1a 12 73712802 17014658381415679_at Psenen 7 30270655 10171686951415680_at Anapc1 2 128304204 323353069

E.g. probe annotation data.Rows = probes

cols = attributes of each probe.


Morris Swertz

Software: exchange an experiment Described on

http://gbic.biol.rug.nl/dbgg

dbGG database

dbGG Importtool

dbGG Exporttool

annotations

Raw and processed data




Morris Swertz

Software: web user interface

Software

http://gbicserver1.biol.rug.nl:8080/dbgg/molgenis.do

http://gbicserver1.biol.rug.nl:8080/dbgg/molgenis.do


Morris Swertz

Software: interface to Rsource(“http://localhost:8080/molgenis4gg/R”)

#download data use.experiment(name=“metanetwork”) #set default traits <- get.metabolitedata(name=“mytraits”) genotypes <- get.markerdata(name=“mygenotypes")

#calculate mQTLslibrary(“MetaNetwork”) qtls <- qtlMapTwoPart(genotypes=genotypes,

traits=traits, spike=4)

#upload results for others to useadd.mqtldata(qtls, name=“myqtls”)

RIL1 RIL3 RIL4 … LCavg.1537 NA 942 2402 … LCavg.1594 NA 4 10 … LCvag.1610 NA 55 62 … … … … … …

Input markers,traits, genotypes

AMap QTLs(qtlMapTwoPart)

QTL profiles{qtlProfiles}

QTL threshold{qtlThres}

BSimulation/FDR(qtlThreshold/qtlFDR)

QTL summary{qtlSumm}

Input mass/chargepeaks

CQTL summary(qtlSummary) Significant QTLs

DZero-ordercorrelation

Peak multiplicity{peakMultiplicity}

HPeak multiplicity(findPeakultiplicity)

Correlation matrix{corrZeroOrder}

FPermutation(qtlCorrThreshold)

E2nd-order correlation(qtlCorrSecondOrder )

Correlation matrix{corrSecondOrder}

Correlation threshold{corrThres}

GCreate network(createCytoFiles)

Network files[network.sif,

network.eda]

inspectMetaNetwork protocol:Fu, Swertz, Keurentjes, Jansen, Nature Protocols, 2007.

http://localhost:8080/molgenis4gg/R


Morris Swertz

Software: interface to Taverna

add dbGG interface


Morris Swertz

Software: interface to TavernaUse data in

dbGG


Morris Swertz

This enables automatic processing(see also CASIMIR use ‘case 1’)

Smedley, Swertz, Wolstencroft et al, Submitted.

dbGG


Morris Swertz

Use BioMART and MOLGENIS to access data and Taverna to automate the workflows

Smedley, Swertz, Wolstencroft et al, Submitted.

ws

ws

ws

SNPsStrain SNP Alleles

Pathways ws

Gene symbols

YourdbGG


Morris Swertz

Reusable assets and generator/interpreter

Little language<entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int"

Domain specific language<entity name="Experiment" label="Experiment"> <field name="ExperimentID" key="1“ readonly="true" label="ExperimentID(autonum)"/> <field name="Medium" type="xref" xref_field="Medium.name"/> /> <field name="Protocol" label="Experiment Protocol"/> <field name="Temperature" type="int" +

Software: extension procedure(using MOLGENIS)

dbGG v1: for microarrays

dbGG v2: for mass

spectrometry


Morris Swertz

Software: extension procedure

<entity name="Metabolite" extends="Trait"> <field name="Formula" nillable="true" description="The chemical formula of a metabolite." /> <field name="Mass" type="decimal" nillable="true" description="The mass of this metabolite" /> <field name="Structure" type="text" nillable="true" description="The chemical structure of this metabolite." /> </entity>


Morris Swertz

Website: demos and downloads




Morris Swertz

Outline› To share genotype/phenotype data and

tools:1. Interoperable software

• Flat file exchange format• Database server• R/web-service interfaces• A procedure to extend the software


› Next steps


Morris Swertz

BxD1 BxD2 BxD3 BxD4 BxD5 BxD6 BxD7rs13475697 1 1 0 1 0 1 0rs13475698 1 0 0 0 0 0 1rs13475699 0 0 0 1 0 1 1rs13475700 1 1 1 1 0 1 0rs13475701 1 0 1 0 0 1 1rs2228909 1 1 0 1 0 0 0rs2228910 0 0 1 1 0 0 0rs3022775 0 0 0 1 1 0 1rs3024102 1 0 1 0 0 0 0rs3024103 1 0 0 1 0 0 0rs3024104 0 1 0 0 0 0 0rs3024105 0 0 1 0 0 0 1rs30462182 1 0 0 0 0 0 0rs30522279 0 1 0 0 1 0 0

Data› Simple and close to current practice:

Genotype data

MARKERS

Subjects: STRAINS

DATA ELEMENTS

Traits:

TRAIT SUBJECT


Morris Swertz


Genotype dataExpression data

BxD1 BxD2 BxD3 BxD4 BxD5 BxD6 BxD71415670_at 0,293493 0,687197 0,137687 0,5992 0,691055 0,644053 0,9387541415671_at 0,124305 0,261548 0,771756 0,022287 0,374063 0,711998 0,5262771415672_at 0,592037 0,334535 0,173969 0,516279 0,21625 0,970534 0,1927341415673_at 0,555223 0,992222 0,17998 0,79899 0,505028 0,776323 0,7361551415674_a_at 0,585366 0,61328 0,448061 0,977578 0,746478 0,937131 0,7829041415675_at 0,938431 0,272201 0,477756 0,374765 0,840321 0,187776 0,540691415676_a_at 0,700227 0,971044 0,486389 0,236767 0,717116 0,714643 0,4434471415677_at 0,716683 0,380579 0,592676 0,224927 0,304563 0,285177 0,6874261415678_at 0,086303 0,069413 0,601634 0,289336 0,197956 0,820493 0,0721611415679_at 0,669657 0,578992 0,373976 0,581597 0,561598 0,051069 0,0701441415680_at 0,277747 0,716174 0,73642 0,428784 0,614857 0,763586 0,7042631415681_at 0,208313 0,279458 0,063052 0,077388 0,577486 0,087832 0,0638261415682_at 0,94562 0,077064 0,735568 0,081915 0,109705 0,278815 0,350941415683_at 0,308529 0,008908 0,793956 0,304491 0,613119 0,055048 0,698222

PROBES

Subjects: INDIVIDUALS

DATA ELEMENTS

Traits:

TRAIT SUBJECT


Morris Swertz


Genotype dataExpression data

Classic phenotype dataMetabolite abundance data

Protein abundance dataAnd so on…

TRAIT SUBJECT


Morris Swertz

Data with any Dimension Type

TRAIT

SUBJECT

DATA ELEMENT

• Individual,

• Strain,• Sample,• …

• Probe• Marker• Mass

Peak• …

TRAIT SUBJECT


Morris Swertz


What about QTL data?

rs13475697rs13475698rs13475699rs13475700rs13475701rs2228909 rs22289101415670_at 0,981848 0,293227 0,034092 0,360978 0,298958 0,466545 0,3703691415671_at 0,464346 0,817348 0,990231 0,204923 0,353808 0,668164 0,4493541415672_at 0,243834 0,900083 0,69971 0,217804 0,471408 0,701617 0,0266091415673_at 0,712543 0,001536 0,209082 0,196611 0,191452 0,91619 0,5356591415674_a_at 0,159777 0,101577 0,678902 0,233476 0,251812 0,349968 0,5671711415675_at 0,777691 0,371057 0,670919 0,410665 0,742277 0,142381 0,5409451415676_a_at 0,320175 0,358505 0,207274 0,952688 0,615915 0,07167 0,2258231415677_at 0,840063 0,281845 0,773908 0,396397 0,482995 0,56668 0,199461415678_at 0,880974 0,471662 0,906012 0,711181 0,622078 0,575441 0,8688161415679_at 0,164846 0,957785 0,794479 0,207902 0,091649 0,727786 0,7960581415680_at 0,56679 0,823206 0,321578 0,513087 0,593739 0,272818 0,6208171415681_at 0,215698 0,384919 0,691254 0,550108 0,603988 0,110792 0,3801261415682_at 0,45273 0,36089 0,733234 0,911573 0,549316 0,086473 0,6396251415683_at 0,526019 0,740045 0,955297 0,797566 0,149079 0,370645 0,57789

PROBES

Traits: MARKERS

DATA

Traits:


Morris Swertz

rs13475697rs13475698rs13475699rs13475700rs13475701rs2228909 rs22289101415670_at 0,981848 0,293227 0,034092 0,360978 0,298958 0,466545 0,3703691415671_at 0,464346 0,817348 0,990231 0,204923 0,353808 0,668164 0,4493541415672_at 0,243834 0,900083 0,69971 0,217804 0,471408 0,701617 0,0266091415673_at 0,712543 0,001536 0,209082 0,196611 0,191452 0,91619 0,5356591415674_a_at 0,159777 0,101577 0,678902 0,233476 0,251812 0,349968 0,5671711415675_at 0,777691 0,371057 0,670919 0,410665 0,742277 0,142381 0,5409451415676_a_at 0,320175 0,358505 0,207274 0,952688 0,615915 0,07167 0,2258231415677_at 0,840063 0,281845 0,773908 0,396397 0,482995 0,56668 0,199461415678_at 0,880974 0,471662 0,906012 0,711181 0,622078 0,575441 0,8688161415679_at 0,164846 0,957785 0,794479 0,207902 0,091649 0,727786 0,7960581415680_at 0,56679 0,823206 0,321578 0,513087 0,593739 0,272818 0,6208171415681_at 0,215698 0,384919 0,691254 0,550108 0,603988 0,110792 0,3801261415682_at 0,45273 0,36089 0,733234 0,911573 0,549316 0,086473 0,6396251415683_at 0,526019 0,740045 0,955297 0,797566 0,149079 0,370645 0,57789

PROBES

Traits: MARKERS

DATA


What about QTL data?Probe association data?

Interaction network data?

TRAIT TRAITSUBJECT SUBJECT

Traits:


Morris Swertz

DATA ELEMENT

Data with any Dimension Type› Minimal data model

TRAIT

SUBJECT

DATA ELEMENT columns

rows

dimension ELEMENT


Morris Swertz

The data model› To share genotype/phenotype data and

tools:1. Extensible data model

• Data• Annotations• Investigations• Integration references


Morris Swertz

Annotations› Simple and close to current practice

Probe annotations

name gene chr bplocal bpglobal1415670_at Copg 6 87875328 9245716701415671_at Atp6v0d1 8 108413750 12349086131415672_at Golga7 8 24706942 11512018051415673_at Psph 5 130080298 8201576541415674_a_at Trappc4 9 44155401 12989088981415675_at Dpm2 2 32395013 2274438781415676_a_at Psmb5 14 53568499 19128940201415677_at Dhrs1 14 54693657 19140191781415678_at Ppm1a 12 73712802 17014658381415679_at Psenen 7 30270655 10171686951415680_at Anapc1 2 128304204 323353069

PROBE IS A VARIANT OF TRAITHAVING:-Name-Gene-Chromosme-Locus


Morris Swertz

DATA ELEMENT

Annotation extends Trait or Subject

TRAIT

SUBJECT

column

row

dimension ELEMENT

PROBE-Name-Gene-Chromosme-Locus

MARKER-Name-Allele-Chromosme-Locus

MASSPEAK-Name-MZ-RetentionTime

STRAIN-Name-Type: CSS, RIL..-Parent Strains

INDIVIDUAL-Name-Strain-Mother-Father-Sex

SAMPLE-Name-Individual-Tissue

And so on…

And so on…


Morris Swertz

DATA ELEMENTMARKER

STRAIN

Annotation simple in practice

DATA ELEMENT

PROBE

MARKER

Genotype data QTL data

DATA ELEMENT

MARKER

INDIVIDL

Expression data Extensions are automatic “under the hood”PROBE isa TRAIT isa DIMENSION ELEMENT PROBE

TRAIT

dimension ELEMENT


Morris Swertz

DATA ELEMENTSBxD1 BxD2 BxD3 BxD4 BxD5 BxD6 BxD7

1415670_at 0,293493 0,687197 0,137687 0,5992 0,691055 0,644053 0,9387541415671_at 0,124305 0,261548 0,771756 0,022287 0,374063 0,711998 0,5262771415672_at 0,592037 0,334535 0,173969 0,516279 0,21625 0,970534 0,1927341415673_at 0,555223 0,992222 0,17998 0,79899 0,505028 0,776323 0,7361551415674_a_at 0,585366 0,61328 0,448061 0,977578 0,746478 0,937131 0,7829041415675_at 0,938431 0,272201 0,477756 0,374765 0,840321 0,187776 0,540691415676_a_at 0,700227 0,971044 0,486389 0,236767 0,717116 0,714643 0,4434471415677_at 0,716683 0,380579 0,592676 0,224927 0,304563 0,285177 0,6874261415678_at 0,086303 0,069413 0,601634 0,289336 0,197956 0,820493 0,0721611415679_at 0,669657 0,578992 0,373976 0,581597 0,561598 0,051069 0,0701441415680_at 0,277747 0,716174 0,73642 0,428784 0,614857 0,763586 0,7042631415681_at 0,208313 0,279458 0,063052 0,077388 0,577486 0,087832 0,0638261415682_at 0,94562 0,077064 0,735568 0,081915 0,109705 0,278815 0,350941415683_at 0,308529 0,008908 0,793956 0,304491 0,613119 0,055048 0,698222

PROBES

Data and annotations

name gene chr bplocal bpglobal1415670_at Copg 6 87875328 9245716701415671_at Atp6v0d1 8 108413750 12349086131415672_at Golga7 8 24706942 11512018051415673_at Psph 5 130080298 8201576541415674_a_at Trappc4 9 44155401 12989088981415675_at Dpm2 2 32395013 2274438781415676_a_at Psmb5 14 53568499 19128940201415677_at Dhrs1 14 54693657 19140191781415678_at Ppm1a 12 73712802 17014658381415679_at Psenen 7 30270655 10171686951415680_at Anapc1 2 128304204 323353069


Morris Swertz





Morris Swertz

Investigation workflow in the lab

?

?

?DATA ELEMENTMARKER

STRAIN

DATA ELEMENT

PROBE

MARKER

DATA ELEMENT

MARKER

INDIVIDL

DATA DATA

DATA

Genotype data QTL data

Expression data


Morris Swertz

DATA

Investigation building on FuGE

DATA

Genotype data QTL dataQTL

MappingAffy

Array

SNPArray DATA

Expression data

FuGE: Jones et al Nature Biotech 25, 1127-1133

MappingProtocol

Illumina

RSoftware

IlluminaProtocol

Affy M430Protocol

BeadStudio

DATA

application

Protocol

Software

Equipment

BioconductorNorm.

Affy M430platform

DATA DATA

DATA

FuGE:


Morris Swertz

Summary of data model

DATA ELEMENT

TRAIT

SUBJECT

dimension ELEMENT

DATA PROTOCOLAPPLICTION

PROTOCOL

INVESTIGATION

column

row Equipment

Software

STRAINPROBE INDIVIDLMARKER

…


Morris Swertz





Morris Swertz

DATABASE REFERENCE

Id = ENSMU0S98Db=ENSEMBL

References for integration› Ontology references and database references

GENEName = Mip1alpha

GENEName = Mip1a

INVESTIGATION 1

INVESTIGATION 2

DATABASE REFERENCE

Id = ENSMUS098Db=ENSEMBL

DATABASE REFERENCE

Id = ENSMUS98Db=ENSEMBL

DATABASE REFERENCE

Id = 1419561_ATDb=AFFY 430

ONTOLOGYENTRY

Id = 0005615Term = ABC

Ontology=GO

Hyperlink…

FuGE: Jones et al Nature Biotech 25, 1127-1133

ONTOLOGYENTRY

Id = MP:0005385Term = cardiovascular

Ontology=MP

Incompatible naming

CompatibleIdentifiers

Map mouse on human ontologies


Morris Swertz

Summary of data model

DATA ELEMENT

TRAIT

SUBJECT

dimension ELEMENT

DATA PROTOCOLAPPLICTION

PROTOCOL

INVESTIGATION

column

row Equipment

Software

DATABASE REFERENCE

ONTOLOGYENTRY

Hyperlink…

STRAINPROBE INDIVIDLMARKER

extensible to more experiments…


Morris Swertz

What is on the todo


Morris Swertz

Todo› Publication: submitted

› Building a catalog of tools on top of dbGG•Experiments: in Braunschweig and Groningen

• Illumina, Affy, Metabolites•Tool ‘plug-ins’

• QTL graphs, import of annotations etc.

› Exploit interoperability•E.g. integrate mouse & human with ontologies•Load annotations from other dbGG/BioMARTs•Build on and extend R/Taverna interaction


Morris Swertz

Summary and questions› Share genotype/phenotype data and tools:



› Next steps


Morris Swertz

Thank [email protected]

Morris A. SwertzBruno M. TessonRichard A. ScheltemaGonzalo VeraRudi AlbertsDamian SmedleyKaty WolstencroftAndrew R. Jones

Klaus SchughartJohn M. HancockHelen E. Parkinson Engbert O. de BrockCarole GoblePaul SchofieldRitsert C. Jansenthe GEN2PHEN consortiumthe CASIMIR consortium


Morris Swertz

Appendix:Procedure to (re)generate a MOLGENIS


Morris Swertz

MOLGENIS for data


Morris Swertz

Describe in little language

Assay

ID : autoidName : varchar

ID : autoidValue : object

DataColumn

1

Assay 1Row 1


Experiment

Experiment 1Experiment1


Trait


Subject

Experiment1

individuals

expressions

probes


Morris Swertz

Assay



DataColumn

1

Assay 1Row 1


Experiment



Trait


Subject

Experiment1



Morris Swertz

Describe in little languageAssay



DataColumn

1

Assay 1Row 1


Experiment



Trait


Subject

Experiment1


Morris Swertz

Case GG: Generate and evaluate

http://gbic.biol.rug.nl/supplementary/2007/molgenis_showcase



Morris Swertz

Documents

dbgg – database for genetical genomics update