MIAMExpress and the development of annotation

ontologies for gene expression experiments

Ele Holloway

Microarray Informatics

European Bioinformatics InstituteMicroarrays and Data Mining 10th-11th December 2002

Outline

Capturing information

Ontologies

MIAMExpress

Capturing information

Lab book – only useful for the individual

Annotate in a controlled way

Submit information to a database / LIMS

Need information understandable by all

Allows easy retrieval

Available to other researchers

What is an ontology?

A kind of controlled vocabulary (CV) expressed in a structured way.

Components of an ontology

Class

Instance

Has a definition and a relationship to other classes (is-a, part-of, kind-of).

Terms that are contained within a class.

= container for information.

e.g. An exon is part of a gene

An ontology – what can it do?

Captures knowledge

Shared understanding

Structure enriches CV

Computer ‘readable’

Why do we need an ontology for the database?

To help users annotate their data usefully and easily

To perform structured queries

To accurately compare data

To avoid problems with free text searching

To avoid excessive curation workload in future

Annotation

Data mining

Controlled vocabulary

Free text

Database

Natural language processing

Standards and Ontologiesfor Functional Genomics

Aim: To bring together scientists (biologists and bioinformaticians) developing standards and ontologies

17 – 20th November 2002Hinxton

http://www.ebi.ac.uk/SOFG

Examples of ontologies and CVs

MGED Ontology

– For describing samples used in microarray experiments

– Gene Ontology

– Edinburgh Mouse Atlas Project

– Drosophila genome database

NCBI Taxonomy

GO

EMAP

FlyBase

- All organisms represented in the genetic databases

Infrastructure

EBI

ExpressionProfiler

Externalbioinformatics

databases

www

Submissions

Queries

www

Dataanalysis

www

MAGE-ML

Local MIAMExpressinstallations

Arraymanufacturers

LIMSData

pip

elin

es

ArrayExpress(Oracle)

Othermicroarraydatabases

Data analysissoftware

Microarraysoftware

MA

GE-M

L im

port

/exp

ort

MIAMExpress

MAGE-ML

MIAME requirements

Experimental design

Array design

Samples

Measurements

Normalization controls

Hybridizations

Nature Genetics 29(4): 365-371

External links

Normalization Data

ArrayHybridizationSample

Experiment

6 parts of a microarray experiment

MEDLINE

Publicationdetails

MGED

Experimentdetails

NCBItaxonomy

CAS/Merck

EMAP

Mousestage

Species

Chemicalcompd.

EMBL

Geneacc. no.

Genename

GO

Genew

MGED Ontology

Community effort

Supports efforts of MAGE

- MGED Society

Describes the parts of a microarray experiment

References out to external ontologies

MGED Ontology

Structured in DAML+OIL using OilEd 3.4

MIAMExpress

Submission and annotation toolBased on MIAME concepts

Array, Experiment and Protocol submissions

Perl-CGI, MySQL database

Login

New/Pending Experiment

Combined Experiment Data

Submit

Sample 1 Sample 2 Sample 3 Sample 4

Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….nE1 E1 E1 E1E2 E2 E2 E2En En En En

LE LE LE LE LE LE LE LE LE LELE LE

HybridizationsArray1 Array2 Array3 Arrayn

Data1 Data2 Data3 Datan

Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….nLab. Extr. 1….n

Image analysis protocol

Transformation protocol

Sample protocol

Hybridization protocol

Extraction protocol

Labeling protocol

Scanning protocol

Submission process

http://www.ebi.ac.uk/miamexpress

Tour of MIAMExpress

Login +Password

Multi-user environment

Control over data access

Login

New/Pending Experiment

Sample 1 Sample 2 Sample 3 Sample 4

Login

New/Pending Experiment

Sample 1 Sample 2 Sample 3 Sample 4

Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….nE1 E1 E1 E1E2 E2 E2 E2En En En En

Login

New/Pending Experiment

Sample 1 Sample 2 Sample 3 Sample 4

Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….nE1 E1 E1 E1E2 E2 E2 E2En En En En

LE LE LE LE LE LE LE LE LE LELE LELab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….nLab. Extr. 1….n

Login

New/Pending Experiment

Sample 1 Sample 2 Sample 3 Sample 4

Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….nE1 E1 E1 E1E2 E2 E2 E2En En En En

LE LE LE LE LE LE LE LE LE LELE LELab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….nLab. Extr. 1….n

HybridizationsArray1 Array2 Array3 Arrayn

Data1 Data2 Data3 Datan

Submission successful

Curation

Export of MAGE-ML

Loading to ArrayExpress

ArrayExpress

MIAMExpress

RADMAGE-ML data exchange

Ontology instances propagated to

submission/annotation web forms

Curation of user defined terms, before inclusion in the ontology

User defined terms collected via forms

MGED Ontology

BiomaterialDescription

SexC

C

C

C Genderdocumentation: Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender.

used in individuals: female,hermaphrodite,male,mixed_sex,unknown_sex

ResourcesMicroarray Informatics Group

http://www.ebi.ac.uk/microarray/

MIAMExpress

http://www.ebi.ac.uk/miamexpress/

MGED Ontology Working Group

http://mged.sourceforge.net/ontologies/

Sourceforge

http://sourceforge.net/

Acknowledgements

ArrayExpressUgis SarkansGonzalo GarciaAhmet OezcimenAnjan Sharma

Curation

Helen Parkinson

Gaurab Mukherjee

Philippe Rocca-Serra

Susanna Sansone

MIAMExpress

Mohammad Shojatalab

Niran Abeygunawardena

Sergio Contrino

Alvis Brazma

MGED OntologyChris Stoeckert(U. Penn)

GO

http://www.geneontology.org

EMAP

http://genex.hgu.mrc.ac.uk/

FlyBase

http://flybase.bio.indiana.edu/

NCBI Taxonomy

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/