The MGED OntologyThe MGED Ontology

W3C Workshop on Semantic Web for life W3C Workshop on Semantic Web for life SciencesSciences

October 27, 2004October 27, 2004

Presented by Presented by

Liju FanLiju Fan

MGED Ontology Working Group MGED Ontology Working Group

Senior Scientist, KEVRICSenior Scientist, KEVRIC

MGED SocietyMGED Society

International organizationInternational organization Comprised of biologists, Comprised of biologists,

computer scientists, and computer scientists, and data analystsdata analysts

Aims to facilitate the sharing Aims to facilitate the sharing and evaluation of microarray and evaluation of microarray data data Establish standards for Establish standards for

microarray data annotationmicroarray data annotation Create microarray databasesCreate microarray databases Promote sharing of high Promote sharing of high

quality, well-annotated dataquality, well-annotated data Extends to cover data Extends to cover data

generated by functional generated by functional genomics and proteomics genomics and proteomics experimentsexperiments

http://www.mged.org

MGED Standardization MGED Standardization EffortsEfforts

MIAMEMIAME The formulation of the minimum information about a microarray The formulation of the minimum information about a microarray

experiment required to interpret and verify the results. experiment required to interpret and verify the results. MAGEMAGE

The establishment of a data exchange format (MAGE-ML) and object The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments. model (MAGE-OM) for microarray experiments.

MGED OntologyMGED Ontology The development of an ontology for microarray experiment The development of an ontology for microarray experiment

description, with particular emphasis on biological material description, with particular emphasis on biological material (biomaterial) annotation. (biomaterial) annotation.

Data Transformation and NormalizationData Transformation and Normalization The development of recommendations regarding microarray data The development of recommendations regarding microarray data

transformations and normalization methods.transformations and normalization methods. RSBIRSBI

The development of a public and compatible reporting structure for The development of a public and compatible reporting structure for biological investigations (array-based data of Toxicogenomics, biological investigations (array-based data of Toxicogenomics, Nutrigenomics, and Environmental Genomics)Nutrigenomics, and Environmental Genomics)

MGED Ontology (MO)MGED Ontology (MO)

PurposePurpose Provide standard terms for the annotation of Provide standard terms for the annotation of

microarray experiments microarray experiments Not to model biology but to provide descriptors for Not to model biology but to provide descriptors for

experiment components experiment components BenefitsBenefits

Unambiguous description of how the experiment was Unambiguous description of how the experiment was performedperformed

Structured queries can be generatedStructured queries can be generated

Ontology concepts derived from the MIAME Ontology concepts derived from the MIAME guidelines/MAGE-OMguidelines/MAGE-OM Also incorporating concepts from Transformations and Also incorporating concepts from Transformations and

RSBIRSBI

MGED Ontology MGED Ontology developmentdevelopment

http://mged.sourceforge.net/ontologies/MGEDontology.phhttp://mged.sourceforge.net/ontologies/MGEDontology.phpp

OilEd OilEd File formatsFile formats

DAML fileDAML file HTML fileHTML file NCI DTS BrowserNCI DTS Browser

ChangesChanges NotesNotes Term TrackerTerm Tracker

MGED Ontology MGED Ontology Class HierarchyClass Hierarchy

MGED CoreOntologyMGED CoreOntology Coordinated development Coordinated development

with MAGE-OMwith MAGE-OM Ease of locating Ease of locating

appropriate class to select appropriate class to select terms fromterms from

MGED MGED ExtendedOntologyExtendedOntology Classes for additional Classes for additional

terms as the usage of terms as the usage of genomics technologies genomics technologies expandexpand

Relationship of Relationship of MO to MAGE-OMMO to MAGE-OM

MO class hierarchy follows that of MO class hierarchy follows that of MAGE-OMMAGE-OM Association to OntologyEntryAssociation to OntologyEntry

MO provides terms for these MO provides terms for these associations by: associations by: Instances internal to MOInstances internal to MO Instances from external ontologiesInstances from external ontologies

Take advantage of existing ontologiesTake advantage of existing ontologies

MO and MAGEMO and MAGE

MO and References to MO and References to External OntologiesExternal Ontologies

MO and references to MO and references to External OntologiesExternal Ontologies

MO and Structured MO and Structured QueriesQueries

Other Sites Using MOOther Sites Using MO

Future Development of Future Development of MOMO

Areas of DevelopmentAreas of Development Ongoing maintenance Ongoing maintenance Ontology languageOntology language Non-array technologiesNon-array technologies Biological domain extensions Biological domain extensions MO v2. developmentMO v2. development

Proposed Development of MGED Proposed Development of MGED OntologyOntology

MO 1.x

MO 2.x

Sept. 2004 Jan. 2005 March 2005 Sept. 2005

Move to OWL/Protege

Proteomics in ExtendedOntology

RSBI in ExtendedOntologyRSBI in CoreOntology

AcknowledgementsAcknowledgements

MGED Ontology Working GroupMGED Ontology Working Group Chris Stoeckert, Trish Whetzel (Penn)Chris Stoeckert, Trish Whetzel (Penn) Helen Parkinson (EBI)Helen Parkinson (EBI) Joe White (TIGR)Joe White (TIGR) Gilberto Fragoso, Mervi Heiskanen Gilberto Fragoso, Mervi Heiskanen

(NCI)(NCI) Many others!Many others!

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