the mged ontology w3c workshop on semantic web for life sciences october 27, 2004 presented by liju...
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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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