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MGED Ontology Working Group Report

MGED Ontology Working Group Report. MGED Advisory Committee Meeting Bethesda, MD, USA Nov. 9, 2001 Chris Stoeckert, U. Penn. Ontology Working Group Highlights. First pass ontology of biomaterial descriptions Participated in Bio-ontologies Consortium Meeting at ISMB 2001.

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MGED Ontology Working Group Report

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  1. MGED Ontology Working Group Report MGED Advisory Committee Meeting Bethesda, MD, USA Nov. 9, 2001 Chris Stoeckert, U. Penn

  2. Ontology Working Group Highlights • First pass ontology of biomaterial descriptions • Participated in Bio-ontologies Consortium Meeting at ISMB 2001. • Mail list of about 200 subscribers

  3. What is an ontology?(In the computer science not philosophy sense) • An ontology is a specification of concepts that includes the relationships between those concepts. • Removes ambiguity. Provides semantics and constraints. • Allows for computational inferences and reliable comparisons

  4. http://www.cbil.upenn.edu/Ontology/

  5. Species Resources

  6. Concept Definitions

  7. Excerpts from a Sample Descriptioncourtesy of M. Hoffman, S. Schmidtke, Lion BioSciences • Organism: mus musculus [ NCBI taxonomy browser ] • Cell source: in-house bred mice (contact: norma.howells@itg.fzk.de) • Sex: female [ MGED ] • Age: 3 - 4 weeks after birth [ MGED ] • Growth conditions: normal • controlled environment • 20 - 22 oC average temperature • housed in cages according to German and EU legislation • specified pathogen free conditions (SPF) • 14 hours light cycle • 10 hours dark cycle • Developmental stage: stage 28(juvenile (young) mice) [ GXD "Mouse Anatomical Dictionary" ] • Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ] • Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice] • Genetic Variation: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ] • Treatment: in vivo [MGED] intraperitoneal injection of Dexamethasone into mice, 10 microgram per 25 g bodyweight of the mouse • Compound: drug [MGED] synthetic glucocorticoid Dexamethasone, dissolved in PBS

  8. OWG Use Cases • Return a summary of all experiments that use a specified type of biosource. • Group the experiments according to treatment. • Return a summary of all experiments done examining effects of a specified treatment • Group the experiments according to biosource. • Return a summary of all experiments measuring the expression of a specified gene. • Indicate when experiments confirm results, provide new information, or conflict. • Generate a distance metric for experiment types • Generate an error estimation for experimental descriptions

  9. MGED Biomaterial Ontology • Under construction • Using OILed (May use others) • Generate multiple formats: RDFS, DAML+OIL • Motivated by MIAME and coordinated with MAGE • Extend classes, provide constraints, provide terms to use

  10. MIAME Section on Sample Source and Treatment • sample source and treatment ID as used in section 1 • organism (NCBI taxonomy) • additional "qualifier, value, source" list; the list includes: • cell source and type (if derived from primary sources (s)) • sex • age • growth conditions • development stage • organism part (tissue) • animal/plant strain or line • genetic variation (e.g., gene knockout, transgenic variation) • individual • individual genetic characteristics (e.g., disease alleles, polymorphisms) • disease state or normal • target cell type • cell line and source (if applicable) • in vivo treatments (organism or individual treatments) • in vitro treatments (cell culture conditions) • treatment type (e.g., small molecule, heat shock, cold shock, food deprivation) • compound • is additional clinical information available (link) • separation technique (e.g., none, trimming, microdissection, FACS) • laboratory protocol for sample treatment

  11. MAGE BioMaterial Model

  12. Building a Microarray Ontology http://www.cbil.upenn.edu/Ontology/Build_Ontology2.html

  13. Ontology Available as RDFS

  14. Ontology in Browseable Form

  15. Example of Internal Terms

  16. Example of External Terms

  17. Relationship of MGED Efforts MIAME DB MAGE MGED Ontology MIAME DB External Ontologies/CVs

  18. Ontology Working Group Issues • Building a biomaterial description ontology • Coordinating with MAGE • Goal for MGED4 • Expanding efforts to include rest of microarray experiments • Funding • Timing • Acceptance by microarray community • Examples of usage • Publication

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