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

5. Species
Resources

7. Concept
Definitions

9. Excerpts from a Sample Description courtesy of M. Hoffman, S
Excerpts from a Sample Description courtesy of M. Hoffman, S. Schmidtke, Lion BioSciences
Organism: mus musculus [ NCBI taxonomy browser ]
Cell source: in-house bred mice (contact:
Sex: female [ MGED ]
Age: weeks after birth [ MGED ]
Growth conditions: normal
controlled environment
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 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

10. 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

11. 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

12. 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

13. MAGE BioMaterial Model

14. Building a Microarray Ontology

15. Ontology Available as RDFS

16. Ontology in Browseable Form

17. Example of Internal Terms

18. Example of External Terms

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

20. 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