1. 2007 Mouse All Hands Meeting BIRN Ontology Day Jeff Grethe & Bill Bug (BIRN OTF) - March 7th, 2007

2. BIRN Ontology Day Agenda  Review Ontology Construction/Use SOPs Update on Biomedical Ontology Dev. Community Update on BIRN & BIRNLex SOPs Use of Ontologies within BIRN  BIRNLex Semantic Domain Review Main Semantic Domain Branches Domain Branch Details  Ontology-related Tools for use in BIRN Ontology Curation Ontology/Controlled Term-based Annotation Ontology-driven Query Support

3. BIRN Ontology Day  Review Ontology Construction/Use of SOPs Update on Biomedical Ontology Dev. Community  Foundational ontologies  Relations ontologies & their use  Ontology sharing - subclasses, owl:imports, bridging Foundational Level  Basic Formal Ontology (BFO)  OBO Relation Ontology (RO)  Ontology of Phenotypic Qualities (PATO)  BioTOP - a biomedical context for BFO + RO Biomedical Ontology Aggregation Sites  OBO Sourceforge Site ( http://obo.sourceforge.net/ )  NCBO BioPortal ( http://www.bioontology.org/ncbo/faces/index.xhtml )  EBI Ontology Lookup Service ( http://www.ebi.ac.uk/ontology-lookup/ )  NCBC Endorsed Ontologies ( http://www.berkeleybop.org/sowg/table.cgi )  OBO Ontology Download Matrix ( http://www.berkeleybop.org/ontologies/ )

4. BIRN Ontology Day  Review Ontology Construction/Use of SOPs Update on BIRN OTF & BIRNLex SOPs  Curation Procedure (on BIRN OTF Wiki)  BIRN OTF Community Participation: Basic Formal Ontology (BFO) Ontology of Biomedical Investigation (OBI) The Ontology of Phenotypic Qualities (PATO) Common Anatomy Reference Ontology (CARO) Use of Ontologies within BIRN  Tools (later)  Data Exchange/Annotation BIRNLex semantic description both for:  schema structure  instance values Data exchange schemas in use in BIRN  XCEDE (imaging data)  MAGE (gene expression data)

5. BIRN Ontology Day  Data Exchange Annotation using BIRNLex XCEDE (imaging data) Example: Subject level information If a required value is not present In BIRNLex, submit request to BONFIRE or BIRNLex Wiki

6. BIRN Ontology Day  BIRNLex Structure: Semantic Domain Review Main Domain Branches  Organism taxonomy  Neuroanatomy  Cognition and behavior  Investigation provenance Domain Details  Inter-Atlas Anatomy: brief review  Organisms: Mouse Strains IMSR nomenclature rules Precision required to interpret genetic impact on complex phenotypes  Investigational Metadata Behavioral paradigms Image device detail & provenance Image processing Gene expression study details

7. BIRN Ontology Day  BIRNLex Structure: Constructing Complex Relations Descriptive Logic restrictions  works for related, immutable facts  All viable nucleated eukaryotic cells contain functional mitochondria Rule-based logic  bridge to data where interpretation still debated  For males in age range X, MCI given by neuropsychological assessment score Y correlates with a mean amyloid plaque load of Z W3C Semantic Web representation (RDF)  Less constrained  :alpha_synuclein :accumulates_in :nigral_dopamine_neurons

8. BIRN Ontology Day  Ontology-related Tools Ontology Curation  Tools for ontology development experts Protégé-OWL  http://protege.stanford.edu/overview/protege-owl.html  NCI Edit Protégé-OWL Tab OBO-Edit  http://www.oboedit.org SWOOP  http://www.mindswap.org/2004/SWOOP  Tools for broader BIRN community BIRNLex Wiki BIRNLex in NCBO BioPortal  http://www.bioontology.org/ncbo/faces/index.xhtml BONFIRE Terminology Server  http://imhotep.ucsd.edu:7873/knowme/umls.html

9. BIRN Ontology Day  Ontology-related Tools Ontology/Controlled Term-based Annotation  Use of PATO Phenote OBO Phenotype Assertion syntax (HCLS example)  http://esw.w3.org/topic/HCLS/OntologyTaskForce/OboPhenotypeSyntaxE xperiment  Algorithmically-generated XCEDE & MAGE  Other Ontology-driven Query Support  Mediator Web Services supporting BIRNLex+BONFIRE  MBAT use  Atlas-Interoperability Web Services

10. BIRN Ontology Day Activities  Reviewed previous slides in detail Especially the BIRNLex curation procedure  Contributed to the BIRNLex FBIRN MRI Glossary entities  Jessica Turner Submitted additional terms:  animal behavior  mouse strains

11. BIRN Ontology Day Activities  Semantic DB Markup (new CC Tool) Identify required terms from BIRNLex Aids in gap analysis of BIRNLex  Clustering DB terms by BIRNLex type indicates BIRNLex candidates  Discussed Technical Plans Alterations to BONFIRE Web Services  Search by term (LUI) - return BIRNLex concept (CUI)  Filter on BIRNLex Relation to mediation and AIDB construction BrainGraph & BONFIRE search (Java tools by Heng)  Use to construct adaptable BIRNLex Portlet