2007 Mouse All Hands Meeting BIRN Ontology Day Jeff Grethe & Bill Bug (BIRN OTF) - March 7th, 2007 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 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 () NCBO BioPortal () EBI Ontology Lookup Service () NCBC Endorsed Ontologies () OBO Ontology Download Matrix () 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) 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 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 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 BIRN Ontology Day Ontology-related Tools Ontology Curation Tools for ontology development experts Protg-OWL NCI Edit Protg-OWL Tab OBO-Edit SWOOP Tools for broader BIRN community BIRNLex Wiki BIRNLex in NCBO BioPortal BONFIRE Terminology Server BIRN Ontology Day Ontology-related Tools Ontology/Controlled Term-based Annotation Use of PATO Phenote OBO Phenotype Assertion syntax (HCLS example) xperiment Algorithmically-generated XCEDE & MAGE Other Ontology-driven Query Support Mediator Web Services supporting BIRNLex+BONFIRE MBAT use Atlas-Interoperability Web Services 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 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