OBI – Communities and Structure

1. -> cBiO will oversee the Open BioMedical Ontology (OBO) initiative OBI – Communities and Structure 1.Coordination Committee (CC): Representatives of the communities -> Monthly conferences 2. Developers WG: CC and other communities’ members Weekly conferences calls 3. Advisors:

2. OBI – Heterogeneity but for Good • Diverse background • Omics standardization effort people (MGED, PSI, MSI) • People ‘running’ (public) repositories, primary + secondary databases • - Software engineers, modellers, biologists, data-miners • People from the semantic web technology • Vendors and manufacturers (new) • Different maturity stages • Some needs to ‘rebuild’, e.g. MGED Ontology • Some are starting now, e.g. MSI • Plurality of (prospective) usage • Driving data entry and annotation • - Indexing of experimental data, minimal information lists, x-db queries • Applying it to text-mining • - Benchmarking, enrichment, annotation • Encoding facts from literature • - Building knowledge bases relying on RDF triple stores

3. OBI – Development Strategy • Collaborative activities • Decide on athe top-level ontology to hook-up to - Leverage on Basic Formal Ontology (BFO) • Agree on an initial structure (trunk) with is_a relationship - Rely on Relation Ontology (RO) -> part_of (currently expressed in the taxonomy as cardinal_part_of) -> participates_in (input) and derives_from (output), located_in etc. • Agree on naming convention and metadata tags - Common working practices, for building, editing etc. • Within community activities • Collect use cases: real examples and potential usage of the ontology • Gather terms and definitions: the bottom-up approach • Branch activities • Split the development in branches for focused working groups • BioMaterial, Data Transformation, Instrument • Plan (design and protocol), Role, Protocol Application • Plan for distributed development: SVN, import functions, merging

4. OBI – Tools and Documentation • Open source, standards compliant and version management • Ontology Web Language (OWL) using Protégé editor • OBI.owl files are available from the OBI SVN Repository

5. OBI – Top Level Classes • Continuant: an entity that endure/remains the same through time • Independent Continuant: stands on its own E.g. All physical entities (instrument, technology platform, document etc.) E.g. Biological material (organism, population etc.) • Dependent Continuant: inheres from another entity E.g. Environment (depend on the set of ranges of conditions, e.g. geographic location) E.g. Characteristics (entity that can be measured, e.g. temperature, unit) - Realizable: an entity that is realized through a process(executed/run) E.g. Software (a set of machine instructions) E.g. Design (the plan that can be realized in a process) • E.g. Role (the part played by an entity within the context of a process) • Occurrent: an entity that occurs/unfolds in time E.g. Temporal Regions, Spatio-Temporal Regions (single actions or Event) • Process E.g. Investigation (the entire ‘experimental’ process) E.g. Assay (process of performing some tests and recording the results)

6. OBI – Main Activities and Timelines • Continue branches activities (iterative process) • Branches editors collect terms from the communities (APRIL 07) • Sort terms by relevance to one or other branch, or to other ontologies • Normalize terms, add metadata tags (e.g. definition and source) • Bin terms into the relevant top level classes • Finalize the first draft of OBI Core • Review branches and merge with the trunk into a core (JULY 07) • - 4th Face-2-face workshop for Coordinators and Developers • Test the first draft of OBI Core • Out to user communities for testing(OCTOBER 07) • - Set up tracker tool for gathering comments and suggestions • Enrich the ontology • Branches editors collect other terms (OCTOBER 07) • Lay out landscape of missing communities • Recruit new communities

7. Approach • Transparency and inclusivity (http://www.bioontology.org/wiki/index.php/OCI:Main_Page; Google “OCI wiki”) • Combined top down/bottom up approach • Assembled term lists • Combine terms • Separate homonyms • Combine synonyms • Assigned membership into BFO/OBI branches • Position terms within branches • Define terms • Testing

8. OCI Wiki

9. Term lists

10. Study Design • Descriptive research – research in which the investigator attempts to describe a group of individuals based on a set of variable in order to document their characteristics • Case study – description of one or more patients • Developmental research – description of pattern of change over time • Normative research – establishing normal values • Qualitative research – gathering data through interview or observation • Evaluation research – objectively assess a program or policy by describing the needs for the services or policy, often using surveys or questionnaires • Exploratory research • Cohort or case-control studies – establish associations through epidemiological studies • Methodological studies – establish reliability and validity of a new method • Secondary analysis – exploring new relationships in old data • Historical research – reconstructing the past through an assessment of archives or other records • Experimental research • Randomized clinical trial – controlled comparison of an experimental intervention allowing the assessment of the causes of outcomes • Single-subject design • Sequential clinical trial • Evaluation research – assessment of the success of a program or policy • Quasi-experimental research • Meta-analysis – statistically combining findings from several different studies to obtain a summary analysis

11. Populations • Recruited population • Randomized population • Enrolled population • Eligible population • Screened population • Completer population • Premature termination population • Excluded population • Excluded post-randomization population • Not-randomized-population • Not-enrolled-population • Not-eligible-population • Analyzed-population • All subjects • Study arm population • Crossover population • Subgroup population • Intent-to-treat population - based on randomization • per-protocol population - exclude those with serious protocol violations

12. Homonyms sample size: 1. A subset of a larger population, selected for investigation to draw conclusions or make estimates about the larger population. 2. The number of subjects in a clinical trial. 3. Number of subjects required for primary analysis.