1. 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: -> cBiO will oversee the Open BioMedical Ontology (OBO) initiative

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 a the 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) - 4 th 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_Pa ge; Google “OCI wiki”)http://www.bioontology.org/wiki/index.php/OCI:Main_Pa ge 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.