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

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

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

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

OBI – Top Level Classes

Continuant: an entity that endure/remains the same through time

• Independent Continuant: stands on its ownE.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 timeE.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)

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

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

OCI Wiki

Term lists

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

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

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.