Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an open access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository.

The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptomics domain by the FGED Society, which developed the MGED Ontology as an annotation resource for microarray data. OBI uses the Basic Formal Ontologyupper level ontology as a means of describing general entities that do not belong to a specific problem domain. As such, all OBI classes are a subclass of some BFO class.

The ontology has the scope of modeling all biomedical investigations and as such contains ontology terms for aspects such as:

Less 'concrete' aspects such as the role a given entity may play in a particular scenario (for example the role of a chemical compound in an experiment) and the function of an entity (for example the digestive function of the stomach to nutriate the body) are also covered in the ontology.

The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. Following a mutual decision to collaborate, this effort later became a wider collaboration between groups such as FGED, PSI and MSI in response to the needs of areas such as transcriptomics, proteomics and metabolomics and the FuGO (Functional Genomics Investigation Ontology) was created. This later became the OBI covering the wider scope of all biomedical investigations.

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