Ontology for Biomedical Investigations

The OBI Consortium logo.

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 protocols 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^[1]

Scope of the Ontology

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.^[2] OBI uses the Basic Formal Ontology^[3] upper 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:

• biological material - for example blood plasma
• instrument (and parts of an instrument therein) - for example DNA microarray, centrifuge
• information content - such as an image or a digital information entity such as an electronic medical record
• design and execution of an investigation (and individual experiments therein) - for example study design, electrophoresis material separaition
• data transformation (incorporating aspects such as data normalization and data analysis) - for example principal components analysis dimensionality reduction, mean calculation

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.

OBI Consortium

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)^[4] was created. This later became the OBI covering the wider scope of all biomedical investigations.

As an international, cross-domain initiative, the OBI consortium draws upon a pool of experts from a variety of fields, not limited to biology. The current list of OBI consortium members is available at the OBI consortium website. The consortium is made up of a coordinating committee which is a combination of two subgroups, the Community Representative (those representing a particular biomedical community) and the Core Developers (ontology developers who may or may not be members of any single community). Separate to the coordinating committee is the Developers Working Group which consists of developers within the communities collaborating in the development of OBI at the discretion of current OBI Consortium members.

References

1. Ontology for Biomedical Investigations (OBI) | Home
2. Smith et al. (2007) Nature Biotechnology 25, 1251 - 1255 (2007)
3. Basic Formal Ontology (BFO) | Home
4. Whetzel, PL et al. Development of FuGO: an ontology for functional genomics investigations. OMICS 10, 199–204

External links

• The OBI Consortium project homepage http://obi-ontology.org/
• The OBI Consortium SVN Repository homepage http://obi.svn.sourceforge.net/viewvc/obi/
• The OBI Consortium mailing list homepage http://obi-ontology.org/page/Mailing_lists

Papers on OBI

• J Biomed Semantics. 2010. Modeling biomedical experimental processes with OBI, Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jr., Jessica A Turner, Jie Zheng, and the OBI consortium

• OWLED 2008. The OWL of Biomedical Investigations, Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Brinkman and Alan Ruttenberg.

• Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations

J Zheng, E Manduchi, CJ Stoeckert J. 2013

• The Semanticscience Integrated Ontology (SIO) for Biomedical Research and Knowledge Discovery

M Dumontier, CJO Baker, J Baran, A Callahan … 2013

• Workshop on laboratory protocol standards for the molecular methods database

MK Müller, P Lambrix, MJ Taussig, JE Litton… 2013

• The representation of biomedical protocols

Larisa N. Soldatova, Ross D. King, Piyali S. Basu, Emma Haddi, Nigel Saunders 2013

• Modeling biomedical experimental processes with OBI RR Brinkman, M Courtot, D Derom, JM Fostel, Y He… - 2010