Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an
Scope
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
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, electrophoresismaterial separation
- data transformation (incorporating aspects such as principal components analysisdimensionality 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
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.
Papers on OBI
- Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, et al. (June 2010). "Modeling biomedical experimental processes with OBI". Journal of Biomedical Semantics. 1 (Suppl 1): S7. PMID 20626927.
- Courtot M, Bug WJ, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A (1 January 2008). The OWL of Biomedical Investigations. Proceedings of the Fifth Owled Workshop on Owl: Experiences and Directions. p. 432. CiteSeerX 10.1.1.142.9206.
- Zheng J, Manduchi E, Stoeckert Jr CJ (7 July 2013). "Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations" (PDF). ICBO: 62–67.
- Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, et al. (March 2014). "The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery". Journal of Biomedical Semantics. 5 (1): 14. PMID 24602174.
- Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, et al. (January 2013). "Workshop on laboratory protocol standards for the Molecular Methods Database". New Biotechnology. 30 (2): 109–13. PMID 22687389.
- Soldatova LN, King RD, Basu PS, Haddi E, Saunders N (October 2013). "The representation of biomedical protocols". EMBnet Journal. 19 (B): 56–8. .
References
- PMID 27128319.
- ^ Ontology for Biomedical Investigations (OBI) | Home
- ^ "Basic Formal Ontology (BFO)". Institute for Formal Ontology and Medical Information Science. Universität des Saarlandes.
- ^ Whetzel, PL et al. Development of FuGO: an ontology for functional genomics investigations. OMICS 10, 199–204
External links
- "The OBI Consortium project homepage".
- "The OBI Consortium SVN Repository homepage". 22 February 2017.