Award details

Ontology development for the study of metabolism and functional genomics

Reference	BB/D524283/1
Principal Investigator / Supervisor	Dr Susanna-Assunta Sansone
Co-Investigators / Co-Supervisors	Dr Philippe Rocca-Serra
Institution	EMBL - European Bioinformatics Institute
Department	Wellcome Trust Genome Campus
Funding type	Research
Value (£)	60,599
Status	Completed
Type	Research Grant
Start date	01/01/2006
End date	31/12/2006
Duration	12 months

Abstract

The MGED ontology (http:mged.sourceforge.net ontologies) is an ontology describing microarray experiments and a framework that references external ontologies and vocabularies unambiguously, providing vocabularies only when these are not available from other sources. It is clear that many useful domain and species-specific ontologies exist and that reinvention of these is neither practical nor desirable. MO is extensible to other types of functional genomics investigation. The development to `convert¿ MO into an ontology that will support multiple omics technologies is a collaborative effort between the generators of the MGED Ontology (web reference given above), MGED RSBI (http:www.mged.org workgroups rsbi), PSI (http:psidey.sf.net) and SMRS (http:www.smrsgroup.org) groups. There is a consensus to develop this technology-specific ontology in a wider functional genomics context. Ontologies specific to each of the domains dealt with by the above groups (transcriptomics, proteomics and metabolomics respectively) should stand alone (ie. Be modular), but should also function together to support functional genomics investigations. The ontology for metabolomic study we plan to develop will be an `extension¿ of this main functional genomics ontology project into this technical domain (although in fact the technology-specific `module¿ will precede the main functional genomics ontology itself by some time). The result of this open, collaborative development effort will be an ontology that will cater to the needs of large numbers of life scientists; allowing them to describe their work in a manner that facilitates comparison between omics datasets, and with other researchers; data, however generated. This will be possible because the ontology will provide both common and domain-specific terms that are well defined and richly contextualised, thereby adding great value to data sets. The massively-collaborative nature of this project requires that, in addition to frequent face-to-face meetings, there is a virtual resource through which development is carried out. A SourceForge project site can provide exactly that sort of collaborative development environment; it offers a free Concurrent Versions System for collaborative code development, unlimited email discussion lists, issue trackers and so on. It is also the case that this collaborative project requires that all participants work in the same format, ideally with the same (free) development tool; it has been decided that we will therefore encode the metabolomics ontology in the OWL format and do our development with the (freeware) Protégé tool. We have carried out work internally at the EBI to assess the best methodology to capture requirements and to begin to accrue new terms. The results of this exploratory work have been submitted to the journal BMC Bioinformatics; the current draft is attached as an annex to this application (Garcia et al.), which also describes the following series of steps for the process of developing the ontology, each except the last resulting in a more developed product: Step one: Identification of purpose, scope, competency questions and scenarios ¿ Product one: Questions, Scenarios. Step two: Identification of those ontologies we could reuse ¿ Product two: Reusable ontologies. Step three: domain analysis and knowledge acquisition ¿ Product three: Baseline ontology. Step four: Iteratively building informal ontologies models ¿ Products four: Refined ontology. Step five: Formalisation ¿ Product five: Ontology. Step six: Evaluation. All novel ontology terms will, as previously stated, be added to the general reworking of MO, along with the products of the RSBI working groups¿ deliberations with respect to high-level project description, resulting ultimately in three omics-specific ontologies, sensibly embedded in a robust, flexible all-encompassing functional genomics ontology.

Summary

unavailable

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	EDF (e-science Development Fund) (EDF) [2003-2005]
Funding Scheme	X – not Funded via a specific Funding Scheme

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