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Bioinformatics 2008 24(13):i295-i303; doi:10.1093/bioinformatics/btn156
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The EXACT description of biomedical protocols

Larisa N. Soldatova *,{dagger}, Wayne Aubrey {dagger}, Ross D. King and Amanda Clare

Department of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB, Wales, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Many published manuscripts contain experiment protocols which are poorly described or deficient in information. This means that the published results are very hard or impossible to repeat. This problem is being made worse by the increasing complexity of high-throughput/automated methods. There is therefore a growing need to represent experiment protocols in an efficient and unambiguous way.

Results: We have developed the Experiment ACTions (EXACT) ontology as the basis of a method of representing biological laboratory protocols. We provide example protocols that have been formalized using EXACT, and demonstrate the advantages and opportunities created by using this formalization. We argue that the use of EXACT will result in the publication of protocols with increased clarity and usefulness to the scientific community.

Availability: The ontology, examples and code can be downloaded from http://www.aber.ac.uk/compsci/Research/bio/dss/EXACT/

Contact: Larisa Soldatova lss{at}aber.ac.uk

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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