The EXACT description of biomedical protocols

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....

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Bibliographic Details
Published in:Bioinformatics 2008-07, Vol.24 (13), p.i295-i303
Main Authors: Soldatova, Larisa N., Aubrey, Wayne, King, Ross D., Clare, Amanda
Format: Article
Language:English
Subjects:
Database Management Systems
Databases, Factual
Documentation - methods
Information Storage and Retrieval - methods
Internet
Research - classification
Research - standards
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Summary: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@aber.ac.uk
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn156