The EXACT description of biomedical protocols

Larisa Nikolaevna Soldatova; Wayne Aubrey; Ross Donald King; Amanda Janet Clare

doi:10.1093/bioinformatics/btn156

The EXACT description of biomedical protocols

Larisa Nikolaevna Soldatova, Wayne Aubrey, Ross Donald King, Amanda Janet Clare

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	i295-i303
Number of pages	9
Journal	Bioinformatics
Volume	24
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btn156
Publication status	Published - 01 Jul 2008

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title = "The EXACT description of biomedical protocols",

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.",

author = "Soldatova, {Larisa Nikolaevna} and Wayne Aubrey and King, {Ross Donald} and Clare, {Amanda Janet}",

note = "Soldatova, L. N., Aubrey, W., King, R. D., Clare, A. J. (2008). The EXACT description of biomedical protocols. Bioinformatics, 24 (13), i295-i303 Sponsorship: BBSRC / RAEng / EPSRC specialissue: ISMB ",

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AU - Soldatova, Larisa Nikolaevna

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AU - Clare, Amanda Janet

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N2 - 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.

AB - 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.

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M3 - Article

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SP - i295-i303

JO - Bioinformatics

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The EXACT description of biomedical protocols

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