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

^*Awdur cyfatebol y gwaith hwn

Adran Cyfrifiadureg

Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid

36 Dyfyniadau (Scopus)

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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/

Iaith wreiddiol	Saesneg
Tudalennau (o-i)	i295-i303
Nifer y tudalennau	9
Cyfnodolyn	Bioinformatics
Cyfrol	24
Rhif cyhoeddi	13
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1093/bioinformatics/btn156
Statws	Cyhoeddwyd - 01 Gorff 2008

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10.1093/bioinformatics/btn156

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@article{29ab494c7f6848399670c8b25880e737,

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

keywords = "Database Management Systems, Databases, Factual, Documentation/methods, Information Storage and Retrieval/methods, Internet, Research/classification",

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 ",

year = "2008",

month = jul,

day = "1",

doi = "10.1093/bioinformatics/btn156",

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publisher = "Oxford University Press",

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T1 - The EXACT description of biomedical protocols

AU - Soldatova, Larisa Nikolaevna

AU - Aubrey, Wayne

AU - King, Ross Donald

AU - Clare, Amanda Janet

N1 - 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

PY - 2008/7/1

Y1 - 2008/7/1

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

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

KW - Database Management Systems

KW - Databases, Factual

KW - Documentation/methods

KW - Information Storage and Retrieval/methods

KW - Internet

KW - Research/classification

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SN - 1367-4803

VL - 24

SP - i295-i303

JO - Bioinformatics

JF - Bioinformatics

IS - 13

ER -

The EXACT description of biomedical protocols

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