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EXACT2: the semantics of biomedical protocols

BACKGROUND: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ens...

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Autores principales: Soldatova, Larisa N, Nadis, Daniel, King, Ross D, Basu, Piyali S, Haddi, Emma, Baumlé, Véronique, Saunders, Nigel J, Marwan, Wolfgang, Rudkin, Brian B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255744/
https://www.ncbi.nlm.nih.gov/pubmed/25472549
http://dx.doi.org/10.1186/1471-2105-15-S14-S5
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author Soldatova, Larisa N
Nadis, Daniel
King, Ross D
Basu, Piyali S
Haddi, Emma
Baumlé, Véronique
Saunders, Nigel J
Marwan, Wolfgang
Rudkin, Brian B
author_facet Soldatova, Larisa N
Nadis, Daniel
King, Ross D
Basu, Piyali S
Haddi, Emma
Baumlé, Véronique
Saunders, Nigel J
Marwan, Wolfgang
Rudkin, Brian B
author_sort Soldatova, Larisa N
collection PubMed
description BACKGROUND: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. METHODS: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2) protocols. RESULTS: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. CONCLUSIONS: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.
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spelling pubmed-42557442014-12-05 EXACT2: the semantics of biomedical protocols Soldatova, Larisa N Nadis, Daniel King, Ross D Basu, Piyali S Haddi, Emma Baumlé, Véronique Saunders, Nigel J Marwan, Wolfgang Rudkin, Brian B BMC Bioinformatics Research BACKGROUND: The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. METHODS: We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2) protocols. RESULTS: The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. CONCLUSIONS: The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format. BioMed Central 2014-11-27 /pmc/articles/PMC4255744/ /pubmed/25472549 http://dx.doi.org/10.1186/1471-2105-15-S14-S5 Text en Copyright © 2014 Soldatova et al.; licensee BioMed Central. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Soldatova, Larisa N
Nadis, Daniel
King, Ross D
Basu, Piyali S
Haddi, Emma
Baumlé, Véronique
Saunders, Nigel J
Marwan, Wolfgang
Rudkin, Brian B
EXACT2: the semantics of biomedical protocols
title EXACT2: the semantics of biomedical protocols
title_full EXACT2: the semantics of biomedical protocols
title_fullStr EXACT2: the semantics of biomedical protocols
title_full_unstemmed EXACT2: the semantics of biomedical protocols
title_short EXACT2: the semantics of biomedical protocols
title_sort exact2: the semantics of biomedical protocols
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255744/
https://www.ncbi.nlm.nih.gov/pubmed/25472549
http://dx.doi.org/10.1186/1471-2105-15-S14-S5
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