التفاصيل البيبلوغرافية
| العنوان: |
EXACT2: the semantics of biomedical protocols |
| المؤلفون: |
Nigel J. Saunders, Piyali Basu, Brian B. Rudkin, Ross D. King, Daniel Nadis, Wolfgang Marwan, Véronique Baumle, Larisa N. Soldatova, Emma Haddi |
| المصدر: |
BMC Bioinformatics |
| بيانات النشر: |
BioMed Central, 2014. |
| سنة النشر: |
2014 |
| مصطلحات موضوعية: |
Computer science, Semantics (computer science), Ontology (information science), computer.software_genre, Biochemistry, Text mining, Software, Structural Biology, Data Mining, Biomedical protocols, Molecular Biology, Reference model, Biomedicine, Language, Reproducibility, Electronic Data Processing, business.industry, Applied Mathematics, Research, Reproducibility of Results, Biological Ontologies, Construct (python library), Replication (computing), Computer Science Applications, Semantics, EXACT2, Ontology, Data mining, business, Software engineering, computer, Natural language |
| الوصف: |
© 2014 Soldatova et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0Test), 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/1.0Test/) applies to the data made available in this article, unless otherwise stated. This article has been made available through the Brunel Open Access Publishing Fund. 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. This work has been partially funded by the Brunel University BRIEF award and a grant from Occams Resources. |
| وصف الملف: |
application/pdf |
| اللغة: |
English |
| تدمد: |
1471-2105 |
| الوصول الحر: |
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::af3ede507715cfddc71573c17a981cf8Test
http://bura.brunel.ac.uk/handle/2438/9597Test |
| حقوق: |
OPEN |
| رقم الانضمام: |
edsair.doi.dedup.....af3ede507715cfddc71573c17a981cf8 |
| قاعدة البيانات: |
OpenAIRE |
