ArticleBMC bioinformatics2014
EXACT2: the semantics of biomedical protocols.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation.Journal of biomedical semantics · 2022Article
- Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora.Frontiers in research metrics and analytics · 2021Article
- Article
- Using semantics for representing experimental protocols.Journal of biomedical semantics · 2017Article
- Robotic crowd biology with Maholo LabDroids.Nature biotechnology · 2017Article
- Knowledge Representation and Management. From Ontology to Annotation. Findings from the Yearbook 2015 Section on Knowledge Representation and Management.Yearbook of medical informatics · 2015Review
- Building an Ontology for Identity Resolution in Healthcare and Public Health.Online journal of public health informatics · 2015Article
- NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories.BMC bioinformatics · 2014Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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. 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.
methodsWe have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility.
resultsThe 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.
conclusionsThe 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.