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An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows
With the capacity to produce and record data electronically, Scientific research and the data associated with it have grown at an unprecedented rate. However, despite a decent amount of data now existing in an electronic form, it is still common for scientific research to be recorded in an unstructu...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10416407/ https://www.ncbi.nlm.nih.gov/pubmed/37568227 http://dx.doi.org/10.1186/s13326-023-00288-6 |
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author | Penn, Steve Lomax, Jane Karlsson, Anneli Antonucci, Vincent Zachmann, Carl-Dieter Kanza, Samantha Schurer, Stephan Turner, John |
author_facet | Penn, Steve Lomax, Jane Karlsson, Anneli Antonucci, Vincent Zachmann, Carl-Dieter Kanza, Samantha Schurer, Stephan Turner, John |
author_sort | Penn, Steve |
collection | PubMed |
description | With the capacity to produce and record data electronically, Scientific research and the data associated with it have grown at an unprecedented rate. However, despite a decent amount of data now existing in an electronic form, it is still common for scientific research to be recorded in an unstructured text format with inconsistent context (vocabularies) which vastly reduces the potential for direct intelligent analysis. Research has demonstrated that the use of semantic technologies such as ontologies to structure and enrich scientific data can greatly improve this potential. However, whilst there are many ontologies that can be used for this purpose, there is still a vast quantity of scientific terminology that does not have adequate semantic representation. A key area for expansion identified by the authors was the pharmacokinetic/pharmacodynamic (PK/PD) domain due to its high usage across many areas of Pharma. As such we have produced a set of these terms and other bioassay related terms to be incorporated into the BioAssay Ontology (BAO), which was identified as the most relevant ontology for this work. A number of use cases developed by experts in the field were used to demonstrate how these new ontology terms can be used, and to set the scene for the continuation of this work with a look to expanding this work out into further relevant domains. The work done in this paper was part of Phase 1 of the SEED project (Semantically Enriching electronic laboratory notebook (eLN) Data). |
format | Online Article Text |
id | pubmed-10416407 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-104164072023-08-12 An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows Penn, Steve Lomax, Jane Karlsson, Anneli Antonucci, Vincent Zachmann, Carl-Dieter Kanza, Samantha Schurer, Stephan Turner, John J Biomed Semantics Database With the capacity to produce and record data electronically, Scientific research and the data associated with it have grown at an unprecedented rate. However, despite a decent amount of data now existing in an electronic form, it is still common for scientific research to be recorded in an unstructured text format with inconsistent context (vocabularies) which vastly reduces the potential for direct intelligent analysis. Research has demonstrated that the use of semantic technologies such as ontologies to structure and enrich scientific data can greatly improve this potential. However, whilst there are many ontologies that can be used for this purpose, there is still a vast quantity of scientific terminology that does not have adequate semantic representation. A key area for expansion identified by the authors was the pharmacokinetic/pharmacodynamic (PK/PD) domain due to its high usage across many areas of Pharma. As such we have produced a set of these terms and other bioassay related terms to be incorporated into the BioAssay Ontology (BAO), which was identified as the most relevant ontology for this work. A number of use cases developed by experts in the field were used to demonstrate how these new ontology terms can be used, and to set the scene for the continuation of this work with a look to expanding this work out into further relevant domains. The work done in this paper was part of Phase 1 of the SEED project (Semantically Enriching electronic laboratory notebook (eLN) Data). BioMed Central 2023-08-11 /pmc/articles/PMC10416407/ /pubmed/37568227 http://dx.doi.org/10.1186/s13326-023-00288-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Database Penn, Steve Lomax, Jane Karlsson, Anneli Antonucci, Vincent Zachmann, Carl-Dieter Kanza, Samantha Schurer, Stephan Turner, John An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title | An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title_full | An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title_fullStr | An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title_full_unstemmed | An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title_short | An extension of the BioAssay Ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
title_sort | extension of the bioassay ontology to include pharmacokinetic/pharmacodynamic terminology for the enrichment of scientific workflows |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10416407/ https://www.ncbi.nlm.nih.gov/pubmed/37568227 http://dx.doi.org/10.1186/s13326-023-00288-6 |
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