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The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of...

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Autores principales: Hastings, Janna, Chepelev, Leonid, Willighagen, Egon, Adams, Nico, Steinbeck, Christoph, Dumontier, Michel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184996/
https://www.ncbi.nlm.nih.gov/pubmed/21991315
http://dx.doi.org/10.1371/journal.pone.0025513
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author Hastings, Janna
Chepelev, Leonid
Willighagen, Egon
Adams, Nico
Steinbeck, Christoph
Dumontier, Michel
author_facet Hastings, Janna
Chepelev, Leonid
Willighagen, Egon
Adams, Nico
Steinbeck, Christoph
Dumontier, Michel
author_sort Hastings, Janna
collection PubMed
description Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).
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spelling pubmed-31849962011-10-11 The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web Hastings, Janna Chepelev, Leonid Willighagen, Egon Adams, Nico Steinbeck, Christoph Dumontier, Michel PLoS One Research Article Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA). Public Library of Science 2011-10-03 /pmc/articles/PMC3184996/ /pubmed/21991315 http://dx.doi.org/10.1371/journal.pone.0025513 Text en Hastings et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Hastings, Janna
Chepelev, Leonid
Willighagen, Egon
Adams, Nico
Steinbeck, Christoph
Dumontier, Michel
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title_full The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title_fullStr The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title_full_unstemmed The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title_short The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
title_sort chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184996/
https://www.ncbi.nlm.nih.gov/pubmed/21991315
http://dx.doi.org/10.1371/journal.pone.0025513
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