Large-scale reasoning over functions in biomedical ontologies

Robert Hoehndorf; Liam Mencel; Georgios V. Gkoutos; Paul N. Schofield

doi:10.3233/978-1-61499-660-6-299

Large-scale reasoning over functions in biomedical ontologies

Robert Hoehndorf^*, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield

^*Corresponding author for this work

Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

4 Scopus citations

Abstract

A large number of biomedical resources have been developed to represent the functions of biological entities, and these resources are widely used for data integration and analysis. Expressing functions in biomedical ontologies currently uses formal representation patterns that renders basic reasoning tasks to fall in complexity classes beyond polynomial time, thereby limiting the potential of using knowledge-based methods for data integration, querying or quality control. Here, we propose an alternative representation pattern for expressing knowledge about biological functions, together with a biological and ontological justification, which can be expressed using the description logic EL++ and implemented using the OWL 2 EL profile. To demonstrate the utility of our account of biological functions, we apply it to all proteins contained in the SwissProt database and evaluate its utility with respect to answering complex queries as well with respect to the classification and query times.

Original language	English (US)
Title of host publication	Formal Ontology in Information Systems - Proceedings of the 9th International Conference, FOIS 2016
Editors	Roberta Ferrario, Werner Kuhn
Publisher	IOS Press BV
Pages	299-312
Number of pages	14
ISBN (Electronic)	9781614996590
DOIs	https://doi.org/10.3233/978-1-61499-660-6-299
State	Published - 2016
Event	9th Formal Ontology in Information Systems Conference, FOIS 2016 - Annecy, France Duration: Jul 6 2016 → Jul 9 2016

Publication series

Name	Frontiers in Artificial Intelligence and Applications
Volume	283
ISSN (Print)	0922-6389
ISSN (Electronic)	1879-8314

Conference

Conference	9th Formal Ontology in Information Systems Conference, FOIS 2016
Country/Territory	France
City	Annecy
Period	07/6/16 → 07/9/16

Bibliographical note

Publisher Copyright:
© 2016 The authors and IOS Press.

Keywords

Big ontologies
Biological function
Protein
Tractable reasoning

ASJC Scopus subject areas

Artificial Intelligence

Access to Document

10.3233/978-1-61499-660-6-299

Cite this

Hoehndorf, R., Mencel, L., Gkoutos, G. V., & Schofield, P. N. (2016). Large-scale reasoning over functions in biomedical ontologies. In R. Ferrario, & W. Kuhn (Eds.), Formal Ontology in Information Systems - Proceedings of the 9th International Conference, FOIS 2016 (pp. 299-312). (Frontiers in Artificial Intelligence and Applications; Vol. 283). IOS Press BV. https://doi.org/10.3233/978-1-61499-660-6-299

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title = "Large-scale reasoning over functions in biomedical ontologies",

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author = "Robert Hoehndorf and Liam Mencel and Gkoutos, {Georgios V.} and Schofield, {Paul N.}",

note = "Publisher Copyright: {\textcopyright} 2016 The authors and IOS Press.; 9th Formal Ontology in Information Systems Conference, FOIS 2016 ; Conference date: 06-07-2016 Through 09-07-2016",

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doi = "10.3233/978-1-61499-660-6-299",

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Hoehndorf, R, Mencel, L, Gkoutos, GV & Schofield, PN 2016, Large-scale reasoning over functions in biomedical ontologies. in R Ferrario & W Kuhn (eds), Formal Ontology in Information Systems - Proceedings of the 9th International Conference, FOIS 2016. Frontiers in Artificial Intelligence and Applications, vol. 283, IOS Press BV, pp. 299-312, 9th Formal Ontology in Information Systems Conference, FOIS 2016, Annecy, France, 07/6/16. https://doi.org/10.3233/978-1-61499-660-6-299

Large-scale reasoning over functions in biomedical ontologies. / Hoehndorf, Robert; Mencel, Liam; Gkoutos, Georgios V. et al.
Formal Ontology in Information Systems - Proceedings of the 9th International Conference, FOIS 2016. ed. / Roberta Ferrario; Werner Kuhn. IOS Press BV, 2016. p. 299-312 (Frontiers in Artificial Intelligence and Applications; Vol. 283).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Mencel, Liam

AU - Gkoutos, Georgios V.

AU - Schofield, Paul N.

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N2 - A large number of biomedical resources have been developed to represent the functions of biological entities, and these resources are widely used for data integration and analysis. Expressing functions in biomedical ontologies currently uses formal representation patterns that renders basic reasoning tasks to fall in complexity classes beyond polynomial time, thereby limiting the potential of using knowledge-based methods for data integration, querying or quality control. Here, we propose an alternative representation pattern for expressing knowledge about biological functions, together with a biological and ontological justification, which can be expressed using the description logic EL++ and implemented using the OWL 2 EL profile. To demonstrate the utility of our account of biological functions, we apply it to all proteins contained in the SwissProt database and evaluate its utility with respect to answering complex queries as well with respect to the classification and query times.

AB - A large number of biomedical resources have been developed to represent the functions of biological entities, and these resources are widely used for data integration and analysis. Expressing functions in biomedical ontologies currently uses formal representation patterns that renders basic reasoning tasks to fall in complexity classes beyond polynomial time, thereby limiting the potential of using knowledge-based methods for data integration, querying or quality control. Here, we propose an alternative representation pattern for expressing knowledge about biological functions, together with a biological and ontological justification, which can be expressed using the description logic EL++ and implemented using the OWL 2 EL profile. To demonstrate the utility of our account of biological functions, we apply it to all proteins contained in the SwissProt database and evaluate its utility with respect to answering complex queries as well with respect to the classification and query times.

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Large-scale reasoning over functions in biomedical ontologies

Abstract

Publication series

Conference

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this