@inproceedings{863e4e89c9f34be58f61dc5b80170b42,
title = "Large-scale reasoning over functions in biomedical ontologies",
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.",
keywords = "Big ontologies, Biological function, Protein, Tractable reasoning",
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",
year = "2016",
doi = "10.3233/978-1-61499-660-6-299",
language = "English (US)",
series = "Frontiers in Artificial Intelligence and Applications",
publisher = "IOS Press BV",
pages = "299--312",
editor = "Roberta Ferrario and Werner Kuhn",
booktitle = "Formal Ontology in Information Systems - Proceedings of the 9th International Conference, FOIS 2016",
}