Enriching the gene ontology via the dissection of labels using the ontology pre-processor language

Jesualdo Tomas Fernandez-Breis; Luigi Iannone; Ignazio Palmisano; Alan L. Rector; Robert Stevens

doi:10.1007/978-3-642-16438-5_5

Enriching the gene ontology via the dissection of labels using the ontology pre-processor language

Jesualdo Tomas Fernandez-Breis, Luigi Iannone, Ignazio Palmisano, Alan L. Rector, Robert Stevens

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

Abstract

In this paper we describe the process of taking an axiomatically lean ontology and enriching it through the automatic application of axioms using ontology design patterns (ODP). Our exemplar is the Gene Ontology's Molecular Function Ontology; this describes an important part of biology and is widely used to describe data. Yet much of the knowledge within the GO's MF is captured within the term's that label the concepts and within the natural language definitions for those concepts. Whilst both of these are absolutely necessary for an ontology, it is also useful to have the knowledge within the textual part of the ontology exposed for computational use. In this work we use an extension to the Ontology PreProcessor Language (OPPL) to dissect terms within the ontology and add axiomatisation, through OPPL's application of ODP, that make the knowledge explicit for computational use. We show the axiomatic enriching of the GO MF; that this can be accomplished both rapidly and consistently; that there is an audit trail for the transformation; and that the queries supported by the ontology are greatly increased in number and complexity. © 2010 Springer-Verlag.

Original language	English
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)\|Lect. Notes Comput. Sci.
Publisher	Springer Nature
Pages	59-73
Number of pages	14
Volume	6317
ISBN (Print)	3642164374, 9783642164378
DOIs	https://doi.org/10.1007/978-3-642-16438-5_5
Publication status	Published - 2010
Event	17th International Conference on Knowledge Engineering and Management by the Masses, EKAW 2010 - Lisbon Duration: 1 Jul 2010 → … http://link.springer.com/chapter/10.1007%2F978-3-642-16438-5_5

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Name	Lecture Notes in Computer Science LNCS

Conference

Conference	17th International Conference on Knowledge Engineering and Management by the Masses, EKAW 2010
City	Lisbon
Period	1/07/10 → …
Internet address	http://link.springer.com/chapter/10.1007%2F978-3-642-16438-5_5

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10.1007/978-3-642-16438-5_5

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Fernandez-Breis, J. T., Iannone, L., Palmisano, I., Rector, A. L., & Stevens, R. (2010). Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci. (Vol. 6317, pp. 59-73). (Lecture Notes in Computer Science LNCS). Springer Nature. https://doi.org/10.1007/978-3-642-16438-5_5

Fernandez-Breis, Jesualdo Tomas ; Iannone, Luigi ; Palmisano, Ignazio et al. / Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. Vol. 6317 Springer Nature, 2010. pp. 59-73 (Lecture Notes in Computer Science LNCS).

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abstract = "In this paper we describe the process of taking an axiomatically lean ontology and enriching it through the automatic application of axioms using ontology design patterns (ODP). Our exemplar is the Gene Ontology's Molecular Function Ontology; this describes an important part of biology and is widely used to describe data. Yet much of the knowledge within the GO's MF is captured within the term's that label the concepts and within the natural language definitions for those concepts. Whilst both of these are absolutely necessary for an ontology, it is also useful to have the knowledge within the textual part of the ontology exposed for computational use. In this work we use an extension to the Ontology PreProcessor Language (OPPL) to dissect terms within the ontology and add axiomatisation, through OPPL's application of ODP, that make the knowledge explicit for computational use. We show the axiomatic enriching of the GO MF; that this can be accomplished both rapidly and consistently; that there is an audit trail for the transformation; and that the queries supported by the ontology are greatly increased in number and complexity. {\textcopyright} 2010 Springer-Verlag.",

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Fernandez-Breis, JT, Iannone, L, Palmisano, I, Rector, AL & Stevens, R 2010, Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. vol. 6317, Lecture Notes in Computer Science LNCS, Springer Nature, pp. 59-73, 17th International Conference on Knowledge Engineering and Management by the Masses, EKAW 2010, Lisbon, 1/07/10. https://doi.org/10.1007/978-3-642-16438-5_5

Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. / Fernandez-Breis, Jesualdo Tomas; Iannone, Luigi; Palmisano, Ignazio et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. Vol. 6317 Springer Nature, 2010. p. 59-73 (Lecture Notes in Computer Science LNCS).

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

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Fernandez-Breis JT, Iannone L, Palmisano I, Rector AL, Stevens R. Enriching the gene ontology via the dissection of labels using the ontology pre-processor language. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. Vol. 6317. Springer Nature. 2010. p. 59-73. (Lecture Notes in Computer Science LNCS). doi: 10.1007/978-3-642-16438-5_5

Enriching the gene ontology via the dissection of labels using the ontology pre-processor language

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