Applying ontology design patterns in bio-ontologies

Mikel Egaña; Alan Rector; Robert Stevens; Erick Antezana

doi:10.1007/978-3-540-87696-0-4

Applying ontology design patterns in bio-ontologies

Mikel Egaña, Alan Rector, Robert Stevens, Erick Antezana

Research output: Chapter in Book/Conference proceeding › Conference contribution

Abstract

Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent "modifiers" of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it. © 2008 Springer-Verlag Berlin Heidelberg.

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	7-16
Number of pages	9
Volume	5268
ISBN (Print)	3540876952, 9783540876953
DOIs	https://doi.org/10.1007/978-3-540-87696-0-4
Publication status	Published - 2008
Event	16th International Conference on Knowledge Engineering and Knowledge Management, EKAW 2008 - Acitrezza Duration: 1 Jul 2008 → …

Conference

Conference	16th International Conference on Knowledge Engineering and Knowledge Management, EKAW 2008
City	Acitrezza
Period	1/07/08 → …

Keywords

Computer Science, Artificial Intelligence

Access to Document

10.1007/978-3-540-87696-0-4

Cite this

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title = "Applying ontology design patterns in bio-ontologies",

abstract = "Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent {"}modifiers{"} of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it. {\textcopyright} 2008 Springer-Verlag Berlin Heidelberg.",

keywords = "Computer Science, Artificial Intelligence",

author = "Mikel Ega{\~n}a and Alan Rector and Robert Stevens and Erick Antezana",

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language = "English",

isbn = "3540876952",

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Egaña, M, Rector, A, Stevens, R & Antezana, E 2008, Applying ontology design patterns in bio-ontologies. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. vol. 5268, Springer Nature, pp. 7-16, 16th International Conference on Knowledge Engineering and Knowledge Management, EKAW 2008, Acitrezza, 1/07/08. https://doi.org/10.1007/978-3-540-87696-0-4

Applying ontology design patterns in bio-ontologies. / Egaña, Mikel; Rector, Alan; Stevens, Robert et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. Vol. 5268 Springer Nature, 2008. p. 7-16.

Research output: Chapter in Book/Conference proceeding › Conference contribution

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T1 - Applying ontology design patterns in bio-ontologies

AU - Egaña, Mikel

AU - Rector, Alan

AU - Stevens, Robert

AU - Antezana, Erick

N1 - Consiglio Nazl Rice, Inria Reinvent Technol NeOn Bony Yahoo Res Egana, Mikel Rector, Alan Stevens, Robert Antezana, Erick 13 BERLIN BIL15

PY - 2008

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N2 - Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent "modifiers" of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it. © 2008 Springer-Verlag Berlin Heidelberg.

AB - Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent "modifiers" of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it. © 2008 Springer-Verlag Berlin Heidelberg.

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M3 - Conference contribution

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SN - 9783540876953

VL - 5268

SP - 7

EP - 16

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.

PB - Springer Nature

T2 - 16th International Conference on Knowledge Engineering and Knowledge Management, EKAW 2008

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ER -

Applying ontology design patterns in bio-ontologies

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