Relational patterns in OWL and their application to OBO

Robert Hoehndorf; Anika Oellrich; M. Dumontier; Janet Kelso; Heinrich Herre; D. Rebholz Schuhmann

Relational patterns in OWL and their application to OBO

Robert Hoehndorf, Anika Oellrich, M. Dumontier, Janet Kelso, Heinrich Herre, D. Rebholz Schuhmann

Research output: Contribution to journal › Conference article in journal › Academic › peer-review

Abstract

Directed acyclic graphs are commonly used to represent ontologies in the biomedical domain. They provide an intuitive means to formalize relations that hold between ontological categories. However, their semantics is usually not explicit. We provide a semantics for a part of the OBO Flatfile Format by extending OWL with a method to express relational patterns. These patterns are OWL axioms with variables for classes. The variables can only be filled with named classes. Addition- Ally, we provide a semantics for open patterns in OWL. Our method is applicable to the OBO Flatfile Format, and provides a means to design OWL ontologies using complex ontology design patterns. Therefore, it leads not only to an integration of the OBO Flatfile Format and OWL, but extends OWL with an intuitive interface for designing ontologies using complex definition patterns. A prototypic implementation and test results are available at http://bioonto.de/obo2owl.

Original language	English
Article number	1
Number of pages	10
Journal	CEUR Workshop Proceedings
Volume	614
Publication status	Published - 2010
Externally published	Yes

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title = "Relational patterns in OWL and their application to OBO",

abstract = "Directed acyclic graphs are commonly used to represent ontologies in the biomedical domain. They provide an intuitive means to formalize relations that hold between ontological categories. However, their semantics is usually not explicit. We provide a semantics for a part of the OBO Flatfile Format by extending OWL with a method to express relational patterns. These patterns are OWL axioms with variables for classes. The variables can only be filled with named classes. Addition- Ally, we provide a semantics for open patterns in OWL. Our method is applicable to the OBO Flatfile Format, and provides a means to design OWL ontologies using complex ontology design patterns. Therefore, it leads not only to an integration of the OBO Flatfile Format and OWL, but extends OWL with an intuitive interface for designing ontologies using complex definition patterns. A prototypic implementation and test results are available at http://bioonto.de/obo2owl.",

author = "Robert Hoehndorf and Anika Oellrich and M. Dumontier and Janet Kelso and Heinrich Herre and {Rebholz Schuhmann}, D.",

year = "2010",

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journal = "CEUR Workshop Proceedings",

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T1 - Relational patterns in OWL and their application to OBO

AU - Hoehndorf, Robert

AU - Oellrich, Anika

AU - Dumontier, M.

AU - Kelso, Janet

AU - Herre, Heinrich

AU - Rebholz Schuhmann, D.

PY - 2010

Y1 - 2010

N2 - Directed acyclic graphs are commonly used to represent ontologies in the biomedical domain. They provide an intuitive means to formalize relations that hold between ontological categories. However, their semantics is usually not explicit. We provide a semantics for a part of the OBO Flatfile Format by extending OWL with a method to express relational patterns. These patterns are OWL axioms with variables for classes. The variables can only be filled with named classes. Addition- Ally, we provide a semantics for open patterns in OWL. Our method is applicable to the OBO Flatfile Format, and provides a means to design OWL ontologies using complex ontology design patterns. Therefore, it leads not only to an integration of the OBO Flatfile Format and OWL, but extends OWL with an intuitive interface for designing ontologies using complex definition patterns. A prototypic implementation and test results are available at http://bioonto.de/obo2owl.

AB - Directed acyclic graphs are commonly used to represent ontologies in the biomedical domain. They provide an intuitive means to formalize relations that hold between ontological categories. However, their semantics is usually not explicit. We provide a semantics for a part of the OBO Flatfile Format by extending OWL with a method to express relational patterns. These patterns are OWL axioms with variables for classes. The variables can only be filled with named classes. Addition- Ally, we provide a semantics for open patterns in OWL. Our method is applicable to the OBO Flatfile Format, and provides a means to design OWL ontologies using complex ontology design patterns. Therefore, it leads not only to an integration of the OBO Flatfile Format and OWL, but extends OWL with an intuitive interface for designing ontologies using complex definition patterns. A prototypic implementation and test results are available at http://bioonto.de/obo2owl.

M3 - Conference article in journal

SN - 1613-0073

VL - 614

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

M1 - 1

ER -

Relational patterns in OWL and their application to OBO

Abstract

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