Relational patterns in OWL and their application to OBO

Robert Hoehndorf; Anika Oellrich; Michel Dumontier; Janet Kelso; Heinrich Herre; Dietrich Rebholz-Schuhmann

Relational patterns in OWL and their application to OBO

Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Heinrich Herre, Dietrich Rebholz-Schuhmann

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (Non-Journal item)

1 Citation (Scopus)

Abstract

Directed acyclic graphs are commonly used to represent on-tologies in the biomedical domain. They provide an intuitive means toformalize relations that hold between ontological categories. However,their semantics is usually not explicit. We provide a semantics for a partof the OBO Flatfile Format by extending OWL with a method to expressrelational patterns. These patterns are OWL axioms with variables forclasses. The variables can only be filled with named classes. Addition-ally, we provide a semantics for open patterns in OWL. Our method isapplicable to the OBO Flatfile Format, and provides a means to designOWL ontologies using complex ontology design patterns. Therefore, itleads not only to an integration of the OBO Flatfile Format and OWL,but extends OWL with an intuitive interface for designing ontologies us-ing complex definition patterns. A prototypic implementation and testresults are available at http://bioonto.de/obo2owl.

Original language	English
Title of host publication	OWL: Experiences and Directions (OWLED)
Number of pages	10
Publication status	Published - 01 Jun 2010
Event	OWL: Experiences and Directions - San Francisco, United States of America Duration: 21 Jun 2010 → 22 Jun 2010

Workshop

Workshop	OWL: Experiences and Directions
Country/Territory	United States of America
City	San Francisco
Period	21 Jun 2010 → 22 Jun 2010

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@inproceedings{bc1ebec8eaa94274849b9f3f01a2aa12,

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

abstract = "Directed acyclic graphs are commonly used to represent on-tologies in the biomedical domain. They provide an intuitive means toformalize relations that hold between ontological categories. However,their semantics is usually not explicit. We provide a semantics for a partof the OBO Flatfile Format by extending OWL with a method to expressrelational patterns. These patterns are OWL axioms with variables forclasses. The variables can only be filled with named classes. Addition-ally, we provide a semantics for open patterns in OWL. Our method isapplicable to the OBO Flatfile Format, and provides a means to designOWL ontologies using complex ontology design patterns. Therefore, itleads not only to an integration of the OBO Flatfile Format and OWL,but extends OWL with an intuitive interface for designing ontologies us-ing complex definition patterns. A prototypic implementation and testresults are available at http://bioonto.de/obo2owl.",

author = "Robert Hoehndorf and Anika Oellrich and Michel Dumontier and Janet Kelso and Heinrich Herre and Dietrich Rebholz-Schuhmann",

year = "2010",

month = jun,

day = "1",

language = "English",

booktitle = "OWL: Experiences and Directions (OWLED)",

note = "OWL: Experiences and Directions ; Conference date: 21-06-2010 Through 22-06-2010",

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TY - GEN

T1 - Relational patterns in OWL and their application to OBO

AU - Hoehndorf, Robert

AU - Oellrich, Anika

AU - Dumontier, Michel

AU - Kelso, Janet

AU - Herre, Heinrich

AU - Rebholz-Schuhmann, Dietrich

PY - 2010/6/1

Y1 - 2010/6/1

N2 - Directed acyclic graphs are commonly used to represent on-tologies in the biomedical domain. They provide an intuitive means toformalize relations that hold between ontological categories. However,their semantics is usually not explicit. We provide a semantics for a partof the OBO Flatfile Format by extending OWL with a method to expressrelational patterns. These patterns are OWL axioms with variables forclasses. The variables can only be filled with named classes. Addition-ally, we provide a semantics for open patterns in OWL. Our method isapplicable to the OBO Flatfile Format, and provides a means to designOWL ontologies using complex ontology design patterns. Therefore, itleads not only to an integration of the OBO Flatfile Format and OWL,but extends OWL with an intuitive interface for designing ontologies us-ing complex definition patterns. A prototypic implementation and testresults are available at http://bioonto.de/obo2owl.

AB - Directed acyclic graphs are commonly used to represent on-tologies in the biomedical domain. They provide an intuitive means toformalize relations that hold between ontological categories. However,their semantics is usually not explicit. We provide a semantics for a partof the OBO Flatfile Format by extending OWL with a method to expressrelational patterns. These patterns are OWL axioms with variables forclasses. The variables can only be filled with named classes. Addition-ally, we provide a semantics for open patterns in OWL. Our method isapplicable to the OBO Flatfile Format, and provides a means to designOWL ontologies using complex ontology design patterns. Therefore, itleads not only to an integration of the OBO Flatfile Format and OWL,but extends OWL with an intuitive interface for designing ontologies us-ing complex definition patterns. A prototypic implementation and testresults are available at http://bioonto.de/obo2owl.

UR - http://hdl.handle.net/2160/11693

M3 - Conference Proceeding (Non-Journal item)

BT - OWL: Experiences and Directions (OWLED)

T2 - OWL: Experiences and Directions

Y2 - 21 June 2010 through 22 June 2010

ER -

Relational patterns in OWL and their application to OBO

Abstract

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