Limits...
Mapping between the OBO and OWL ontology languages.

Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP - J Biomed Semantics (2011)

Bottom Line: Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness.Our Java implementation of the mapping is part of the official Gene Ontology project source.In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA. hamid@cs.utexas.edu.

ABSTRACT

Background: Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL.

Results: We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source.

Conclusions: Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

No MeSH data available.


Related in: MedlinePlus

Layer cakes for OBO and the Semantic Web A layer cake for OBO, with some examples and a comparison with the Semantic Web layers; the mapping between the two layer cakes is generally quite straightforward, which makes it easy to understand the constructs in OBO and their mappings in OWL.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3105495&req=5

Figure 1: Layer cakes for OBO and the Semantic Web A layer cake for OBO, with some examples and a comparison with the Semantic Web layers; the mapping between the two layer cakes is generally quite straightforward, which makes it easy to understand the constructs in OBO and their mappings in OWL.

Mentions: The Semantic Web is an evolving extension of the World Wide Web based on ontologies. Intended to facilitate search and information integration, and built on the foundations of artificial intelligence, the Semantic Web envisions the Web becoming a global knowledgebase through distributed development of ontologies using formally defined semantics, global identifiers and expressive languages for defining rules and queries on ontologies. The Semantic Web has been organized in the form of a layer cake where each layer provides a representation language of increasing expressive power (see Figure 1). The Web Ontology Language (OWL) [7], a component of the Semantic Web, provides the capability of expressing ontologies in multiple dialects. OWL-DL, a Description Logics based dialect, has become its language of choice due to the availability of reasoning tools. In the biomedical domain, some important ontologies such as NCI Thesaurus [8] and BioPAX [9] have been modelled in OWL.


Mapping between the OBO and OWL ontology languages.

Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP - J Biomed Semantics (2011)

Layer cakes for OBO and the Semantic Web A layer cake for OBO, with some examples and a comparison with the Semantic Web layers; the mapping between the two layer cakes is generally quite straightforward, which makes it easy to understand the constructs in OBO and their mappings in OWL.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105495&req=5

Figure 1: Layer cakes for OBO and the Semantic Web A layer cake for OBO, with some examples and a comparison with the Semantic Web layers; the mapping between the two layer cakes is generally quite straightforward, which makes it easy to understand the constructs in OBO and their mappings in OWL.
Mentions: The Semantic Web is an evolving extension of the World Wide Web based on ontologies. Intended to facilitate search and information integration, and built on the foundations of artificial intelligence, the Semantic Web envisions the Web becoming a global knowledgebase through distributed development of ontologies using formally defined semantics, global identifiers and expressive languages for defining rules and queries on ontologies. The Semantic Web has been organized in the form of a layer cake where each layer provides a representation language of increasing expressive power (see Figure 1). The Web Ontology Language (OWL) [7], a component of the Semantic Web, provides the capability of expressing ontologies in multiple dialects. OWL-DL, a Description Logics based dialect, has become its language of choice due to the availability of reasoning tools. In the biomedical domain, some important ontologies such as NCI Thesaurus [8] and BioPAX [9] have been modelled in OWL.

Bottom Line: Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness.Our Java implementation of the mapping is part of the official Gene Ontology project source.In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA. hamid@cs.utexas.edu.

ABSTRACT

Background: Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL.

Results: We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source.

Conclusions: Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

No MeSH data available.


Related in: MedlinePlus