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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

Mappings between OBO Ids and URIs A mapping between the existing OBO Ids, newly recommended Foundry-compliant URIs, and the URIs produced by the standard mapping, mentioned as OBO legacy URI. This figure has been taken from the draft of the recommendation, and refers to the mappings of Ids described in the recommendation document.
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Figure 2: Mappings between OBO Ids and URIs A mapping between the existing OBO Ids, newly recommended Foundry-compliant URIs, and the URIs produced by the standard mapping, mentioned as OBO legacy URI. This figure has been taken from the draft of the recommendation, and refers to the mappings of Ids described in the recommendation document.

Mentions: ● The new version of OBO will accompany a recommendation [36] for globally unique identifiers for OBO that will have a one to one mapping with OBO Foundry compliant URIs, hence making the ID mapping obvious. The design goals behind this recommendation are to make sure that the URIs resolve to useful information about an OBO term, and that it is possible to maintain those URIs over time so they keep pointing to useful information. The recommendation document provides an example of how existing OBO IDs, new URIs, and existing transformed URI from the standard mapping may be related in the future (see Figure 2).


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)

Mappings between OBO Ids and URIs A mapping between the existing OBO Ids, newly recommended Foundry-compliant URIs, and the URIs produced by the standard mapping, mentioned as OBO legacy URI. This figure has been taken from the draft of the recommendation, and refers to the mappings of Ids described in the recommendation document.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Mappings between OBO Ids and URIs A mapping between the existing OBO Ids, newly recommended Foundry-compliant URIs, and the URIs produced by the standard mapping, mentioned as OBO legacy URI. This figure has been taken from the draft of the recommendation, and refers to the mappings of Ids described in the recommendation document.
Mentions: ● The new version of OBO will accompany a recommendation [36] for globally unique identifiers for OBO that will have a one to one mapping with OBO Foundry compliant URIs, hence making the ID mapping obvious. The design goals behind this recommendation are to make sure that the URIs resolve to useful information about an OBO term, and that it is possible to maintain those URIs over time so they keep pointing to useful information. The recommendation document provides an example of how existing OBO IDs, new URIs, and existing transformed URI from the standard mapping may be related in the future (see Figure 2).

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