Abstract
AbstractTwo of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Page
Highlights
With the explosion of ontologies used to drive work in ecommerce, e-science, and many other application areas, the World Wide Web Consortium (W3C) initiated a standards process that led to the recommendation of OWL (McGuinness and Harmelen, 2004), the Web Ontology Language
If the Open Biomedical Ontologies Format (OBOF) default-namespace is not declared, the ID will be mapped to the base Uniform Resource Identifiers (URIs)’s namespace or, if the ID refers to a relationship definition, it can be explicitly assigned to a particular namespace where this relationship is defined
OBOF provides a uniform mean of encoding relationships holding among a set of entities, terminological and lexical aspects of those entities, and information pertaining to the ontology lifecycle
Summary
With the explosion of ontologies used to drive work in ecommerce, e-science, and many other application areas, the World Wide Web Consortium (W3C) initiated a standards process that led to the recommendation of OWL (McGuinness and Harmelen, 2004), the Web Ontology Language. There is a significant interest in using the life sciences domain as a “focus” for W3C semantic web activity (Ruttenberg et al, 2007) In this light, biological data described using OBOF (Open Biomedical Ontologies Format) ontologies are a prime resource, and there is great interest from the Semantic Web community to access both the ontologies and the data that have been described (annotated) using these ontologies. Our conversion software uses the respective OBO-Edit API and Protégé OWL API to carry out the actual transformation from OBOF to OWL format and vice-versa. This implementation was written in Java 1.5. We have to note the exception that OBOF instances (Instance stanzas) and certain tags (is_anonymous, transitive_over, is_reflexive, is_anti_symmetric, builtin and is_metadata_tag) are not mapped into OWL in this mapping. These constructs will not be fully specified in OBOF until its release
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