ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Journal article, Peer reviewed
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Date
2010Metadata
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- Institutt for biologi [2596]
- Publikasjoner fra CRIStin - NTNU [38294]
Abstract
Background: The biosciences increasingly face the challenge of integrating a wide variety of available data,
information and knowledge in order to gain an understanding of biological systems. Data integration is supported
by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant
hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes
misconnected. The need to address this terminology problem has spawned the building of a large number of bioontologies.
OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in
the Life Sciences, opening the potential to use the Semantic Web to support data integration and further
exploitation of integrated resources via automated retrieval and reasoning procedures.
Methods: We extended the Perl suite ONTO-PERL and functionally integrated it into the Galaxy platform. The
resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface,
and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology
terms that match specific search criteria.
Results: ONTO-ToolKit is available as a tool suite for Galaxy. Galaxy not only provides a user friendly interface
allowing the interested biologist to manipulate OBO ontologies, it also opens up the possibility to perform further
biological (and ontological) analyses by using other tools available within the Galaxy environment. Moreover, it
provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL.
Conclusions: ONTO-ToolKit reaches out to researchers in the biosciences, by providing a user-friendly way to
analyse and manipulate ontologies. This type of functionality will become increasingly important given the wealth
of information that is becoming available based on ontologies.