Abstract
BackgroundOntology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.FindingsOntoFox http://ontofox.hegroup.org/ is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.ConclusionsOntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.
Highlights
Ontology development is a rapidly growing area of research, especially in the life sciences domain
Ontology developers may want the flexibility of including no superclasses, only one direct superclass, all superclasses to the top class, or a subset of all superclasses for a term, in order to provide additional relevant domain terms for their users. To address these needs for ontology reuse, we have developed OntoFox http://ontofox.hegroup.org/, a webbased application implementing the MIREOT and related ontology term extraction strategies
MIREOT implementation The MIREOT guideline suggests the following minimal set: (1) source term URI, (2) target direct superclass URI, and (3) source ontology URI [14]. These are the first parameters taken as input by OntoFox: 1) Source ontology URI Box 1 of the OntoFox web input system includes a list of the 15 ontologies a user can select as source ontology (Figure 2 and [Additional file 1)
Summary
Ontology development is a rapidly growing area of research, especially in the life sciences domain. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Biomedical ontologies are sets of terms and relations that represent entities in the scientific world and how they relate to each other. Ontologies have dramatically changed how biomedical research is conducted. Since the Gene Ontology (GO) was first published in 2000 [1], it has been used and cited in more than 2000 peer-reviewed journal articles [4]. Ontologies have been used in various applications, such as gene expression data analysis [1], literature mining [5], and as the underpinning of a semantic web [6]. There are currently more than 150 biomedical ontologies and 700,000 entities in the NCBO BioPortal http:// bioportal.bioontology.org/.
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