Xiang et al. BMC Research Notes 2010, 3:175 http://www.biomedcentral.com/1756-0500/3/175 Open Access TECHNICAL NOTE © 2010 He et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attri- bution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Technical Note OntoFox: web-based support for ontology reuse Zuoshuang Xiang 1,2,3 , Mélanie Courtot 4 , Ryan R Brinkman 4,5 , Alan Ruttenberg 6 and Yongqun He* 1,2,3 Abstract Background: Ontology 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. Findings: OntoFox 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. Conclusions: OntoFox 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. Background Biomedical ontologies are sets of terms and relations that represent entities in the scientific world and how they relate to each other. Terms are associated with documen- tation and definitions, which are, ideally, expressed in for- mal logic in order to support automated reasoning [1-3]. Ontologies have dramatically changed how biomedical research is conducted. For example, 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 applica- tions, 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 ontol- ogies and 700,000 entities in the NCBO BioPortal http:// bioportal.bioontology.org/ . With new resources continu- ously being developed, maximizing ontology sharing and interoperability has become a growing concern [7,8]. The development of a new biomedical ontology cover- ing a specific domain is often an ambitious, time-con- suming project, usually requiring extensive cross- community collaboration. The OBO Foundry is an open community that has established a set of principles for ontology development with the goal of creating a suite of interoperable reference ontologies in the biomedical domain [3]. These principles require that member ontol- ogies be open, orthogonal, expressed in a common shared syntax, and designed to possess a common space of iden- tifiers. One way of meeting the goal of interoperability is to reuse existing resources by importing them into the to- be-created ontology. For example, the Vaccine Ontology (VO, http://www.violinet.org/vaccineontology ) [9] relies on many terms (e.g., administering substance in vivo) already described by other biomedical ontologies, such as the Ontology for Biomedical Investigations (OBI; http:// purl.obolibrary.org/obo/obi ). * Correspondence: yongqunh@umich.edu 1 Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA Full list of author information is available at the end of the article