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. 2017 Jan 4;45(D1):D347-D352.
doi: 10.1093/nar/gkw918. Epub 2016 Oct 12.

Ontobee: A Linked Ontology Data Server to Support Ontology Term Dereferencing, Linkage, Query and Integration

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Free PMC article

Ontobee: A Linked Ontology Data Server to Support Ontology Term Dereferencing, Linkage, Query and Integration

Edison Ong et al. Nucleic Acids Res. .
Free PMC article

Abstract

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.

Figures

Figure 1.
Figure 1.
Basic Ontobee system design. An ontology term Internationalized Resource Identifier (IRI) query will be processed by Ontobee system against the Resource Description Frameworks (RDF) triple store, and then Ontobee will return an RDF document dereferencing the term IRI. This RDF document can be directly output for a Semantic web and Linked Data application. If the ontology term IRI query is requested by a web browser, the eXtensible Stylesheet Language Transformation (XSLT) statement in the RDF document will render an HTML page to display the information of the term IRI. See more explanation in the text.
Figure 2.
Figure 2.
(A–D) Ontobee dereferencing of VO term ‘vaccine’ (VO_0000001). Different approaches can be used for dereferencing ontology URIs in Ontobee. Using a web browser, a direct browser query of an (A) ontology URI or an (B and C) Ontobee website query could lead to the HTML visualization page of the (E) ontology URI. (B) The Ontobee query builder allows a keyword-based simple textual search. As the user types, commencing on the third character, (B) a drop-down menu with terms whose label (or synonym) contains the string typed so far will show up. (E) A selection of a specific term in the drop-down menu will then lead to the web page dereferencing the ontology term. Alternatively the ‘Search terms’ tab can be clicked to obtain a page that lists all matches, sorted in order to first show terms that start with the search string, (C) shortest to longest. (E) A selection of a term on this page also leads to page. The HTML web page of the (E) term URI shows different levels of details about the ontology term. (D) If a non-browser web program (like a Linux terminal command call using the ‘curl’ command) is used, or if the source of the web visualization page is checked, the content of the deferenced URI is provided with the (F and G) RDF/OWL format. The contents of (F) in the Linux terminal and (G) in a web browser are the same.

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