Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

doi:10.1093/nar/gkw918

Title: Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Journal Article · Wed Oct 12 00:00:00 EDT 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw918· OSTI ID:1625557

Ong, Edison ^[1]; Xiang, Zuoshuang ^[1]; Zhao, Bin ^[1]; Liu, Yue ^[1]; Lin, Yu ^[1]; Zheng, Jie ^[2]; Mungall, Chris ^[3]; Courtot, Mélanie ^[4]; Ruttenberg, Alan ^[5]; He, Yongqun ^[1]

Univ. of Michigan Medical School, Ann Arbor, MI (United States)
Univ. of Pennsylvania Perelman School of Medicine, Philadelphia, PA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
European Bioinformatics Inst., Cambridge (United Kingdom). European Molecular Biology Lab. (EMBL)
Univ. at Buffalo, NY (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231; (NIAID) [R01AI081062]

OSTI ID:: 1625557

Journal Information:: Nucleic Acids Research, Vol. 45, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 56 works

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