Ontobee


NAR Molecular Biology Database Collection entry number 1938
Edison Ong1, Zuoshuang Xiang1, Bin Zhao1, Yue Liu1, Yu Lin1, Jie Zheng2, Chris Mungall3, Mélanie Courtot5, Alan Ruttenberg5, Yongqun He1
1. University of Michigan Medical School, Ann Arbor, MI 48109, USA
2. University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
3. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4. EMBL-European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
5. University at Buffalo, Buffalo, NY 14203, USA

Database Description

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 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

Acknowledgements

We thank James A. Overton, Bjoern Peters, Melissa Haendel, Jonathan Rees, Maryanne Martone, Philippe Rocca-Serra, Helen Parkinson, Barry Smith, Robert Hoehndorf and many others, for their valuable comments, suggestions and encouragements. The authors appreciate the strong support from the OBI developers, the OBO Foundry and all Ontobee users.

References

1. Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query, and integration. Nucleic Acid Research. 2017 Jan 4;45(D1):D347-D352. PMID: 27733503. PMCID: PMC5210626.


Go to the abstract in the NAR 2017 Database Issue.
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