Bioinformatics pp 123-135 | Cite as

Working with Ontologies

Part of the Methods in Molecular Biology book series (MIMB, volume 1525)


Ontologies are powerful and popular tools to encode data in a structured format and manage knowledge. A large variety of existing ontologies offer users access to biomedical knowledge. This chapter contains a short theoretical background of ontologies and introduces two notable examples: The Gene Ontology and the ontology for Biological Pathways Exchange. For both ontologies a short overview and working bioinformatic applications, i.e., Gene Ontology enrichment analyses and pathway data visualization, are provided.

Key words

Data management Knowledge management Ontologies BioPAX rBiopaxParser Gene ontology topGO GOstat 



This work was funded by the German ministry of education and research (BMBF) grants FKZ01ZX1508 and FKZ031L0024A.


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Medical StatisticsUniversity Medical Center GöttingenGöttingenGermany

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