Working with Ontologies

Frank Kramer; Tim Beißbarth

doi:10.1007/978-1-4939-6622-6_6

Working with Ontologies

Methods Mol Biol. 2017:1525:123-135. doi: 10.1007/978-1-4939-6622-6_6.

Authors

Frank Kramer¹, Tim Beißbarth²

Affiliations

¹ Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073, Göttingen, Germany. frank.kramer@med.uni-goettingen.de.
² Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073, Göttingen, Germany.

PMID: 27896720
DOI: 10.1007/978-1-4939-6622-6_6

Abstract

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.

Keywords: BioPAX; Data management; GOstat; Gene ontology; Knowledge management; Ontologies; rBiopaxParser; topGO.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Gene Ontology
Information Storage and Retrieval
Natural Language Processing