title: Working with Ontologies.
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.
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073, Göttingen, Germany. frank.kramer@med.uni-goettingen.de.
authors.forename: Frank
authors.initials: F
authors.lastname: Kramer
authors.affiliation: Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073, Göttingen, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: Beißbarth
mesh_terms: D019295:Computational Biology / Q000379:methods*; D063990:Gene Ontology; D016247:Information Storage and Retrieval; D009323:Natural Language Processing
keywords: BioPAX; Data management; GOstat; Gene ontology; Knowledge management; Ontologies; rBiopaxParser; topGO