Volume 1525 of the series Methods in Molecular Biology pp 123-135


Working with Ontologies

  • Frank KramerAffiliated withDepartment of Medical Statistics, University Medical Center Göttingen Email author 
  • , Tim BeißbarthAffiliated withDepartment of Medical Statistics, University Medical Center Göttingen

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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