Biomedical Ontology

A Biomedical Ontology is a biomedical knowledge base that is a domain-specific ontology (for a biomedical domain of biomedical concept records that represent biomedical concepts).

• Context:
  • It can (typically) be associated with a Biological Ontology and a Healthcare Ontology.
  • It can range from being a Lightweight Biomedical Ontology (such as a BiomedKG) to being a Formal Biomedical Ontology.
  • …
• Example(s):
  • a BioMedical Chemical Ontology, such as GO Gene Ontology, or PRO Protein Ontology.
  • a Disease Ontology, such as an infectious disease ontology.
  • a Clinical Research Ontology (for clinical research), such as a CTO clinical trial ontology.
  • …
• Counter-Example(s):
  • a Chemistry Ontology.
  • a Data Mining Ontology.
• See: Biomedical Text Mining.

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References

2008

• (Rubin et al., 2008) ⇒ Daniel L. Rubin, Nigam H. Shah, and Natalya F. Noy. (2008). “Biomedical Ontologies: A Functional Perspective.” Briefings in Bioinformatics, 9(1).

2007

• (Smith et al., 2007) ⇒ Barry Smith, Michael Ashburner, … . (2007). “The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.” In: Nature Biotechnology, 25. doi:10.1038/nbt1346.
  • QUOTE: The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development.

2006

• (Bodenreider, 2006) ⇒ Olivier Bodenreide. (2006). “Lexical, Terminological and Ontological Resources for Biological Text Mining.” In: Sophia Ananiadou, and McNaught J, (editors). Text mining for biology and biomedicine biomedicine. Artech House. ISBN:978-1-58053-984-5

2005

• (Hu, 2005) ⇒ X. Hu. (2005). “Mining Novel Connections from Large Online Digital Library Using Biomedical Ontologies.” In: Library Management Journal, 26 (4/5).

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