IDEAS home Printed from https://ideas.repec.org/h/spr/ihichp/978-3-540-92673-3_20.html
   My bibliography  Save this book chapter

Ontologies for Formal Representation of Biological Systems

In: Handbook on Ontologies

Author

Listed:
  • Nigam Shah

    (Stanford Medical Informatics)

  • Mark Musen

    (Stanford Medical Informatics)

Abstract

Summary This chapter provides an overview of how the use of ontologies may enhance biomedical research by providing a basis for a formalized, and shareable descriptions, of models of biological systems. A wide variety of artifacts are labeled as “ontologies” in the Biomedical domain, leading to much debate and confusion. The most widely used ontological artifact are controlled vocabularies (CVs). A CV provides a list of terms whose meanings are specifically defined. Terms from a CV are usually used for indexing records in a database. The Gene Ontology (GO) is the most widely used CV in databases serving biomedical researchers. The GO provides term for declaring the molecular function (MF), biological process (BP) and cellular component (CC) of gene products. The statements comprising these MF, BP and CC declaration are called annotations [51], which are predominantly used to interpret results from high throughput gene expression experiments [27, 53]. Arguably, CVs provide the most value for effort in terms of facilitating database search and interoperability.

Suggested Citation

  • Nigam Shah & Mark Musen, 2009. "Ontologies for Formal Representation of Biological Systems," International Handbooks on Information Systems, in: Steffen Staab & Rudi Studer (ed.), Handbook on Ontologies, pages 445-461, Springer.
    • Handle: RePEc:spr:ihichp:978-3-540-92673-3_20
    DOI: 10.1007/978-3-540-92673-3_20
    as

    Download full text from publisher

    To our knowledge, this item is not available for download. To find whether it is available, there are three options:
    1. Check below whether another version of this item is available online.
    2. Check on the provider's web page whether it is in fact available.
    3. Perform a search for a similarly titled item that would be available.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:ihichp:978-3-540-92673-3_20. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.