Controlled vocabularies in bioinformatics: A case study in the Gene Ontology

Drug Discovery Today: Biosilico 2 (6):246-252 (2004)

Barry Smith
State University of New York, Buffalo
The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation.
Keywords information integration  biomedical ontology  Gene Ontology (GO)
Categories (categorize this paper)
Edit this record
Mark as duplicate
Export citation
Find it on Scholar
Request removal from index
Revision history

Download options

Our Archive
External links

Setup an account with your affiliations in order to access resources via your University's proxy server
Configure custom proxy (use this if your affiliation does not provide a proxy)
Through your library

References found in this work BETA

SNAP and SPAN: Towards Dynamic Spatial Ontology.Pierre Grenon & Barry Smith - 2004 - Spatial Cognition and Computation 4 (1):69–103.

Add more references

Citations of this work BETA

Oncology Ontology in the NCI Thesaurus.Anand Kumar & Barry Smith - 2005 - Artificial Intelligence in Medicine:213-220.

Add more citations

Similar books and articles

Ontology for the Intelligence Analyst.Barry Smith - 2012 - CrossTalk 14 (Nov/Dec):18-25.
What is a Gene For?Lindell Bromham - 2016 - Biology and Philosophy 31 (1):103-123.
Biometaphysics.Barry Smith - 2009 - In Robin Le Poidevin, Peter Simons, Andrew McGonigal & Ross Cameron (eds.), The Routledge Companion to Metaphysics. Routledge. pp. 537-544.
Ontologies of Cellular Networks. Arp - 2008 - Science Signalling 1 (50):1-3.


Added to PP index

Total views
157 ( #51,576 of 2,285,433 )

Recent downloads (6 months)
59 ( #14,092 of 2,285,433 )

How can I increase my downloads?


My notes

Sign in to use this feature