<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology.
GO is a controlled vocabulary that is intended to facilitate communication between
biologists by standardizing usage of terms in database annotations. Making such
controlled vocabularies maximally useful in support of bioinformatics applications
requires explicating in machine-processible form the implicit background information
that enables human users to interpret the meaning of the vocabulary terms.
In the case of GO, this process would involve rendering the meanings of GO into
a formal (logical) language with the help of domain experts, and adding additional
information required to support the chosen formalization. A controlled vocabulary
augmented in these ways is commonly called an <italic>ontology</italic>. In this paper, we make a
modest exploration to determine the ontological requirements for this extended version
of GO. Using the terms within the three GO hierarchies (molecular function,
biological process and cellular component), we investigate the facility with which
GO concepts can be ontologized, using available tools from the philosophical and
ontological engineering literature.</p>
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Comp Funct Genomics. 2003 Feb; 4(1):90-93