Abstract
Ontologies are intended to capture and formalize a domain of knowledge. The ontologies comprising the Open Biological Ontologies (OBO) project, which includes the Gene Ontology (GO), are formalizations of various domains of biological knowledge. Ontologies within OBO typically lack computable definitions that serve to differentiate a term from other similar terms. The computer is unable to determine the meaning of a term, which presents problems for tools such as automated reasoners. Reasoners can be of enormous benefit in managing a complex ontology. OBO term names frequently implicitly encode the kind of definitions that can be used by computational tools, such as automated reasoners. The definitions encoded in the names are not easily amenable to computation, because the names are ostensibly natural language phrases designed for human users. These names are highly regular in their grammar, and can thus be treated as valid sentences in some formal or computable language.With a description of the rules underlying this formal language, term names can be parsed to derive computable definitions, which can then be reasoned over. This paper describes the effort to elucidate that language, called Obol, and the attempts to reason over the resulting definitions. The current implementation finds unique non-trivial definitions for around half of the terms in the GO, and has been used to find 223 missing relationships, which have since been added to the ontology. Obol has utility as an ontology maintenance tool, and as a means of generating computable definitions for a whole ontology.
The software is available under an open-source license from: http://www.fruitfly. org/~cjm/obol. Supplementary material for this article can be found at: http://www. interscience.wiley.com/jpages/1531-6912/suppmat.
Full Text
The Full Text of this article is available as a PDF (208.5 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Drysdale R. Phenotypic data in FlyBase. Brief Bioinform. 2001 Mar;2(1):68–80. doi: 10.1093/bib/2.1.68. [DOI] [PubMed] [Google Scholar]
- Gkoutos G. V., Green E. C. J., Mallon A. M., Hancock J. M., Davidson D. Building mouse phenotype ontologies. Pac Symp Biocomput. 2004:178–189. doi: 10.1142/9789812704856_0018. [DOI] [PubMed] [Google Scholar]
- Harris M. A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(DATABASE):D258–D261. doi: 10.1093/nar/gkh036. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hill David P., Blake Judith A., Richardson Joel E., Ringwald Martin. Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res. 2002 Dec;12(12):1982–1991. doi: 10.1101/gr.580102. [DOI] [PMC free article] [PubMed] [Google Scholar]
- July Laura V., Beraldi Eliana, So Alan, Fazli Ladan, Evans Kenneth, English John C., Gleave Martin E. Nucleotide-based therapies targeting clusterin chemosensitize human lung adenocarcinoma cells both in vitro and in vivo. Mol Cancer Ther. 2004 Mar;3(3):223–232. [PubMed] [Google Scholar]
- Lord P. W., Stevens R. D., Brass A., Goble C. A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003 Jul 1;19(10):1275–1283. doi: 10.1093/bioinformatics/btg153. [DOI] [PubMed] [Google Scholar]
- Ogren P. V., Cohen K. B., Acquaah-Mensah G. K., Eberlein J., Hunter L. The compositional structure of Gene Ontology terms. Pac Symp Biocomput. 2004:214–225. doi: 10.1142/9789812704856_0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smith Barry, Williams Jennifer, Schulze-Kremer Steffen. The ontology of the gene ontology. AMIA Annu Symp Proc. 2003:609–613. [PMC free article] [PubMed] [Google Scholar]
- Wroe C. J., Stevens R., Goble C. A., Ashburner M. A methodology to migrate the gene ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput. 2003:624–635. doi: 10.1142/9789812776303_0058. [DOI] [PubMed] [Google Scholar]
- Yeh Iwei, Karp Peter D., Noy Natalya F., Altman Russ B. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics. 2003 Jan 22;19(2):241–248. doi: 10.1093/bioinformatics/19.2.241. [DOI] [PubMed] [Google Scholar]