Abstract
The Gene Ontology (GO) is a controlled vocabulary used for annotation of genes. Assigning such terms to uncategorized genes is time-consuming work, and a recurring task in biomedicine. The biomedical citations of the literature database MEDLINE are indexed with terms from the Medical Subject Headings (MeSH). We studied whether MeSH terms from gene-related MEDLINE entries could be translated to GO, and be used automatically for annotation purposes. We explored three MeSH to GO alignments: pairing similar MeSH and GO term synonyms, indirect linking through MeSH’s associations with Enzyme Commission (EC) terms and the official EC2GO translation table, and using association analysis to indicate which MeSH and GO terms that co-occurred most frequently for existing annotations. We here show that an alignment can be found, and, despite inconsistency in the use of MeSH terms as MEDLINE indexes, we conclude that GO annotation prediction using this alignment is useful in manual annotation of genes.
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Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al.: Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000)
Lægreid, A., Hvidsten, T.R., Midelfart, H., Komorowski, J., Sandvik, A.: Predicting gene ontology biological process from temporal gene expression patterns. Genome Res. 13(5), 965–979 (2003)
Hvidsten, T.R., Lægreid, A., Komorowski, J.: Learning rule-based models from gene expression time profiles annotated using Gene Ontology. Bioinformatics 19, 1116–1123 (2003)
Raychaudhuri, S., Chang, J.T., Sutphin, P.D., Altman, R.: Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 12, 203–214 (2002)
National Library of Medicine. Medical Subject Headings, http://www.nlm.nih.gov/mesh/meshhome.html
Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. Enzyme Nomenclature, http://www.chem.qmul.ac.uk/iubmb/enzyme/
Agrawal, R., Imielinski, T., Swami, A.: Mining association rules between sets of items in large databases. In: Proceedings of the ACM SIGMOD Conference on Management of Data, pp. 207–216 (1993)
Funk, M.E., Reid, C.: Indexing Consistency in MEDLINE. Bulletin of the Medical Library Association 71(2), 176–183 (1983)
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© 2004 Springer-Verlag Berlin Heidelberg
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Tveit, H., Mollestad, T., Lægreid, A. (2004). The Alignment of the Medical Subject Headings to the Gene Ontology and Its Application in Gene Annotation. In: Tsumoto, S., Słowiński, R., Komorowski, J., Grzymała-Busse, J.W. (eds) Rough Sets and Current Trends in Computing. RSCTC 2004. Lecture Notes in Computer Science(), vol 3066. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-25929-9_102
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DOI: https://doi.org/10.1007/978-3-540-25929-9_102
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