Ontological realism, concepts and classification in molecular biology: Development and application of the gene ontology

Journal of Documentation

Volumn 70, Issue 1, 2014, Pages 173-193

  Mayor, Charlie ^a   Robinson, Lyn ^a  

^a CITY UNIVERSITY   (United Kingdom)

Author keywords

Bibliometrics; Classification; Content analysis; Discourse analysis; Molecular biology; Ontologies

Indexed keywords

EID: 84890331663     PISSN: 00220418     EISSN: None     Source Type: Journal    
DOI: 10.1108/JD-06-2013-0076     Document Type: Article

References (29)

1. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S. (2000), "Gene ontology: tool for the unification of biology" in Nature Genetics, Vol. 25, No. 1, pp. 25-29.
2. Bard, J.B.L., Rhee, S.Y. (2004), "Ontologies in biology: design, applications and future challenges" in Nature Reviews Genetics, Vol. 5, No. 3, pp. 213-222.
3. Bawden, D., Robinson, L. (2012), Introduction to Information Science, Facet, London.
4. Bowker, G.C., Star, S.L. (1999), Sorting Things Out: Classification and its Consequences, MIT Press, Cambridge, MA.
5. Budd, J.M. (2006), "Discourse analysis and the study of communication in LIS" in Library Trends, Vol. 55, No. 1, pp. 65-82.
6. Ceusters, W. (2009), "Applying evolutionary terminology auditing to the gene ontology" in Journal of Biomedical Informatics, Vol. 42, No. 3, pp. 518-529.
7. Chiluwa, I. (2009), "The discourse of digital deceptions and '419' emails" in Discourse Studies, Vol. 11, No. 6, pp. 635-660.
8. de Keyser, P. (2012), Indexing: from Thesauri to the Semantic Web, Chandos, Oxford.
9. Fairclough, N. (1989), Language and Power, Longman, London.
10. Fairclough, N. (2001), "Critical discourse analysis as a method in social science research" in Wodak, R. and Meyer, M. (Eds.), Methods of Critical Discourse Analysis, Sage, London, pp. 121-138.
11. Fayard, A.L., de Sanctis, G. (2010), "Enacting language games: the development of a sense of 'we-ness' in online forums" in Information Systems Journal, Vol. 20, No. 4, pp. 383-416.
12. Fowler, R. (1985), "Power" van Dijk, T.A. (Ed.), Handbook of Discourse Analysis, Academic Press, London.
13. Gene Ontology Consortium (2013a), "Gene ontology annotations and resources" in Nucleic Acids Research, Vol. 41, D1, pp. D530-D535, available at: http://nar.oxfordjournals.org/content/41/D1/D530 (accessed 11 March 2013).
14. Gene Ontology Consortium (2013b), "Gene ontology documentation", available at: www.geneontology.org/GO.contents.doc.shtml (accessed 23 July 2013).
15. Haider, J., Bawden, D. (2007), "Conceptions of 'information poverty' in LIS: a discourse analysis" in Journal of Documentation, Vol. 63, No. 4, pp. 534-557.
16. Hughes, A.V., Rafferty, P. (2011), "Inter-indexer consistency in graphic materials indexing at the National Library of Wales" in Journal of Documentation, Vol. 67, No. 1, pp. 9-32.
17. Humphrey, S.M. (1984), "File maintenance of MeSH headings in MEDLINE" in Journal of the American Society for Information Science, Vol. 35, No. 1, pp. 34-44.
18. Knowlton, S.A. (2005), "Three decades since prejudices and antipathies: a study of changes in the Library of Congress Subject Headings" in Cataloging and Classification Quarterly, Vol. 40, No. 2, pp. 123-145.
19. Leonelli, S. (2012), "Classificatory theory in data-intensive science: the case of Open Biomedical Ontologies" in International Studies in the Philosophy of Science, Vol. 26, No. 1, pp. 47-65.
20. Leonelli, S., Diehl, A.D., Christie, K.R., Harris, M.A., Lomax, J. (2011), "How the gene ontology evolves" in BMC Bioinformatics, Vol. 12, p. 325, available at: www.biomedcentral.com/content/pdf/1471-2105-12-325.pdf (accessed 13 March 2013).
21. MacMullen, W.J., Denn, S.O. (2005), "Information problems in molecular biology and bioinformatics" in Journal of the American Society for Information Science and Technology, Vol. 56, No. 5, pp. 447-456.
22. Mayor, C. (2012), "The classification of gene products in the molecular biology domain: realism, objectivity, and the limitations of the gene ontology", PhD thesis, City University London, London, available at: http://openaccess.city.ac.uk.
23. Mayor, C., Robinson, L. (2013), "Ontological realism and classification: structures and concepts in the gene ontology", Journal of the American Society for Information Science and Technology, in press.
24. Nahl, D. (2007), "A discourse analysis technique for charting the flow of micro-information behaviour" in Journal of Documentation, Vol. 63, No. 3, pp. 323-339.
25. Park, J-R. (2007), "Interpersonal and affective communication in synchronous online discourse" in Library Quarterly, Vol. 77, No. 2, pp. 133-155.
26. Soler Monreal, M.C., Gil-Leva, I. (2011), "Evaluation of controlled vocabularies by inter-indexer consistency", Information Research, Vol. 16, No. 4, paper 502, available at: http://InformationR.net/ir/16-4/paper502.html (accessed 16 March 2013).
27. Song, M., Kim, S.Y. (2013), "Detecting the knowledge structure of bioinformatics by mining full-text collections" in Scientometrics, Vol. 96, No. 1, pp. 183-201.
28. White, H., Willis, C., Greenberg, J. (2013), "HIVEing: the effect of a semantic web technology on inter-indexer consistency", Journal of Documentation, Vol. 70, No. 3, in press.
29. Xia, J., Liu, Y. (2013), "Usage patterns of open genomic data" in College and Research Libraries, Vol. 74, No. 2, pp. 195-208.