BIOTOP: An upper domain ontology for the life sciences: A description of its current structure, contents and interfaces to OBO ontologies

Applied Ontology

Volumn 3, Issue 4, 2008, Pages 205-212

  Beisswanger, Elena ^a   Schulz, Stefan ^b   Stenzhorn, Holger ^b,c   Hahn, Udo ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

^c Institute for Formal Ontology and Medical Information Science   (Germany)

Author keywords

Annotation vocabulary; Bio ontology; Biomedical terminologies; Ontology integration; Upper domain ontology

Indexed keywords

EID: 85013619452     PISSN: 15705838     EISSN: 18758533     Source Type: Journal    
DOI: 10.3233/AO-2008-0057     Document Type: Article

References (28)

1. 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., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S.E., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M. & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25(1), 25-29.
2. Bada M., Turi, D., McEntire, R. & Stevens, R. (2004). Using reasoning to guide annotation with Gene Ontology terms in GOAT. ACM SIGMOD Record, Special Issue: Data Engineering for Life Sciences, 33(2), 27-32.
3. Bada, M. & Hunter, L. (2007). Enrichment of OBO ontologies. Journal of Biomedical Informatics, 40(3), 300-315.
4. Bard, J., Rhee, S.Y. & Ashburner, M. (2005). An ontology for cell types. Genome Biology, 6(2), R21.
5. Bodenreider, O. & Stevens, R. (2006). Bio-ontologies: Current trends and future directions. Briefings in Bioinformatics, 7(3), 256-274.
6. Burgun, A. & Bodenreider, O. (2005). An ontology of chemical entities helps identify dependence relations among Gene Ontology terms. In U. Hahn& A. Valencia (eds), SMBM 2005 - Proceedings of the 1st International Symposium on Semantic Mining in Biomedicine, Hinxton, England, UK, April 10-13, 2005 (pp. 6-12).
7. Cohen, A.M. & Hersh, W.R. (2005). A survey of current work in biomedical text mining. Briefings in Bioinformatics, 6(1), 57-71.
8. Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. & Ashburner, M. (2008). CHEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research, 36, 344-350 (Database-Issue).
9. Grenon, P., Smith, B. & Goldberg, L. (2003). Biodynamic ontology: Applying BFO in the biomedical domain. In D.M. Pisanelli (ed.), Ontologies in Medicine - Proceedings of the Workshop on Medical Ontologies, Rome, Italy, October 2003. Studies in Health Technology and Informatics (Vol. 102, pp. 20-38). Amsterdam: IOS Press.
10. Hahn, U., Romacker, M. & Schulz, S. (1999). Discourse structures in medical reports - watch out! The generation of referentially coherent and valid text knowledge bases in the MEDSYNDIKATE system. International Journal of Medical Informatics, 53(1), 1-28.
11. Herre, H., Heller, B., Burek, P., Hoehndorf, R., Loebe, F. & Michalek, H. (2006). General Formal Ontology (GFO): A foundational ontology integrating objects and processes. Part I: Basic principles. Technical report, Research Group Ontologies in Medicine (Onto-Med), University of Leipzig.
12. Horrocks, I.R., Patel-Schneider, P.F. & van Harmelen, F. (2003). From SHIQ and RDF to OWL: The making of a Web ontology language. Journal of Web Semantics, 1(1), 7-26.
13. Jensen, L.J., Saric, J. & Bork, P. (2006). Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics, 7(2), 119-129.
14. Kawazoe, A., Jin, L., Shigematsu, M., Barerro, R., Taniguchi, K. & Collier, N. (2006). The development of a schema for the annotation of terms in the BioCaster disease detecting/tracking system. In O. Bodenreider (ed.), Proceedings of the KR-MED 2006 Workshop, Baltimore, MD, USA, November 8, 2006. CEUR Workshop Proceedings (Vol. 222, pp. 77-85).
15. MacGregor, R. (1991). The evolving technology of classification-based knowledge representation systems. In J.F. Sowa (ed.), Principles of Semantic Networks. Explorations in the Representation of Knowledge (pp. 385-400). San Mateo, CA: Morgan Kaufmann.
16. Mungall, C.J. (2004). Obol: integrating language and meaning in bio-ontologies. Comparative and Functional Genomics, 5, 509-520.
17. Myhre, S., Tveit, H., Mollestad, T. & Laegreid, A. (2006). Additional Gene Ontology structure for improved biological reasoning. Bioinformatics, 22(16), 2020-2027.
18. Ogren, P.V., Cohen, K.B., Acquaah-Mensah, G.K., Eberlein, J. & Hunter, L. (2004). The compositional structure of Gene Ontology terms. In R.B. Altman, A.K. Dunker, L. Hunter, T.A. Jung & T.E. Klein (eds), PSB 2004 - Proceedings of the Pacific Symposium on Biocomputing 2004, Hawaii, USA, January 6-10, 2004 (pp. 214-225). Singapore: World Scientific Publishing.
19. Ohta, T., Tateisi, Y. & Kim, J.-D. (2002). The GENIA corpus: an annotated research abstract corpus in molecular biology domain. In M.P. Marcus (ed.), HLT 2002 - Human Language Technology Conference. Proceedings of the 2nd International Conference on Human Language Technology Research, San Diego, CA, USA, March 24-27, 2002 (pp. 82-86). San Francisco, CA: Morgan Kaufmann.
20. Poprat, M. & Hahn, U. (2007). An investigation into the reusability of biomedical terminologies for the resolution of referential expressions. In Proceedings of the ISMB/ECCB 2007 Special Interest Group "BioLink", Vienna, Austria, July 19, 2007 (pp. 39-42).
21. Rector, A.L., Rogers, J. & Bittner, T. (2006). Granularity, scale and collectivity: when size does and does not matter. Journal of Biomedical Informatics, 39(3), 333-349.
22. Rosse, C., Kumar, A., Mejino Jr., J.L.V., Cook, D.L., Detwilern, L.D. & Smith, B. (2005). A strategy for improving and integrating biomedical ontologies. In C.P. Friedman (ed.), AMIA 2005 - Proceedings of the Annual Symposium of the American Medical Informatics Association. Biomedical and Health Informatics: From Foundations, to Applications to Policy, Washington, DC, USA, October 22-26, 2005 (pp. 639-643).
23. Schulz, S., Beisswanger, E., Hahn, U., Wermter, J., Kumar, A. & Stenzhorn, H. (2006). From GENIA to BIOTOP: towards a toplevel ontology for biology. In B. Bennett & C. Fellbaum (eds), FOIS 2006 - Proceedings of the 4th International Conference on Formal Ontology in Information Systems, Baltimore, MD, USA, November 9-11, 2006. Frontiers in Artificial Intelligence and Applications (Vol. 150, pp. 103-114). Amsterdam: IOS Press.
24. Schulz, S., Boeker, M. & Stenzhorn, H. (2008). How granularity issues concern biomedical ontology integration. In MIE 2008 -Proceedings of the 21st International Congress of the European Federation for Medical Informatics, Göteborg, Sweden, May 25-28, 2008. Studies in Health Technology and Informatics (Vol. 136, pp. 863-868).
25. Sioutos, N., de Coronado, S., Haber, M.W., Hartel, F.W., Shaiu, W.-L. & Wright, L.W. (2007). NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics, 40(1), 30-43.
26. Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C.J., Neuhaus, F., Rector, A.L. & Rosse, C. (2005). Relations in biomedical ontologies. Genome Biology, 6(5), R46 (1: 15).
27. Spasic, I., Ananiadou, S., McNaught, J. & Kumar, A. (2005). Text mining and ontologies in biomedicine: making sense of raw text. Briefings in Bioinformatics, 6(3), 239-251.
28. Wroe, C.J., Stevens, R., Goble, C.A. & Ashburner, M. (2003). A methodology to migrate the Gene Ontology to a description logic environment using DAML OIL. In R.B. Altman, A.K. Dunker, L. Hunter, T.A. Jung & T.E. Klein (eds), PSB 2003 -Proceedings of the Pacific Symposium on Biocomputing 2003, Kauai, HI, USA, January 3-7, 2003 (pp. 624-635). Singapore: World Scientific Publishing.