Biomedical Engineering through Ontologies
Seremeti Lambrini, Kameas Achilles
2014
Abstract
Biomedical engineering is the application of scientific and mathematical principles to practical ends in the medicine and biology fields. It comprises many research directions including computational model of HIV infection, integration of clinical and experimental data, etc. Much of the work in biomedical engineering consists in providing solutions to the problem of securing an effective integration of biomedical content. To this end, ontologies, as sharable, reusable and machine-readable artifacts capable of knowledge representation, contribute to the interoperability between systems, the access of heterogeneous information sources, and the reuse of voluminous and complex information. The aim of this paper is to present the literature on biomedical ontologies in order to highlight how current research of the ontology field can be brought to bear on the practical problems associated with biomedical engineering. Thus, we discuss the fundamental role of ontologies in biomedical engineering, we review several methodologies suitable for building specialized biomedical ontologies, and we present some peculiarities related to the creation of biomedical ontologies that continue to constitute research challenges.
References
- Ananiadou, S., Albert, S., Schumann, D., 2000. Evaluation of automatic term recognition of nuclear receptors from MEDLINE. In Genome Informatics, Vol. 11, pp. 450-451.
- Ba, M., Diallo, G., 2013. Large-scale biomedical ontology matching with ServOMAP. In IRBM, Vol. 34, Issue 1, pp. 56-59.
- Baneyx, A., Charlet, J., Jaulent, M., 2007. Building an ontology of pulmonary diseases with natural language processing tools using textual corpora. In International Journal of Medical Informatics, Vol. 76, No. 2, pp. 208-215.
- Bard, J., Rhee, S.Y., 2004. Ontologies in biology: Design, applications and future challenges. In Nature Reviews Genetics, Vol. 5, pp. 213-222.
- Beisswanger, E., Porpat, M., Hahn, U., 2008. Lexical properties of OBO ontology class names and synonyms. In Foreword to the 3rd International Symposium for semantic mining in Biomedicine (SMBM), pp. 13-20.
- Bittner, T., Smith, B., 2003. A theory of granular partition. In M. Duckham, M. Goodchild, M. Worboys (eds), Foundations of geographic information science, London, Taylor & Francis Books, pp. 117-151.
- Blake, J., 2004. Bio-ontologies - fast and furious. In Nat Biotechnol, Vol. 22, pp. 773-774.
- Bodenreider, O., Burgun, A., 2005. Biomedical ontologies. In H. Chen, S.S. Fuller, C. Friedman, W. Hersh (eds), Medical Informatics: Integrated Series in Information Systems, Vol. 8, pp. 211-236, Springer.
- Bodenreider, O., 2008. Biomedical ontologies in action: Role in knowledge management, data integration and decision support. Yearbook of Medical Informatics, Issue 1, pp. 67-79.
- Boeker, M., Schober, D., Raufie, D., Grewe, N., Röhl, J., Janses, L., Schulz, S., 2012. Teaching good biomedical ontology design. In R. Cornet, R. Stevens (eds), ICBO, Proceedings of the CEUR Workshop, Vol. 897.
- Brand, J., 2003. Ontologies formalizing biological knowledge for bioinformatics. In Bioessays, Vol. 25, No. 5, pp. 501-506.
- Chandrasekaran, B., Josephson, J.R., Benjamins, V.R., 1999. Ontologies: What are they? Why do we need them? In IEEE Intelligent Systems and Their Applications, Special Issue on Ontologies, Vol. 14, No. 1, pp. 20-26.
- Cinimo, J.J., 2000. From data to knowledge through concept-oriented terminologies: experience with the Medical Entities Dictionary. In J Am Med Inform Assoc, Vol. 7, No. 3, pp. 288-297.
- Cowell, L.G., Smith, B., 2010. Infectious disease ontology. In V. Sintchenko, Infectious Disease Informatics, New York: Springer, pp. 373-395.
- Daramola, O., Fatumo, S., 2009. Developing ontology support for human malaria control initiatives. In International Conference on Biomedical Ontology.
- Donnelly, M., 2004. On parts and holes: The spatial structure of the human body. In M. Fieschi et al., (eds), MEDINFO2004, IOS Press, pp. 351-356.
- Fonseca, F., 2007. The double role of ontologies in inflrmation science research. In Journal of the American Society for Information Science and Technology, Vol. 58, No. 6, pp. 786-793.
- Freitas, F., Schultz, S., Moreas, E., 2009. Survey of current terminologies and ontologies in biology and medicine. In RECIIS, Electronic Journal of Communication Information & Innovation in Health, Vo. 3, No. 1.
- Goh, C.H., 1997. Representing and reasoning about semantic conflicts in heterogeneous information sources. MIT.
- Gruber, T.R., 1993. Towards principles for the design of ontologies used for knowledge sharing. In R. Poli, N. Guarino (eds), International Workshop on Formal Ontology.
- Guarino, N., Giaretta, P., 1995. Ontologies and knowledge bases: Towards a terminological classification. In Towards Very Large Knowledge Bases: Knowledge Building & Knowledge Sharing, IOS Press.
- Horrocks, I., 2013. What are ontologies good for? In B.O. Küppers et al. (eds), Evolution of Semantic Systems, pp. 175-188, Springer-Verlag Berlin Heidelberg.
- Hudelot, C., Atif, J., Bloch, I., 2008. Fuzzy spatial relation ontology for image interpretation. In Fuzzy Sets and Systems, Vol. 159, pp. 1929-1951.
- Jonquet, C., Musen, M.A., Shah, N.H., 2010. Building a biomedical ontology recommender web service. In Journal of Biomedical Semantics, Vol. 1.
- Kayaalp, M., 2005. Why do we need probabilistic approaches to ontologies and the associated data? In AMIA Annual Symposium Proceedings.
- Keet, M.C., 2009. Constraints for representing transforming entities in bio-ontologies. Knowledge Representation Centre Technical Report, Free University of Bozen-Bolzno, Italy.
- Lin, Y., He, Y., 2013. Ontology modelling of genetic susceptibility to adverse events following vaccination. In Proceedings of the International Conference on Biomedical Ontology (ICBO).
- Madsen, B.N., Thomsen, H.E., Vinker, C., 2005. Multidimensionality in terminological concept modelling. In Proceedings of the 7th International Conference on Terminology and Knowledge Engineering, pp. 161-173.
- McGarry, K., Garfield, S., Morris, N., 2006. Recent trends in knowledge and data integration for the life sciences. In Expert Systems: The Journal of Knowledge Engineering, Vol. 23, No. 5, pp. 337-348.
- McGarry, K., Garfield, S., Morris, N., Wemster, S., 2007. Integration of hubrid bio-ontologies using baeysian networks for knowledge discovery. In Proceedings of the 3rd International Workshop on Neural-Symbolic Learning and Reasoning.
- Melton, G.B., Moon, S., McInnes, B., Pakhomov, S., 2010. Automated identification of synonyms in biomedical acronym sense inventories. In Proceedings of the NAACL HLT2010 Second ouhi Workshop on Text and Data Mining of Health Documents, pp. 46- 52.
- Mortensen, J.M., Musen, M.A., Noy, N.F., 2013. Crowdsourcing the verification of relationships in biomedical ontologies. In AMIA Annual Symposium.
- Musen, M.A., 2006. Don't know much about philosophy: The confusion over bio-ontologies. In Proceedings of the Computational Systems Bioinformatics (CSB), pp. 3-5.
- Neches, R., Fikes, R., Finin, T., Gruber, T., Patil, R., Senator, T., Swartout, W.R., 1991. Enabling technology for knowledge sharing. In AI Magazine, pp. 36-56.
- Pathak, J., Johnson, T.M., Chute, C.G., 2008. Modular ontology techniques and their applications in the biomedical domain. In IEEE IRI2008, pp. 351-357.
- Rector, A., 2003. Medical Informatics. In F. Baader, D. Calvanese, D. McGuinness, D. Nardi, P. PatelShneider (eds), The description logic handbook, Cambridge University Press, pp. 406-426.
- Rubin, D.L., Lewis, S.E., Mungall, C.J., Misra, S., Westerfield, M., Ashburner, M., Sim, I., Chute, C.G., Solbriq, H., Storey, M.A., Smith, B., Day-Richter, J., Noy, N.F., Musen, M.A., 2006. National center for biomedical ontology: Advancing biomedicine through structured organization of scientific knowledge. In Omics, Vol. 10, No. 2, pp. 185-198.
- Rubin, D., Shah, N., Noy, N., 2007. Biomedical ontologies: A functional perspective. In Briefings in Bioinformatics, Vol. 19, No. 1, pp. 75-90.
- Sahay, S., Li, B., Garcia, E.V., Agichtein, E., Ram, A., 2007. Domain ontology construction from biomedical text. In International Conference on Artificial Intelligence (ICAI), pp. 28-34.
- Saripalle, R.K., 2013. Current status of ontologies in biomedical and clinical informatics. In J.J. Cinimo, E.H. Shortliffe, (eds), Biomedical Informatics: Computed Applications in Health Care and Biomedicine (Health Informatics.
- Satria, H., Priya, R.S., Ismail, L.H., Supriyanto, E., 2012. Building and reusing medical ontology for tropical diseases management. In International Journal of Education and Information Technologies, Vol. 6, Issue 1, pp. 52-61.
- Schulz, S., Hahn, U., 2001. Mereotopological reasoning about parts and (w)holes in bio-ontologies. In C.W.B. Smith (ed), Formal Ontology in Information System, ACM Press, pp. 210-221.
- Schulz, S., Kumar, A., Bittner, T., 2006. Biomedical ontologies: What part-of is and isn't. In Journal of Biomedical Informatics, Vol. 39, Issue 3, pp. 350-361.
- Schulz, S., Jansen, L., 2009. Molecular interactions: On the ambiguity of ordinary statements in biomedical literature. In Applied Ontology, Vol. 4, No. 1, pp. 21- 34.
- Schulz, S., Lopez-Garcia, P., 2011. Modularity issues in biomedical ontologies. In Proceedings of the 5th International Workshop (WoMo), IOS Press, pp. 7-9.
- Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C., 2005. Relations in biomedical ontologies. In Genome Biology, Vol. 6.
- Stevens, R., Goble, C., Becchofer, S., 2000. Ontologybased knowledge representation for bioinformatics. In Briefings in Bioinformatics, Vol. 1, No. 4, pp. 398- 414.
- Tan, H., Lambrix, P., 2009. Selecting an ontology for biomedical text mining. In Proceedings of the Workshop on BioNLP, pp. 55-62.
- Valarakos, A., Karkaletsis, V., Alexopoulou, D., Papadimitriou, E., Spyropoulos, C., Vouros, G., 2006. Building an allergens ontology and maintaining it using machine learning techniques. In Computers in Biology and Medicine, Vol. 36, No. 10, pp. 1155- 1184.
- Wächter, T., 2010. Semi-automated ontology generation for biocuration and semantic search. PhD dissertation, Technischen Universität Dresden.
- Warrender, J.D., 2013. Building a logical model of mitochondrial disease. School of Computing Science, Newcastle University.
- Xiang, Z., He, Y., 2013. HINO: BFO-aligned ontology representation of human molecular interactions and pathways. In Proceedings of the 4th International Conference on Biomedical Ontology.
- Yu, A., 2006. Methods in biomedical ontology. In Journal of Biomedical Informatics, Vol. 39, pp. 252-266.
Paper Citation
in Harvard Style
Lambrini S. and Achilles K. (2014). Biomedical Engineering through Ontologies . In Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2014) ISBN 978-989-758-049-9, pages 240-247. DOI: 10.5220/0005073802400247
in Bibtex Style
@conference{keod14,
author={Seremeti Lambrini and Kameas Achilles},
title={Biomedical Engineering through Ontologies},
booktitle={Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2014)},
year={2014},
pages={240-247},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005073802400247},
isbn={978-989-758-049-9},
}
in EndNote Style
TY - CONF
JO - Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K 2014)
TI - Biomedical Engineering through Ontologies
SN - 978-989-758-049-9
AU - Lambrini S.
AU - Achilles K.
PY - 2014
SP - 240
EP - 247
DO - 10.5220/0005073802400247