Abstract
Despite the dramatic growth of online genomic data, their understanding is still in early stage. To have meaningful interpretation, it requires the integration of various types of data that are relevant, such as gene sequence, protein interaction and metabolic pathway. Gene Ontology, an ontology proposed by molecular biologist community, is a possible tool to help address some of the difficulties in such integration. In this paper, we exam the formality of Gene Ontology, and study the possibilities and potential problems in applying Gene Ontology to both structured (such as database) and semi-structured (such as the publications in the literature) data integration for online genomic information.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Hernandez, T., Kambhampati, S.: Integration of biological sources: current systems and challenges ahead. ACM SIGMOD Record 33, 51–60 (2004)
The Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nature Genetics 25, 25–29 (2000)
Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., Stoeckert Jr., C.J.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal 40, 512–531 (2001)
Haas, L.M., Kodali, P., Rice, J.E., Schwarz, P.M., Swope, W.C.: Integrating life sciences data-with a little garlic. In: Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering, pp. 5–12 (2000)
Lenzerini, M.: Data integration: a theoretical perspective. In: Symposium on Principles of Database Systems, pp. 233–246 (2002)
Gruber, T.: A translation approach to portable ontology specifications. Knowledge Acquisition 5, 199–220 (1993)
The Gene Ontology Consortium: Creating the gene ontology resource: Design and implementation. Genome Research 11, 1425–1433 (2001)
Wache, H., Vogele, T., Visser, U., Stuckenschmidt, H., Schuster, G., Neumann, H., Hubner, S.: Ontology-based integration of information - a survey of existing approaches. In: Proceedings of the 17th International Joint Conference on Artificial Intelligence (IJCAI 2001) Workshop: Ontologies and Information Sharing, pp. 108–117 (2001)
Uschold, M., Gruninger, M.: Ontologies and semantics for seamless connectivity. SIGMOD Record 33(4), 58–64 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Xu, K. (2006). Web-Based Genomic Information Integration with Gene Ontology. In: Zhou, X., Li, J., Shen, H.T., Kitsuregawa, M., Zhang, Y. (eds) Frontiers of WWW Research and Development - APWeb 2006. APWeb 2006. Lecture Notes in Computer Science, vol 3841. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11610113_78
Download citation
DOI: https://doi.org/10.1007/11610113_78
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-31142-3
Online ISBN: 978-3-540-32437-9
eBook Packages: Computer ScienceComputer Science (R0)