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Knowledge modeling and its application in life sciences: a tale of two ontologies

Published: 23 May 2006 Publication History

Abstract

High throughput glycoproteomics, similar to genomics and proteomics, involves extremely large volumes of distributed, heterogeneous data as a basis for identification and quantification of a structurally diverse collection of biomolecules. The ability to share, compare, query for and most critically correlate datasets using the native biological relationships are some of the challenges being faced by glycobiology researchers. As a solution for these challenges, we are building a semantic structure, using a suite of ontologies, which supports management of data and information at each step of the experimental lifecycle. This framework will enable researchers to leverage the large scale of glycoproteomics data to their benefit.In this paper, we focus on the design of these biological ontology schemas with an emphasis on relationships between biological concepts, on the use of novel approaches to populate these complex ontologies including integrating extremely large datasets ( 500MB) as part of the instance base and on the evaluation of ontologies using OntoQA [38] metrics. The application of these ontologies in providing informatics solutions, for high throughput glycoproteomics experimental domain, is also discussed. We present our experience as a use case of developing two ontologies in one domain, to be part of a set of use cases, which are used in the development of an emergent framework for building and deploying biological ontologies.

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      cover image ACM Conferences
      WWW '06: Proceedings of the 15th international conference on World Wide Web
      May 2006
      1102 pages
      ISBN:1595933239
      DOI:10.1145/1135777
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      Published: 23 May 2006

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      Author Tags

      1. ProPreO
      2. bioinformatics ontology
      3. biological ontology development
      4. glycO
      5. glycoproteomics
      6. ontology population
      7. ontology structural metrics
      8. semantic bioinformatics

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      • (2021)Beware of the hierarchy - An analysis of ontology evolution and the materialisation impact for biomedical ontologiesJournal of Web Semantics10.1016/j.websem.2021.100658(100658)Online publication date: Aug-2021
      • (2014)Toolboxes for a standardised and systematic study of glycansBMC Bioinformatics10.1186/1471-2105-15-S1-S915:S1Online publication date: 10-Jan-2014
      • (2012)Efficient query processing in the semantic model approach to information integration2012 IEEE 13th International Conference on Information Reuse & Integration (IRI)10.1109/IRI.2012.6303030(348-355)Online publication date: Aug-2012
      • (2011)Ontology module extraction based on semantic query2011 International Conference on Electrical and Control Engineering10.1109/ICECENG.2011.6057464(2406-2409)Online publication date: Sep-2011
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