Abstract
Biological ontologies define the basic terms and relations in biological domains and are being used among others, as community reference, as the basis for interoperability between systems, and for search, integration and exchange of biological data. In this chapter we present examples of biological ontologies and ontology-based knowledge, show how biological ontologies are used and discuss some important issues in ontology engineering.
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Baker C.J.O., Shaban-Nejad A., Su X., Haarslev V., and Butler G. Semantic Web Infrastructure for Fungal Enzyme Biotechnologists, Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences 4(3), 2006.
BioCreAtlvE, Critical Assessment for Information Extraction in Biology; http://biocreative.sourceforge.net/.
BioPAX, Biological Pathway Exchange; http://www.biopax.org/.
Blaschke C., Hirschman L., and Valencia A. Information extraction in molecular biology, Briefings in Bioinformatics 3(2):154–165, 2002.
Coté R., Jones P., Apweiler R., and Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries, BMC Bioinformatics 7:97, 2006.
Collins F., Green E., Guttmacher A., and Guyer M. A vision for the future of genomics research, Nature 422:835–847, 2003.
GO, The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology, Nature Genetics 25(1):25–29, 2000; http://www.geneontology.org/.
Goble C, Stevens R., Ng G., Bechhofer S., Paton N., Baker P., Peim M., and Brass A. Transparent access to multiple bioinformatics information sources, IBM Systems Journal 40(2):532–551, 2001.
Gómez-Pérez A. Ontological Engineering: A state of the Art, Expert Update 2(3):33–43, 1999.
Guarino N. and Giaretta P. Ontologies and Knowledge Bases: Towards a Terminological Clarification, in: Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing, Mars, ed., IOS Press, 25–32, 1995.
Hermjakob H., Montecchi-Palazzi L., Bader G., Wojcik J., Salwinski L., Ceol A., et al. The HUPO PSI’s Molecular Interaction format-a community standard for the representation of protein interaction data, Nature Biotechnology 22(2): 177–183, 2004.
Hucka M., Finney A., Sauro H., Bolouri H., Doyle J., Kitano H., and the rest of the SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics 19(4):524–531, 2003.
Jakoniene V. and Lambrix P. Ontology-based integration for bioinformatics, in: Proceedings of the VLDB Workshop on Ontologies-based techniques for DataBases and Information Systems, 55–58, 2005.
Jakoniene V., Rundqvist D., and Lambrix P. A method for similarity-based grouping of biological data, in: Proceedings of the 3rd International Workshop on Data Integration in the Life Sciences, LNBI 4075, 136–151, 2006.
Jasper R. and Uschold M. A Framework for Understanding and Classifying Ontology Applications, in: Proceedings of the IJCAI-99 Workshop on Ontologies and Problem-Solving Methods: Lessons Learned and Future Trends, 1999.
Köhler J., Munn K., Rüegg A., Skusa A, and Smith B. Quality control for terms and definitions in ontologies and taxonomies, BMC Bioinformatics 7:212, 2006.
Lambrix, P. Ontologies in Bioinformatics and Systems Biology, in: Artificial Intelligence Methods and Tools for Systems Biology, Dubitzky and Azuaje, eds., Springer, chapter 8, 129–146, 2004.
Lambrix, P. Towards a Semantic Web for Bioinformatics using Ontology-based Annotation, in: Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises, 3–7. Invited talk, 2005.
Lambrix P. and Tan H. SAMBO-A System for Aligning and Merging Biomedical Ontologies, Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences 4(3), 2006a.
Lambrix, P. and Tan H. Ontology Alignment and Merging, in: Anatomy Ontologies for Bioinformatics: Principles and Practice, Burger, Davidson and Baldock, eds., Springer. To appear, 2006b.
Lord P., Stevens R., Brass A., and Goble C. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation, Bioinformatics 19(10): 1275–1283, 2003.
MeSH, Medical Subject Headings; http://www.nlm.nih.gov/mesh/.
Mukherjea S. Information retrieval and knowledge discovery utilising a biomedical Semantic Web, Briefings in Bioinformatics 6(3):252–262, 2005.
Neches R., Fikes R., Finin T., Gruber T., Senator T., and Swartout, W. Enabling technology for knowledge engineering, AI Magazine 12(3):26–56, 1991.
OBO, Open Biomedical Ontologies; http://obo.sourceforge.net/.
OBO Foundry; http://obofoundry.org/.
OntoWeb, 2002, Deliverable 1.3: A survey on ontology tools; 2002, Deliverable 2.1: Successful Scenarios for Ontology-based Applications; 2002, Deliverable 2.2: Guidelines for the selection of techniques for kinds of ontology-based applications; 2004, Deliverable 1.6: A survey on ontology-based applications. E-commerce, knowledge management, multimedia, information sharing and educational applications; http://www.ontoweb.org/.
Orchard S., Montecchi-Palazzi L., Hermjakob H., and Apweiler R. The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments, in: Proceedings of the Pacific Symposium on Biocomputing 10:186–196, 2005.
Protégé; http://protege.stanford.edu/.
REWERSE, EU Network of Excellence on Reasoning on the Web with Rules and Semantics, Working group A2; http://rewerse.net/.
Rojas I., Ratsch E., Saric J., and Wittig U. Notes on the use of ontologies in the biochemical domain, In Silico Biology 4:0009, 2003.
SBML, Systems Biology Markup Language; http://sbml.org.
Schulze-Kremer S. Ontologies for molecular biology and bioinformatics, In Silico Biology 2:0017, 2002.
Smith B., Ceusters W., Klagges B., Köhler J., Kumar A., Lomax J., Mungall C, Neuhaus F., Rector A., and Rosse C. Relations in biomedical ontologies, Genome Biology 6:R46, 2005.
SOFG, Standards and Ontologies for Functional Genomics; http://www.sofg.org/.
Stevens R., Goble C., and Bechhofer S. Ontology-based knowledge representation for bioinformatics, Briefings in Bioinformatics 1(4):398–414, 2000.
Strömbäck L., Hall D., and Lambrix P. A review of standards for data exchange within systems biology, Proteomics. Invited contribution. To appear, 2006a.
Strömbäck L., Jakoniene V., Tan H., and Lambrix P. Representing, storing and accessing molecular interaction data: a review of models and tools, Briefings in Bioinformatics. Invited contribution. To appear, 2006b.
Strömbäck L., and Lambrix P. Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX, Bioinformatics 21(24):4401–4407, 2005.
UMLS, Unified Medical Language System; http://www.nlm.nih.gov/pubs/factsheets/umls.html.
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Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L. (2007). Biological Ontologies. In: Baker, C.J.O., Cheung, KH. (eds) Semantic Web. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-48438-9_5
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DOI: https://doi.org/10.1007/978-0-387-48438-9_5
Publisher Name: Springer, Boston, MA
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