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Ontologies and Life Science Data Management

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  1. Altman R, Bada M, Chai X, Whirl CM, Chen R, Abernethy N. RiboWeb: an ontology-based system for collaborative molecular biology. IEEE Intell Syst. 1999;14(5):68–76.

    Article  Google Scholar 

  2. Baader F, Calvanese D, McGuinness D, Nardi D, Patel-Schneider P, editors. The description logic handbook: theory, implementation and applications. Cambridge: Cambridge University Press; 2003.

    MATH  Google Scholar 

  3. Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform. 2006;7(3):256–74.

    Article  Google Scholar 

  4. Brenchley R, Tariq H, McElhinney H, Szoor B, Stevens R, Matthews K, Tabernero L. The TriTryp Phosphatome analysis of the protein phosphatase catalytic domains. BMC Genome. 2007;8:434.

    Article  Google Scholar 

  5. Davidson S, Overton C, Buneman P. Challenges in integrating biological data sources. J Comput Biol. 1995;2(4):557–72.

    Article  Google Scholar 

  6. Fernàndez-Lòpez M, Gòmez-Pèrez A. Overview and analysis of methodologies for building ontologies. Knowl Eng Rev. 2002;17(2):129–56.

    Article  Google Scholar 

  7. Goble CA, Stevens R, Ng G, Bechhofer S, Paton NW, Baker P, Peim M, Brass A. Transparent access to multiple bioinformatics information sources. IBM Syst J, Special issue on deep computing for the life sciences. 2001;40(2e):532–52.

    Google Scholar 

  8. Karp P, Riley M, Saier M, Paulsen I, Paley S, Pellegrini-Toole A. The EcoCyc and metacyc databases. Nucleic Acids Res. 2000;28:56–9.

    Article  Google Scholar 

  9. Lord PW, Stevens R, Brass A, Goble CA. Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation. Bioinformatics. 2003;19(10):1275–83.

    Article  Google Scholar 

  10. Luciano J. PAX of mind for pathway researchers. Drug Discov Today. 2005;10:937–42.

    Article  Google Scholar 

  11. Ringland G, Duce D. Approaches to knowledge representation: an introduction knowledge-based and expert systems series. Chichester: John Wiley; 1988.

    Google Scholar 

  12. Rosse C, Mejino JLV. A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inform. 2003;36:478–500.

    Article  Google Scholar 

  13. Taylor C, Paton N, Lilley K, Binz P, Julian Jr R, Jones A, Zhu W, Apweiler R, Aebersold R, Deutsch E, Dunn M, Heck A, Leitner A, Macht M, Mann M, Martens L, Neubert T, Patterson S, Ping P, Seymour S, Souda P, Tsugita A, Vandekerckhove J, Vondriska T, Whitelegge J, Wilkins M, Xenarios I, Yates 3rd J, Hermjakob H. The Minimum Information About a Proteomics Experiment (MIAPE). Nat Biotechnol. 2007;25:887–93.

    Article  Google Scholar 

  14. Ashburner M et al. The gene ontology consortium gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.

    Article  Google Scholar 

  15. Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. In: Proceedings IEEE symposium on computational intelligence in bioinformatics and computational biology. 2004. p. 25–31.

    Google Scholar 

  16. Whetzel P, Brinkman R, Causton H, Fan L, Field D, Fostel J, Fragaso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert C, Taylor C, White J, Wood A. The FuGo working group development of FuGo: an ontology for functional genomics investigations. OMICS J Integrat Biol. 2006;10:199–204.

    Article  Google Scholar 

  17. Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ. The mged ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006;22(7):866–73.

    Article  Google Scholar 

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Correspondence to Robert Stevens .

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Stevens, R., Lord, P. (2016). Ontologies and Life Science Data Management. In: Liu, L., Özsu, M. (eds) Encyclopedia of Database Systems. Springer, New York, NY. https://doi.org/10.1007/978-1-4899-7993-3_631-2

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  • DOI: https://doi.org/10.1007/978-1-4899-7993-3_631-2

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  • Online ISBN: 978-1-4899-7993-3

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