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Semantic Technologies and Bio-Ontologies

  • Fernando GutierrezEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1617)

Abstract

As information available through data repositories constantly grows, the need for automated mechanisms for linking, querying, and sharing data has become a relevant factor both in research and industry. This situation is more evident in research fields such as the life sciences, where new experiments by different research groups are constantly generating new information regarding a wide variety of related study objects. However, current methods for representing information and knowledge are not suited for machine processing. The Semantic Technologies are a set of standards and protocols that intend to provide methods for representing and handling data that encourages reusability of information and is machine-readable. In this chapter, we will provide a brief introduction to Semantic Technologies, and how these protocols and standards have been incorporated into the life sciences to facilitate dissemination and access to information.

Key words

Semantic Web Resources Ontology Bio-ontology 

References

  1. 1.
    Gruber TR (1993) A translation approach to portable ontology specifications. Knowl Acquis 5(2):199–220. doi: 10.1006/knac.1993.1008 CrossRefGoogle Scholar
  2. 2.
    Parsia B, Sirin E (2004) Pellet: an owl dl reasoner. In: 3rd international Semantic Web conference (ISWC2004), Hiroshima, Japan, 2004Google Scholar
  3. 3.
    Motik B, Shearer R, Horrocks I (2009) Hypertableau reasoning for description logics. J Artif Int Res 36(1):165–228Google Scholar
  4. 4.
    Calvanese D, De Giacomo G, Lemho D, Lenzerini M, Rosati R (2005) DL-lite: tractable description logics for ontologies. AAAI Press, Pittsburgh, PA, pp 602–607Google Scholar
  5. 5.
    Barzdins G, Rikacovs S, Zviedris M (2009) Graphical query language as SPARQL frontend. In: 13th east-European conference on advances in databases and information systems (ADBIS-2009), Riga, Latvia, 2009, pp 93–107Google Scholar
  6. 6.
    Bizer C, Seaborne A (2004) D2RQ-treating non-RDF databases as virtual RDF graphs. In: 3rd international Semantic Web conference (ISWC2004), Hiroshima, JapanGoogle Scholar
  7. 7.
    Hemmer M (2008) Expert systems in chemistry research. CRC Press, Boca Raton, FLGoogle Scholar
  8. 8.
  9. 9.
    Stevens R, Jupp S, Klein J, Schanstra J (2011) Using Semantic Web technologies to manage complexity and change in biomedical data. Conf Proc IEEE Eng Med Biol Soc 2011:3708–3711. doi: 10.1109/IEMBS.2011.6090629 PubMedGoogle Scholar
  10. 10.
    Wong N, Wang X (2014) miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res 43(D1):D146–D152. doi: 10.1093/nar/gku1104 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F (2013) The cancer imaging archive (TCIA): maintaining and operating a public information repository. J Digit Imaging 26(6):1045–1057. doi: 10.1007/s10278-013-9622-7 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    National Institute on Drug Abuse Data Share. https://datashare.nida.nih.gov/
  13. 13.
    National Center for Biotechnology Information PubMed. https://www.ncbi.nlm.nih.gov/pubmed/
  14. 14.
    Splendiani A, Burger A, Paschke A, Romano P, Marshall MS (2011) Biomedical semantics in the Semantic Web. J Biomed Semantics 2(Suppl 1):S1. doi: 10.1186/2041-1480-2-S1-S1 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    SWAT4LS '11 (2012) Proceedings of the 4th international workshop on Semantic Web applications and tools for the life sciences. ACM, New York, NYGoogle Scholar
  16. 16.
    Melzi S, Jonquet C (2014) Scoring semantic annotations returned by the NCBO annotator. In: 7th international workshop on Semantic Web applications and tools for life sciences (SWAT4LS2014), BerlinGoogle Scholar
  17. 17.
    Koutkias V, Jaulent M-C (2014) Leveraging post-marketing drug safety research through semantic technologies: the pharmacovigilance signal detectors ontology. In: 7th international workshop on Semantic Web applications and tools for life sciences (SWAT4LS2014), BerlinGoogle Scholar
  18. 18.
    Herrero Zazo M, Hastings J, Segura Bedmar I, Croset S, Martínez P, Steinbeck C (2014) An ontology for drug-drug interactions. In: 7th international workshop on Semantic Web applications and tools for life sciences (SWAT4LS2014), BerlinGoogle Scholar
  19. 19.
    Grenon P, Smith B, Goldberg L (2004) Biodynamic ontology: applying BFO in the biomedical domain. Ontol Med 102:20–38Google Scholar
  20. 20.
    Chen X, Chen H, Bi X, Gu P, Chen J, Wu Z (2014) BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine. Comput Math Methods Med 2014:957231. doi: 10.1155/2014/957231 PubMedPubMedCentralGoogle Scholar
  21. 21.
    Thomas P, Starlinger J, Vowinkel A, Arzt S, Leser U (2012) GeneView: a comprehensive semantic search engine for PubMed. Nucleic Acids Res 40(Web Server issue):W585–W591. doi: 10.1093/nar/gks563 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Computer and Information ScienceUniversity of OregonEugeneUSA

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