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Logical Reasoning (Inferencing) on MicroRNA Data

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

Abstract

Logical reasoning played an important role in artificial intelligence. Applying logical reasoning on microRNA data brings intelligence into data analysis. Here, we provide basic introduction about logic (especially propositional logic) and automated reasoning based on knowledge described in the form of logic rules. We also introduce tools that could be used for building automated reasoning systems with microRNA data.

Key words

Logical reasoning Propositional logic Inference rule 

References

  1. 1.
    McCarthy J (1960) Programs with common sense. RLE and MIT Computation Center, pp 300–307Google Scholar
  2. 2.
    Darwiche A (2009) Modeling and reasoning with Bayesian networks. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  3. 3.
    Schönіng U (2001) Logic for computer scientists. Birkhäuser Boston, c/o Springer-Verlag New York, Inc., New York, NYGoogle Scholar
  4. 4.
    Rosen KH, Krithivasan K (1995) Discrete mathematics and its applications, vol 6. McGraw-Hill, New York, NYGoogle Scholar
  5. 5.
    Russell SJ, Norvig P, Canny JF, Malik JM, Edwards DD (2003) Artificial intelligence: a modern approach, vol 2. Prentice Hall, Upper Saddle RiverGoogle Scholar
  6. 6.
    Robinson JA (1965) A machine-oriented logic based on the resolution principle. JACM 12(1):23–41CrossRefGoogle Scholar
  7. 7.
    Forgy CL (1982) Rete: a fast algorithm for the many pattern/many object pattern match problem. Artif Intell 19:17–37. doi: 10.1016/0004-3702(82)90020-0 CrossRefGoogle Scholar
  8. 8.
    Robinson JA (1971) Computational logic: the unification computation. In: Meltzer B, Michie D (eds) Machine intelligence, vol 6. Edinburgh University Press, Edinburgh, Scotland, pp 63–72Google Scholar
  9. 9.
    Wang J, Byrnes J, Valtorta M, Huhns M (2012) On the combination of logical and probabilistic models for information analysis. Appl Intell 36(2):472CrossRefGoogle Scholar
  10. 10.
    Tran DH, Satou K, Ho TB (2008) Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics 9(12):1Google Scholar
  11. 11.
    Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC et al (2016) The ontology for biomedical investigations. PLoS One 11(4):e0154556CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake AJ, Eilbeck K, Natale DA, Lin Y, Wu B, de Silva N, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A (2016) OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J Biomed Semantics 7:25CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Baader F, Sattler U (2001) An overview of tableau algorithms for description logics. Stud Logica 69(1):5–40CrossRefGoogle Scholar
  14. 14.
    Calvanese D, De Giacomo G, Lenzerini M, Nardi D (2001) Reasoning in expressive description logics. In: Robinson A, Voronkov A (eds) Handbook of automated reasoning, vol 2. Elsevier Science, Amsterdam, pp 1581–1634Google Scholar
  15. 15.
    Roussel F (1975) Prolog: Manuel de reference et d’Utilisation. Groupe d’Intelligence Artificielle, Marseille-LuminyGoogle Scholar
  16. 16.
    Kowalski R, Kuehner D (1971) Linear resolution with selection function. Artif Intell 2(3–4):227–260CrossRefGoogle Scholar
  17. 17.
    Browne P (2009) JBoss Drools business rules. Packt Publishing Ltd., Birmingham, UKGoogle Scholar
  18. 18.
    Jess, the Rule Engine for the Java Platform (Sept 2009) by Sandia National Laboratories. http://www.jessrules.com/jess
  19. 19.
    Apache Jena, A free and open source Java framework for building Semantic Web and Linked Data applications. https://jena.apache.org
  20. 20.
    Musen MA (2015) The Protégé project: a look back and a look forward. AI Matters 1(4):4–12. doi: 10.1145/2757001.2757003, http://protege.stanford.edu

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Oracle CorporationRedwood ShoresUSA

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