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Creating Biomedical Ontologies Using mOntage

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Data Integration in the Life Sciences (DILS 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9162))

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Abstract

The growing volume of biomedical data available on the Web has contributed to numerous scientific advancements. At the same time, the complex, versatile and disparate nature of the data can overburden the knowledge discovery and data-driven hypothesis generation by scientists. Ontologies have been proposed to address the data integration challenge, however, creating useful domain-specific ontologies and populating them with high quality instances is tedious and time-consuming. In this paper, we present the mOntage framework to rapidly create ontologies representing data in a specific area of interest. We show how the mOntage framework can be used to create and populate biomedical ontologies from existing data sources. The classes and properties of the ontology being created are mapped to and instantiated from the existing data sources by executing suitable SPARQL queries. We illustrate our framework by creating a Phosphatase Ontology and show how it can serve as an important source of knowledge in the area of phosphatases.

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Notes

  1. 1.

    http://disease-ontology.org/.

  2. 2.

    http://people.cis.ksu.edu/~rpr/TR/.

  3. 3.

    http://linkedlifedata.com/.

  4. 4.

    http://tarql.github.io/.

  5. 5.

    http://d2rq.org/.

  6. 6.

    http://void.rkbexplorer.com/.

  7. 7.

    http://spinrdf.org/.

References

  1. A prototype knowledge base for the life sciences. Available from: http://www.w3.org/TR/hcls-kb/

  2. Bizer, C., Heath, T., Berners-Lee, T.: Linked data - the story so far. Int. J. Seman. Web Inf. Syst. 5, 21 (2009)

    Google Scholar 

  3. Gruber, T.R.: Toward principles for the design of ontologies used for knowledge sharing. Int. J. Hum. Comput. Stud. 43(4–5), 907–928 (1995)

    Article  Google Scholar 

  4. Smith, B., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. BioTechnol. 25(11), 1251–1255 (2007)

    Article  Google Scholar 

  5. Noy, N.F., et al.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucl. Acids Res. 37(suppl. 2), W170–W173 (2009)

    Article  MathSciNet  Google Scholar 

  6. Ashburner, M., et al.: Gene ontology: tool for the unification of biology. Gene Ontol. Consortium. Nat. Genet. 25(1), 25–29 (2000)

    MATH  Google Scholar 

  7. Natale, D.A., et al.: The protein ontology: a structured representation of protein forms and complexes. Nucl. Acids Res. 39(Database issue), D539–D545 (2011)

    Article  MathSciNet  Google Scholar 

  8. Dastgheib, S., Mesbah, A., Kochut, K.: Montage: creating self-populating domain ontologies from linked open data. Int. J. Seman. Comput. 7(04), 427–453 (2013)

    Article  Google Scholar 

  9. Dastgheib, S., Mesbah, A., Kochut, K.: mOntage: building domain ontologies from linked open data. In: International Conference on Semantic Computing (ICSC). IEEE, Irvine (2013)

    Google Scholar 

  10. Gosal, G., Kochut, K.J., Kannan, N.: ProKinO: an ontology for integrative analysis of protein kinases in cancer. PLoS ONE 6(12), e28782 (2011)

    Article  Google Scholar 

  11. McSkimming, D.I., et al.: ProKinO: a unified resource for mining the cancer kinome. Hum. Mutat. 36(2), 175–186 (2015)

    Article  Google Scholar 

  12. Gosal, G.P.S., Kannan, N., Kochut, K.J.: ProKinO: a framework for protein kinase ontology. In: 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE (2011)

    Google Scholar 

  13. Forbes, S.A., et al.: The catalogue of somatic mutations in cancer (COSMIC). Current Protoc. Hum. Genet. 10–11 (2008)

    Google Scholar 

  14. Croft, D., et al.: Reactome: a database of reactions, pathways and biological processes. Nucl. Acids Res. 39(suppl. 1), D691–D697 (2011)

    Article  MathSciNet  Google Scholar 

  15. Bairoch, A., et al.: The universal protein resource (UniProt). Nucl. Acids Res. 33(suppl. 1), D154–D159 (2005)

    Google Scholar 

  16. He, R.-J., et al.: Protein tyrosine phosphatases as potential therapeutic targets. Acta Pharmacologica Sinica 35, 1227–1246 (2014)

    Article  Google Scholar 

  17. McConnell, J.L., Wadzinski, B.E.: Targeting protein serine/threonine phosphatases for drug development. Mol. Pharmacol. 75(6), 1249–1261 (2009)

    Article  Google Scholar 

  18. Zhang, M., et al.: Viewing serine/threonine protein phosphatases through the eyes of drug designers. FEBS J. 280(19), 4739–4760 (2013)

    Article  Google Scholar 

  19. Wolstencroft, K., et al.: PhosphaBase: an ontology-driven database resource for protein phosphatases. Proteins: Struct. Funct. Bioinf. 58(2), 290–294 (2005)

    Article  Google Scholar 

  20. Horrocks, I.: DAML+OIL: a description logic for the semantic web. IEEE Data Eng. Bull. 25(1), 4–9 (2002)

    MathSciNet  Google Scholar 

  21. Apweiler, R., et al.: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucl. Acids Res. 29(1), 37–40 (2001)

    Article  Google Scholar 

  22. Hamosh, A., et al.: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucl. Acids Res. 33(suppl. 1), D514–D517 (2005)

    Google Scholar 

  23. Duan, G., Li, X., Köhn, M.: The human DEPhOsphorylation database DEPOD: a 2015 update. Nucl. Acids Res. 43, D531–D535 (2014). doi:10.1093/nar/gku1009

    Article  Google Scholar 

  24. Composer, T.: TopBraid Composer 2007 features and getting started guide version 1.0, created by TopQuadrant, US (2007)

    Google Scholar 

  25. Weiten, M.: OntoSTUDIO® as a ontology engineering environment. In: Davies, J., Grobelnik, M., Mladenić, D. (eds.) Semantic Knowledge Management, pp. 51–60. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  26. http://protege.stanford.edu/

  27. von Eschenbach, A.C., Buetow, K.: Cancer informatics vision: caBIGâ„¢. Cancer Inf. 2, 22 (2006)

    Google Scholar 

  28. Knoblock, C.A., Szekely, P., Ambite, J.L., Goel, A., Gupta, S., Lerman, K., Muslea, M., Taheriyan, M., Mallick, P.: Semi-automatically mapping structured sources into the semantic web. In: Simperl, E., Cimiano, P., Polleres, A., Corcho, O., Presutti, V. (eds.) ESWC 2012. LNCS, vol. 7295, pp. 375–390. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  29. Sahoo, S.S., et al.: An ontology-driven semantic mash-up of gene and biological pathway information: application to the domain of nicotine dependence. J. Biomed. Inf. 41(5), 752 (2008)

    Article  Google Scholar 

  30. Jentzsch, A., et al.: Linking open drug data. In: Triplification Challenge of the International Conference on Semantic Systems (2009)

    Google Scholar 

  31. Hassanzadeh, O., et al.: Linkedct: a linked data space for clinical trials (2009). arXiv preprint arXiv:0908.0567

  32. Lenzerini, M.: Data integration: a theoretical perspective. In: Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems. ACM (2002)

    Google Scholar 

  33. Queralt-Rosinach, N., Furlong, L.I.: DisGeNET RDF: a gene-disease association linked open data resource. In: SWAT4LS (2013)

    Google Scholar 

  34. Lin, Y.-C., et al.: SCP phosphatases suppress renal cell carcinoma by stabilizing PML and inhibiting mTOR/HIF signaling. Cancer Res. 74(23), 6935–6946 (2014)

    Article  Google Scholar 

  35. Humtsoe, J.O., et al.: Lipid phosphate phosphatase 3 stabilization of β-catenin induces endothelial cell migration and formation of branching point structures. Mol. Cell. Biol. 30(7), 1593–1606 (2010)

    Article  Google Scholar 

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Acknowledgment

Funding for NK from the National Science Foundation (MCB-1149106) is acknowledged.

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Authors and Affiliations

  1. Department of Computer Science, University of Georgia, Athens, GA, 30602, USA

    Shima Dastgheib & Krys Kochut

  2. Institute of Bioinformatics; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA

    Daniel Ian McSkimming & Natarajan Kannan

Authors
  1. Shima Dastgheib
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  2. Daniel Ian McSkimming
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  3. Natarajan Kannan
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  4. Krys Kochut
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Corresponding author

Correspondence to Shima Dastgheib .

Editor information

Editors and Affiliations

  1. USC Stevens Neuroimaging and Informatics Institute, Los Angeles, California, USA

    Naveen Ashish

  2. USC Information Sciences Institute, Marina del Rey, California, USA

    Jose-Luis Ambite

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Dastgheib, S., McSkimming, D.I., Kannan, N., Kochut, K. (2015). Creating Biomedical Ontologies Using mOntage. In: Ashish, N., Ambite, JL. (eds) Data Integration in the Life Sciences. DILS 2015. Lecture Notes in Computer Science(), vol 9162. Springer, Cham. https://doi.org/10.1007/978-3-319-21843-4_9

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  • DOI: https://doi.org/10.1007/978-3-319-21843-4_9

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  • Publisher Name: Springer, Cham

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