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Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics

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Reasoning Web

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 5224))

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Abstract

Semantic Web technologies are appealing for biomedical researchers since they promise to solve many of the daily problems they face while accessing and integrating biological information that is distributed over the Internet and managed by using tools which are extremely heterogeneous and largely not compatible. On the other hand, the complexity of biomedical information and its heterogeneity, together with the need of keeping current production services steadily up and running, make the transition from current semantic-less to future semantic-aware services a huge problem.

In this paper, authors present the characteristics of biomedical information that make adoption of semantic web technologies both desirable and complex at the same time. They then present the tools and the applications that have been developed so far, including biomedical ontologies, RDF/OWL data stores, query systems and semantic-aware tools and browsers. Finally, they present community efforts and the perspectives that can be sought for short- and mid-term developments in the field.

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References

  1. Spear, A.D.: Ontology for the Twenty First Century: An Introduction with Recommendations, Saarbruecken, Germany (2006), http://www.ifomis.uni-saarland.de/bfo/manual/manual.pdf

  2. Lodish, H., Berk, A., Kaiser, C.A., Krieger, M., Scott, M.P., Bretscher, A., Ploegh, H., Matsudaira, P.: Molecular Cell Biology, 6th edn. W.H.Freeman, New York (2000)

    Google Scholar 

  3. Rebholz-Schuhmann, D., Arregui, M., Gaudan, S., Kirsh, H., Jimeno, A.: Text processing through Web services: calling Whatizit. Bioinformatics 24(2), 296–298 (2008)

    Article  Google Scholar 

  4. Fink, J.L., Kushch, S., Williams, P.R., Bourne, P.E.: BioLit: integrating biological literature with databases. Nucleic Acids Res. (May 31, 2008)

    Google Scholar 

  5. Bourne, P.: Will a biological database be different from a biological journal? PloS Comp. Biol. 1(3), 34 (2005)

    Article  Google Scholar 

  6. Bons, M.: Which gene did you mean? BMC Bioinformatics 6, 142 (2005)

    Article  Google Scholar 

  7. Bourne, P.E., Fink, J.L., Gerstein, M.: Open Access: Taking Full Advantage of the Content. PloS Comput. Biol. 4(3), 1000037 (2008)

    Article  Google Scholar 

  8. Ball, A.C., Sherlock, G., Parkinson, H., Rocca-Serra, P., Brooksbank, C., Causton, H.C., Cavaliaeri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C.J., Stewart, J.E., Taylor, R., Brazma, A., Quackenbush, J.: An open letter to the scientific journals. Bioinformatics 18(1), 1409 (2002)

    Article  Google Scholar 

  9. Internationl Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)

    Google Scholar 

  10. Lin, S., Lopez, Q., Lorenc, R., McWilliam, D., Mukherjee, H., Nardone, G., Plaister, F., Robinson, S., Sobhany, S., Vaughan, S., Wu, R., Zhu, D.: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acid Res. 36(Database issue), D5–D12 (2008)

    Google Scholar 

  11. Parkinson, H., Kapushesky, M., Shojatalab, M., Abeygunawardena, N., Coulson, R., Farne, A., Holloway, E., Kolesnykov, N., Lilja, P., Mani, R., Rayner, T., Sharma, A., William, E., Sarkans, U., Brazma, A.: ArrayExpress – a pcublic database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35(DB issue), D747–750 (2007)

    Article  Google Scholar 

  12. Galperin, M.Y.: The Molecular Biology Database Collection: 2007 update. Nucleic Acids Res. 35, D3–D4 (2007)

    Article  Google Scholar 

  13. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Res. 36 (January 2008) (Database issue)

    Google Scholar 

  14. Sugawara, H., Ogasawara, O., Okubo, K., Gojobori, T., Tateno, Y.: DDBJ with new system and face. Nucleic Acids Res. 36 (January 2008) (Database issue)

    Google Scholar 

  15. Olivier, M., Eeles, R., Hollstein, M., Khan, M.A., Harris, C.C., Hainaut, P.: The IARC TP53 database: new online mutation analysis and recommendation to users. Hum. Mutat. 19(6), 607–614 (2002)

    Article  Google Scholar 

  16. Hamroun, D., Kato, S., Ishioka, C., Claustres, M., Béroud, C., Soussi, T.: The UMD TP53 database and website: update and revisions. Hum. Mutat. 27(1), 14–20 (2006)

    Article  Google Scholar 

  17. Forbes, S.A., Bharma, G., Bamford, S., Dawson, E., Kok, C., Clements, J., Menzies, A., Teague, J.W., Futreal, P.A., Stratton, M.R.: The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008, ch. 10: Unit 10.11 (April 2008)

    Google Scholar 

  18. The UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008)

    Google Scholar 

  19. Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., Doh, G., Fieri, W., Kronenberg, M., Kubo, R., Lund, O., Nemazee, D., Ponomarenko, J.V., Sathiamurthy, M.S., Choenberger, S., Stewart, S., Surko, P., Way, S., Wilson, S., Sette, A.: The immune epitope database and analysis resource: from vision to blueprint. PloS Biol. 3(3), 91 (2005)

    Article  Google Scholar 

  20. Karp, P.D., Christos, A., Ouzounis, A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., Lopez-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33(19), 6083–6089 (2005)

    Article  Google Scholar 

  21. Paley, S.M., Karp, P.D.: The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 34(13), 3771–3778 (2006)

    Article  Google Scholar 

  22. Krummenacker, M., Paley, S., Mueller, L., Yan, T., Karp, P.D.: Querying and computing with BioCyc databases. Bioinformatics 21(16), 3454–3455 (2005)

    Article  Google Scholar 

  23. Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M., Karp, P.D.: Computational prediction of human metabolic pathways from the complete human genome. Genome Biology 6, R2 (2004)

    Article  Google Scholar 

  24. Vastrik, I., D’Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L.: Reactome: a knowledge base of biologic pathways and processes. Genome Biology 8, R39 (2007)

    Article  Google Scholar 

  25. Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., Kitano, H., Arkin, A., Bornstein, B., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novère, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: SBML Forum: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)

    Article  Google Scholar 

  26. Le Novère, N., Borsntein, B., Broicher, A., Courtout, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, J.L., Hucka, M.: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689–D691 (2006)

    Article  Google Scholar 

  27. LSR: Life Sciences Identifiers RFP Response, http://www.omg.org/docs/lifesci/03-12-02.pdf

  28. Clark, T., Martin, S., Liefeld, T.: Globally distributed object identification for biological knowledgebases. Briefings in Bioinformatics 5, 59–70 (2004)

    Article  Google Scholar 

  29. Etzold, T., Ulyanov, A., Argos, P.: SRS: information retrieval system for molecular biology data banks. Meth. Enzymol. 266, 114–128 (1996)

    Article  Google Scholar 

  30. Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G.-J., Musen, M., Cockerill, M., Hermjakob, H., Mons, A., Packer, A., Pacheco, R., Lewis, S., Berkeley, A., Melton, W., Barris, N., Wales, J., Meijssen, G., Moeller, E., Roes, P.J., Borner, K., Bairoch, A.: Calling on a million minds for community annotation in WikiProteins. Genome Biology 9, R89 (2008)

    Article  Google Scholar 

  31. Salzberg, S.L.: Genome re-annotation: a wiki solution? Genome Biology 8, 102 (2007)

    Article  Google Scholar 

  32. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25(1), 25–29 (2000)

    Google Scholar 

  33. Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Res. 36(Database issue), D440–444 (January 2008)

    Google Scholar 

  34. Mungall, C.J.: Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics 5, 509–520 (2004)

    Article  Google Scholar 

  35. Moreira, D.A., Musen, M.A.: OBO to OWL: a protege OWL tab to read/save OBO ontologies. Bioinformatics 23(14), 1868–1870 (2007)

    Article  Google Scholar 

  36. Aranguren, M.E., Bechhofer, S., Lord, P., Sattler, U., Stevens, R.: Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 8, 57 (2007)

    Article  Google Scholar 

  37. Khatri, P., Drăghici, S.: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21(18), 3587–3595 (2005)

    Article  Google Scholar 

  38. Lord, P.W., Stevens, R.D., Brass, A., Goble, C.A.: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19(10), 1275–1283 (2003)

    Article  Google Scholar 

  39. Côté, R.G., Jones, P., Apweiler, R., Hermjakob, H.: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7, 97 (2006)

    Article  Google Scholar 

  40. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, J., Ceusters, W., Goldberg, J.L., Eilbeck, K., Ireland, A., Mungall, C.J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Scheuermann, R.H., Shah, N., Whetzel, P.L., Lewis, S.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251–1255 (2007)

    Article  Google Scholar 

  41. Bada, M., Hunter, L.: Enrichment of OBO ontologies. J. Biomed. Inform. 40(3), 300–315 (2007)

    Article  Google Scholar 

  42. Myhre, S., Tveit, H., Mollestad, T., Laegreid, A.: Additional gene ontology structure for improved biological reasoning. Bioinformatics 22(16), 2020–2027 (2006)

    Article  Google Scholar 

  43. Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biol. 6(5), R46 (2005)

    Article  Google Scholar 

  44. Cheung, K.-H., Qi, P., Tuck, D., Krauthammer, M.: A semantic web approach to biological pathway data reasoning and integration. Web Semantics: Science, Services and Agents on the World Wide Web (Journal of Web Semantics) 4, 207–215 (2006)

    Article  Google Scholar 

  45. Chen, H., Doherty, D., Forsberg, K., Gao, Y., Kashyap, V., Kinoshita, J., Luciano, J., Marshall, M.S., Ogbuji, C., Rees, J., Stephens, S., Wong, G.T., Wu, E., Zaccagnini, D., Hongsermeier, T., Neumann, E., Herman, I., Cheung, K.-H.: Advancing translational research with the Semantic Web. BMC Bioinformatics 8(suppl. 3), S2 (2007)

    Article  Google Scholar 

  46. Splendiani, A.: RDFScape: Semantic Web meets Systems Biology. BMC Bioinformatics 9(suppl. 4), S6 (2008)

    Article  Google Scholar 

  47. Chatraryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G.: MINT: the Molecular INTeraction database. Nucleic Acids Res. 35, D572–D574 (2007)

    Article  Google Scholar 

  48. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29(4), 365–371 (2001)

    Article  Google Scholar 

  49. Ball, C.A., Brazma, A.: MGED standards: work in progress. OMICS 10(2), 138–144 (2006)

    Article  Google Scholar 

  50. Soldatova, L.N., King, R.D.: Are the current ontologies in biology good ontologies? Nat. Biotechnol. 23(9), 1095–1098 (2005)

    Article  Google Scholar 

  51. Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L.: Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23(12), 1509–1515 (2005)

    Article  Google Scholar 

  52. Whetzel, P.L., Brinkman, R.R., Causton, H.C., Fan, L., Field, D., Fostel, J., Fragoso, G., Gray, T., Heiskanen, M., Hernandez-Boussard, T., Morrison, N., Parkinson, H., Rocca-Serra, P., Sansone, S.A., Schober, D., Smith, B., Stevens, R., Stoeckert, C.J.: FuGO Working Group.: Development of FuGO: an ontology for functional genomics investigations. OMICS 10(2), 199–204 (2006) (review)

    Article  Google Scholar 

  53. Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings in Bioinformatics 3, 331–341 (2002)

    Article  Google Scholar 

  54. Wroe, C., Stevens, R., Goble, C., Roberts, A., Greenwod, M.: A suite of DAML+OIL ontologies to describe bioinformatics web services and data. International Journal of Cooperative Information Systems – Special issue on Bioinformatics 12, 197–224 (2003)

    Article  Google Scholar 

  55. Romano, P.: Automation of in-silico data analysis processes through workflow management systems. Briefings in Bioinformatics 9(1), 57–68 (2008)

    Article  Google Scholar 

  56. Mahoui, M., Ben-Miled, Z., Srinivasan, S., Dippold, M., Yang, B., Li, N.: SIBIOS Ontology: a robust package for the integration and pipelining of bioinformatics services. In: Leser, U., Naumann, F., Eckman, B. (eds.) DILS 2006. LNCS (LNBI), vol. 4075. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  57. Leser, U.: A query language for biological networks. Bioinformatics 21(suppl. 2), 33–39 (2005)

    Google Scholar 

  58. Ruttenberg, A., Rees, J., Zucker, J.: What BioPAX communicates and how to extend OWL to help it. In: Proceeding of OWLed (2006), http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-216/

  59. Karp, P.D., Paley, S.: Automated drawing of metabolic pathways. In: Lim, H., Cantor, C., Robbins, R. (eds.) Proceedings of the Third International Conference on Bioinformatics and Genome Research. Florida State Conference Center, pp. 225–238. Tallahassee, Florida (1994)

    Google Scholar 

  60. Good, B.M., Wilkinson, M.D.: The Life Sciences Semantic Web is full of creeps. Brief Bioinform. 7(3), 275–286 (2006)

    Article  Google Scholar 

  61. Cannata, N., Merelli, E., Altman, R.B.: Time to Organize the Bioinformatics Resourceome. PLoS Computational Biology 1(7), 76 (2007)

    Article  Google Scholar 

  62. Cannata, N., Corradini, F., Gabrielli, S., Leoni, L., Merelli, E., Piersigilli, F., Vito, L.: Intuitive and machine understandable representation of the bioinformatics domain and of related resources with Resourceomes. In: Felicioli, C., Romano, P., Marangoni, R. (eds.) Proc. of the 7th International Workshop NETTAB 2007 on A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications, Pisa, June 12-15, 2007, pp. 35–46 (2007)

    Google Scholar 

  63. Dinov, I.D., Rubin, D., Lorensen, W., Dugan, J., Ma, J., Murphy, S., Kirschner, B., Bug, W., Sherman, M., Floratos, A., Kennedy, D., Jagadish, H.V., Schmidt, J., Athey, B., Califano, A., Musen, A., Altman, R., Kikinis, R., Kohane, I., Delp, S., Parker, D.S., Toga, A.W.: iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. PLoS ONE 3(5), 2265 (2008)

    Article  Google Scholar 

  64. Schröder, M., Burger, A., Kostkova, P., Stevens, R., Habermann, B., Dieng-Kuntz, R.: From a Services-based eScience Infrastructure to a Semantic Web for the Life Sciences: The Sealife Project. In: NETTAB 2006, Santa Margherita di Pula, CA, July 10-13 (2006)

    Google Scholar 

  65. Alexopoulou, D., Wachter, T., Pickersgill, L., Eyre, C., Schroeder, M.: Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. BMC Bioinformatics 9(Suppl. 4), S2 (2008)

    Article  Google Scholar 

  66. Neumann, E.K., Quan, D.: BioDash: a Semantic Web dashboard for drug development. In: Proc. Pacific Symposium Biocomputing (PSB 2006), pp. 176–187 (2006)

    Google Scholar 

  67. HCLS Charter, http://www.w3.org/2008/05/HCLSIGCharter

  68. A Prototype Knowledge Base for the Life Sciences, W3C Interest Group Note (June 4, 2008), http://www.w3.org/TR/hcls-kb/

  69. Lam, H.Y.K., Marenco, L., Clark, T., Gao, Y., Kinoshita, J., Shepherd, G., Miller, P., Wu, E., Wong, G.T., Liu, N., Crasto, C., Morse, T., Stephens, S., Cheung, K.-H.: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 8(suppl. 3), S4 (2007)

    Article  Google Scholar 

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Authors and Affiliations

  1. National Cancer Research Institute, Largo Rosanna Benzi 10, I-16132, Genova, Italy

    Paolo Romano

  2. University of Rennes 1, 2, rue Henri Le Guilloux, F-35033, Rennes, France

    Andrea Splendiani

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  1. Paolo Romano
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Cristina Baroglio Piero A. Bonatti Jan Małuszyński Massimo Marchiori Axel Polleres Sebastian Schaffert

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Romano, P., Splendiani, A. (2008). Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics. In: Baroglio, C., Bonatti, P.A., Małuszyński, J., Marchiori, M., Polleres, A., Schaffert, S. (eds) Reasoning Web. Lecture Notes in Computer Science, vol 5224. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85658-0_6

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