Reasoning Web pp 200-239 | Cite as

Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics

  • Paolo Romano
  • Andrea Splendiani
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5224)

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.

Keywords

biological data integration molecular biology databases bio-ontologies semantic web applications 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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. 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. 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)CrossRefGoogle Scholar
  4. 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. 5.
    Bourne, P.: Will a biological database be different from a biological journal? PloS Comp. Biol. 1(3), 34 (2005)CrossRefGoogle Scholar
  6. 6.
    Bons, M.: Which gene did you mean? BMC Bioinformatics 6, 142 (2005)CrossRefGoogle Scholar
  7. 7.
    Bourne, P.E., Fink, J.L., Gerstein, M.: Open Access: Taking Full Advantage of the Content. PloS Comput. Biol. 4(3), 1000037 (2008)CrossRefGoogle Scholar
  8. 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)CrossRefGoogle Scholar
  9. 9.
    Internationl Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)Google Scholar
  10. 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. 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)CrossRefGoogle Scholar
  12. 12.
    Galperin, M.Y.: The Molecular Biology Database Collection: 2007 update. Nucleic Acids Res. 35, D3–D4 (2007)CrossRefGoogle Scholar
  13. 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. 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. 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)CrossRefGoogle Scholar
  16. 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)CrossRefGoogle Scholar
  17. 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. 18.
    The UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008)Google Scholar
  19. 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)CrossRefGoogle Scholar
  20. 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)CrossRefGoogle Scholar
  21. 21.
    Paley, S.M., Karp, P.D.: The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 34(13), 3771–3778 (2006)CrossRefGoogle Scholar
  22. 22.
    Krummenacker, M., Paley, S., Mueller, L., Yan, T., Karp, P.D.: Querying and computing with BioCyc databases. Bioinformatics 21(16), 3454–3455 (2005)CrossRefGoogle Scholar
  23. 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)CrossRefGoogle Scholar
  24. 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)CrossRefGoogle Scholar
  25. 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)CrossRefGoogle Scholar
  26. 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)CrossRefGoogle Scholar
  27. 27.
    LSR: Life Sciences Identifiers RFP Response, http://www.omg.org/docs/lifesci/03-12-02.pdf
  28. 28.
    Clark, T., Martin, S., Liefeld, T.: Globally distributed object identification for biological knowledgebases. Briefings in Bioinformatics 5, 59–70 (2004)CrossRefGoogle Scholar
  29. 29.
    Etzold, T., Ulyanov, A., Argos, P.: SRS: information retrieval system for molecular biology data banks. Meth. Enzymol. 266, 114–128 (1996)CrossRefGoogle Scholar
  30. 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)CrossRefGoogle Scholar
  31. 31.
    Salzberg, S.L.: Genome re-annotation: a wiki solution? Genome Biology 8, 102 (2007)CrossRefGoogle Scholar
  32. 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. 33.
    Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Res. 36(Database issue), D440–444 (January 2008)Google Scholar
  34. 34.
    Mungall, C.J.: Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics 5, 509–520 (2004)CrossRefGoogle Scholar
  35. 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)CrossRefGoogle Scholar
  36. 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)CrossRefGoogle Scholar
  37. 37.
    Khatri, P., Drăghici, S.: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21(18), 3587–3595 (2005)CrossRefGoogle Scholar
  38. 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)CrossRefGoogle Scholar
  39. 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)CrossRefGoogle Scholar
  40. 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)CrossRefGoogle Scholar
  41. 41.
    Bada, M., Hunter, L.: Enrichment of OBO ontologies. J. Biomed. Inform. 40(3), 300–315 (2007)CrossRefGoogle Scholar
  42. 42.
    Myhre, S., Tveit, H., Mollestad, T., Laegreid, A.: Additional gene ontology structure for improved biological reasoning. Bioinformatics 22(16), 2020–2027 (2006)CrossRefGoogle Scholar
  43. 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)CrossRefGoogle Scholar
  44. 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)CrossRefGoogle Scholar
  45. 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)CrossRefGoogle Scholar
  46. 46.
    Splendiani, A.: RDFScape: Semantic Web meets Systems Biology. BMC Bioinformatics 9(suppl. 4), S6 (2008)CrossRefGoogle Scholar
  47. 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)CrossRefGoogle Scholar
  48. 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)CrossRefGoogle Scholar
  49. 49.
    Ball, C.A., Brazma, A.: MGED standards: work in progress. OMICS 10(2), 138–144 (2006)CrossRefGoogle Scholar
  50. 50.
    Soldatova, L.N., King, R.D.: Are the current ontologies in biology good ontologies? Nat. Biotechnol. 23(9), 1095–1098 (2005)CrossRefGoogle Scholar
  51. 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)CrossRefGoogle Scholar
  52. 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)CrossRefGoogle Scholar
  53. 53.
    Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings in Bioinformatics 3, 331–341 (2002)CrossRefGoogle Scholar
  54. 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)CrossRefGoogle Scholar
  55. 55.
    Romano, P.: Automation of in-silico data analysis processes through workflow management systems. Briefings in Bioinformatics 9(1), 57–68 (2008)CrossRefGoogle Scholar
  56. 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)CrossRefGoogle Scholar
  57. 57.
    Leser, U.: A query language for biological networks. Bioinformatics 21(suppl. 2), 33–39 (2005)Google Scholar
  58. 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. 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. 60.
    Good, B.M., Wilkinson, M.D.: The Life Sciences Semantic Web is full of creeps. Brief Bioinform. 7(3), 275–286 (2006)CrossRefGoogle Scholar
  61. 61.
    Cannata, N., Merelli, E., Altman, R.B.: Time to Organize the Bioinformatics Resourceome. PLoS Computational Biology 1(7), 76 (2007)CrossRefGoogle Scholar
  62. 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. 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)CrossRefGoogle Scholar
  64. 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. 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)CrossRefGoogle Scholar
  66. 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. 67.
  68. 68.
    A Prototype Knowledge Base for the Life Sciences, W3C Interest Group Note (June 4, 2008), http://www.w3.org/TR/hcls-kb/
  69. 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)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Paolo Romano
    • 1
  • Andrea Splendiani
    • 2
  1. 1.National Cancer Research InstituteGenovaItaly
  2. 2.University of Rennes 1RennesFrance

Personalised recommendations