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eScience

  • Jun Zhao
  • Oscar Corcho
  • Paolo Missier
  • Khalid Belhajjame
  • David Newmann
  • David de Roure
  • Carole A. Goble

Abstract

This chapter looks into how the use of semantic technologies can provide support to common needs in eScience projects, including data-intensive science, facilitating experiment knowledge reuse and recycle among scientists, lowering the barriers of knowledge exchange for interdisciplinary research, and bridging the gap between data from different sources and the gap between data sharing and digital scholarly publication. To illustrate this, we describe a set of pioneering semantic eScience projects that cover a diversity of application domains including bioinformatics, biology, chemistry, physics, environmental science, and astronomy, and we summarize some of the open issues and future lines of research and development in this area.

Keywords

Data integration e-Science knowledge transfer provenance quality semantic publishing semantic Web trust usability Web of Data 

References

  1. 1.
    Galperin, M., Cochrane, G.: Nucleic acids research annual database issue and the NAR online molecular biology database collection in 2009. Nucleic Acids Res. 37(Database issue), 1–4 (2009)CrossRefGoogle Scholar
  2. 2.
    Clery, D., Voss, D.: All for one and one for all. Science 308(5723), 809 (2005)CrossRefGoogle Scholar
  3. 3.
    McGuinness, D., Fox, P., Brodaric, B., Kendall, E.: The emerging field of semantic scientific knowledge integration. IEEE Intell. Syst. 24(1), 25–26 (2009)CrossRefGoogle Scholar
  4. 4.
    McGuinness, D., Fox, P., Cinquini, L., West, P., Garcia, J., Benedict, J., Middleton, D.: The virtual solar-terrestrial observatory: a deployed semantic web application case study for scientific research. In: Proceedings of the 22nd AAAI Conference on Artificial Intelligence (AAAI-07), Vancouver, pp. 1730–1737 (2007)Google Scholar
  5. 5.
    Ludascher, B., Goble, C.: Guest editors’ introduction to the special section on scientific workflows. SIGMOD Rec. 34(3), 2 (2005)CrossRefGoogle Scholar
  6. 6.
    Web Services activity statement: World Wide Web Consortium (W3C) activity statement. http://www.w3.org/2002/ws/Activity.html (Apr 2004). Accessed Dec 2010
  7. 7.
    Moreau, L., Ludascher, B., Altintas, I., Barga, R., Bowers, S., Callahan, S., Chin, J.R., Clifford, B., Cohen, S., Cohen-Boulakia, S.: Special issue: the first provenance challenge. Concurr. Comput Pract. Exp. 20(5), 409–418 (2008)CrossRefGoogle Scholar
  8. 8.
    W3C semantic web activity. http://www.w3.org/2001/sw/ (2001). Accessed 14 July 2009
  9. 9.
    Klyne, G., Carroll, J.J., McBride, B.: Resource Description Framework (RDF): concepts and abstract syntax, W3C recommendation. http://www.w3.org/TR/rdf-concepts/ (2004). Accessed Dec 2010
  10. 10.
    Gruber, T.: A translation approach to portable ontology specifications. Knowl. Acquis. 5, 199–220 (1993)CrossRefGoogle Scholar
  11. 11.
    Brickley, D., Guha, R.: RDF vocabulary description language 1.0: RDF schema, W3C recommendation (2004)Google Scholar
  12. 12.
    McGuinness, D., Van Harmelen, F.: OWL web ontology language overview, W3C recommendation (2004)Google Scholar
  13. 13.
    Brickley, D., Miller, L.: FOAF vocabulary specification 0.9. Namespace document (2007)Google Scholar
  14. 14.
    Breslin, J., Harth, A., Bojars, U., Decker, S.: Towards semantically-interlinked online communities. In: Proceedings of the Second European Semantic Web Conference (ESWC 2005), Heraklion. Lecture Notes in Computer Science, vol. 3532, pp. 500–514. Springer, Berlin (2005)Google Scholar
  15. 15.
    Prud’hommeaux, E., Seaborne, A.: SPARQL query language for RDF, W3C Recommendation. http://www.w3.org/TR/rdf-sparql-query/ (2008). Accessed 15 Jan 2008
  16. 16.
    Clark, K.G., Feigenbaum, L., Torres, E.: SPARQL protocol for RDF, W3C Recommendation. http://www.w3.org/TR/rdf-sparql-protocol/ (2008). Accessed 15 Jan 2008
  17. 17.
    Berners-Lee, T., Cailliau, R.: The world-wide web. Commun. ACM 37(8), 76–82 (1992)CrossRefGoogle Scholar
  18. 18.
    Berners-Lee, T.: Linked data-design issues. http://www.w3.org/DesignIssues/LinkedData.html (2006). Accessed 14 July 2009
  19. 19.
    Bizer, C., Health, T., Berners-Lee, T.: Linked Data – the story so far. Int. J. Semant. Web Inf. Syst. 5(3), 1–22 (2009). (Special Issue on Linked Data)CrossRefGoogle Scholar
  20. 20.
    Fielding, R., Gettys, J., Mogul, J., Frystyk, H., Berners-Lee, T.: RFC2616: hypertext transfer protocol – HTTP/1.1. Internet RFCs (1999). Accessed Dec 2010Google Scholar
  21. 21.
    Berners-Lee, T., Fielding, R., Masinter, L.: RFC 2396: Uniform Resource Identifiers (URI): generic syntax. Internet RFCs (1998)Google Scholar
  22. 22.
    Fox, P., McGuinness, D., Cinquini, L., West, P., Garcia, J., Benedict, J., Middleton, D.: Ontology-supported scientific data frameworks: the virtual solar-terrestrial observatory experience. Comput. Geosci. 35(4), 724–738 (2009)CrossRefGoogle Scholar
  23. 23.
    Fox, P., Cinquini, L., McGuinness, D., West, P., Garcia, J., Benedict, J., Zednik, S.: Semantic web services for interdisciplinary scientific data query and retrieval. In: Proceedings of the AAAI Semantic e-Science Workshop, Vancouver, pp. 42–50 (2007)Google Scholar
  24. 24.
    Wright, R., Sánchez-Gestido, M., Gómez-Pérez, A., Pérez-Hernández, M.S., González-Cabero, R., Corcho, O.: A semantic data grid for satellite mission quality analysis. In: Proceedings of the Seventh International Semantic Web Conference (ISWC 2008), Karlsruhe. Lecture Notes in Computer Science, vol. 5318, pp. 818–832. Springer, Heidelberg (2008)Google Scholar
  25. 25.
    ESA bulletin number 106, “EnviSat special issue”. http://www.esa.int/esapub/pi/bulletinPI.htm. Accessed Dec 2010
  26. 26.
    De Roure, D., Goble, C., Stevens, R.: Designing the myexperiment virtual research environment for the social sharing of workflows. In: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing, Bangalore, pp. 603–610 (2007)Google Scholar
  27. 27.
    De Roure, D., Goble, C., Aleksejevs, S., Bechhofer, S., Bhagat, J., Cruickshank, D., Fisher, P., Hull, D., Michaelides, D., Newman, D.: Towards open science: the myExperiment approach. Concurr. Comput. Pract. Exp. 22(17), 2335–2353 (2010)CrossRefGoogle Scholar
  28. 28.
    De Roure, D., Goble, C., Bhagat, J., Cruickshank, D., Goderis, A., Michaelides, D., Newman, D.: myExperiment: defining the social virtual research environment. In: Proceedings of the Fourth IEEE International Conference on e-Science, Indianapolis, pp. 182–189 (2008)Google Scholar
  29. 29.
    Newman, D., Bechhofer, S., De Roure, D.: myExperiment: an ontology for e-research. In: Workshop on Semantic Web Applications in Scientific Discourse, Washington, DC (2009)Google Scholar
  30. 30.
    Preece, A., Jin, B., Pignotti, E., Missier, P., Embury, S., Stead, D., Brown, A.: Managing information quality in e-Science using semantic web technology. In: Proceedings of the Third European Semantic Web Conference (ESWC 2006), Budva. Lecture Notes in Computer Science, vol. 4011, pp. 472–486. Springer, Berlin (2006)Google Scholar
  31. 31.
    Missier, P., Embury, S., Greenwood, M., Preece, A., Jin, B.: Quality views: capturing and exploiting the user perspective on data quality. In: Proceedings of the 32nd Very Large Data Bases (VLDB 2006), Seoul, pp. 977–988 (2006)Google Scholar
  32. 32.
    Missier, P., Embury, S., Greenwood, M., Preece, A., Jin, B.: Managing information quality in e-Science: the qurator workbench. In: Proceedings of the 2007 ACM SIGMOD International Conference on Management of Data, Beijing, pp. 1150–1152 (2007)Google Scholar
  33. 33.
    Belhajjame, K., Embury, S., Paton, N.: On characterising and identifying mismatches in scientific workflows. In: Proceedings of the Third International Workshop on Data Integration in the Life Sciences (DILS 2006), Hinxton. Lecture Notes in Computer Science, vol. 4075, pp. 240–247. Springer, Berlin (2006)Google Scholar
  34. 34.
    Goble, C., Belhajjame, K., Tanoh, F., Bhagat, J., Wolstencroft, K., Stevens, R., Nzuobontane, E., McWilliam, H., Laurent, T., Lopez, R.: BioCatalogue: a curated web service registry for the life science community. In: Microsoft eScience Conference, Nature Precedings, Indianapolis, p. 3132 (2008)Google Scholar
  35. 35.
    Wolstencroft, K., Alper, P., Hull, D., Wroe, C., Lord, P.W., Stevens, R.D., Goble, C.A.: The myGrid ontology: bioinformatics service discovery. Int. J. Bioinform. Res. Appl. 3(3), 303–325 (2007)CrossRefGoogle Scholar
  36. 36.
    Belhajjame, K., Embury, S., Paton, N., Stevens, R., Goble, C.: Automatic annotation of web services based on workflow definitions. ACM Trans. Web 2(2), 1–34 (2008)CrossRefGoogle Scholar
  37. 37.
    Stein, L.: Integrating biological databases. Nat. Rev. Genet. 4(5), 337–345 (2003)CrossRefGoogle Scholar
  38. 38.
    Stein, L.: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat. Rev. Genet. 9(9), 678–688 (2008)CrossRefGoogle Scholar
  39. 39.
    Hull, D., Stevens, R., Lord, P., Goble, C.: Integrating bioinformatics resources using shims. Poster Abstract in Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology, Glasgow (2004)Google Scholar
  40. 40.
    Bizer, C., Cyganiak, R.: D2R server-publishing relational databases on the semantic web. Poster Session of the Fifth International Semantic Web Conference (ISWC 2006), Athens (2006)Google Scholar
  41. 41.
    Barrasa, J., Corcho, O., Gómez-Pérez, A.: R2O, an extensible and semantically based database-to-ontology mapping language. In: Proceedings of the Second Workshop on Semantic Web and Databases (SWDB 2004), Toronto (2004)Google Scholar
  42. 42.
    Auer, S., Dietzold, S., Lehmann, J., Hellmann, S., Aumueller, D.: Triplify: light-weight linked data publication from relational databases. In: Proceedings of the 18th International Conference on the World Wide Web (WWW 2009), Madrid, pp. 621–630 (2009)Google Scholar
  43. 43.
    Berners-Lee, T., Chen, Y., Chilton, L., Connolly, D., Dhanaraj, R., Hollenbach, J., Lerer, A., Sheets, D.: Tabulator: exploring and analyzing linked data on the semantic web. In: Proceedings of the Third International Semantic Web User Interaction Workshop (SWUT 2006), Athens, GA (2006)Google Scholar
  44. 44.
    Jentzsch, A., Zhao, J., Hassanzadeh, O., Cheung, K.-H., Samwald, M., Andersson, B.: Linking open drug data. In: Triplification Challenge of I-Semantics’09, Graz (2009)Google Scholar
  45. 45.
    Volz, J., Bizer, C., Gaedke, M., Kobilarov, G.: Silk – a link discovery framework for the web of data. In: Proceedings of the Linked Data on the Web Workshop at WWW 2009, Madrid (2009)Google Scholar
  46. 46.
    Hassanzadeh, O.: A framework for semantic link discovery over relational data. In: Proceedings of the 18th ACM Conference on Information and Knowledge Management (CIKM 2009), Hong Kong, pp. 1027–1036 (2009)Google Scholar
  47. 47.
    Volz, J., Bizer, C., Gaedke, M., Kobilarov, G.: Discovering and maintaining links on the web of data. In: Proceedings of the Eighth International Semantic Web Conference (ISWC 2009), Chantilly. Lecture Notes in Computer Science, vol. 5823, pp. 650–665. Springer, Berlin (2009)Google Scholar
  48. 48.
    Murray-Rust, P.: Chemistry for everyone. Nature 451(7179), 648–651 (2008)CrossRefGoogle Scholar
  49. 49.
    Shotton, D.: Semantic publishing: the coming revolution in scientific journal publishing. Learn. Publ. 22(2), 85–94 (2009)CrossRefGoogle Scholar
  50. 50.
    Corbett, P., Murray-Rust, P.: High-throughput identification of chemistry in life science texts. Comput. Life Sci. II 4216, 107–118 (2006)CrossRefGoogle Scholar
  51. 51.
    Degtyarenko, K., Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., Ashburner, M.: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350 (2007)CrossRefGoogle Scholar
  52. 52.
    Weininger, D.: SMILES, a chemical language and information system. J. Chem. Inf. Comput. Sci. 28(1), 31–36 (1988)CrossRefGoogle Scholar
  53. 53.
    Research Information: Semantic enrichment boosts information retrieval. http://www.researchinformation.info/features/feature.php?feature_id=127 (2007). Accessed Dec 2010
  54. 54.
    Shotton, D., Portwin, K., Klyne, G., Miles, A.: Adventures in semantic publishing: exemplar semantic enhancements of a research article. PLoS Comput. Biol. 5(4), e1000361 (2009)CrossRefGoogle Scholar
  55. 55.
    Shotton, D.: CiTO, the Citation Typing Ontology, and its use for annotation of reference lists and visualization of citation networks. In: Proceedings of the 12th Annual Bio-Ontologies Meeting, Stockholm (2009)Google Scholar
  56. 56.
    Pafilis, E., O’Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., Schneider, R.: Reflect: augmented browsing for the life scientist. Nat. Biotechnol. 27(6), 508–510 (2009)CrossRefGoogle Scholar
  57. 57.
    Ding, L., Finin, T., Joshi, A., Pan, R., Cost, R., Peng, Y., Reddivari, P., Doshi, V., Sachs, J.: Swoogle: a search and metadata engine for the semantic web. In: Proceedings of the 13th ACM International Conference on Information and Knowledge Management (CIKM 2004), Washington, DC, pp. 652–659 (2004)Google Scholar
  58. 58.
    d’Aquin, M., Sabou, M., Motta, E.: Reusing knowledge from the semantic web with the Watson Plugin. In: Demo, Proceedings of the Seventh International Semantic Web Conference (ISWC 2008), Karlsruhe. Lecture Notes in Computer Science, vol. 5318. Springer, Berlin (2008)Google Scholar
  59. 59.
    Harth, A., Umbrich, J., Decker, S.: Multicrawler: A pipelined architecture for crawling and indexing semantic web data. In: Proceedings of the International Semantic Web Conference (ISWC 2006), Sardinia. Lecture Notes in Computer Science, vol. 3729, pp. 258–271. Springer, Heidelberg (2006)Google Scholar
  60. 60.
    Tummarello, G., Delbru, R., Oren, E.: Sindice. com: weaving the open linked data. In: Proceedings of the Sixth International Semantic Web Conference (ISWC 2007), Busan. Lecture Notes in Computer Science, vol. 4825, pp. 552–565. Springer, Heidelberg (2007)Google Scholar
  61. 61.
    Cheung, K., Frost, H., Marshall, M., Prud’hommeaux, E., Samwald, M., Zhao, J., Paschke, A.: A journey to semantic web query federation in life sciences. BMC Bioinform. 10(Suppl 10), S10 (2009)CrossRefGoogle Scholar
  62. 62.
    Belleau, F., Nolin, M., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41(5), 706–716 (2008)CrossRefGoogle Scholar
  63. 63.
    Sahoo, S.S.,Halb, W., Hellmann, S., Idehen, K., Thibodeau Jr, T., Auer, S., Sequeda, J., Ezzat, A.: A survey of current approaches for mapping of relational databases to RDF. W3C Technical Report. http://www.w3.org/2005/Incubator/rdb2rdf/RDB2RDF_SurveyReport.pdf (2009)

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Jun Zhao
    • 1
  • Oscar Corcho
    • 2
  • Paolo Missier
    • 3
  • Khalid Belhajjame
    • 3
  • David Newmann
    • 4
  • David de Roure
    • 5
  • Carole A. Goble
    • 3
  1. 1.Department of ZoologyOxford UniversityOxfordUK
  2. 2.Ontology Engineering Group, Departamento de Inteligencia Artificial, Facultad de InformáticaUniversidad Politécnica de MadridBoadilla del MonteSpain
  3. 3.School of Computer ScienceUniversity of ManchesterManchesterUK
  4. 4.School of Electronics and Computer ScienceUniversity of SouthamptonSouthamptonUK
  5. 5.Oxford e-Research CentreUniversity of OxfordOxfordUK

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