Abstract
The amount of bioinformatics services available over the web has dramatically increased over the last years. Generalist on-line catalogs help identifying a particular service in such a pool. Unfortunately, most of the time, querying those catalogs is only based on a textual search for a particular datatype or a domain of interest. In this context, we have developed the Structural Bioinformatics Semantic Map (SBMap), a dual level ontology that allows users to discover structural bioinformatics resources through the exploration of a graph of high level concepts. In this paper, we present how participative design workshops helped us to improve the navigation experiment. The SBMap discovery tool (release-candidate) is available at: http://sbmap.rpbs.univ-paris-diderot.fr
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Brazas, M.D., Yamada, J.T., Ouellette, B.F.F.: Evolution in bioinformatic resources: 2009 update on the bioinformatics links directory. Nucleic Acids Res. 37, W3–W5 (2009)
Cochrane, G.R., Galperin, M.Y.: The 2010 nucleic acids research database issue and online database collection: a community of data resources. Nucleic Acids Res. 38, D1–D4 (2010)
Benson, G.: Editorial. nucleic acids research annual web server issue in 2010. Nucleic Acids Res. 38(suppl.), W1–W2 (2010)
Tufféry, P., Lacroix, Z., Ménager, H.: Semantic map of services for structural bioinformatics. In: 18th International Conference on Scientific and Statistical Database Management (SSDBM), pp. 217–224. IEEE Press, Los Alamitos (2006)
Ménager, H., Tufféry, P., Lacroix, Z.: Bioinformatics services discovery using ontology classification. In: 1st IEEE International Workshop on Service Oriented Technologies for Biological Databases and Tools, In conjunction with ICWS/SCC, pp. 106–113. IEEE Press, Los Alamitos (2007)
Wilkinson, M.D., Senger, M., Kawas, E., et al.: Interoperability with moby 1.0–it’s better than sharing your toothbrush! Brief Bioinform. 9, 220–231 (2008)
Oinn, T., Addis, M., Ferris, J., et al.: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics Journal 20, 3045–3054 (2004)
Carrere, S., Gouzy, J.: Remora: a pilot in the ocean of biomoby web-services. Bioinformatics 22, 900–901 (2006)
Lacroix, Z., Ménager, H.: SemanticBio: Building conceptual scientific workflows over web services. In: Ludäscher, B., Raschid, L. (eds.) DILS 2005. LNCS (LNBI), vol. 3615, pp. 296–299. Springer, Heidelberg (2005)
Wang, R., Brewer, D., Shastri, S., Swayampakula, S., Miller, J.A., Kraemer, E., Kissinger, J.C.: Adapting the galaxy bioinformatics tool to support semantic web service composition. In: SERVICES I, pp. 283–290 (2009)
Néron, B., Ménager, H., Maufrais, C., et al.: Mobyle: a new full web bioinformatics framework. Bioinformatics 25, 3005–3011 (2009)
Kawas, E., Senger, M., Wilkinson, M.D.: Biomoby extensions to the taverna workflow management and enactment software. BMC Bioinformatics 7, 523 (2006)
Wilkinson, M.D., Vandervalk, B.P., McCarthy, E.L.: SADI semantic web services–’cause you can’t always GET what you want. In: Kirchberg, M., Hung, P.C.K., Carminati, B., Chi, C.H., Kanagasabai, R., Valle, E.D., Lan, K.C., Chen, L.J. (eds.) APSCC, pp. 13–18. IEEE, Los Alamitos (2009)
Matos, E.E., Campos, F., Braga, R.M.M., Palazzi, D.: CelOWS: An ontology based framework for the provision of semantic web services related to biological models. Journal of Biomedical Informatics 43, 125–136 (2010)
Sbodio, M.L., Martin, D., Moulin, C.: Discovering semantic web services using SPARQL and intelligent agents. J. Web Sem. 8, 310–328 (2010)
Bhagat, J., Tanoh, F., Nzuobontane, E., et al.: Biocatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 38(supl.), W689–694 (2010)
Lacroix, Z., Aziz, M.: Resource descriptions, ontology, and resource discovery. Int. J. of Metadata and Semantics and Ontologies 5, 194–207 (2010)
Lacroix, Z., Morris, T., Parekh, K.: et al.: Exploiting multiple paths to express scientific queries. In: Scientific and Statistical Database Management (SSDBM), pp. 357–360. IEEE Computer Society, Los Alamitos (2004)
Cohen-Boulakia, S., Davidson, S., Froidevaux, C., Lacroix, Z., Vidal, M.E.: Path-based systems to guide scientists in the maze of biological data sources. J. Bioinform Comput. Biol. 4, 1069–1095 (2006)
Côté, R.G., Jones, P., Martens, L., et al.: The ontology lookup service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res. 36, W372–376 (2008)
Noy, N.F., Shah, N.H., Whetzel, P.L., et al.: Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 37, W170–173 (2009)
McGuinness, D.L., van Harmelen, F.: Owl web ontology language overview. W3C Recommendation (2004), http://www.w3.org/TR/owl-features/
Gansner, E.R., North, S.C.: An open graph visualization system and its applications to software engineering. Software - Practice and Experience, 1203–1233 (2000)
Sabou, M., Pan, J.Z.: Towards semantically enhanced web service repositories. J. Web Sem. 5, 142–150 (2007)
Hao, Y., Zhang, Y., Cao, J.: Web services discovery and rank: An information retrieval approach. Future Generation Comp. Syst. 26, 1053–1062 (2010)
Liu, M., Shen, W., Hao, Q., Yan, J.: An weighted ontology-based semantic similarity algorithm for web service. Expert Syst. Appl. 36, 12480–12490 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Strauser, E., Naveau, M., Ménager, H., Maupetit, J., Lacroix, Z., Tufféry, P. (2012). Semantic Map for Structural Bioinformatics: Enhanced Service Discovery Based on High Level Concept Ontology. In: Lacroix, Z., Vidal, M.E. (eds) Resource Discovery. RED 2010. Lecture Notes in Computer Science, vol 6799. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27392-6_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-27392-6_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-27391-9
Online ISBN: 978-3-642-27392-6
eBook Packages: Computer ScienceComputer Science (R0)