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Semantic Web pp 317–340Cite as

Sembowser - Semantic Biological Web Services Registry

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Abstract

There are now more than a thousand Web Services [22] offering access to disparate biological resources namely data and computational tools. It is extremely difficult for biological researchers to search in a Web Services (WS) registry for a relevant WS using the standard (primarily computational) descriptions used to describe it. Semantic Biological Web Services Registry (SemBOWSER) is an ontology-based implementation of the UDDI specification, which enables, at present, glycoproteomics researchers to publish, search and discover WS using semantic, service-level, descriptive domain keywords. SemBOWSER classifies a WS along two dimensions- the task they implement and the domain they are associated with. Each published WS is associated with the relevant ProPreO (comprehensive process ontology for glycoproteomics experimental lifecycle) ontology-based keywords (implemented as part of the registry). A researcher, in turn, can search for relevant WS using only the descriptive keywords, part of their everyday working lexicon. This intuitive search is underpinned by the ProPreO ontology, thereby making use of the inherent advantages of a semantic search, as compared to a purely syntactic search, namely disambiguation and use of named relationships between concepts. SemBOWSER is part of the glycoproteomics web portal’ stargate’.

Key words

  • Semantic Web services
  • Web services registry
  • ProPreO ontology
  • SemBOWSER registry
  • WSDL-S
  • biomedical glycomics
  • service-level semantic annotation

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References

  1. Aleman-Meza B., Halaschek-Wiener C., Arpinar I.A., Ramakrishnan C., and Sheth, A., Ranking Complex Relationships on the Semantic Web, IEEE Internet Computing, 9(3), pp. 37–44, May/June 2005

    CrossRef  Google Scholar 

  2. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. “Basic local alignment search tool. J. Mol. Biol. 215:403–410, 1990

    PubMed  CAS  Google Scholar 

  3. Anyanwu K., Maduko A., and Sheth. A. SemRank: Ranking Complex Relationship Search Results on the Semantic Web. In the Proceedings of the 14th International World Wide Web Conference (WWW2005), May 2005. Chiba Japan, 117–127.

    Google Scholar 

  4. 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 Nature Genet. 25: 25–29, 2000.

    PubMed  CrossRef  CAS  Google Scholar 

  5. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L.L., Studholme D.J., Yeats C, and Eddy S.R., “The Pfam Protein Families Database”, Nucleic Acids ResearchDatabase Issue 32:D138–D141, 2004 (http://www.sanger.ac.uk/Software/Pfam/)

    CrossRef  CAS  Google Scholar 

  6. Cardoso J., Sheth A., Miller J., Arnold J., and Kochut K., Quality of Service for Workflows and Web Service Processes, Journal of Web Semantics, Elsevier, 1(3), 281–308, 2004.

    Google Scholar 

  7. Goble C, Using the Semantic Web for e-Science: Inspiration, Incubation, Irritation Lecture Notes in Computer Science 3729:1–3

    Google Scholar 

  8. Gomadam K., Verma K., Brewer D., Sheth A.P., and Miller, J.A. Radiant: A tool for semantic annotation of Web Services, 4th International Semantic Web Conference (ISWC 2005) Galway, Ireland

    Google Scholar 

  9. http://bioontology.org/resources-obo.html, Open Biomedical Ontologies-OBO

    Google Scholar 

  10. http://lsdis.cs.uga.edu/projects/meteor-s/, METEOR-S: Semantic Web services and processes

    Google Scholar 

  11. http://www.ncbi.nlm.nih.gov/, NCBI homepage

    Google Scholar 

  12. http://www.rosettanet.org/Rosettanet/Public/PublicHomePage, RosettaNet Standard

    Google Scholar 

  13. http://www.snomed.org/snomedct/, SNOMED-CT

    Google Scholar 

  14. http://www.uddi.org/, UDDI

    Google Scholar 

  15. http://www.w3.org/2001/sw/hcls/, W3C Semantic Web Health Care and Life Sciences Interest Group

    Google Scholar 

  16. http://www.w3.org/2002/ws/sawsdl/#Charter, Semantic Annotations for WSDL Working Group charter

    Google Scholar 

  17. http://www.w3.org/Submission/OWL-S/, OWL-S

    Google Scholar 

  18. http://www.w3.org/TR/wsdl, Web Services Description Language-WSDL

    Google Scholar 

  19. http://www.w3.org/Submission/WSDL-S/, WSDL-S

    Google Scholar 

  20. http://www.w3.org/TR/owl-features/, Web Ontology Language-OWL

    Google Scholar 

  21. http://www.wsmo.org/TR/d16/d16.l/v0.21/, Web Service Modeling Language (WSML)

    Google Scholar 

  22. Hull D., Stevens R., and Lord P. Describing Web Services for user-oriented retrieval W3C Workshop on Frameworks for Semantics in Web Services, Digital Enterprise Research Institute (DERI), Innsbruck, Austria. 2005.

    Google Scholar 

  23. Li K., Verma K., Miller J., Gomadam K., and Sheth A., Semantic Web Process Design, in Semantic Web Processes and Their Applications. J. Cardiso, A. Sheth, Editors. Springer, 2006 (in print)

    Google Scholar 

  24. Lord P., Bechhofer S., Wilkinson M.D., Schiltz G., Gessler D.

    Google Scholar 

  25. Hull D., Goble C, Stein L. Applying semantic web services to Bioinformatics: Experiences gained, lessons learnt in ISWC 2004. Springer-Verlag Berlin Heidelberg, p350–364.

    Google Scholar 

  26. Lord P., Alper P., Wroe C, and Goble C., Feta: A light-weight architecture for user oriented semantic service discovery in Proc of 2 nd European Semantic Web Conference, Crete, June 2005.

    Google Scholar 

  27. Nagarajan M., Verma K., Sheth A.P., Miller J., and Lathem J., Semantic Interoperability of Web Services-Challenges and Experiences, ICWS 2006

    Google Scholar 

  28. Navas-Delgado I., Rojano-Muñoz M., Ramírez S., Pérez A.J., Andrés León E., Aldana-Montes J.F., and Trelles O. Intelligent client for integrating bioinformatics services, Bioinformatics Advance Access published on January 1, 2006, DOI 10.1093/bioinformatics/bti740. Bioinformatics 22: 106–111., 2006.

    PubMed  CrossRef  CAS  Google Scholar 

  29. Oinn T., Greenwood M., Addis M., Alpdemir M.N., Ferris J., Glover K., Goble C, Goderis A., Hull D., Marvin D., Li P., Lord P., Pocock M.R., Senger M., Stevens R., Wipat A., and Wroe C. Taverna: Lessons in creating a workflow environment for the life sciences Concurrency Computat. Pract. Exper. 00:1–7, 2000.

    Google Scholar 

  30. Oldham N., Verma K., Sheth A.P., Hakimpour F., Semantic WS-Agreement Partner Selection, Proceedings of the 15th International World Wide Web (WWW) Conference, Edinburgh, Scotland, May, 2006, 697–706, 2006.

    Google Scholar 

  31. Patil A., Oundhakar S., Sheth A., and Verma K., METEOR-S Web service Annotation Framework, Proceeding of the World Wide Web Conference, New York, NY, May 2004, 553–562, 2004.

    Google Scholar 

  32. Roman D., Keller U., Lausen H., de Bruijn J., Lara R., Stollberg M., Polleres A., Feier C, Bussler C, and Fensel D., Web Service Modeling Ontology, Applied Ontology, 1(1): 77–106, 2005.

    Google Scholar 

  33. Sahoo S.S., Sheth A., York W.S., and Miller J.S., Semantic Web Services for N-glycosylation Process, International Symposium on Web Services for Computational Biology and Bioinformatics, VBI, Blacksburg, VA, USA May 26–27, 2005

    Google Scholar 

  34. Sahoo S.S., Thomas C.J., Sheth A.P., York W.S., and Tartir S., Knowledge Modeling and its Application in Life Sciences: A Tale of two Ontologies, Proceedings of the 15th International World Wide Web (WWW) Conference, Edinburgh, Scotlands, May, 2006, pp. 317–326, 2006.

    Google Scholar 

  35. Sheth A., van der Alst W., and Arpinar I. B. Processes Driving the Networked Economy. IEEE Concurrency 7,3, 18–31, July–September 1999.

    CrossRef  Google Scholar 

  36. Smith B., Kumar A., and Bittner T. Basic Formal Ontology for Bioinformatics, http://www.uni-leipzig.de/~akumar/JAIS.pdf

    Google Scholar 

  37. Wu C.H., Apweiler R., Bairoch A., Natale D.A., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Mazumder R., O’Donovan C, Redaschi N., and Suzek B. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34:D187–D19, 2006. http://www.pir.uniprot.org/

    PubMed  CrossRef  CAS  Google Scholar 

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Sahoo, S.S., Sheth, A., Hunter, B., York, W.S. (2007). Sembowser - Semantic Biological Web Services Registry. In: Baker, C.J.O., Cheung, KH. (eds) Semantic Web. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-48438-9_15

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