BSIS: An Experiment in Automating Bioinformatics Tasks Through Intelligent Workflow Construction

Part of the Annals of Information Systems book series (AOIS, volume 11)


Existing bioinformatics tools are extremely difficult to integrate and inter-operate, because of the diversity of service deployment techniques and the representational heterogeneity of biological data they are interacting with. This chapter presents the BioService Integration System (BSIS), a general framework which provides a graphic-based workflow language. The language enables the description of workflows composed of abstract semantic Web services and references to biologically relevant data. The workflows constructed in BSIS can be instantiated through automated planning techniques and automatically executed by adapting the Web Service Integration Framework (WSIF). A prototype implementation of the system is presented to demonstrate the effectiveness and efficiency of the approach.


Domain Ontology Service Node Data Node Service Instance Operator Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors would like to thank the anonymous reviewers for their insightful comments. The authors wish to thank the following researchers for helping in different stages of this project: Gopal Gupta, Arlin Stoltzfus, Julie Thompson, Francisco Prosdocimi, Brook Milligan, Tu Phan, and Samat Jain.

The research has been partially supported by NSF grants IIS-0812267, HRD-0420407, and CNS-0220590.


  1. 1.
    Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludscher, B., Mock, S.: Kepler: An extensible system for design and execution of scientific workflows. In: Proceedings of the16th International Conference on Scientific and Statistical Database Management (SSDBM’04), IEEE Computer Society, Los Alamitos, CA (2004) 21–23Google Scholar
  2. 2.
    Ankolekar, A., Burstein, M., Hobbs, J., Lassila, O., Martin, D., McIlraith, S., Narayanan, S., Paolucci, M., Payne, T., Sycara, K., Zeng, H.: DAML-S: Semantic markup for web services. In: Proceedings of the International Semantic Web Working Symposium (SWWS) (2001)Google Scholar
  3. 3.
    Balzer, S., Liebig, T., Wagner, M.: Pitfalls of OWL-S: A practical semantic web use case. In: International Conference on Service Oriented Computing, ACM Press, New York, NY (2004)Google Scholar
  4. 4.
    Bechhofer, S., van Harmelen, F., Hendler, J., Horrocks, I., McGuinness, D., Patel-Schneider, P., Stein, L.A.: OWL Web Ontology Language Reference. Technical Report, W3C (2004)Google Scholar
  5. 5.
    Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Scientific American, Harper, San Francisco, CA (2001)Google Scholar
  6. 6.
    Chapman, B., Chang, J.: BioPython: Python tools for computational biology. ACM SIGBIO Newsletter 20(2) 15–19 (2000)CrossRefGoogle Scholar
  7. 7.
    Christensen, E., Curbera, F., Meredith, G., Weeravarana, S.: Web Services Description Language (WSDL) 1.1. Technical Report, W3C (2001)Google Scholar
  8. 8.
    Clement, L., Hately, A., von Riegen, C., Rogers, T.: UDDI Version 3.0.2. Technical Report 20041019, OASIS (2004)Google Scholar
  9. 9.
    Consel, C.: Domain specific languages: What, why, how. Electronic Notes in Theoretical Computer Science 65(3) (2002)Google Scholar
  10. 10.
    De Giacomo, G., Lesp´erance, Y., Levesque, H.: ConGolog, a concurrent programming language based on the situation calculus. Artificial Intelligence 121(1–2) (2000) 109–169CrossRefGoogle Scholar
  11. 11.
    Erl, T.: Service-Oriented Architecture: Concepts, Technology, and Design. Prentice Hall, Upper Saddle River, New Jersey (2005)Google Scholar
  12. 12.
    Fern´andez-Olivares, J., Garz´on, T., Castillo, L., Garcia-P´erez, O., Palao, F.: A middle-ware for the automated composition and invocation of semantic web services based on temporal HTN planning techniques. In: Conference of the Spanish Association for Artificial Intelligence (CAEPIA). Springer, New York (2007) 70–79Google Scholar
  13. 13.
    Fremantle, P.: Applying the Web services invocation framework. IBM DeveloperWorks, Technical Report, IBM, Armonk, NY (2002)Google Scholar
  14. 14.
    Gonnet, G.H., Hallett, M.T., Korostensky, C., Bernardin, L.: Darwin v. 2.0: An interpreted computer language for the biosciences. Bioinformatics 16 101–103 (2000)CrossRefGoogle Scholar
  15. 15.
    Holmes, I.: Use cases for GNU Make in Bioinformatics Analyses. Technical Report, Bio Wiki (2007). Scholar
  16. 16.
    Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M., Li, P., Oinn, T.: Taverna: A tool for building and running workflows of services. Nucleic Acids Research Web Services Issue (2006)Google Scholar
  17. 17.
    Janies, D.A., Wheeler, W.: POY version 3.0, Documentation and Command Summary, Phylogeny Reconstruction Via Direct Optimization of DNA and Other Data. Technical Report, BMI Technical Report:OSUBMI-TR-2002-n03 (2002)Google Scholar
  18. 18.
    Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Research 34 354–357 (2006)CrossRefGoogle Scholar
  19. 19.
    Katayama, T., Nakao, M.C., Goto, N., Tanaka, N.: Bioruby+chemruby: An exploratory software project. GIW 2004 Poster Abstracts, S06 (2005)Google Scholar
  20. 20.
    Kim, H.S., Kim, I.C.: Mapping semantic web service descriptions to planning domain knowledge. In: World Congress on Medical Physics and Biomedical Engineering (2006) 388–391Google Scholar
  21. 21.
    Kosar, T., L´opez, P.M., Barrientos, P., Mernik, M.: A preliminary study on various implementation approaches of domain-specific languages. Information and Software Technology 50(5) (2008)Google Scholar
  22. 22.
    Kumar, S., Dudley, J., Nei, M., Tamura, K.: MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9 (2008)Google Scholar
  23. 23.
    Labarga, A., Valentin, F., Andersson, M., Lopez, R.: Web Services at the European Bioinformatics Institute. Nucleic Acids Research Web Services Issue (2007)Google Scholar
  24. 24.
    Levesque, H., Reiter, R., Lesperance, Y., Lin, F., Scherl, R.: GOLOG: A logic programming language for dynamic domains. Journal of Logic Programming 31(1–3) (1997) 59–84CrossRefGoogle Scholar
  25. 25.
    Lord, P., Wroe, C., Stevens, R., Goble, C., Miles, S., Moreau, L., Decker, K., Payne, T., Papay, J.: Personalised grid service discovery. In: Proceedings of the UK OST e-Science Second All Hands Meeting 2003 (AHM’03), WarwickPrint, University of Warwick, UK (2003)Google Scholar
  26. 26.
    Luo, J., Montrose, B., Kim, A., Khashnobish, A., Kang, M.: Adding OWL-S Support to the Existing UDDI Infrastructure. IEEE International Conference on Web Services (ICWS’06), IEEE Computer Society, Los Alamitos, CA (2006) 153–162Google Scholar
  27. 27.
    Maddison, W.P., Maddison, D.: Mesquite: A modular system for evolutionary analysis. Version 1.05. URL Accessed 21 Jul 2010
  28. 28.
    Maximilien, E., Singh, M.: Reputation and endorsement for web services. ACM SIGecom Exchanges 3(1) (2002) 24–3Google Scholar
  29. 29.
    McIlraith, S., Son, T.: Adapting golog for composition of semantic web services. In: Proceedings of the Eighth International Conference on Principles of Knowledge Representation and Reasoning (KR’2002), Morgan Kaufmann, San Francisco, CA (2002) 482–493Google Scholar
  30. 30.
    Miller, J., Verma, K., Rajasekaran, P., Sheth, A., Aggarwal, R., Sivashanmugan, K.: WSDL-S: Adding Semantic to WSDL. Technical Report, LSDIS Lab, University of Georgia (2004)Google Scholar
  31. 31.
    Moene, I., Subramaniam, S., Darin, D., Leergaard, T., Bjaalie, J.: Toward a workbench for rodent brain image data: Systems architecture and design. Neuroinformatics 5(1) (2007) 35–58Google Scholar
  32. 32.
    Moreau, L., Miles, S., Papay, J., Decker, K., Payne, T.: Publishing Semantic Descriptions of Services. Technical Report, Global Grid Forum (2003)Google Scholar
  33. 33.
    Mungall, C.: BioMake: Specifying Biocompute Pipelines with Makefiles and Beyond. Technical Report, Berkeley Drosophila Genome Project (2006)Google Scholar
  34. 34.
    NCBI: Entrez Help (2006). URL Accessed 21 Jul 2010
  35. 35.
    Pan, Y.: Automating Bioinformatics Tasks Through Intelligent Workflow Construction. Ph.D. Thesis, New Mexico State University, Las Cruces, NM (2007)Google Scholar
  36. 36.
    Papazoglou, M., Dubray, J.J.: A Survey of Web Service Technologies. Technical Report DIT-04-058, University of Trento, Italy (2004)Google Scholar
  37. 37.
    Parker, D., Gorlick, M., Lee, C.: Evolving from bioinformatics in-the-small to Bioinformatics in-the-large. OMICS 7(1) (2003) 37–48CrossRefGoogle Scholar
  38. 38.
    Parkinson, J., Anthony, A., Wasmuth, J., Schmid, R., Hedley, A., Blaxter, M.: PartiGene - constructing partial genomes. Bioinformatics 20(9) (2004) 1398–1404CrossRefGoogle Scholar
  39. 39.
    Pocock, M., Down, T., Hubbard, T.: BioJava: Open source components for bioinformatics. SIGBIO Newsletter 20(2) (2000) 10–12. DOI
  40. 40.
    Qiu, W., Schisler, N., Stoltzfus, A.: The evolutionary gain of spliceosomal introns: Sequence and phase preferences. Molecular Biology Evolution 21(7) (2004) 1252–1263Google Scholar
  41. 41.
    Ran, S.: A model for web services discovery with QoS. ACM SIGecom Exchanges 4(1) (2003) 1–10CrossRefGoogle Scholar
  42. 42.
    Reiter, R.: Knowledge in action: Logical foundations for describing and implementing dynamical systems. MIT Press, Cambridge, MA (2001)Google Scholar
  43. 43.
    Stajich, J., Block, D., Boulez, K., Brenner, S., Chervitz, S., Dagdigian, C., Fuellen, G., Gilbert, J., Korf, I., Lapp, H., Lehvslaiho, H., Matsalla, C., Mungall, C., Osborne, B., Pocock, M., Schattner, P., Senger, M., Stein, L., Stupka, E., Wilkinson, M., Birney, E.: The BioPerl toolkit: Perl modules for the life sciences. Genome Research 12(10) (2002) 1611–1618CrossRefGoogle Scholar
  44. 44.
    Stevens, R., Robinson, A., Goble, C.: myGrid: Personalised bioinformatics on the information grid. Bioinformatics 19(1) (2003) 302–304Google Scholar
  45. 45.
    Stollberg, M., Roman, D., Gomez, J.: A mediated approach towards web service choreography. In: Proceedings of the Workshop “Semantic Web Services: Preparing to Meet the World of Business Applications” Held at the 3rd International Semantic Web Conference, IEEE Computer Society, Los Alamitos, CA (2004)Google Scholar
  46. 46.
    Tamura, K., Dudley, J., Nei, M., Kumar, S.: MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24 (2007) 1596–1599CrossRefGoogle Scholar
  47. 47.
    Thompson, J., Higgins, D., Gibson, T.: CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22 (1994) 4673–4680CrossRefGoogle Scholar
  48. 48.
    Wilkinson, M., Links, M.: BioMOBY: An open-source biological web services proposal. Briefings in Bioinformatics 3(4) (2002) 331–341CrossRefGoogle Scholar
  49. 49.
    Yu, B., Singh, M.: An evidential model for distributed reputation management. In: Proceedings of AAMAS’02, ACM Press, New York, NY (2002)Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Department of Computer ScienceNew Mexico State UniversityLas CrucesUSA

Personalised recommendations