Abstract
In the Taverna workflow design and enactment tool, users often find it difficult to both manually discover a service or workflow fragment that executes a desired operation on a piece of data (both semantically and syntactically), and correctly connect that service into the workflow such that appropriate connections are made between input and output data elements. The BioMoby project, and its successor the SADI project, embed semantics into their data-structures in an attempt to make the purpose and functionality of a Web Service more computable, and thereby facilitate service discovery during workflow construction. In this article, we compare and contrast the functionality of the BioMoby and SADI plug-ins to Taverna, with a particular focus on how they attempt to simplify workflow synthesis by end-users. We then compare these functionalities with other workflow-like clients we (and others) have created for the BioMoby and SADI systems, discuss the limitations to manual workflow synthesis, and contrast these with the opportunities we have found for fully automated workflow synthesis using the semantics of SADI.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Goderis, A., Li, P., Goble, C.: Workflow Discovery: Requirements from E-science and a Graph-based Solution. International Journal of Web Services Research 5(4) (2008)
Goble, C., DeRoure, D.C.: myExperiment: social networking for workflow-using e-scientists. In: Proceedings of the 2nd Workshop on Workflows in Support of Large-Scale Science, pp. 1–2 (2007)
Wroe, C., Goble, C., Goderis, A., Lord, P., Miles, S., Papay, J., Alper, P., Moreau, L.: Recycling workflows and services through discovery and reuse. Concurrency Computat: Pract. Exper. 19(2), 1–7 (2006)
Gordon, P.M.K., Sensen, C.: A Pilot Study into the Usability of a Scientific Workflow Construction Tool. Technical Report #2007-874-26. Department of Computer Science, The University of Calgary (2007)
Goderis, A., Sattler, U., Lord, P., Goble, C.: Seven Bottlenecks to Workflow Reuse and Repurposing. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 323–337. Springer, Heidelberg (2005)
Gordon, P.M.K., Barker, K., Sensen, C.W.: Helping Molecular Biologists Effectively Build Workflows, Without Programming. In: Lambrix, P., Kemp, G. (eds.) Proceedings of 7th International Conference on Data Integration in the Life Sciences (DILS 2010), Gothenburg, Sweden, August 25-27, pp . 74–89 (2010)
Oinn, T., Greenwood, M., Addis, M., Alpdemir, N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M., Senger, M., Stevens, R., Wipat, A., Wroe, C.: Taverna: lessons in creating a workflow environment for the life sciences. Concurrency Computat: Pract. Exper. 18(10), 1067–1100 (2006)
Reichm, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P., Miserov, J.P.: GenePattern 2.0. Nat. Genet. 38(5), 500–501 (2006)
Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., Brass, A.: Tambis: transparent access to multiple bioinformatics information sources. Bioinformatics 16(2), 184–185 (2000)
Lord, P., Bechhofer, S., Wilkinson, M.D., Schiltz, G., Gessler, D., Hull, D., Goble, C., Stein, L.: Applying semantic web services to Bioinformatics: Experiences gained, lessons learnt. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 350–364. Springer, Heidelberg (2004)
The BioMoby Consortium. Interoperability with Moby 1.0 - It’s better than sharing your toothbrush! Briefings in Bioinformatics 9(3), 220–231 (2008)
Wilkinson, M.D. Vandervalk, B. McCarthy, L.: SADI Semantic Web Services - cause you can’t always GET what you want! In: IEEE Asia-Pacific Services Computing Conference, APSCC 2009, pp. 13–18 (2009)
Kawas, E., Senger, M., Wilkinson, M.D.: BioMoby extensions to the Taverna workflow management and enactment software. BMC Bioinformatics 7(523) (2006)
Pignotti, E., Edwards, P., Preece, A., Gotts, N., Polhill, G.: Enhancing Workflow with a Semantic Description of Scientific Intent. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021, pp. 644–658. Springer, Heidelberg (2008)
Taylor, J., Schenck, I., Blankenberg, D., Nekrutenko, A.: Using galaxy to perform large-scale interactive data analyses. Curr. Protoc. Bioinformatics, ch. 10:Unit 10.5 (September 2007)
http://lsdis.cs.uga.edu/projects/meteor-s/downloads/Lumina/files/thesis.pdf (Downloaded May 15, 2010)
http://www.w3.org/2002/ws/sawsdl/ (Downloaded May 15, 2010)
Wolstencroft, K., Alper, P., Hull, D., Wroe, C., Lord, P.W., Stevens, R.D., Goble, C.A.: The myGrid ontology: bioinformatics service discovery. International Journal of Bioinformatics Research and Applications 3(3), 303–325 (2007)
Lord, P., Alper, P., Wroe, C., Goble, C.: Feta: A light-weight architecture for user oriented semantic service discovery. In: Gómez-Pérez, A., Euzenat, J. (eds.) ESWC 2005. LNCS, vol. 3532, pp. 17–31. Springer, Heidelberg (2005)
Gordon, P.M.K., Sensen, C.: Seahawk: moving beyond HTML in Web-based bioinformatics analysis. BMC Bioinformatics 8(208) (2007)
Martín-Requena, V., Ríos, J., García, M., Ramírez, S., Trelles, O.: jORCA: easily integrating bioinformatics Web Services. Bioinformatics 26(4), 553–559 (2010)
Carrere, S., Gouzy, J.: REMORA: a pilot in the ocean of BioMoby web-services. Bioinformatics 22(7), 900–901 (2006)
Wilkinson, M.: Gbrowse Moby: A Web-based browser for BioMOBY Services. Source Code for Biology and Medicine 1(4) (2006)
Navas, I., Rojano, M., Ramirez, S., Pérez, A.J., Aldana, J.F., Trelles, O.: Intelligent client for integrating bioinformatics services. Bioinformatics 22, 106–111 (2006)
Néron, B., Ménager, H., Maufrais, C., Joly, N., Maupetit, J., Letort, S., Carrere, S., Tuffery, P., Letondal, C.: Mobyle: a new full web bioinformatics framework. Bioinformatics 25(22), 3005–3011 (2006)
http://bioinfo.mpiz-koeln.mpg.de/jabba/help.html (Downloaded May 15, 2010)
Song, Y.C., Kawas, E., Good, B.M., Wilkinson, M.D., Tebbutt, S.: DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. Bioinformatics 23(6), 780–782 (2007)
Ríos, J., Karlsson, J., Trelles, O.: Magallanes: a web services discovery and automatic workflow composition tool. BMC Bioinformatics 10(334) (2009)
Vandervalk, B.P., McCarthy, E.L., Wilkinson, M.D.: SHARE: A Semantic Web Query Engine for Bioinformatics. In: Gómez-Pérez, A., Yu, Y., Ding, Y. (eds.) ASWC 2009. LNCS, vol. 5926, pp. 367–369. Springer, Heidelberg (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Withers, D., Kawas, E., McCarthy, L., Vandervalk, B., Wilkinson, M. (2010). Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins. In: Margaria, T., Steffen, B. (eds) Leveraging Applications of Formal Methods, Verification, and Validation. ISoLA 2010. Lecture Notes in Computer Science, vol 6415. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16558-0_26
Download citation
DOI: https://doi.org/10.1007/978-3-642-16558-0_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-16557-3
Online ISBN: 978-3-642-16558-0
eBook Packages: Computer ScienceComputer Science (R0)