article

WOODSS and the Web: annotating and reusing scientific workflows

Authors:

C. B. Medeiros,

J. Perez-Alcazar,

L. Digiampietri,

G. Z. Pastorello, Jr.,

E. BacarinAuthors Info & Claims

ACM SIGMOD Record, Volume 34, Issue 3

Pages 18 - 23

https://doi.org/10.1145/1084805.1084810

Published: 01 September 2005 Publication History

Abstract

This paper discusses ongoing research on scientific workflows at the Institute of Computing, University of Campinas (IC - UNICAMP) Brazil. Our projects with bio-scientists have led us to develop a scientific workflow infrastructure named WOODSS. This framework has two main objectives in mind: to help scientists to specify and annotate their models and experiments; and to document collaborative efforts in scientific activities. In both contexts, workflows are annotated and stored in a database. This "annotated scientific workflow" database is treated as a repository of (sometimes incomplete) approaches to solving scientific problems. Thus, it serves two purposes: allows comparison of distinct solutions to a problem, and their designs; and provides reusable and executable building blocks to construct new scientific workflows, to meet specific needs. Annotations, moreover, allow further insight into methodology, success rates, underlying hypotheses and other issues in experimental activities.The many research challenges faced by us at the moment include: the extension of this framework to the Web, following Semantic Web standards; providing means of discovering workflow components on the Web for reuse; and taking advantage of planning in Artificial Intelligence to support composition mechanisms. This paper describes our efforts in these directions, tested over two domains - agro-environmental planning and bioinformatics.

References

[1]

K. M. Anderson, R. N. Taylor, and E. J. Whitehead Jr. Chimera: hypermedia for heterogeneous software development environments. ACM Transactions on Information Systems (TOIS), 18(3):211--245, 2000.

Digital Library

[2]

E. Bacarin, C. B. Medeiros, and E. Madeira. A Collaborative Model for Agricultural Supply Chains. In Proc COOPIS 2004, volume LNCS 3290, pages 319--336, 2004.

[3]

T. J. Biggerstaff and C. Richter. Reusability framework, assessment, and directions, pages 1--17. ACM Press, 1989.

Digital Library

[4]

M. C. Cavalcanti, R. Targino, F. Baião, S. C. Rössle, P. M. Bisch, P. F. Pires, M. L. M. Campos, and M. Mattoso. Managing structural genomic workflows using Web services. Data & Knowledge Engineering, 53(1):45--74, 2005.

Digital Library

[5]

L. A. Digiampietri, C. B. Medeiros, and J. C. Setubal. A framework based in Web services orchestration for bioinformatics workflow management. In Proc III Brazilian Workshop in Bioinformatics, 2004.

[6]

A. J. G. Simpson et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature, 406(1):151--157, 2000.

[7]

R. Fileto. The POESIA Approach for Services and Data Integration On the Semantic Web. PhD thesis, ICUNICAMP, Campinas-SP, 2003.

[8]

R. Fileto, L. Liu, C. Pu, E. Assad, and C. B. Medeiros. POESIA: An Ontological Workflow Approach for Composing Web Services in Agriculture. VLDB Journal, 12(4):352--367, 2003.

Digital Library

[9]

M. Ghallab, D. Nau, and P. Traverso. Automated Planning, Theory and Practice. Elsevier, 2004.

Digital Library

[10]

Proc. of the Workshop on Planning and Scheduling for Web and Grid Services, June 2004. http://www.isi.edu/ikcap/icaps04-workshop/ (as of 2005-07-11).

[11]

D. Kaster, C. B. Medeiros, and H. Rocha. Supporting Modeling and Problem Solving from Precedent Experiences: The Role of Workflows and Case-Based Reasoning. Environmental Modeling and Software, 20:689--704, 2005.

[12]

J. Kim and Y. Gil. Towards Interactive Composition of Semantic Web Services. In Proc. of the AAAI Spring Symposium on Semantic Web Services, march 2004.

[13]

Oasis-Open. OASIS Web Services Business Process Execution Language Technical Committee. http://www.oasis-open.org/committees/tc_home. php?wg_abbrev-wsbpel (as of 2005-07-11).

[14]

G. Z. Pastorello Jr. Publication and Integration of Scientific Workflows on the Web. Master's thesis, UNICAMP, 2005. In Portuguese.

[15]

G. Z. Pastorello Jr, C. B. Medeiros, S. Resende, and H. Rocha. Interoperability for GIS Document Management in Environmental Planning. Journal on Data Semantics, 3(LNCS 3534):100--124, 2005.

Digital Library

[16]

A. Santanchè and C. B. Medeiros. Geographic Digital Content Components. In Proc. of VI Brazilian Symposium on GeoInformatics, November 2004.

[17]

A. Santanchè and C. B. Medeiros. Managing Dynamic Repositories for Digital Content Components. In EDBT 2004 Workshops, volume LNCS 3268/2004, pages 66--77, 2004.

Digital Library

[18]

A. Santanchè and C. B. Medeiros. Self describing components: Searching for digital artifacts on the web. In Proc. of XX Brazilian Symp. on Databases, October 2005.

[19]

L Seffino, C. B. Medeiros, J. Rocha, and B. Yi. WOODSS - A Spatial Decision Support System based on Workflows. Decision Support Systems, 27(1-2):105--123, 1999.

Digital Library

[20]

E. Sirin, B. Parsia, D. Wu, J. A. Hendler, and D. S. Nau. HTN planning for Web Service composition using SHOP2. Journal of Web Semantics, 1(4):377--396, 2004.

Digital Library

[21]

R. D. Stevens, H. J. Tipney, C. J. Wroe, T. M. Oinn, M. Senger, P. W. Lord, C. A. Goble, A. Brass, and M. Tassabehji. Exploring Williams-Beuren syndrome using myGrid. Bioinformatics, 20(suppl_1):i303--310, 2004.

Digital Library

[22]

The myGrid Consortium. myGrid: Middleware for in silico experiments in biology. http://www.mygrid.org.uk/ (as of 2005-07-11).

[23]

J. Wainer, M. Weske, G. Vossen, and C. B. Medeiros. Scientific Workflow Systems. In Proc. of the NSF Workshop on Workflow and Process Automation Information Systems, 1996.

Cited By

Werneck Rde Almeida WStein BPazinato DJúnior PPenatti ORocha ATorres R(2018)Kuaa: A unified framework for design, deployment, execution, and recommendation of machine learning experimentsFuture Generation Computer Systems10.1016/j.future.2017.06.01378(59-76)Online publication date: Jan-2018
https://doi.org/10.1016/j.future.2017.06.013
Tang WFeng WJia MShi JZuo HStringer CTrettin C(2017)A cyber-enabled spatial decision support system to inventory Mangroves in MozambiqueInternational Journal of Geographical Information Science10.1080/13658816.2016.124541931:5(907-938)Online publication date: 1-May-2017
https://dl.acm.org/doi/10.1080/13658816.2016.1245419
Digiampietri LMaruyama WSantiago CLima JSiqueira SCarvalho S(2015)A Link Prediction System in Social NetworksProceedings of the annual conference on Brazilian Symposium on Information Systems: Information Systems: A Computer Socio-Technical Perspective - Volume 110.5555/2814058.2814082(139-146)Online publication date: 26-May-2015
https://dl.acm.org/doi/10.5555/2814058.2814082
Show More Cited By

Index Terms

WOODSS and the Web: annotating and reusing scientific workflows

Recommendations

BPEL Workflows Combining Standard OGC Web Services and Grid-enabled OGC Web Services
SEAA '08: Proceedings of the 2008 34th Euromicro Conference Software Engineering and Advanced Applications

When designing a Grid workflow, it might be necessary to integrate different kinds of services. In an ideal scenario all services are Grid-enabled. But real workflows often consist of Grid-enabled andnon Grid-enabled services. One reason is that Grid-...
Delivering web service coordination capability to users
WWW Alt. '04: Proceedings of the 13th international World Wide Web conference on Alternate track papers & posters

As web service technology matures there is growing interest in exploiting workflow techniques to coordinate web services. Bioinformaticians are a user community who combine web resources to perform in silico experiments. These users are scientists and ...
Making Scientific Applications as Web Services

In past columns, the authors discussed Grid technology in e-Science (large-scale, distributed scientific research). Here, we make the ideas more concrete by describing how to convert (or build from scratch) a scientific resource (a software program) to ...

Comments

Information & Contributors

Information

Published In

cover image ACM SIGMOD Record

ACM SIGMOD Record Volume 34, Issue 3

September 2005

115 pages

ISSN:0163-5808

DOI:10.1145/1084805

Issue’s Table of Contents

Copyright © 2005 Authors.

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 01 September 2005

Published in SIGMOD Volume 34, Issue 3

Check for updates

Qualifiers

Article

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

38
Total Citations
View Citations
381
Total Downloads

Downloads (Last 12 months)2
Downloads (Last 6 weeks)0

Reflects downloads up to

Other Metrics

View Author Metrics

Citations

Cited By

Werneck Rde Almeida WStein BPazinato DJúnior PPenatti ORocha ATorres R(2018)Kuaa: A unified framework for design, deployment, execution, and recommendation of machine learning experimentsFuture Generation Computer Systems10.1016/j.future.2017.06.01378(59-76)Online publication date: Jan-2018
https://doi.org/10.1016/j.future.2017.06.013
Tang WFeng WJia MShi JZuo HStringer CTrettin C(2017)A cyber-enabled spatial decision support system to inventory Mangroves in MozambiqueInternational Journal of Geographical Information Science10.1080/13658816.2016.124541931:5(907-938)Online publication date: 1-May-2017
https://dl.acm.org/doi/10.1080/13658816.2016.1245419
Digiampietri LMaruyama WSantiago CLima JSiqueira SCarvalho S(2015)A Link Prediction System in Social NetworksProceedings of the annual conference on Brazilian Symposium on Information Systems: Information Systems: A Computer Socio-Technical Perspective - Volume 110.5555/2814058.2814082(139-146)Online publication date: 26-May-2015
https://dl.acm.org/doi/10.5555/2814058.2814082
Digiampietri LPereira VCosta Cdos Santos Júnior GStefanini FSantiago C(2014)An Extensible Framework for Genomic and Metagenomic AnalysisAdvances in Bioinformatics and Computational Biology10.1007/978-3-319-12418-6_1(1-8)Online publication date: 2014
https://doi.org/10.1007/978-3-319-12418-6_1
Acuña RLacroix ZChomilier J(2013)A workflow for the prediction of the effects of residue substitution on protein stabilityProceedings of the 8th IAPR international conference on Pattern Recognition in Bioinformatics10.1007/978-3-642-39159-0_23(253-264)Online publication date: 17-Jun-2013
https://dl.acm.org/doi/10.1007/978-3-642-39159-0_23
Naik P(2012)Design of Framework for Semantic Annotation ofGeospatial DataInternational Journal of Information and Electronics Engineering10.7763/IJIEE.2012.V2.128Online publication date: 2012
https://doi.org/10.7763/IJIEE.2012.V2.128
Acuna RLacroix. ZChomilier J(2012)Refurbishing Legacy Biological Workflows SPROUTS Case StudyProceedings of the 2012 IEEE Eighth World Congress on Services10.1109/SERVICES.2012.81(41-49)Online publication date: 24-Jun-2012
https://dl.acm.org/doi/10.1109/SERVICES.2012.81
Cerezo NMontagnat JTaylor IMontagnat J(2011)Scientific workflow reuse through conceptual workflows on the virtual imaging platformProceedings of the 6th workshop on Workflows in support of large-scale science10.1145/2110497.2110499(1-10)Online publication date: 14-Nov-2011
https://dl.acm.org/doi/10.1145/2110497.2110499
Liu ZShao QChen Y(2010)Searching workflows with hierarchical viewsProceedings of the VLDB Endowment10.14778/1920841.19209583:1-2(918-927)Online publication date: 1-Sep-2010
https://dl.acm.org/doi/10.14778/1920841.1920958
Geovana N. Macário Cdos Santos JMedeiros Cda S. Torres RPurves RClough PJones C(2010)Annotating data to support decision-makingProceedings of the 6th Workshop on Geographic Information Retrieval10.1145/1722080.1722106(1-7)Online publication date: 18-Feb-2010
https://dl.acm.org/doi/10.1145/1722080.1722106
Show More Cited By

View Options

Get Access

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Issue’s Table of Contents