Wf4Ever project

Wf4Ever was a research object funded by EU Framework 7 to investigate how scientific workflows and their data could be better preserved for reproducibility, reuse and resiliance against workflow decay.

For instance, a particular computational analysis may require certain software preinstalled, and rely on web services and databases on the network. The workflow is also executed in a particular workflow engine, possibly using plugins or additional shims for data conversations etc. Reference datasets are used for comparisons. All of these components are however subject to change, both desirable (e.g. a web service gets new feature) and undesirable (e.g. a software binary no longer run on newer OS), and this can make the computational method captured in the form of a workflow over time turn inaccessible, incomprehensible, incompatible or unavailable.

In the project, researchers from Spain, UK, Poland and The Netherlands collaborated to develop methods and demonstrators for workflow preservation in bioinformatics and astrophysics, developing the concept of Research Objects to maturity, adding detailed provenance capture and metadata support for the workflow systems Taverna and WINGS while co-developing Linked Data standards like W3C PROV and W3C Web Annotation model.

Publications

See also:

Khalid Belhajjame, Jun Zhao, Daniel Garijo, Matthew Gamble, Kristina Hettne, Raul Palma, Eleni Mina, Oscar Corcho, José Manuel Gómez-Pérez, Sean Bechhofer, Graham Klyne, Carole Goble (2015) Using a suite of ontologies for preserving workflow-centric research objects, Web Semantics: Science, Services and Agents on the World Wide Web, https://doi.org/10.1016/j.websem.2015.01.003

Stian Soiland-Reyes, Pinar Alper, Carole Goble (2016): Tracking workflow execution with TavernaProv. At: PROV: Three Years Later, Provenance Week 2016. https://doi.org/10.5281/zenodo.51314 [html] [pdf] [source]

Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Eelke van der Horst, Zuotian Tatum, Kristina M Hettne, Erik A Schultes, Barend Mons, Marco Roos (2015): Nanopublications for exposing experimental data in the life-sciences: a Huntington’s Disease case study. Journal of Biomedical Semantics 6(5). https://doi.org/10.1186/2041-1480-6-5

Daniel Garijo, Nandana Mihindukulasooriya, Oscar Corcho (2015): LDP4ROs: Managing Research Objects with the W3C Linked Data Platform. WWW ’15 Companion. Proceedings of the 24th International Conference on World Wide Web. https://doi.org/10.1145/2740908.2742016 [pdf]

Kristina M Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A `t Hoen, Sean Bechhofer, Carole Goble, Marco Roos (2014) Structuring research methods and data with the research object model: genomics workflows as a case study, Journal of Biomedical Semantics 5(1), p. 41, https://doi.org/10.1186/2041-1480-5-41

Palma Raul, Piotr Hołubowicz, Kevin Page, Stian Soiland-Reyes, Graham Klyne, Cezary Mazurek (2014) A Suite of APIs for the Management of Research Objects, Proceedings of the ISWC Developers Workshop 2014, ISWC-DEV 2014, CEUR-WS.org, online http://ceur-ws.org/Vol-1268/paper8.pdf

Raúl Palma, Piotr Hołubowicz, Oscar Corcho, José Manuel Gómez-Pérez, Cezary Mazurek (2014): ROHub — A Digital Library of Research Objects Supporting Scientists Towards Reproducible Science. Semantic Web Evaluation Challenge. SemWebEval 2014 at ESWC 2014. https://doi.org/10.1007/978-3-319-12024-9_9 [pdf, archived 2016-04-12] [preprint o:378711] [proceedings p361]

Kevin R. Page, Raul Palma, Piotr Hołubowicz, Graham Klyne, Stian Soiland-Reyes, Daniel Garijo, Khalid Belhajjame, and Rudolf Mayer: Research Objects for Audio Processing: Capturing Semantics for Reproducibility, 53rd Audio Engineering Society International Conference on Semantic Audio, January 2014. ISBN: 978-0-937803-96-7 [Proceedings] [Preprint] [escholar]

David De Roure (2014): Executable Music Documents. DLfM ’14 Proceedings of the 1st International Workshop on Digital Libraries for Musicology.https://doi.org/10.1145/2660168.2660183 [preprint] [preprint server]

Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Phillip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Danius Michaelides, Stuart Owen, David Newman, Shoaib Sufi, Carole Goble (2013) Why Linked Data is Not Enough for Scientists, Future Generation Computer Systems 29(2), February 2013, Pages 599-611, ISSN 0167-739X, https://doi.org/10.1016/j.future.2011.08.004 [preprint] [researchgate]

Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble (2013): A Checklist-Based Approach for Quality Assessment of Scientific Information. 3rd International Workshop on Linked Science 2013—Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013). [preprint] [slides]

Carole Goble, David De Roure, Sean Bechhofer (2013) Accelerating Scientists’ Knowledge Turns, Communications in Computer and Information Science 348, p. 3-25, https://doi.org/10.1007/978-3-642-37186-8_1

David De Roure (2013) Towards Computational Research Objects, Proceedings of the 1st International Workshop on Digital Preservation of Research Methods and Artefacts, p. 16-19, ACM, https://doi.org/10.1145/2499583.2499590

Khalid Belhajjame, Oscar Corcho, Daniel Garijo, Jun Zhao, Paolo Missier, David R. Newman, Raul Palma, Sean Bechhofer, Esteban Garcia Cuesta, Jose Manuel Gomez-Perez, Graham Klyne, Kevin Page, Marco Roos, José Enrique Ruiz, Stian Soiland-Reyes, Lourdes Verdes-Montenegro, David De Roure, Carole Goble (2012): Workflow-Centric Research Objects: A First Class Citizen in the Scholarly Discourse. Proceedings of the Workshop on the Semantic Publishing (SePublica 2012) (i), p. 1-12. CEUR Workshop Proceedings 903. http://ceur-ws.org/Vol-903/paper-01.pdf

Jun Zhao, Jose Manuel Gomez-perez, Khalid Belhajjame, Graham Klyne, Esteban Garcia-cuesta (2012) Why Workflows Break – Understanding and Combating Decay in Taverna Workflows, 8th International Conference on E-Science (e-Science), IEEE. https://doi.org/10.1109/eScience.2012.6404482

Matthew Gamble, Carole Goble, Graham Klyne, Jun Zhao (2012) MIM: A minimum information model vocabulary and framework for scientific linked data, 2012 IEEE 8th International Conference on E-Science, e-Science 2012. https://doi.org/10.1109/eScience.2012.6404489 [preprint]

David De Roure, Khalid Belhajjam, Paolo Missier, José Manuel Gómez-Pérez, Raúl Palma, José Enrique Ruiz, Kristina Hettne, Marco Roos, Graham Klyne, Carole Goble (2011): Towards the Preservation of Scientific Workflows. iPRES 2011 – 8th International Conference on Preservation of Digital Objects. https://doi.org/11353/10.294253 [researchgate] [preprint o:294253] [proceedings p228]

Sean Bechhofer, John Ainsworth, Jiten Bhagat, Iain Buchan, Phillip Couch, Don Cruickshank, David De Roure, Mark Delderfield, Ian Dunlop, Matthew Gamble, Carole Goble, Danius Michaelides, Paolo Missier, Stuart Owen, David Newman, Shoaib Sufi (2010): Why Linked Data is Not Enough for Scientists, Sixth IEEE e-Science conference (e-Science 2010) https://doi.org/10.1109/eScience.2010.21 [preprint] [pdf]

Sean Bechhofer, David De Roure, Matthew Gamble, Carole Goble, Iain Buchan (2010): Research Objects: Towards Exchange and Reuse of Digital Knowledge, The Future of the Web for Collaborative Science (FWCS 2010). https://doi.org/10.1038/npre.2010.4626.1

Deliverables

This list of project deliverables is adapted from http://wf4ever.org/web/guest/deliverables.html with updated hyperlinks as repo.wf4ever-project.org is no longer available. Except where noted as confidential, these project deliverables are all Open Access licensed Creative Commons Attribution 3.0 (CC-BY-3.0).