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2014

Journals

  1. 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: Structuring research methods and data with the research object model: genomics workflows as a case study. Journal of Biomedical Semantics 2014, 5:41. doi:10.1186/2041-1480-5-41 [preprint]

Conference/Workshop Proceedings

  1. Kevin R. Page, Raul Palma, Piotr Ho?ubowicz, 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

2013

Journals

  1. Carole Goble, Sean Bechhofer, David De Roure and Tim Clark (2012), Accelerating Scientists' Knowledge Turns, Selected papers of Proc of IC3K 2010, Springer LNCS in press
  2. Daniel Garijo, et al. Common Motifs in Scientific Workflows: An Empirical Analysis, Selected papers of IEEE eScience 2012, FGCS, submitted
  3. Kristina Hettne et al. Structuring research methods and data with the Research Object model: genomics workflows as a case study submitted to Journal of Biomedical Semantics 2013-05-13, resubmitted after peer review 2013-11-09. (Preprint: http://arxiv.org/abs/1311.2789)
  4. Kevin Page, Ben Fields, David De Roure, Tim Crawford, J. Stephen Downie. Capturing the Workflows of Music Information Retrieval for Repeatability and Reuse. Journal of Intelligent Information Systems, Springer, 2013 doi:10.1007/s10844-013-0260-9.
  5. Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair J G Gray, Carole Goble, Tim Clark (2013): PAV ontology: Provenance, Authoring and Versioning. Journal of Biomedical Semantics 2013 4:37. doi:10.1186/2041-1480-4-37 (arXiv)
  6. Paolo Ciccarese, Stian Soiland-Reyes, Tim Clark: Web Annotation as a First-Class Object (2013) IEEE Internet Computing 17(6) 71-75 doi:10.1109/MIC.2013.123
  7. Harish Dharuri, Peter Henneman, Ayse Demirkan, Jan B van Klinken, Dennis O Mook-Kanamori, Rui Wang-Sattler, Christian Gieger, Jerzy Adamski, Kristina Hettne, Marco Roos, Karsten Suhre, Cornelia M van Duijn, Ko Willems van Dijk and Peter A.C. 't Hoen. Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles. BMC Genomics 2013 14:865. doi:10.1186/1471-2164-14-865

Conference/Workshop Proceedings

  1. Pinar Alper, Khalid Belhajjame, Carole A. Goble and Pinar Karagoz, Enhancing and Abstracting Scientific Workflow Provenance for Data Publishing Proc BigProv'13 Workshop, co-located EDBT March 2013
  2. Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian Soiland-Reyes, Pinar Alper, and Oscar Corcho, A Workflow PROV-Corpus based on Taverna and Wings Proc BigProv'13 Workshop, co-located EDBT March 2013
  3. José Manuel Gómez-Pérez, Esteban Garc?a-Cuesta, Jun Zhao, Aleix Garrido, José Enrique Ruiz. How Reliable is Your workflow: Monitoring Decay in Scholarly Publications. sepublica 2013 May 2013
  4. Daniel Garijo, Oscar Corcho, and Yolanda Gil. Detecting common scientific workflow fragments using templates and execution provenance Proc K-CAP 2013 June 2013
  5. De Roure, D., Towards computational research objects, Proc. 1st International Workshop on the Digital Preservation of Research Methods and Artefacts (DPRMA 2013), pp.16-19, July 2013, doi:10.1145/2499583.2499590
  6. Raúl Palma, Oscar Corcho, Piotr Ho?ubowicz, Sara Pérez, Kevin Page, Cezary Mazurek , Digital libraries for the preservation of research methods and associated artifacts, Proc. 1st International Workshop on the Digital Preservation of Research Methods and Artefacts (DPRMA 2013), pp.8-15, July 2013, doi:10.1145/2499583.2499589
  7. Jun Zhao, Mark Thompson, Kristina Hettne, Katy Wolstencroft, Erik A. Schultes, Mark Wilkinson, Barend Mons, Carole Goble, Marco Roos. Technology for sharing methods and data of computational experiments in a digital era. ISMB Technical Track. July 2013
  8. Kristina M. Hettne, Harish Dharuri, Reinout van Schouwen, Peter A.C. 'T Hoen, Barend Mons and Marco Roos: Explaining genome-wide association study results using concept profile analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database. Extended abstract. In BioLINK SIG 2013: Roles for text mining in biomedical knowledge discovery and translational medicine, The Annual Meeting of the ISMB BioLINK Special Interest Group, In Association with ISMB/ECCB 2013, Berlin, Germany, July 20, 2013. (Proceedings, pp.60)
  9. Pinar Alper,Khalid Belhajjame, Carole Goble, and Pinar Karagoz. Small Is Beautiful: Summarizing Scientific Workflows Using Semantic Annotations IEEE Big Data'13 October 2013
  10. Hyde Zhang, Stian Soiland-Reyes, Carole Goble (2013): Taverna Mobile: Taverna workflows on Android. Extended abstract. EMBnet.Journal, 19(B), pp. 43-45. In NETTAB 2013, Workshop on "Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories", 16-18 October 2013, Lido of Venice, Italy. (Preprint: http://arxiv.org/abs/1309.2787)
  11. Ruiz, J.E., Verdes-Montenegro, L. Sánchez Expósito, S., Garrido, J., Santander-Vela, J.D. Digital Science: reproducibility and visibility in Astronomy Highlights of Spanish Astrophysics VII, Proceedings of the X Scientific Meeting of the Spanish Astronomical Society (SEA), held in Valencia, July 9 - 13, 2012, Eds.: J.C. Guirado, L.M. Lara, V. Quilis, and J. Gorgas., pp.910-915
  12. Jose Manuel Gomez-Perez, Esteban Garc?a-Cuesta, Aleix Garrido, Jose Enrique Ruiz, Jun Zhao, Graham Klyne, When History Matters - Assessing Reliability for the Reuse of Scienti?c Work?ows, Proceedings of the International Semantic Web Conference 2013 InUse Track, October 2013, Sydney, Australia
  13. Jun Zhao, Graham Klyne, Matthew Gamble, and Carole Goble: A Checklist-Based Approach for Quality Assessment of Scienti?c Information, Proceedings of the Third Linked Science Workshop co-located at the International Semantic Web Conference 2013, October 2013, Sydney, Australia
  14. Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Zuotian Tatum, Kristina Hettne, Erik A. Schultes, and Marco Roos: Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study, International SWAT4LS Workshop December 2013, Accepted.

2012

Journals

none

Conference/Workshop Proceedings

  1. Khalid Belhajjame, Paolo Missier, and Carole Goble. Detecting Duplicate Records in Scientific Workflow Results. In the proceedings of IPAW, Springer, 2012.
  2. Paolo Missier and Khalid Belhajjame. A PROV encoding for provenance analysis using deductive rules. In the proceedings of IPAW, Springer, 2012.
  3. Khalid Belhajjame, Oscar Corcho, Daniel Garijo, Jun Zhao, et al. Workflow-Centric Research Objects: A First Class Citizen in the Scholarly Discourse. In the proceedings of SEPUBLICA, CEUR-WS, 2012.
  4. Khalid Belhajjame, José-Manuel Gomez-Perez, Paolo Missier, Jun Zhao (Eds). The 3rd International Workshop on Semantic Web for Provenance Management. CEUR-WS, 2012.
  5. Khalid belhajjame, David De Roure, and Carole Goble. Research Object Management: Opportunities and Challenges. Data Intensive Collaboration in Science and Engineering (DISCOSE) workshop, collocated with CSCW. 2012
  6. Jun Zhao, Jose Manuel Gomez-Perez, Khalid Belhajjame, Graham Klyne, Esteban Garcia-Cuesta, Aleix Garrido, Kristina Hettne, Marco Roos, David De Roure, Carole Goble. Why workflows break- Understanding and combating decay in Taverna Workflows, IEEE 8th International Conference on eScience 2012 Chicago 8-12 October, 2012.
  7. Daniel Garijo, Pinar Alper, Khalid Belhajjame, Yolanda Gil, Carole Goble. Common Motifs in Scientific Workflows: An Empirical Analysis IEEE eScience 2012 Chicago, USA October, 2012
  8. Matthew Gamble, Jun Zhao, Graham Klyne, Carole Goble. MIM: A Minimum Information Model Vocabulary and Framework for Scientific Linked Data. IEEE eScience 2012 Chicago, USA October, 2012
  9. Daniel Garijo and Yolanda Gil. Augmenting PROV with Plans in P-PLAN: Scientific Processes as Linked Data. The Second Linked Science Workshop at ISWC Boston, USA November, 2012
  10. Kevin Page, Raúl Palma, Piotr Ho?ubowicz, Graham Klyne, Stian Soiland-Reyes, Don Cruickshank, Rafael González Cabero, Esteban García, David De Roure Cuesta, Jun Zhao, José Manuel Gómez-Pérez. From workflows to Research Objects: an architecture for preserving the semantics of science. The Second Linked Science Workshop at ISWC Boston, USA November, 2012
  11. Jun Zhao, Graham Klyne, Piotr Ho?ubowicz, Raúl Palma, Stian Soiland-Reyes, Kristina Hettne, José Enrique Ruiz, Marco Roos, Kevin Page, José Manuel Gómez-Pérez, David De Roure, Carole Goble. RO-Manager: A Tool for Creating and Manipulating Research Objects to Support Reproducibility and Reuse in Sciences. The Second Linked Science Workshop at ISWC Boston, USA November, 2012
  12. Kristina Hettne, Katherine Wolstencroft, Khalid Belhajjame, Carole Goble, Eleni Mina, Harish Dharuri, David De Roure, Lourdes Verdes-Montenegro, Julian Garrido and Marco Roos. Best Practices for workflow design: how to prevent workflow decay. Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2012 Paris, France November, 2012
  13. K  R Page, B Fields, D De Roure, T Crawford, and J S Downie. Reuse, Remix, Repeat: the workflows of MIR. Proc International Society for Music Information Retrieval Conference Porto, Portugal October, 2012
  14. A. Schaaff, L. Verdes-Montenegro, J.E. Ruiz, J. Santander-Vela. Scientific Workflows in Astronomy. Astronomical Data Analysis Software and Systems XXI. Proceedings of a Conference held at Marriott Rive Gauche Conference Center, Paris, France, 6-10 November, 2011. ASP Conference Series, Vol. 461. Edited by P. Ballester, D. Egret, and N.P.F. Lorente. San Francisco: Astronomical Society of the Pacific, 2012., p.875

2011

Journals

  • Sean Bechhofer, Iain Buchan, David De Roure et al (2011) Why Linked Data is Not Enough for Scientists, Future Generation Computer Systems, February 2013. Future Generation Computer Systems, Special section: Recent advances in e-Science. 29(2), 599--611 doi:10.1016/j.future.2011.08.004 [preprint]

Conference/Workshop Proceedings

  1. Khalid Belhajjame, Carole Goble, Stian Soyland-Reyes, and David De Roure. Fostering Scientific Workflow Preservation through Discovery of Substitute Services. IEEE eScience Conference. IEEE CS. 97-104, 2011.
  2. David De Roure, Khalid Belhajjame, 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. in Proc 8th International Conference on Preservation of Digital Objects (iPRES 2011)
  3. De Roure, D., Bechhofer, S., Goble, C. and Newman, D. (2011) Scientific Social Objects: The Social Objects and Multidimensional Network of the myExperiment Website. in Proc1st International Workshop on Social Object Networks (SocialObjects 2011), October 2011, Boston, MA, US
  4. Gamble M and Goble CA (2011)  Quality vs. Trust of Scientific Data on the Web: Towards a Joint Model. Proc 3rd Intl Conference on Web Science, Koblenz, Germany,
  5. Force11 White Paper: Improving the Future of Research Communication and e-Scholarship (2011) (eds Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E and Shotton D), http://force11.org/white-paper Contributors: David De Roure and Carole Goble
  6. Hettne, K., Soiland-Reyes, S., Klyne, G., Belhajjame, K., Gamble, M., Bechhofer, S., Roos, M., Corcho, O., . Workflow forever: semantic web semantic models and tools for preserving and digitally publishing computational experiments Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences 2011 (SWAT4LS)  p.36-37
  7. Garijo D, Gil Y. A new approach for publishing workflows: Abstractions, standards, and linked data. Proceedings of the 6th workshop on Workflows in support of large-scale science, 2011.

Related Publications

  1. Missier, P., and Goble, C. (2011) Workflows to Open Provenance Graphs, round-trip. Future Generation Computer Systems (FGCS), Volume 27, Issue 6, June 2011, pp: 812-819
  2. Zhao, Jun; Sahoo, Satya S.; Missier, Paolo; Sheth, Amit; Goble, Carole (2011) Extending Semantic Provenance into the Web of Data, IEEE Internet Computing, vol.15, no.1, pp.40-48, Jan.-Feb
  3. Garijo, Daniel and Gil, Yolanda. A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data. WORKS11. Link: http://www.isi.edu/~gil/papers/garijo-gil-works11.pdf
  4. Garijo, Daniel and Gil, Yolanda. Towards Open Publication of Reusable Scientific Workflows: Abstractions, Standards and Linked Data (Submitted to JWS).
  5. Patrinos, G.P., Cooper, D.N., van Mulligen, E., Gkantouna, V., Tzimas, G., Tatum, Z., Schultes, E., Roos, M., Mons, B., . Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain Human Mutation 2012
  6. Karasavvas, K., Wolstencroft, K., Mina, E., Cruickshank, D., Williams, A., De Roure, D., Goble, C., Roos, M., . Opening new gateways to workflows for life scientists. Studies in health technology and informatics 2012 175  p.131
  7. Roos, M., Schultes, E.A., Mons, B., . Speeding up research with the Semantic Web Orphanet Journal of Rare Diseases 2012 7 Suppl 2 p.A11
  8. Mons, B., van Haagen, H., Chichester, C., den Dunnen, J.T., van Ommen, G., van Mulligen, E., Singh, B., Hooft, R., Roos, M., Hammond, J., . The value of data Nature genetics 2011 43 4 p.281-283
  9. A. Schaaff and José Enrique Ruiz. Scientific Workflows in the VO. IVOA Technical Note
  10. Akhondi, SA., Singh, B., van der Host, E., van Mulligen, EM., Hettne, K., Kors JA., (2013). A dictionary- and grammar-based chemical named entity recognizer Proceedings of the 4th BioCreative challenge evaluation workshop 2013