This is a list of recent publications made by the eScience lab team. This page might not be complete, please help us to improve this page.

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Open Access logo © 2012 Nick Shockey, distributed under a Creative Commons Attribution 4.0 License. Source: openaccessweek.org

The University of Manchester strive to publish as open access, or to provide green open access preprints where gold open access is not possible. Please let us know if you are unable to access any of our publications.

2016

Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole Goble (2016): FAIRDOMHub: a repository and collaboration environment for sharing systems biology research Nucleic Acids Research. doi:10.1093/nar/gkw1032 [pdf] [html]

Kyle Chard, Mike D’ Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga (2016): I’ll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets. Accepted at IEEE International Conference on Big Data 2016. [preprint] [pdf] [researchgate]

Antonis Troumpoukis, Angelos Charalambidis, Giannis Mouchakis, Stasinos Konstantopoulos, Ronald Siebes, Victor de Boer, Stian Soiland-Reyes, Daniela Digles (2016): Developing a Benchmark Suite for Semantic Web Data from Existing Workflows Accepted at BLINK 2016 Workshop on Benchmarking Linked Data. Kobe, Japan. [pdf] [preprint]

Julie A McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Janna Hastings, Melissa A Haendel, Henning Hermjakob, Jean-Karim Hériché, Jon C Ison, Rafael C Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Christopher J Mungall, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L Snoep, Natalie J Stanford, Stian Soiland-Reyes, Neil Swainston, Nicole Washington, Alan R Williams, Katherine Wolstencroft, Carole Goble, Helen Parkinson (2016): Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize data utility and impact. Submitted to PLOS Biology 2016-10-04. [preprint] [pdf] doi:10.5281/zenodo.163459

Pablo Carbonell, Andrew Currin, Mark Dunstan, Donal Fellows, Adrian Jervis, Nicholas J.W. Rattray, Christopher J. Robinson, Neil Swainston, Maria Vinaixa, Alan Williams, Cunyu Yan, Perdita Barran, Rainer Breitling, George Guo-Qiang Chen, Jean-Loup Faulon, Carole Goble, Royston Goodacre, Douglas B. Kell, Rosalind Le Feuvre, Jason Micklefield, Nigel S. Scrutton, Philip Shapira, Eriko Takano, Nicholas J. Turner (2016): SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals. Biochemical Society Transactions 44(3) 675-677 doi:10.1042/BST20160009

Pinar Alper, Khalid Belhajjame, Carole A. Goble (2016): Automatic Versus Manual Provenance Abstractions: Mind the Gap. 8th USENIX Workshop on the Theory and Practice of Provenance (TaPP 16). [usenix] arxiv:1605.06669 [pdf]

Alex R. Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J. Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito, Donal Fellows, Antonio Fernandez Guerra, Nuno Ferreira, Yuliya Fetyukova, Bruno Fosso, Jonathan Giddy, Carole Goble, Anton Güntsch, Robert Haines, Vera Hernández Ernst, Hannes Hettling, Dóra Hidy, Ferenc Horváth, Dóra Ittzés, Péter Ittzés, Andrew Jones, Renzo Kottmann, Robert Kulawik, Sonja Leidenberger, Päivi Lyytikäinen-Saarenmaa, Cherian Mathew, Norman Morrison, Aleksandra Nenadic, Abraham Nieva de la Hidalga, Matthias Obst, Gerard Oostermeijer, Elisabeth Paymal, Graziano Pesole, Salvatore Pinto, Axel Poigné, Francisco Quevedo Fernandez, Monica Santamaria, Hannu Saarenmaa, Gergely Sipos, Karl-Heinz Sylla, Marko Tähtinen, Saverio Vicario, Rutger Aldo Vos, Alan R. Williams, Pelin Yilmaz (2016): BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. BMC Ecology 16(49) doi:10.1186/s12898-016-0103-y PMID:27765035

Caroline Jay, Simon Harper, Ian Dunlop, Sam Smith, Shoaib Sufi, Carole Goble, Iain Buchan (2016): Natural Language Search Interfaces: Health Data Needs Single-Field Variable Search. Journal of Medical Internet Research 18(1):e13 doi:10.2196/jmir.4912 PMID:26769334

Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao & Barend Mons (2016) The FAIR Guiding Principles for scientific data management and stewardship. Nature Scientific Data 3, 2016 doi:10.1038/sdata.2016.18

David Nickerson, Koray Atalag, Bernard de Bono, Jörg Geiger, Carole Goble, Susanne Hollmann, Joachim Lonien, Wolfgang Müller, Babette Regierer, Natalie J. Stanford, Martin Golebiewski, Peter Hunter (2016): The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable Interface Focus 6:20150103. [pdf] doi:10.1098/rsfs.2015.0103

Alice Allen, Cecilia Aragon, Christoph Becker, Jeffrey Carver, Andrei Chis, Benoit Combemale, Mike Croucher, Kevin Crowston, Daniel Garijo, Ashish Gehani, Carole Goble, Robert Haines, Robert Hirschfeld, James Howison, Kathryn Huff, Caroline Jay, Daniel Katz, Claude Kirchner, Kateryna Kuksenok, Ralf Lämmel, Oscar Nierstrasz, Matthew Turk, Rob Van Nieuwpoort, Matthew Vaughn, Jurgen Vinju (2016): Lightning Talk: “I solemnly pledge” A Manifesto for Personal Responsibility in the Engineering of Academic Software Proceedings of the Fourth Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4), CEUR 1686 http://ceur-ws.org/Vol-1686/WSSSPE4_paper_15.pdf

2015

Katherine Wolstencroft, Stuart Owen, Olga Krebs, Quyen Nguyen, Natalie J Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lihua An, David Shockley, Jacky L Snoep, Wolfgang Mueller, Carole Goble (2015): SEEK: a systems biology data and model management platform. BMC Systems Biology 20, 9:33 doi:10.1186/s12918-015-0174-y

Natalie J Stanford, Katherine Wolstencroft, Martin Golebiewski, Renate Kania, Nick Juty, Christopher Tomlinson, Stuart Owen, Sarah Butcher, Henning Hermjakob, Nicolas Le Novère, Wolfgang Mueller, Jacky Snoep, Carole Goble (2015): The evolution of standards and data management practices in systems biology. Molecular Systems Biology 11:851 doi:10.15252/msb.20156053

Kristian Garza, Carole A. Goble, John M. Brooke, Caroline Jay (2015): Framing the community data system interface. BCS HCI 2015: Proceedings of the 2015 British HCI Conference: pp 269-270 doi:10.1145/2783446.2783605 [preprint] [escholar]

Aleksandra Pawlik, Judith Segal, Helen Sharp, Marian Petre (2015): Crowdsourcing Scientific Software Documentation: A Case Study of the NumPy documentation project. Computing in Science & Engineering, 17 (1), January/February 2015. doi:10.1109/MCSE.2014.93 [preprint]

Jinhui Yao, Wei Tan, Surya Nepal, Shiping Chen, Jia Zhang, David De Roure, Carole Goble (2015): ReputationNet: Reputation-Based Service Recommendation for e-Science. IEEE Transactions on Services Computing 8(3) doi:10.1109/TSC.2014.2364029 [preprint] [researchgate]

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. Journal of Web Semantics: Scence, Services and Agents on the World Wide Web 32 May 2015 pp 16-, doi:10.1016/j.websem.2015.01.003

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau,, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens,, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li,, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti,, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen1 and Søren Brunak (2015): Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 2015 gkv1116. doi:10.1093/nar/gkv1116

2014

Carole Goble (2014): Better Software, Better Research. IEEE Internet Computing 18(5) pp.4-, Sept/Oct 2014. Editorial. doi:10.1109/MIC.2014.88 [preprint]

Carole Goble, Alasdair J G Gray, Eleftherios Tatakis (2014): Help me describe my data: A demonstration of the Open PHACTS VoID Editor. ISWC-P&D 2014: Proceedings of the ISWC 2014 Posters & Demonstrations Track, CEUR-WS.org online http://ceur-ws.org/Vol-1272/paper_33.pdf

Cherian Mathew, Anton Güntsch, Matthias Obst, Saverio Vicario, Robert Haines, Alan R. Williams, Yde de Jong, Carole Goble (2014): A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control. Biodiversity Data Journal 12/2014; 2:e4221. doi:10.3897/BDJ.2.e4221

Paul Groth, Antonis Loizou, Alasdair J.G. Gray, Carole Goble, Lee Harland, Steve Pettifer (2014): API-centric Linked Data integration: The Open PHACTS Discovery Platform case study Web Semantics: Science, Services and Agents on the World Wide Web doi:10.1016/j.websem.2014.03.003 [researchgate]

Pinar Alper, Khalid Belhajjame, Carole A. Goble, Pinar Karagoz (2014): LabelFlow: Exploiting Workflow Provenance to Surface Scientific Data Provenance. Provenance and Annotation of Data and Processes, 5th International Provenance and Annotation Workshop, IPAW 20, Cologne, Germany, June 9-, 2014. Revised Selected Papers. doi:10.1007/978-3-319-16462-5_7 [preprint] [escholar]

Sarah Cohen Boulakia, Jiuqiang Chen, Paolo Missier, Carole A. Goble, Alan R. Williams (2014): Distilling structure in Taverna scientific workflows: a refactoring approach. BMC Bioinformatics 15 (Suppl 1), S12. doi:10.1186/1471-2105-15-S1-S12

Judy Qiu, Ian T. Foster, Carole A. Goble (2014): Emerging Computational Methods for the Life Sciences Workshop 2012. Concurrency and Computation: Practice and Experience 26(6): 1231-1233 doi:10.1002/cpe.3101

Pinar Alper, Carole A Goble, Khalid Belhajjame (2014): On assisting scientific data curation in collection-based dataflows using labels. Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science. pp 7-16 doi:10.1145/2534248.2534249 [escholar] [preprint]

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

Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg (2014): A Quick Guide for Establishing a Successful Bioinformatics Community. PLoS Computational Biology 11(2): e1003972 doi:10.1371/journal.pcbi.1003972

Rutger Aldo Vos, Jordan Valkov Biserkov, Bachir Balech, Niall Beard, Matthew Blissett, Christian Brenninkmeijer, Tom van Dooren, David Eades, George Gosline, Quentin John Groom, Thomas D. Hamann, Hannes Hettling, Robert Hoehndorf, Ayco Holleman, Peter Hovenkamp, Patricia Kelbert, David King, Don Kirkup, Youri Lammers, Thibaut DeMeulemeester, Daniel Mietchen, Jeremy A. Miller, Ross Mounce, Nicola Nicolson, Rod Page, Aleksandra Pawlik, Serrano Pereira, Lyubomir Penev, Kevin Richards, Guido Sautter, David Peter Shorthouse, Marko Tähtinen, Claus Weiland, Alan R. Williams, Soraya Sierra (2014): Enriched biodiversity data as a resource and service. Biodiversity Data Journal 2: e1125 doi:10.3897/BDJ.2.e1125

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]

Steffen Möller, Enis Afgan, Michael Banck, Raoul J P Bonnal, Timothy Booth, John Chilton, Peter J A Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, David R. Powell, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett, Stian Soiland-Reyes, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Valls Guimera, Toshiaki Katayama, Brad A. Chapman (2014): Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics 15(Suppl 14):S7 Supplement NETTAB 2013. doi:10.1186/1471-2105-15-S14-S7

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère (2014): COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, BMC Bioinformatics 15(1), p. 3, doi:10.1186/s12859-014-0369-z

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

Emily Merrill, Stéphane Corlosquet, Paolo Ciccarese, Tim Clark, Sudeshna Das (2014): Semantic Web repositories for genomics data using the eXframe platform Journal of Biomedical Semantics 5(Suppl 1):S3 doi:10.1186/2041-1480-5-S1-S3

Shoaib Sufi, Neil Chue Hong, Simon Hettrick, Mario Antonioletti, Stephen Crouch, Alexander Hay, Devasena Inupakutika, Mike Jackson, Aleksandra Pawlik, Giacomo Peru, John Robinson, Les Carr, David De Roure, Carole Goble, Mark Parsons (2014): Software in reproducible research: advice and best practice collected from experiences at the collaborations workshop. Proceedings of the 1st ACM SIGPLAN Workshop on Reproducible Research Methodologies and New Publication Models in Computer Engineering. 2014.
doi:10.1145/2618137.2618140 [preprint] [escholar]

Ramona L. Walls, John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Leonard Krishtalka, Andréa Matsunaga, Peter Midford, Norman Morrison, Éamonn Ó. Tuama, Mark Schildhauer, Barry Smith, Brian J. Stucky, Andrea Thomer, John Wieczorek, Jamie Whitacre, John Wooley (2014): Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE 9(3): e89606 doi:10.1371/journal.pone.0089606

Neil Davies, Dawn Field, Linda Amaral-Zettler, Katharine Barker, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, Alexei Drummond, Jack A. Gilbert, Frank Oliver Glöckner, Renzo Kottmann, Chris Meyer, Norman Morrison, Matthias Obst, Robert Robbins, Lynn Schriml, Peter Sterk, Steven Stones-Havas (2014): Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. Standards in Genomics Disease 9(3): 1236–1250. doi:10.4056/sigs.4319681 pubmed:PMC4148987

Dawn Field, Peter Sterk, Renzo Kottmann, J. Wim De Smet, Linda Amaral-Zettler, Guy Cochrane, James R. Cole, Neil Davies, Peter Dawyndt, George M. Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Hans-Peter Klenk, Rob Knight, Nikos Kyrpides, Folker Meyer, Ilene Karsch-Mizrachi, Norman Morrison, Robert Robbins, Inigo San Gil, Susanna Sansone, Lynn Schriml, Tatiana Tatusova, Dave Ussery, Pelin Yilmaz, Owen White, John Wooley, Gregory Caporaso (2014) Genomic Standards Consortium Projects. Standards in Genomics Disease 9(3): 599–601. doi:10.4056/sigs.5559680 pubmed:PMC4148985

Neil Davies, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, Jonathan Geller, Jack Gilbert, Frank Oliver Glöckner, Penny R Hirsch, Jo-Ann Leong, Chris Meyer, Matthias Obst, Serge Planes, Chris Scholin, Alfried P Vogler, Ruth D Gates, Rob Toonen, Véronique Berteaux-Lecellier, Michèle Barbier, Katherine Barker, Stefan Bertilsson, Mesude Bicak, Matthew J Bietz, Jason Bobe, Levente Bodrossy, Angel Borja, Jonathan Coddington, Jed Fuhrman, Gunnar Gerdts, Rosemary Gillespie, Kelly Goodwin, Paul C Hanson, Jean-Marc Hero, David Hoekman, Janet Jansson, Christian Jeanthon, Rebecca Kao, Anna Klindworth, Rob Knight, Renzo Kottmann, Michelle S Koo, Georgios Kotoulas, Andrew J Lowe, Viggó Thór Marteinsson, Folker Meyer, Norman Morrison, David D Myrold, Evangelos Pafilis, Stephanie Parker, John Jacob Parnell, Paraskevi N Polymenakou, Sujeevan Ratnasingham, George K Roderick, Naiara Rodriguez-Ezpeleta, Karsten Schonrogge, Nathalie Simon, Nathalie J Valette-Silver, Yuri P Springer, Graham N Stone, Steve Stones-Havas, Susanna-Assunta Sansone, Kate M Thibault, Patricia Wecker, Antje Wichels, John C Wooley, Tetsukazu Yahara, Adriana Zingone, GOs-COS (2014): The founding charter of the Genomic Observatories Network. GigaScience 3:2 doi:10.1186/2047-217X-3-2

Alasdair J. G. Gray, Paul Groth, Antonis Loizou, Sune Askjaer, Christian Brenninkmeijer, Kees Burger, Christine Chichester, Chris T. Evelo, Carole Goble, Lee Harland, Steve Pettifer, Mark Thompson, Andra Waagmeester, Antony J. Williams (2014): Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semantic Web 5(3), 1–13. [pdf] [journal article] [doi:10.3233/SW-2012-0088

2013

Katherine Wolstencroft, Robert Haines, Donal Fellows, Alan Williams, David Withers, Stuart Owen, Stian Soiland-Reyes, Ian Dunlop, Aleksandra Nenadic, Paul Fisher, Jiten Bhagat, Khalid Belhajjame, Finn Bacall, Alex Hardisty, Abraham Nieva de la Hidalga, Maria P. Balcazar Vargas, Shoaib Sufi, Carole Goble (2013): The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud, Nucleic Acids Research 41(W1), W557-W561. doi:10.1093/nar/gkt328

Hyde Zhang, Stian Soiland-Reyes, Carole Goble (2013): Taverna Mobile: Taverna workflows on Android, EMBnet.journal 19(B). doi:10.14806/ej.19.B.727 [pdf]

Paolo Ciccarese, Stian Soiland-Reyes, Tim Clark (2013): Web Annotation as a First Class Object. IEEE Internet Computing. 2013 December; 17(6): 71-75. doi:10.1109/MIC.2013.123 [preprint] [escholar] arXiv:1310.6555

Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Mueller, Quyen Nguyen, Jacky L. Snoep, Carole Goble (2013) Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform The Semantic Web – ISWC 2013, October 21-25, 2013, Proceedings, Part II pp 212-227. doi:10.1007/978-3-642-41338-4_14

Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Philip 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), 599 - 611. doi:10.1016/j.future.2011.08.004 [preprint] [escholar]

Paolo Ciccarese, Stian Soiland-Reyes, Khalid Belhajjame, Alasdair JG Gray, Carole Goble, Tim Clark (2013): PAV ontology: provenance, authoring and versioning. Journal of Biomedical Semantics 4:1, 37. doi:10.1186/2041-1480-4-37

Daniel Garijo, Pinar Alper, Khalid Belhajjame, Oscar Corcho, Yolanda Gil, Carole Goble (2013): Common motifs in scientific workflows: An empirical analysis. Future Generation Computer Systems, 36 pp 338-351. doi:10.1016/j.future.2013.09.018 [preprint]

Carole Goble, David De Roure and Sean Bechhofer (2013): Accelerating Scientists’ Knowledge Turns. Knowledge Discovery, Knowledge Engineering and Knowledge Management (Revised Selected Papers of Third International Joint Conference, IC3K 2011, Paris, France, October 26-29, 2011, editors: Ana Fred, Jan L. G. Dietz, Kecheng Liu, Joaquim Filipe). Communications in Computer and Information Science 348 Springer Berlin Heidelberg, 2013. 3-25. 8 June 2013. doi:10.1007/978-3-642-37186-8_1 [preprint server] [preprint].

Khalid Belhajjame, Jun Zhao, Daniel Garijo, Aleix Garrido, Stian Soiland-Reyes, Pinar Alper, Oscar Corcho (2013): A workflow PROV-corpus based on Taverna and Wings. Proceedings of the Joint EDBT/ICDT 2013 Workshops, ACM, New York, NY, USA, pp. 331–332. doi:10.1145/2457317.2457376 [pdf] [related website]

Christian Brenninkmeijer, Chris Evelo, Carole Goble, Alasdair J G Gray, Paul Groth, Steve Pettifer, Robert Stevens, Antony J Williams, Egon L Willighagen (2013): Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets. Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2013), Berlin, Germany, July 2013. [pdf]

Tim Clark, Paolo Ciccarese, Carole A Goble (2013): Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications. Journal of Biomedical Semantics 5:28 doi:10.1186/2041-1480-5-28 [poster]

Christian Y A Brenninkmeijer, Ian Dunlop, Carole Goble, Alasdair J G Gray, Steve Pettifer, Robert Stevens (2013): Computing Identity Co-Reference Across Drug Discovery Datasets. Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS); CEUR-WS.org; 2013. http://ceur-ws.org/Vol-1114/Session4_Brenninkmeijer.pdf

Pinar Alper, Khalid Belhajjame, Carole Goble, Pinar Karagoz (2013): Small Is Beautiful: Summarizing Scientific Workflows Using Semantic Annotations. 2013 IEEE International Congress on Big Data doi:10.1109/BigData.Congress.2013.49 [pdf]

Pinar Alper, Khalid Belhajjame, Carole A. Goble, Pinar Karagoz (2013): Enhancing and abstracting scientific workflow provenance for data publishing. Proceedings of the Joint EDBT/ICDT 2013 Workshops, pp. 313-318. ACM, 2013. doi:10.1145/2457317.2457370 [escholar] [preprint]

Blanc, A.; Brooke, J.; Fellows, D.; Soldati, M.; Perez-Suarez, D.; Marassi, A. & Santin, A. (2013), Workflows for Heliophysics. Journal of Grid Computing 11(3), 481-503. doi:10.1007/s10723-013-9256-5 [researchgate]

Stephen Crouch, Neil Chue Hong, Simon Hettrick, Mike Jackson, Aleksandra Pawlik, Shoaib Sufi, Les Carr, David De Roure, Carole Goble, Mark Parsons (2013): The Software Sustainability Institute: Changing Research Software Attitudes and Practices. Computing in Science and Engineering 15(6) pp 74-80 doi:10.1109/MCSE.2013.133 [postprint]

Paolo Missier, Saumen Dey, Khalid Belhajjame, Victor Cuevas-Vicenttín, Bertram Ludäscher (2013): D-PROV: Extending the PROV Provenance Model with Workflow Structure. 5th USENIX Workshop on the Theory and Practice of Provenance (TaPP ‘13)., Lombard, IL, USA. 2013-04-02. [pdf] [presentation]

Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J Mungall, Suzanna E Lewis, the ENVO Consortium (2013): The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics 2013, 4:43
doi:10.1186/2041-1480-4-43

John Deck, Katharine Barker, Reed Beaman, Pier Luigi Buttigieg, Gabriele Dröge, Robert Guralnick, Chuck Miller, Éamonn Ó Tuama, Zack Murrell, Cynthia Parr, Bob Robbins, Dmitry Schigel, Brian Stucky, Ramona Walls, John Wieczorek, Norman Morrison, John Wooley (2013): Clarifying Concepts and Terms in Biodiversity Informatics. Standards in Genomics Sciences 8(2): 352–359. doi:10.4056/sigs.3907833 pubmed:PMC3746421

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 (LISC2013). [preprint] [slides]

2002-2012

See also the archived publications covering the group activity for the period 2002-2012.