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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
Peer Reviewed
Scientific Data, Issue 3, 2016. 10.1038/sdata.2016.18.
There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these […]
Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F
Peer Reviewed
Bioinformatics, Issue 4, pages 638-40, 2016. 10.1093/bioinformatics/btv606.
Summary: The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a […]
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, and Carole Goble
Peer Reviewed
Nucleic Acids Research, 2016. 10.1093/nar/gkw1032.
The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of […]
Wolstencroft, K, Owen, S, Krebs, O, Nguyen, Q, Stanford, NJ, Golebiewski, M, Weidemann, A, Bittkowski, M, An, L, Shockley, D, Snoep, JL, Mueller, W, Goble, C
Peer Reviewed
BMC Systems Biology, Issue 9:33, pages 33, 2015. 10.1186/s12918-015-0174-y.
BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing […]
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
Peer Reviewed
Molecular Systems Biology, Issue 11:12, 2015. 10.15252/msb.20156053.
Bergmann, FT, Adams, R, Moodie, S, Cooper, J, Glont, M, Golebiewski, M, Hucka, M, Laibe, C, Miller, AK, Nickerson, DP, Olivier, BG, Rodriguez, N, Sauro, HM, Scharm, M, Soiland-Reyes, S, Waltemath, D, Yvon, F, Le Novère, N
Peer Reviewed
BMC Bioinformatics, Issue 15:1, pages 369, 2014. 10.1186/s12859-014-0369-z.
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. […]
Bechhofer, S, Buchan, I, De Roure, D, Missier, P, Ainsworth, J, Bhagat, J, Couch, P, Cruickshank, D, Delderfield, M, Dunlop, I, Gamble, M, Michaelides, D, Owen, S, Newman, D, Sufi, S, Goble, C
Peer Reviewed
Future Generation Computer Systems, Issue 29:2, pages 599 - 611, 2013. 10.1016/j.future.2011.08.004.
Scientific data represents a significant portion of the linked open data cloud and scientists stand to benefit from the data fusion capability this will afford. Publishing linked data into the cloud, however, does not ensure the required reusability. Publishing has requirements of provenance, quality, credit, attribution and methods to provide the reproducibility that enables validation […]
Wolstencroft, K, Owen, S, Horridge, M, Jupp, S, Krebs, O, Snoep, J, du Preez, F, Mueller, W, Stevens, R, Goble, C
Peer Reviewed
Concurrency and Computation: Practice and Experience, Issue 25:4, pages 467 - 480, 2013. 10.1002/cpe.2941.
Wolstencroft, K, Owen, S, Krebs, O, Mueller, W, Nguyen, Q, Snoep, JL, Goble, C
Book Chapter
Book title: Springer, Berlin, Heidelberg, 2013.
Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. Semantic web technologies should be ideal for exploring the complex networks of genes, proteins and metabolites that interact, but much of this data is not natively available to the semantic web. Data […]
Sansone, S-A, Rocca-Serra, P, Field, D, Maguire, E, Taylor, C, Hofmann, O, Fang, H, Neumann, S, Tong, W, Amaral-Zettler, L, Begley, K, Booth, T, Bougueleret, L, Burns, G, Chapman, B, Clark, T, Coleman, L-A, Copeland, J, Das, S, de Daruvar, A, de Matos, P, Dix, I, Edmunds, S, Evelo, CT, Forster, MJ, Gaudet, P, Gilbert, J, Goble, C, Griffin, JL, Jacob, D, Kleinjans, J, Harland, L, Haug, K, Hermjakob, H, Sui, SJHo, Laederach, A, Liang, S, Marshall, S, McGrath, A, Merrill, E, Reilly, D, Roux, M, Shamu, CE, Shang, CA, Steinbeck, C, Trefethen, A, Williams-Jones, B, Wolstencroft, K, Xenarios, I, Hide, W
Peer Reviewed
Nature Genetics, Issue 44:2, pages 121 - 126, 2012. 10.1038/ng.1054.
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared ‘Investigation-Study-Assay’ framework to support that […]