Cite Us

To reference Research Objects in your work, please use the following citation:

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

If you would like to cite the Research Object model, please use:

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, doi:10.1016/j.websem.2015.01.003

Related Publications

Papers relevant to all aspects of Research Objects, and the future of scholarly publishing. To suggest corrections or new publications, please raise an issue.

2016

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. Scientific Data 3:160018. doi:10.1038/sdata.2016.18

Sarven Capadisli, Amy Guy, Christoph Lange, Sören Auer, Nicola Greco (2015): Linked Research: An Approach for Scholarly Communication. Submitted to ACM Hypertext 2016. http://csarven.ca/linked-research-scholarly-communication

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. IEEE International Conference on Big Data 2016. [pdf[preprint server] [researchgate]

Scott C Edmunds, Peter Li, Christopher I Hunter, Si Zhe Xiao, Robert L Davidson, Nicole Nogoy, Laurie Goodman (2016): Experiences in integrated data and research object publishing using GigaDB. International Journal on Digital Libraries 2016 1–13. doi:10.1007/s00799-016-0174-6

A. Bánáti, P. Kacsuk, M. Kozlovszky (2016): Classification of Scientific Workflows Based on Reproducibility AnalysisMIPRO 2016 – 39th International Convention DC VIS – Distributed Computing, Visualization and Biomedical Engineering. [pdf]

2015

Alejandra González-Beltrán, Peter Li, Jun Zhao, Maria Susana Avila-Garcia, Marco Roos, Mark Thompson, Eelke van der Horst, Rajaram Kaliyaperumal, Ruibang Luo, Tin-Lap Lee, Tak-wah Lam, Scott C. Edmunds, Susanna-Assunta Sansone, Philippe Rocca-Serra (2015): From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics, PLoS ONE 10(7): e0127612 doi:10.1371/journal.pone.0127612

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, doi:10.1016/j.websem.2015.01.003

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). doi: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.  doi:10.1145/2740908.2742016

Anna Bánáti, Péter Kacsuk, Miklós Kozlovszky (2015): Minimal sufficient information about the scientific workflows to create reproducible experiment. IEEE 19th International Conference on Intelligent Engineering Systems (INES) 2015doi:10.1109/INES.2015.7329705  [preprint]

Armel Lefebvre, Marco Spruit and Wienand Omta (2015): Towards Reusability of Computational Experiments: Capturing and Sharing Research Objects from Knowledge Discovery Processes. Proceedings of the 7th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management 1 456–462. doi:10.5220/0005631604560462 [preprint]

2014

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. 369, doi:10.1186/s12859-014-0369-z

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, doi: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

Alejandra González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone,Philippe Rocca-Serra (2014):  linkedISA: semantic representation of ISA-Tab experimental metadata, BMC Bioinformatics 15(Suppl 14): S4. doi:10.1186/1471-2105-15-S14-S4

Herbert Van De Sompel, Robert Sanderson, Harihar Shankar, Martin Klein (2014) Persistent Identifiers for Scholarly Assets and the Web: The Need for an Unambiguous Mapping, IDCC(June 2014), p. 1-10, doi:10.1145/1998076.1998111

Alyssa Goodman, Alberto Pepe, Alexander W. Blocker, Christine L. Borgman, Kyle Cranmer, Merce Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret Hedstrom, David W. Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska, Aleksandra Slavkovic (2014) Ten Simple Rules for the Care and Feeding of Scientific Data, PLoS Computational Biology 10(4). doi:10.1371/journal.pcbi.1003542

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. doi:10.1007/978-3-319-12024-9_9

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]

2013

Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble (2013): A Checklist-Based Approach for Quality Assessment of Scientific Information3rd International Workshop on Linked Science 2013—Supporting  Reproducibility, Scientific Investigations and Experiments (LISC2013).  [preprint] [slides]

Heather A. Piwowar (2013) Value all research products, Nature 493, p. 159, doi:10.1038/493159a

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

Johan Rung, Alvis Brazma (2013) Reuse of public genome-wide gene expression data., Nature reviews. Genetics 14(2), p. 89-99, Nature Publishing Group, pubmed, doi:10.1038/nrg3394

Dennis G Thomas, Sharon Gaheen, Stacey L Harper, Martin Fritts, Fred Klaessig, Elizabeth Hahn-Dantona, David Paik, Sue Pan, Grace a Stafford, Elaine T Freund, Juli D Klemm, Nathan a Baker (2013) ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format., BMC Biotechnology 13, p. 2, pubmed central, doi:10.1186/1472-6750-13-2

Victoria Stodden, Peixuan Guo, Zhaokun Ma (2013) Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals, PLoS ONE 8(6). 10.1371/journal.pone.0067111

Heinz Pampel, Paul Vierkant, Frank Scholze, Roland Bertelmann, Maxi Kindling, Jens Klump, Hans Jürgen Goebelbecker, Jens Gundlach, Peter Schirmbacher, Uwe Dierolf (2013): Making research data repositories visible: The re3data.org registry, PLoS ONE 8(11). doi:10.1371/journal.pone.0078080

Katherine Wolstencroft, Stuart Owen, Olga Krebs (2013): Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform, The Semantic Web, p. 212-227, doi:10.1007/978-3-642-41338-4_14

Daniel Garijo, Sarah Kinnings, Li Xie, Lei Xie, Yinliang Zhang, Philip E. Bourne, Yolanda Gil (2013): Quantifying reproducibility in computational biology: The case of the tuberculosis drugome, PLoS ONE 8(11): e80278, doi:10.1371/journal.pone.0080278

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, doi:10.1145/2499583.2499590

2012

Jennifer M Schopf (2012) Treating data like software, Proceedings of the 12th ACM/IEEE-CS joint conference on Digital Libraries – JCDL ’12, p. 153, doi:10.1145/2232817.2232846

Darrel C Ince, Leslie Hatton, John Graham-Cumming (2012) The case for open computer programs., Nature 482(7386), p. 485-8, pubmed, doi:10.1038/nature10836

A. Morin, J. Urban, P. D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz (2012) Shining Light into Black Boxes, Science 336, p. 159-160, doi:10.1126/science.1218263

Jun Zhao, Jose Manuel Gomez-perez, Khalid Belhajjame, Graham Klyne, Esteban Garcia-cuesta (2012) Why Workflows Break – Understanding and Combating Decay in Taverna Workflows8th International Conference on E-Science (e-Science), IEEE. doi:10.1109/eScience.2012.6404482

Katherine Wolstencroft, Stuart Owen, Carole Goble, Quyen Nguyen, Olga Krebs, Wolfgang Müller (2012) RightField : Semantic Enrichment of Systems Biology Data using Spreadsheets

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. doi:10.1109/eScience.2012.6404489 [preprint]

Ó Corcho, D Garijo Verdejo, Khalid Belhajjame (2012) Workflow-centric research objects: First class citizens in scholarly discourse., Proceedings of the Workshop on the Semantic Publishing (SePublica 2012)(i), p. 1-12, url

2011

Kevin Richards, Richard White, Nicola Nicolson, Richard Pyle (2011) A Beginner’ s Guide to Persistent Identifiers, Global Biodiversity, p. 33, pdf

R. D. Peng (2011) Reproducible Research in Computational Science, Science 334, p. 1226-1227, doi:10.1126/science.1213847

Adam Scott, Will Courtney, Dylan Wood, Raul de la Garza, Susan Lane, Margaret King, Runtang Wang, Jody Roberts, Jessica A. Turner, Vince D. Calhoun (2011) COINS: An Innovative Informatics and Neuroimaging Tool Suite Built for Large Heterogeneous Datasets, Frontiers in Neuroinformatics 5, doi:10.3389/fninf.2011.00033

Mercè Crosas (2011) The Dataverse Network®: An Open-Source Application for Sharing, Discovering and Preserving Data, D-Lib Magazine 17(1/2), url, doi:10.1045/january2011-crosas

S. F. Akkerman, A. Bakker (2011) Boundary Crossing and Boundary Objects, Review of Educational Research 81(2), p. 132-169, doi:10.3102/0034654311404435

2010

Sean Bechhofer, John Ainsworth, Jitenkumar Bhagat, Iain Buchan, Phillip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Carole Goble, Danius Michaelides, Paolo Missier, Stuart Owen, David Newman, David De Roure, Shoaib Sufi (2010) Why Linked Data is Not Enough for Scientists, Sixth IEEE e-Science conference (e-Science 2010), url

Alberto Pepe, Matthew Mayernik, Christine L. Borgman, Herbert De Van Sompel (2010) From artifacts to aggregations: Modeling scientific life cycles on the semantic web, Journal of the American Society for Information Science and Technology 61, p. 567-582, doi:10.1002/asi.21263

Jill P Mesirov (2010) Computer science. Accessible reproducible research., Science (New York, N.Y.) 327, p. 415-416, (preprint), doi:10.1126/science.1179653

Tim Berners-lee (2010) Scientific publishing on the semantic web, Nature, p. 1-2

Dean B Krafft, Nicholas A Cappadona, Brian Medha Devare, Brian J Lowe, Jon Corson-rikert (2010) VIVO : Enabling National Networking of Scientists, Technology, p. 24 months, url

Yale Law School Roundtable on Data and Code Sharing (2010) Reproducible Research: Addressing the Need for Data and Code Sharing in Computational Science, Computing in Science & Engineering 12(sept/oct), p. 8-12, url, doi:10.1109/MCSE.2010.113

Josh Sommer (2010) The delay in sharing research data is costing lives., Nature medicine 16(7), p. 744, doi:10.1038/nm0710-744

Paul Groth, Andrew Gibson, Jan Velterop (2010) The anatomy of a nanopublication, Information Services and Use 30(1-2), p. 51-56

2009

Herbert Van De Sompel, Carl Lagoze, Michael L Nelson, Simeon Warner, Robert Sanderson, Pete Johnston (2009) Adding eScience Assets to the Data Web, Proceedings of the 2nd Workshop on Linked Data on the Web (LDOW2009), p. 10, url

Barend Mons, Jan Velterop (2009) Nano-Publication in the e-science era, Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009)

Bryn Nelson (2009) Data sharing: Empty archives., Nature 461(7261), p. 160-3, pubmed

David De Roure, Carole Goble, Sergejs Aleksejevs, Sean Bechhofer, Jiten Bhagat, Don Cruickshank, Danius Michaelides, David Newman (2009) The myExperiment Open Repository for Scientific Workflows, Analysis, p. 0-3

Iain Buchan, Shoaib Sufi, Sarah Thew, Ian Dunlop, Urara Hiroeh, Dexter Canoy, Georgina Moulton, John Ainsworth, Angela Dale, Sean Bechhofer, Carole Goble (2009) Obesity e-Lab: Connecting Social Science via Research Objects, 5th International Conference on e-Social Science

David De Roure, Carole Goble (2009) Lessons from myExperiment: Research Objects for Data Intensive Research, Microsoft eScience Workshop, url

David De Roure, Carole Goble, Robert Stevens (2009) The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows, Future Generation Computer Systems 25(5), p. 561-567, url, doi:10.1016/j.future.2008.06.010

2008

Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R Brinkman, Adam Michael Clark, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M Hancock, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M Reecy, Donald G Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H Scheuermann, Daniel Schober, Barry Smith, Jason Snape, Christian J Stoeckert, Keith Tipton, Peter Sterk, Andreas Untergasser, Jo Vandesompele, Stefan Wiemann (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project., Nature biotechnology 26, p. 889-896, doi:10.1038/nbt.1411

2006

Brian Caruso, Brian J. Lowe, Jon Corson-Rikert, Medha Devare (2006) VIVO: Case Study of an Ontology-Based Web Site, Artificial Intelligence, p. 2, pdf

2005

Norman Paskin (2005) Digital Object Identifiers for scientific data, Data Science Journal 4, p. 12-20, doi:10.2481/dsj.4.12

JF Claerbout, M Karrenbach (2005) Electronic documents give reproducible research a new meaning, SEG Technical Program Expanded Abstracts 11(1), p. 601, url

2003

J Kunze (2003) Towards electronic persistence using ARK identifiers, Retrieved November, p. 1-9, pdf

1945

Vannevar Bush (1945) As We May Think, The Atlantic Monthly, p. 1-12, url, doi:10.1145/227181.227186