Publications

Cite Us

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

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 [pdf] [preprint]

If you would like to cite the classic 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
Journal of Web Semantics 32
https://doi.org/10.1016/j.websem.2015.01.003

To cite the newer RO-Crate implementation of Research Objects, please use:

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022): Packaging research artefacts with RO-Crate.
Data Science 5(2)
https://doi.org/10.3233/DS-210053

These events cover topics largely overlapping with research objects and modernizing scholarly communication.

2021 onwards

For newer events, see RO-Crate outreach

RO-Crate publications

For the most recent articles, see also RO-Crate publications.

Articles relevant to all aspects of Research Objects, and the future of scholarly publishing. We generally only list publications available as Open Access. To suggest corrections or additions, please raise an issue.

2022

2021

Krzysztof Kurowski, Oscar Corcho, Christine Choirat, Magnus Eriksson, Frederik Coppens, Mark van de Sanden, Milan Ojsteršek (2021):
EOSC Interoperability Framework.
KI-02-21-055-EN-N. Report from the EOSC Executive Board, Working Groups FAIR and Architecture. Publications Office of the EU.
https://doi.org/10.2777/620649

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg (2021):
The role of metadata in reproducible computational research
Patterns 2(1):100322 https://doi.org/10.1016/j.patter.2021.100322

Maxwell Adam Levinson, Justin Niestroy, Sadnan Al Manir, Karen Fairchild, Douglas E. Lake, J. Randall Moorman, Timothy Clark (2020):
FAIRSCAPE: A Framework for FAIR and Reproducible Biomedical Analytics
Neuroinformatics https://doi.org/10.1007/s12021-021-09529-4

2020

Kyle Chard, Niall Gaffney, Mihael Hategan, Kacper Kowalik, Bertram Ludaescher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis (2020):
Toward Enabling Reproducibility for Data-Intensive Research using the Whole Tale Platform
Advances in Parallel Computing 2020 https://doi.org/10.3233/APC200107 preprint arXiv:2005.06087

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober (2020):
FAIR Computational Workflows.
Data Intelligence 2(1):108–121 https://doi.org/10.1162/dint_a_00033

Nick Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John Kunze, Carole A. Goble, Tim Clark (2020):
Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR.
Data Intelligence 2(1):30–39 https://doi.org/10.1162/dint_a_00025

Paul Groth, Helena Cousijn, Tim Clark, Carole Goble (2020):
FAIR Data Reuse – the Path through Data Citation.
Data Intelligence 2(1):78–86 https://doi.org/10.1162/dint_a_00030

Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert W. N. Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia M Santos, Ben Scott, Alan R. Williams, Zhengzhe Wu (2020):
Landscape Analysis for the Specimen Data Refinery
Research Ideas and Outcomes 6:e57602 https://doi.org/10.3897/rio.6.e57602

Mirko Albani, Rosemarie Leone, Federica Foglini, Francesco De Leo, Fulvio Marelli, Iolanda Maggio (2020):
EVER-EST: The Platform Allowing Scientists to Cross-Fertilize and Cross-Validate Data
Data Science Journal 19(1) https://doi.org/10.5334/dsj-2020-021

Nicole A. Vasilevsky, Mohammad Hosseini, Samantha Teplitzky, Violeta Ilik, Ehsan Mohammadi, Juliane Schneider, Barbara Kern, Julien Colomb, Scott C. Edmunds, Karen Gutzman, Daniel S. Himmelstein, Marijane White, Britton Smith, Lisa O’Keefe, Melissa Haendel, Kristi L. Holmes (2020):
Is authorship sufficient for today’s collaborative research? A call for contributor roles
Accountability in Research https://doi.org/10.1080/08989621.2020.1779591

2019

Eoghan Ó Carragáin; Carole Goble; Peter Sefton; Stian Soiland-Reyes (2019):
A lightweight approach to research object data packaging
Bioinformatics Open Source Conference (BOSC2019)
https://doi.org/10.5281/zenodo.3250687

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe (2019):
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.
GigaScience 8(11):giz095 https://doi.org/10.1093/gigascience/giz095

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober (2019):
FAIR Computational Workflows.
Data Intelligence 2(1):108–121 https://doi.org/10.1162/dint_a_00033

Paul Groth, Helena Cousijn, Tim Clark, Carole Goble (2019):
FAIR Data Reuse – the Path through Data Citation.
Data Intelligence 2(1):78–86 https://doi.org/10.1162/dint_a_00030

Katrina Fenlon (2019):
Interactivity, Distributed Workflows, and Thick Provenance: A Review of Challenges Confronting Digital Humanities Research Objects.
RO-2 at Workshop on Research Objects (RO 2019), 24 Sept 2019, San Diego, CA, USA.
2019 IEEE 14th International Conference on e-Science (e-Science), pp. 510–513.
https://doi.org/10.1109/eScience.2019.00067 [preprint]

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludäscher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis (2019):
Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses.
RO-5 at Workshop on Research Objects (RO 2019), 24 Sept 2019, San Diego, CA, USA.
2019 IEEE 15th International Conference on e-Science (e-Science), pp. 514–521.
https://doi.org/10.1109/eScience.2019.00068 [preprint] [BDBag]

Katrina Fenlon (2019): Modeling Digital Humanities Collections as Research Objects
2019 ACM/IEEE Joint Conference on Digital Libraries (JCDL).
https://doi.org/10.1109/JCDL.2019.00029 preprint]

Ravi K Madduri, Kyle Chard, Mike D’Arcy, Segun C Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Ivo Dinov, Gustavo Glusman, Nathan Price, John D Van Horn, Carl Kesselman, Arthur W Toga, Ian Foster (2018):
Reproducible big data science: A case study in continuous FAIRness.
PLoS ONE. 14(4):e0213013
https://doi.org/10.1371/journal.pone.0213013 [preprint bioXriv 268755] Data as BDBag: https://doi.org/10.6084/m9.figshare.5924077.v1

2018

Gil Alterovitz, Dennis A Dean II, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King IV, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Konstantinos Krampis, Krista Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018):
Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results.
PLOS Biology. 16(12):e3000099
https://doi.org/10.1371/journal.pbio.3000099 (bioXriv:191783)

Joshua Borycz, Bonnie Carroll (2018):
Managing Digital Research Objects in an Expanding Science Ecosystem: 2017 Conference Summary
Data Science Journal 17, p16 http://doi.org/10.5334/dsj-2018-016

Zhihao Yuan, Dai Hai Ton That, Siddhant Kothari, Gabriel Fils, Tanu Malik (2018): Utilizing Provenance in Reusable Research Objects
Informatics 5(14).
https://doi.org/10.3390/informatics5010014

Raul Palma, Andrés García-Silva, Jose Manuel Gomez-Perez, Marcin Krystek (2018):
A Research Object-based Toolkit to Support the Earth Science Research Lifecycle.
2018 IEEE 14th International Conference on e-Science (e-Science)
https://doi.org/10.1109/eScience.2018.00020 [preprint] [pdf] [html .zip] [research object]

Stian Soiland-Reyes, Marcos Cáceres (2018):
The Archive and Package (arcp) URI scheme.
2018 IEEE 14th International Conference on e-Science (e-Science) https://doi.org/10.1109/eScience.2018.00018 [preprint] [html] [pdf] [research object]

Bryce Mecum, Matthew Jones, Dave Vieglais, Craig Willis (2018):
Preserving Reproducibility: Provenance and Executable Containers in DataONE Data Packages.
2018 IEEE 14th International Conference on e-Science (e-Science) https://doi.org/10.1109/eScience.2018.00019 [preprint] [pdf]

Beatriz Pérez, Julio Rubio & Carlos Sáenz-Adán (2018):
A systematic review of provenance systems
Knowledge Information Systems 57 pp 495–543
https://doi.org/10.1007/s10115-018-1164-3 [preprint] [supplementary material]

2017

Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D.L. Kelpin, Alasdair J.G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, Michel Dumontier (2017):
Interoperability and FAIRness through a novel combination of Web technologies
PeerJ Computer Science 3:e110 https://doi.org/10.7717/peerj-cs.110

Tobias Kuhn, Michel Dumontier (2017):
Genuine semantic publishing.
Data Science, 1(1-2) https://doi.org/10.3233/DS-170010

Jose Manuel Gomez-Perez, Raul Palma, Andres Garcia-Silva (2017):
Towards a Human-Machine Scientific Partnership Based on Semantically Rich Research Objects.
IEEE 13th International Conference on e-Science (e-Science 2017).
https://doi.org/10.1109/eScience.2017.40 [preprint] [research object]

Andres Garcia-Silva, Raul Palma, Jose Manuel Gomez-Perez (2017):
Ensuring the Quality of Research Objects in the Earth Science Domain. IEEE 13th International Conference on e-Science (e-Science 2017).
https://doi.org/10.1109/eScience.2017.62 [researchgate]

Andres Garcia-Silva, Raul Palma, Jose Manuel Gomez-Perez (2017):
Semantic Technologies and Text Analysis in Support of Scientific Knowledge Reuse.
IEEE 13th International Conference on e-Science (e-Science 2017)
https://doi.org/10.1109/eScience.2017.68 [ResearchGate] no Open Access preprint available?

Dai Hai Ton That, Gabriel Fils, Zhihao Yuan, Tanu Malik (2017):
Sciunits: Reusable Research Objects.
IEEE 13th International Conference on e-Science (e-Science 2017).
https://doi.org/10.1109/eScience.2017.51 [arXiv:1707.05731] [preprint] [slides]

André Giesler, Myriam Czekala, Björn Hagemeier, Richard Grunzke (2017):
UniProv: A Flexible Provenance Tracking System for UNICORE.
JHPCS 2016: High-Performance Scientific Computing, Lecture Notes in Computer Science 10164 pp 233-242.
https://doi.org/10.1007/978-3-319-53862-4_20 [ResearchGate] No Open Access preprint available?

Scott C Edmunds, Peter Li, Christopher I Hunter, Si Zhe Xiao, Robert L Davidson, Nicole Nogoy, Laurie Goodman (2017):
Experiences in integrated data and research object publishing using GigaDB.
International Journal on Digital Libraries 18(99)
https://doi.org/10.1007/s00799-016-0174-6

Markus Stocker (2017):
From Data to Machine Readable Information Aggregated in Research Objects.
D-Lib Magazine 23(1/2).
https://doi.org/10.1045/january2017-stocker

Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blancheto (2017):
Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities.
Future Generation Computer Systems (Available online 6 January 2017).
https://doi.org/10.1016/j.future.2017.01.012 [preprint] [preprint server]

Daniel Nüst, Markus Konkol, Marc Schutzeichel, Edzer Pebesma, Christian Kray, Holger Przibytzin, Jörg Lorenz (2017):
Opening the Publication Process with Executable Research Compendia.
D-Lib Magazine 23(1/2).
https://doi.org/10.1045/january2017-nuest

Tomasz Miksa, Andreas Rauber (2017):
Using ontologies for verification and validation of workflow-based experiments.
Web Semantics: Science, Services and Agents on the World Wide Web 43 March 2017, pages 25–45.
https://doi.org/10.1016/j.websem.2017.01.002 [preprint]

Joachim Van Herwegen, Ruben Taelman, Sarven Capadisli, Ruben Verborgh (2017):
Describing Configurations of Software Experiments as Linked Data.
Proceedings of the First Workshop on Enabling Open Semantic Science, CEUR Workshop Proceedings 1931 pp 23-30.
http://ceur-ws.org/Vol-1931/paper-04.pdf [html] [slides]

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. https://doi.org/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. https://doi.org/10.1109/BigData.2016.7840618 [pdf] [preprint server] [researchgate]

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 45(D1) pp D404–D407. https://doi.org/10.1093/nar/gkw1032

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. https://doi.org/10.1007/s00799-016-0174-6

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

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]

David De Roure, Graham Klyne, Kevin R. Page, John Pybus, David M. Weigl, Matthew Wilcoxson, Pip Willcox (2016): Plans and performances: Parallels in the production of science and music. 2016 IEEE 12th International Conference on e-Science (e-Science). https://doi.org/10.1109/eScience.2016.7870899 [preprint] [preprint server] [slideshare]

Christopher J Playford, Vernon Gayle, Roxanne Connelly, Alasdair JG Gray (2016): Administrative social science data: The challenge of reproducible research. Big Data & Society 3(2). https://doi.org/10.1177/2053951716684143

2015

Adnan Custovic, John Ainsworth, Hasan Arshad, Christopher Bishop, Iain Buchan, Paul Cullinan, Graham Devereux, John Henderson, John Holloway, Graham Roberts, Steve Turner, Ashley Woodcock, Angela Simpson (2015): The Study Team for Early Life Asthma Research (STELAR) consortium ‘Asthma e-lab’: team science bringing data, methods and investigators together. Thorax 70:799-801. https://doi.org/10.1136/thoraxjnl-2015-206781

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 https://doi.org/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, https://doi.org/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). 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]

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) 2015. https://doi.org/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. https://doi.org/10.5220/0005631604560462 [preprint]

Idafen Santana-Perez and María S. Pérez-Hernández (2015): Towards Reproducibility in Scientific Workflows: An Infrastructure-Based Approach. Scientific Programming 2015(243180). https://doi.org/10.1155/2015/243180

David De Roure, Graham Klyne, Kevin R. Page, John P. N. Pybus, David M. Weigl (2015): Music and Science: Parallels in Production. DLfM ’15 Proceedings of the 2nd International Workshop on Digital Libraries for Musicology. https://doi.org/10.1145/2785527.2785530 (No Open Access preprint available)

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, https://doi.org/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, 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

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. https://doi.org/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, https://doi.org/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). https://doi.org/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. 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]

2013

Sonja Holl, Daniel Garijo, Khalid Belhajjame, Olav Zimmermann, Renato De Giovanni, Matthias Obst, Carole Goble (2013): On Specifying and Sharing Scientific Workflow Optimization Results Using Research Objects. Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science (WORKS ’13).
https://doi.org/10.1145/2534248.2534251 [pdf]

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]

Heather A. Piwowar (2013) Value all research products, Nature 493, p. 159, https://doi.org/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, https://doi.org/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, https://doi.org/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, https://doi.org/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). https://doi.org/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, https://doi.org/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, https://doi.org/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, https://doi.org/10.1145/2499583.2499590

2012

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

Jennifer M Schopf (2012) Treating data like software, Proceedings of the 12th ACM/IEEE-CS joint conference on Digital Libraries – JCDL ’12, p. 153, https://doi.org/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, https://doi.org/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, https://doi.org/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 Workflows, 8th International Conference on E-Science (e-Science), IEEE. https://doi.org/10.1109/eScience.2012.6404482 [preprint]

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. https://doi.org/10.1109/eScience.2012.6404489 [preprint]

2011

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]

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, https://doi.org/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, https://doi.org/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, https://doi.org/10.1045/january2011-crosas

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

2010

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

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, https://doi.org/10.1002/asi.21263

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

Tim Berners-Lee, James Handler (2010) Scientific publishing on the semantic web, Nature 410(6832) pp.1023-1024. https://doi.org/10.1038/35074206 https://www.nature.com/nature/debates/e-access/Articles/bernerslee.html

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, https://doi.org/10.1109/MCSE.2010.113

Josh Sommer (2010) The delay in sharing research data is costing lives., Nature medicine 16(7), p. 744, https://doi.org/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, [preprint]

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 [preprint]

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, https://doi.org/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, https://doi.org/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, https://doi.org/10.2481/dsj.4.12

2003

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

1992

Jon F. Claerbout, Martin Karrenbach (1992): Electronic documents give reproducible research a new meaning, SEG Technical Program Expanded Abstracts 1992 11(1), pp. 601–604, https://doi.org/10.1190/1.1822162 [pdf]

1945

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