Publications

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.

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.

2024

Chris Orton, Lara Edwards, David Seymour, Monica Jones, Philip Quinlan, Simon Thompson, Carole Goble, Jennifer Quint, Aziz Sheikh (2024):
Data as infrastructure: Systematic data curation addressing fundamental data content differences across the UK.
Conference Proceedings for International Population Data Linkage Conference 2024, Chicago, USA, 2024-09-15/–18.
International Journal of Population Data Science 9(5)
https://doi.org/10.23889/ijpds.v9i5.2683

Rafael Ferreira da Silva, Deborah Bard, Kyle Chard, Shaun DeWitt, Ian T. Foster, Tom Gibbs, Carole Goble, William Godoy, Johan Gustafsson, Utz−Uwe Haus, Stephen Hudson, Shantenu Jha, Laila Los, Drew Paine, Frederic Suter, Logan Ward, Sean Wilkinson, Marcos Amaris, Yadu Babuji, Jonathan and Bader, Rajat Bhattarai, Wes Brewer, Paul Brunk, Silvina Caino−Lores, Henri Casanova, Daniela Cassol, Jared Coleman, Taina Coleman, Iacopo Colonnelli, Anderson Andrei Da Silva, Daniel de Oliveira, Pascal Elahi, Nour Elfaramawy, Wael Elwasif, Brian Etz, Thomas Fahringer, Wesley Ferreira, Rosa Filgueira, Jacob Fosso Tande, Luiz Gadelha, Andy Gallo, Daniel Garijo, Yiannis Georgiou, Philipp Gritsch, Patricia Grubel, Amal Gueroudji, Quentin Guilloteau, Carlo Hamalainen, Rolando Hong Enriquez, Lauren Huet, Kevin Hunter Kesling, Paula Iborra, Shiva Jahangiri, Jan Janssen, Joe Jordan, Sehrish Kanwal, Liliane Kunstmann, Fabian Lehmann, Ulf Leser, Chen Li, Peini Liu, Jakob Luettgau, Richard Lupat, Jose M. Fernandez, Ketan Maheshwari, Tanu Malik, Jack Marquez, Motohiko Matsuda, Doriana Medic, Somayeh Mohammadi, Alberto Mulone, John−Luke Navarro, Kin Wai Ng, Klaus Noelp, Bruno P. Kinoshita, Ryan Prout, Michael R. Crusoe, Sashko Ristov, Stefan Robila, Daniel Rosendo, Billy Rowell, Jedrzej Rybicki, Hector Sanchez, Nishant Saurabh, Sumit Kumar Saurav, Tom Scogland, Dinindu Senanayake, Woong Shin, Raul Sirvent, Tyler Skluzacek, Barry Sly−Delgado, Stian Soiland−Reyes, Abel Souza, Renan Souza, Domenico Talia, Nathan Tallent, Lauritz Thamsen, Mikhail Titov, Ben Tovar, Karan Vahi, Eric Vardar−Irrgang, Edite Vartina, Yuandou Wang, Merridee Wouters, Qi Yu, Ziad Al Bkhetan, Mahnoor Zulfiqar (2024):
Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows.
Oak Ridge National Laboratory Technical Report ORNL/TM−2024/3573
Zenodo
https://doi.org/10.5281/zenodo.13844759

Ove Johan Ragnar Gustafsson, Sean R. Wilkinson, Finn Bacall, Stian Soiland-Reyes, Simone Leo, Luca Pireddu, Stuart Owen, Nick Juty, José Mª Fernández, Tom Brown, Hervé Ménager, Björn Grüning, Salvador Capella-Gutierrez, Frederik Coppens, Carole Goble (2024):
WorkflowHub: a registry for computational workflows.
arXiv:2410.06941 [cs.DL]
https://doi.org/10.48550/arXiv.2410.06941

Sean Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble (2024):
Applying the FAIR Principles to Computational Workflows.
arXiv 2410.03490 [cs.DL]
https://doi.org/10.48550/arXiv.2410.03490

Simone Leo, Michael R. Crusoe, Laura Rodríguez-Navas, Raül Sirvent, Alexander Kanitz, Paul De Geest, Rudolf Wittner, Luca Pireddu, Daniel Garijo, José M. Fernández, Iacopo Colonnelli, Matej Gallo, Tazro Ohta, Hirotaka Suetake, Salvador Capella-Gutierrez, Renske de Wit, Bruno de Paula Kinoshita, Stian Soiland-Reyes (2024):
Recording provenance of workflow runs with RO-Crate.
PLOS One 19(9):e0309210
https://doi.org/10.1371/journal.pone.0309210

Jana Martínková, Nick Juty, Alejandra Gonzalez Beltran, Carole Goble, Yann Le Franc (2024):
Moving towards FAIR mappings and crosswalks.
FOAM 2024: FAIR principles for Ontologies and Metadata in Knowledge Management, Formal Ontology in Information Systems Conference 2024 (FOIS 2024), 15-19 July 2024, Enschede, Netherlands

Stian Soiland-Reyes, Carole Goble, Paul Groth (2024):
Evaluating FAIR Digital Object and Linked Data as distributed object systems.
PeerJ Computer Science 10:e1781
https://doi.org/10.7717/peerj-cs.1781 [RO-Crate]

Flora D’Anna, Niclas Jareborg, Mijke Jetten, Minna Ahokas, Pinar Alper, Robert Andrews, Korbinian Bösl, Teresa D’Altri, Daniel Faria, Nazeefa Fatima, Siiri Fuchs, Clare Garrard, Wei Gu5, Katharina F. Heil, Yvonne Kallberg, Flavio Licciulli, Nils-Christian Lübke, Ana M. P. Melo, Ivan Mičetić15, Jorge Oliveira, Anastasis Oulas, Patricia M. Palagi, Krzysztof Poterlowicz, Xenia Perez-Sitja, Patrick Ruch, Susanna-Assunta Sansone, Helena Schnitzer, Celia van Gelder, Thanasis Vergoulis, Daniel Wibberg, Ulrike Wittig, Brane Leskošek, Jiri Vondrasek, Munazah Andrabi (2024):
A research data management (RDM) community for ELIXIR.
F1000Research 13(ELIXIR):230
https://doi.org/10.12688/f1000research.146301.2

Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, Herbert Van de Sompel (2024):
Practical webby FDOs with RO-Crate and FAIR Signposting: Experiences and lessons learned.
International FAIR Digital Objects Implementation Summit 2024, Berlin, Germany, 2024-03-20/–21.
Open Conference Proceedings (submitted)
https://s11.no/2024/webby-fdos/

Stian Soiland-Reyes, Peter Sefton, Simone Leo, Leyla Jael Castro, Claus Weiland, RO-Crate community (2024):
RO-Crate community update 2024.
(submitted)
https://research.manchester.ac.uk/en/publications/ro-crate-community-update-2024

Stian Soiland-Reyes, Stuart Wheater, Tom Giles, Carole Goble, Phil Quinlan (2024):
Five Safes RO-Crate: FAIR Digital Objects for Trusted Research Environments.
(submitted)
https://research.manchester.ac.uk/en/publications/five-safes-ro-crate-fair-digital-objects-for-trusted-research-env

Herbert Van de Sompel, Stian Soiland-Reyes (2024):
FAIR Signposting: Exposing the Topology of Digital Objects on the Web.
(submitted)
https://research.manchester.ac.uk/en/publications/fair-signposting-exposing-the-topology-of-digital-objects-on-the-

Peter Sefton, Stian Soiland-Reyes (2024):
Five ways RO-Crate data packages are important for repositories.
(submitted)
https://research.manchester.ac.uk/en/publications/five-ways-ro-crate-data-packages-are-important-for-repositories

Stian Soiland-Reyes, Leyla Jael Castro, Rohitha Ravinder, Claus Weiland, Jonas Grieb, Alexander Rogers, Christophe Blanchi, Herbert Van de Sompel (2024):
BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas.
BioHackrXiv
https://doi.org/10.37044/osf.io/gmk2h

Sebastian Beier, Timo Mühlhaus, Cyril Pommier, Stuart Owen, Dominik Brilhaus, Heinrich Lukas Weil, Florian Wetzels, Gavin Chait, Daniel Arend, Manuel Feser, Gajendra Doniparthi, Jonathan Bauer, Sveinung Gundersen, Pável Vázquez (2024):
BioHackEU23 report: Enabling continuous RDM using Annotated Research Contexts with RO-Crate profiles for ISA.
BioHackrXiv
https://doi.org/10.37044/osf.io/7y2jh

José M. Fernández, Paula Iborra, Sébastien Moretti, Arun Isaac, Paul De Geest, Stian Soiland-Reyes (2024): BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate.
BioHackrXiv https://doi.org/10.37044/osf.io/7f94w

Mark D Wilkinson, Susanna-Assunta Sansone, Marjan Grootveld, Richard Dennis, David Hecker, Robert Huber, Stian Soiland-Reyes, Herbert Van de Sompel, Andreas Czerniak, Milo Thurston, Allyson L. Lister, Alban Gaignard (2024):
Report on “FAIR Signposting” and its uptake by the community.
EOSC FAIR Metrics and Data Quality Task Force
https://doi.org/10.5281/zenodo.10490289

2023

Tom Brown, Nick Juty, Stian Soiland-Reyes, Felix Shaw, Rutger Vos (2023): RO-Crates as a practical implementation of FAIR Digital Object to align biodiversity genomics work streams. (submitted) https://research.manchester.ac.uk/en/publications/ro-crates-as-a-practical-implementation-of-fair-digital-object-to

Romain David, Arina Rybina, Jean‐Marie Burel, Jean‐Karim Heriche, Pauline Audergon, Jan‐Willem Boiten, Frederik Coppens, Sara Crockett, Katrina Exter, Sven Fahrner, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Björn Grüning, Kim Tamara Gurwitz, John M Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean‐Luc Legras, Allyson L Lister, Dario Livio Longo, Rebecca Ludwig, Bénédicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Michaela Th Mayrhofer, Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S Richard, Paolo Romano, Antonio Rosato, Alex Sánchez‐Pla, Susanna‐Assunta Sansone, Ugis Sarkans, Beatriz Serrano‐Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon (2023):
“Be sustainable”: EOSC‐Life recommendatons for implementation of FAIR principles in life science data handling.
The EMBO Journal 42:e115008
https://doi.org/10.15252/embj.2023115008

Romain David, Audrey S. Richard, Claire Connellan, Katharina B. Lauer, Maria Luisa Chiusano, Carole Goble, Martin Houde, Isabel Kemmer, Antje Keppler, Philippe Lieutaud, Christian Ohmann, Maria Panagiotopoulou, Sara Raza Khan, Arina Rybina, Stian Soiland-Reyes, Charlotte Wit, Rudolf Wittner, Rafael Andrade Buono, Sarah Arnaud Marsh, Pauline Audergon, Dylan Bonfils, Jose-Maria Carazo, Remi Charrel, Frederik Coppens, Wolfgang Fecke, Claudia Filippone, Eva Garcia Alvarez, Sheraz Gul, Henning Hermjakob, Katja Herzog, Petr Holub, Lukasz Kozera, Allyson L. Lister, José López-Coronado, Bénédicte Madon, Kurt Majcen, William Martin, Wolfgang Müller, Elli Papadopoulou, Christine M.A. Prat, Paolo Romano, Susanna-Assunta Sansone, Gary Saunders, Niklas Blomberg, Jonathan Ewbank (2023):
Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness.
Data Science Journal 22:52
https://doi.org/10.5334/dsj-2023-035

Rudolf Wittner, Matej Gallo, Simone Leo, Cecilia Mascia, Francesca Frexia, Markus Plass, Stian Soiland-Reyes, Heimo Müller, Jörg Geiger, Petr Holub (2023):
Linking provenance and its metadata in multi-organizational environments of life sciences.
(Submitted) https://research.manchester.ac.uk/en/publications/linking-provenance-and-its-metadata-in-multi-organizational-envir

Marjan Meurisse, Francisco Estupiñán-Romero, Javier González-Galindo, Natalia Martínez-Lizaga, Santiago Royo-Sierra, Simon Saldner, Lorenz Dolanski-Aghamanoukjan, Alexander Degelsegger-Marquez, Stian Soiland-Reyes, Nina Van Goethem, Enrique Bernal-Delgado, On Behalf of BeYond-COVID project contributors (2023):
Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment.
BMC Medical Research Methodology 23:248
https://doi.org/10.1186/s12874-023-02068-3

Ignacio Eguinoa, Marek Suchánek, Vojtěch Knaisl, Jan Slifka, Paul De Geest, David López, Bjorn Gruning, Simone Leo, Stian Soiland-Reyes (2023):
BioHackEU22 Report: Enhancing Research Data Management in Galaxy and Data Stewardship Wizard by utilising RO-Crates.
BioHackrXiv
https://doi.org/10.37044/osf.io/24jst

Carole Goble, Finn Bacall, Stian Soiland-Reyes, Stuart Owen, Ignacio Eguinoa, Bert Droesbeke, Hervé Ménager, Laura Rodriguez-Navas, José M. Fernández, Björn Grüning, Simone Leo, Luca Pireddu, Michael Crusoe, Johan Gustafsson, Salvador Capella-Gutierrez, Frederik Coppens (2023):
EOSC-Life Workflow Collaboratory for the Life Sciences.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.352

Leyla Jael Castro, Stian Soiland-Reyes, Dietrich Rebholz-Schuhmann (2023):
RO-Crates Meets FAIR Digital Objects.
1st Conference on Research Data Infrastructure (CoRDI 2023), 2023-09-12/–14, Karlsruhe, Germany.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.396

Fuqi Xu, Nick Juty, Carole Goble, Simon Jupp, Helen Parkinson, Mélanie Courtot (2023):
Features of a FAIR vocabulary.
Journal of Biomedical Semantics 14:6
https://doi.org/10.1186/s13326-023-00286-8

Alasdair Gray, Leyla J. Castro, Nick Juty, Carole Goble (2023):
Schema.org for Scientific Data.
Artificial Intelligence for Science (Chapter 27) pp 495-51.
https://doi.org/10.1142/9789811265679_0027 [no OA preprint available]

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Mélanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio-De-Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger (2023):
Towards a common standard for data and specimen provenance in life sciences.
Learning Health Systems
https://doi.org/10.1002/lrh2.10365

Ginger Tsueng, Sahar Frika, Alasdair J. G. Gray, Marcos Casado Barbero, Alban Gaignard, Ivan Mičetić, Leyla Jael Castro, Nick Juty (2023):
Enabling profile updates through the Data Discovery Engine (DDE).
BioHackrXiv
https://doi.org/10.37044/osf.io/3b9gp

Finn Bacall, Aitor Apaolaza, Munazah Andrabi, Chris Child, Carole Goble, Olivier Sand, Alexander Botzki (2023):
Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal.
Current Protocols 3:e682
https://doi.org/10.1002/cpz1.682

Brigitte Mathiak, Nick Juty, Alessia Bardi, Julien Colomb, Peter Kraker (2023):
What are Researchers’ Needs in Data Discovery? Analysis and Ranking of a Large-Scale Collection of Crowdsourced Use Cases.
Data Science Journal 22(1)
http://doi.org/10.5334/dsj-2023-003

Ebtisam Alharbi, Rigina Skeva, Nick Juty, Caroline Jay, Carole Goble (2023):
A FAIR-Decide framework for pharmaceutical R&D: FAIR data cost–benefit assessment.
Drug Discovery Today 28(4):103510
https://doi.org/10.1016/j.drudis.2023.103510

Natasha Noy, Carole Goble (2023):
Are We Cobblers without Shoes? Making Computer Science Data FAIR.
Communications of the ACM 66(1)
https://doi.org/10.1145/3528574

Mingfang Wu, Stephen M. Richard, Chantelle Verhey, Leyla Jael Castro, Baptiste Cecconi, Nick Juty (2023):
An analysis of crosswalks from research data schemas to Schema.org.
Data Intelligence
https://doi.org/10.1162/dint_a_00186

Rafael Ferreira da Silva, Rosa M. Badia, Venkat Bala, Debbie Bard, Peer-Timo Bremer, Ian Buckley, Silvina Caino-Lores, Kyle Chard, Carole Goble, Shantenu Jha, Daniel S. Katz, Daniel Laney, Manish Parashar, Frederic Suter, Nick Tyler, Thomas Uram, Ilkay Altintas, Stefan Andersson, William Arndt, Juan Aznar, Jonathan Bader, Bartosz Balis, Chris Blanton, Kelly Rosa Braghetto, Aharon Brodutch, Paul Brunk, Henri Casanova, Alba Cervera Lierta, Justin Chigu, Taina Coleman, Nick Collier, Iacopo Colonnelli, Frederik Coppens, Michael Crusoe, Will Cunningham, Bruno de Paula Kinoshita, Paolo Di Tommaso, Charles Doutriaux, Matthew Downton, Wael Elwasif, Bjoern Enders, Chris Erdmann, Thomas Fahringer, Ludmilla Figueiredo, Rosa Filgueira, Martin Foltin, Anne Fouilloux, Luiz Gadelha, Andy Gallo, Artur Garcia Saez, Daniel Garijo, Roman Gerlach, Ryan Grant, Samuel Grayson, Patricia Grubel, Johan Gustafsson, Valerie Hayot-Sasson, Oscar Hernandez, Marcus Hilbrich, AnnMary Justine, Ian Laflotte, Fabian Lehmann, Andre Luckow, Jakob Luettgau, Ketan Maheshwari, Motohiko Matsuda, Doriana Medic, Pete Mendygral, Marek Michalewicz, Jorji Nonaka, Maciej Pawlik, Loic Pottier, Line Pouchard, Mathias Putz, Santosh Kumar Radha, Lavanya Ramakrishnan, Sashko Ristov, Paul Romano, Daniel Rosendo, Martin Ruefenacht, Katarzyna Rycerz, Nishant Saurabh, Volodymyr Savchenko, Martin Schulz, Christine Simpson, Raul Sirvent, Tyler Skluzacek, Stian Soiland-Reyes, Renan Souza, Sreenivas Rangan Sukumar, Ziheng Sun, Alan Sussman, Douglas Thain, Mikhail Titov, Benjamin Tovar, Aalap Tripathy, Matteo Turilli, Bartosz Tuznik, Hubertus van Dam, Aurelio Vivas , Logan Ward, Patrick Widener, Sean Wilkinson, Justyna Zawalska, Mahnoor Zulfiqar (2023):
Workflows Community Summit 2022: A Roadmap Revolution.
arXiv:2304.00019
https://arxiv.org/abs/2304.00019

2022

Daniel Arend, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, Cyril Pommier, Stuart Owen, Philippe Rocca-Serra, Thomas Rosnet, Stian Soiland-Reyes (2022):
BioHackEU22 Project 22: Plant data exchange and standard interoperability.
BioHackrXiv https://doi.org/10.37044/osf.io/c724r

Yo Yehudi, Lukas Hughes-Noehrer, Carole Goble, Caroline Jay (2022):
Subjective data models in bioinformatics: Do wet-lab and computational biologists comprehend data differently?.
arXiv:2208.12346 [cs.HC]
https://doi.org/10.48550/arXiv.2208.12346

Cyril Pommier, Frederik Coppens, Hanna Ćwiek-Kupczyńska, Daniel Faria, Sebastian Beier, Célia Miguel, Célia Michotey, Flora D’Anna, Stuart Owen & Kristina Gruden (2022):
Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data Lifecycle.
In: Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, Hugh F. Williamson, Sabina Leonelli (eds.)
https://doi.org/10.1007/978-3-031-13276-6_8

Vitor Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F. Heil, Henning Hermjakob, Pascal Kahlem, Maria I. Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, Rahuman S. Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T. Evelo, John M. Hancock (2022):
Systems Biology in ELIXIR: modelling in the spotlight. [version 1; peer review: 1 approved with reservations]
F1000Research 11(ELIXIR):1265
https://doi.org/10.12688/f1000research.126734.1

Stian Soiland-Reyes, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, Paul Groth (2022):
Updating Linked Data practices for FAIR Digital Object principles.
1st International Conference on FAIR Digital Objects (FDO 2022) (presentation).
Research Ideas and Outcomes 8:e94501
https://doi.org/10.3897/rio.8.e94501 [slides]

Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth (2022):
Creating lightweight FAIR Digital Objects with RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e93937
https://doi.org/10.3897/rio.8.e93937 [poster]

Oliver Woolland, Paul Brack, Stian Soiland-Reyes, Ben Scott, Laurence Livermore (2022):
Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e94349
https://doi.org/10.3897/rio.8.e94349 [poster]

Paul De Geest, Frederik Coppens, Stian Soiland-Reyes, Ignacio Eguinoa, Simone Leo (2022):
Enhancing RDM in Galaxy by integrating RO-Crate.
1st International Conference on FAIR Digital Objects (FDO 2022) (poster)
Research Ideas and Outcomes 8:e95164
https://doi.org/10.3897/rio.8.e95164 [poster]

Carlos Martinez-Ortiz, Carole Goble, Daniel S Katz, Tom Honeyman, Paula Andrea Martinez, Michelle Barker, Leyla Jael Castro, Neil Chue Hong, Morane Gruenpeter, Jennifer Harrow, Anna-Lena Lamprecht, Fotis E Psomopoulos (2022):
How does software fit into the FDO landscape?.
1st International Conference on FAIR Digital Objects (FDO 2022) (presentation)
Research Ideas and Outcomes 8:e95164
https://doi.org/10.3897/rio.8.e95724

Laurence Livermore, Paul Brack, Ben Scott, Stian Soiland-Reyes, Oliver Woolland (2022):
The Specimen Data Refinery: Using a scientific workflow approach for information extraction
Biodiversity Information Standards (TDWG 2022).
Biodiversity Information Science and Standards 6:e93500
https://doi.org/10.3897/biss.6.93500 [slides]

Ebtisam Alharbi (2022):
The practices, costs and benefits of FAIR implementation in pharmaceutical Research and Development.
PhD Thesis, The University of Manchester
https://www.research.manchester.ac.uk/portal/en/theses/the-practices-costs-and-benefits-of-fair-implementation-in-pharmaceutical-research-and-development(61faec0b-92d6-4bb6-85ed-c1404cdf510b).html

Jan G. Bjaalie, Carole Goble, Susanna-Assunta Sansone, Richard Nakamura, Maryann E. Martone (2022):
Perspectives on Data Sharing and the New NIH Policy from the European Union.
Harvard Data Science Review 4(3)
https://doi.org/10.1162/99608f92.bcd0b999

Ebtisam Alharbi, Yojana Gadiya, David Henderson, Andrea Zaliani, Alejandra Delfin-Rossaro, Anne Cambon-Thomsen, Manfred Kohler, Gesa Witt, Danielle Welter, Nick Juty, Caroline Jay, Ola Engkvist, Carole Goble, Dorothy S. Reilly, Venkata Satagopam, Vassilios Ioannidis, Wei Gu, Philip Gribbon (2022):
Selection of data sets for FAIRification in drug discovery and development: Which, why, and how?.
Drug Discovery Today 27(8)
https://doi.org/10.1016/j.drudis.2022.05.010

Yo Yehudi, Lukas Hughes-Noehrer, Carole Goble, Caroline Jay (2022):
COVID-19: An exploration of consecutive systemic barriers to pathogen-related data sharing during a pandemic.
arXiv 2205.12098 [cs.CY] (preprint)
https://doi.org/10.48550/arXiv.2205.12098

Rachel Lyne, Adrián Bazaga, Daniela Butano, Sergio Contrino, Joshua Heimbach, Fengyuan Hu, Alexis Kalderimis, Mike Lyne, Kevin Reierskog, Radek Stepan, Julie Sullivan, Archie Wise, Yo Yehudi, Gos Micklem (2022):
HumanMine: advanced data searching, analysis and cross-species comparison.
bioRxiv 2022.05.11.491545
https://doi.org/10.1101/2022.05.11.491545

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
[RO-Crate]

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2022):
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
Communications of the ACM 65(6)
https://doi.org/10.1145/3486897
arXiv:2105.07028 [cs.DC] [pdf] [html]

Anne M. Treasure, Siobhan Mackenzie Hall, Igor Lesko, Derek Moore, Malvika Sharan, Menno van Zaanen, Yo Yehudi, Anelda van der Walt (2022):
Ten simple rules for establishing a mentorship programme.
PLOS Computational Biology 18(5):e1010015
https://doi.org/10.1371/journal.pcbi.1010015

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble (2022):
Ten Simple Rules for making a software tool workflow-ready.
PLOS Computational Biology 18(3):e1009823
https://doi.org/10.1371/journal.pcbi.1009823

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth (2022):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00135

Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (2022): The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00134

Sam Parsons, Flávio Azevedo, Mahmoud M. Elsherif, Samuel Guay, Owen N. Shahim, Gisela H. Govaart, Emma Norris, Aoife O’Mahony, Adam J. Parker, Ana Todorovic, Charlotte R. Pennington, Elias Garcia-Pelegrin, Aleksandra Lazić, Olly Robertson, Sara L. Middleton, Beatrice Valentini, Joanne McCuaig, Bradley J. Baker, Elizabeth Collins, Adrien A. Fillon, Tina B. Lonsdorf, Michele C. Lim, Norbert Vanek, Marton Kovacs, Timo B. Roettger, Sonia Rishi, Jacob F. Miranda, Matt Jaquiery, Suzanne L. K. Stewart, Valeria Agostini, Andrew J. Stewart, Kamil Izydorczak, Sarah Ashcroft-Jones, Helena Hartmann, Madeleine Ingham, Yuki Yamada, Martin R. Vasilev, Filip Dechterenko, Nihan Albayrak-Aydemir, Yu-Fang Yang, Annalise A. LaPlume, Julia K. Wolska, Emma L. Henderson, Mirela Zaneva, Benjamin G. Farrar, Ross Mounce, Tamara Kalandadze, Wanyin Li, Qinyu Xiao, Robert M. Ross, Siu Kit Yeung, Meng Liu, Micah L. Vandegrift, Zoltan Kekecs, Marta K. Topor, Myriam A. Baum, Emily A. Williams, Asma A. Assaneea, Amélie Bret, Aidan G. Cashin, Nick Ballou, Tsvetomira Dumbalska, Bettina M. J. Kern, Claire R. Melia, Beatrix Arendt, Gerald H. Vineyard, Jade S. Pickering, Thomas R. Evans, Catherine Laverty, Eliza A. Woodward, David Moreau, Dominique G. Roche, Eike M. Rinke, Graham Reid, Eduardo Garcia-Garzon, Steven Verheyen, Halil E. Kocalar, Ashley R. Blake, Jamie P. Cockcroft, Leticia Micheli, Brice Beffara Bret, Zoe M. Flack, Barnabas Szaszi, Markus Weinmann, Oscar Lecuona, Birgit Schmidt, William X. Ngiam, Ana Barbosa Mendes, Shannon Francis, Brett J. Gall, Mariella Paul, Connor T. Keating, Magdalena Grose-Hodge, James E. Bartlett, Bethan J. Iley, Lisa Spitzer, Madeleine Pownall, Christopher J. Graham, Tobias Wingen, Jenny Terry, Catia Margarida F. Oliveira, Ryan A. Millager, Kerry J. Fox, Alaa AlDoh, Alexander Hart, Olmo R. van den Akker, Gilad Feldman, Dominik A. Kiersz, Christina Pomareda, Kai Krautter, Ali H. Al-Hoorie, Balazs Aczel (2022):
A community-sourced glossary of open scholarship terms.
Nature Human Behaviour
https://doi.org/10.1038/s41562-021-01269-4 [preprint]

Neil P. Chue Hong, Daniel S. Katz, Michelle Barker; Anna-Lena Lamprecht, Carlos Martinez, Fotis E. Psomopoulos, Jen Harrow, Leyla Jael Castro, Morane Gruenpeter, Paula Andrea Martinez, Tom Honeyman; Alexander Struck, Allen Lee, Axel Loewe, Ben van Werkhoven, Catherine Jones, Daniel Garijo, Esther Plomp, Francoise Genova, Hugh Shanahan, Joanna Leng, Maggie Hellström, Malin Sandström, Manodeep Sinha, Mateusz Kuzak, Patricia Herterich, Qian Zhang, Sharif Islam, Susanna-Assunta Sansone, Tom Pollard, Udayanto Dwi Atmojo; Alan Williams, Andreas Czerniak, Anna Niehues, Anne Claire Fouilloux, Bala Desinghu, Carole Goble, Céline Richard, Charles Gray, Chris Erdmann, Daniel Nüst, Daniele Tartarini, Elena Ranguelova, Hartwig Anzt, Ilian Todorov, James McNally, Javier Moldon, Jessica Burnett, Julián Garrido-Sánchez, Khalid Belhajjame, Laurents Sesink, Lorraine Hwang, Marcos Roberto Tovani-Palone, Mark D. Wilkinson, Mathieu Servillat, Matthias Liffers, Merc Fox, Nadica Miljković, Nick Lynch, Paula Martinez Lavanchy, Sandra Gesing, Sarah Stevens, Sergio Martinez Cuesta, Silvio Peroni, Stian Soiland-Reyes, Tom Bakker, Tovo Rabemanantsoa, Vanessa Sochat, Yo Yehudi, FAIR4RS WG (2022):
FAIR Principles for Research Software version 1.0 (FAIR4RS Principles v1.0).
Research Data Alliance
https://doi.org/10.15497/RDA00068

Peter Wittenburg, Ivonne Anders, Christophe Blanchi, Merret Buurman, Carole Goble, Jonas Grieb, Alex Hardisty, Sharif Islam, Thomas Jejkal, Tibor Kálmán, Christine Kirkpatrick, Laurence Lannom, Thomas Lauer, Giridhar Manepalli, Karsten Peters-von Gehlen, Andreas Pfeil, Robert Quick, Mark van de Sanden, Ulrich Schwardmann, Stian Soiland-Reyes, Rainer Stotzka, Zachary Trautt, Dieter Van Uytvanck, Claus Weiland, Philipp Wieder (2022):
FAIR Digital Object Demonstrators 2021.
Report, FAIR Digital Objects Forum. Zenodo
https://doi.org/10.5281/zenodo.5872645

2021

Shoaib Sufi (2021):
The Rise of a New Digital Third Space Professional in Higher Education: Recognising Research Software Engineering arXiv:2103.01041 [cs.CY]
https://doi.org/10.48550/arXiv.2103.01041

Rebecca Knowles, Bilal A. Mateen, Yo Yehudi (2021):
We need to talk about the lack of investment in digital research infrastructure.
Nature Computational Science 1
https://doi.org/10.1038/s43588-021-00048-5

Lukas Noehrer, Abigail Gilmore, Caroline Jay, Yo Yehudi (2021):
The impact of COVID-19 on digital data practices in museums and art galleries in the UK and the US.
Humanities and Social Sciences Communications 8:236
https://doi.org/10.1057/s41599-021-00921-8

Manuel Spitschan, Yo Yehudi, Laura Acion (2021):
Video grant proposals could be exclusionary.
Nature 592:26 (2021)
https://doi.org/10.1038/d41586-021-00862-x

Andrew J. Stewart, Emily K. Farran, James A. Grange, Malcolm Macleod, Marcus Munafò, Phil Newton, David R. Shanks, the UKRN Institutional Leads (2021):
Improving research quality: the view from the UK Reproducibility Network institutional leads for research improvement.
BMC Research Notes 14:458.
https://doi.org/10.1186/s13104-021-05883-3

Andrew J. Stewart, Henrik Singmann, Matthew Haigh, Jeffrey S. Wood, Igor Douven (2021):
Tracking the eye of the beholder: is explanation subjective?.
Journal of Cognitive Psychology 33(2)
https://doi.org/10.1080/20445911.2020.1870986 [preprint]

Ebtisam Alharbi, Rigina Skeva, Nick Juty, Caroline Jay, Carole Goble (2021):
Exploring the Current Practices, Costs and Benefits of FAIR Implementation in Pharmaceutical Research and Development: A Qualitative Interview Study.
Data Intelligence 3(4):507–-527
https://doi.org/10.1162/dint_a_00109

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft (2021):
Perspectives on automated composition of workflows in the life sciences.
[version 1; peer review: 2 approved]
F1000Research 10:897
https://doi.org/10.12688/f1000research.54159.1

Petr Holub, Rudolf Wittner, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Melanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Elliot Fairweather, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio-De-Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger (2021):
Towards a Common Standard for Data and Specimen Provenance in Life Sciences.
Working Paper.
https://doi.org/10.5281/zenodo.5093125

Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M Badia, Bartosz Balis, Tainã Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf (2021):
A Community Roadmap for Scientific Workflows Research and Development.
2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS), pp 81–90.
https://doi.org/10.1109/WORKS54523.2021.00016 arXiv:2110.02168 [cs.DC]

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodriguez-Navas, José Mª Fernández, Salvador Capella-Gutierrez, Hervé Ménager, Björn Grüning, Beatriz Serrano-Solano, Philip Ewels, Frederik Coppens (2021):
Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory.
Zenodo
https://doi.org/10.5281/zenodo.4605654

Rudolf Wittner, Petr Holub, Heimo Müller, Jörg Geiger, Carole Goble, Stian Soiland-Reyes, Luca Pirredu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio, Gianluigi Zanetti, David Grunwald, Hiroki Nakae (2021):
ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data.
In: Provenance and Annotation of Data and Processes. IPAW 2020, IPAW 2021. Lecture Notes in Computer Science 12839
https://doi.org/10.1007/978-3-030-80960-7_16 [preprint]

Tobias Kuhn, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier (2021):
Semantic micro-contributions with decentralized nanopublication services.
PeerJ Computer Science 7:e387
https://doi.org/10.7717/peerj-cs.387

Jennifer Harrow, John Hancock, ELIXIR‐EXCELERATE Community, Niklas Blomberg (2021):
ELIXIR‐EXCELERATE: establishing Europe’s data infrastructure for the life science research of the future.
EMBO Journal e107409
https://doi.org/10.15252/embj.2020107409

Daniel S. Katz, Morane Gruenpeter, Tom Honeyman, Lorraine Hwang, Mark D. Wilkinson, Vanessa Sochat, Hartwig Anzt, Carole Goble, FAIR4RS Subgroup 1 (2021):
A Fresh Look at FAIR for Research Software.
arXiv:2101.10883 [pdf]
https://doi.org/10.48550/arXiv.2101.10883

Victor Chang, Carole Goble, Muthu Ramachandran, Lazarus Jegatha Deborah, Reinhold Behringer (2021):
Editorial on Machine Learning, AI and Big Data Methods and Findings for COVID-19.
Information Systems Frontiers 23 pp. 1363–1367
https://doi.org/10.1007/s10796-021-10216-7

Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Willighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D’Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID-19 Disease Map Community (2021):
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms.
Molecular Systems Biology 17:e10387
https://doi.org/10.15252/msb.202110387

2020

Elsa Loissel, Emmy Tsang, Sandrine Müller, Julia Deathridge, Helena Pérez Valle, Yo Yehudi, Lucy Cheke (2020):
The experiences of those who support researchers struggling with their mental health.
(Report)
https://doi.org/10.17863/CAM.60247

Yo Yehudi, Kaitlin Stack Whitney, Malvika Sharan (2020):
Enhancing the inclusivity and accessibility of your online calls
OSF Preprints
https://doi.org/10.31219/osf.io/k3bfn

Michelle Phillips, Andrew J. Stewart, J. Matthew Wilcoxson, Luke A. Jones, Emily Howard, Pip Willcox, Marcus du Sautoy, David De Roure (2020):
What Determines the Perception of Segmentation in Contemporary Music?
Frontiers in Psychology 11:1001
https://doi.org/10.3389/fpsyg.2020.01001

Manuel Bernal-Llinares, Javier Ferrer-Gómez, Nick Juty, Carole Goble, Sarala M Wimalaratne, Henning Hermjakob (2020):
Identifiers.org: Compact Identifier services in the cloud.
Bioinformatics btaa864
https://doi.org/10.1093/bioinformatics/btaa864

Niall Beard, Finn Bacall, Aleksandra Nenadic, Milo Thurston, Carole A Goble, Susanna-Assunta Sansone, Teresa K Attwood (2020):
TeSS: a platform for discovering life science training opportunities.
Bioinformatics 6(10)
https://doi.org/10.1093/bioinformatics/btaa047

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

Charles Auffray, Rudi Balling, Niklas Blomberg, MYRNA BONALDO, Bertrand Boutron, Samir Brahmachari, Christian Bréchot, Alfredo Cesario, Sai-Juan Chen, Karine Clément, Daria Danilenko, Alberto Di Meglio, Andrea Gelemanovic, Carole Goble, Takashi Gojobori, Jason D Goldman, Michel Goldman, Yi-Ke Guo, James Heath, Leroy Hood, Peter Hunter, Li Jin, Hiroaki Kitano, Bartha Maria Knoppers, Doron Lancet, Catherine Larue, Mark Lathrop, Martine Laville, Ariel B Lindner, Antoine Magnan, Andres Metspalu, Edgar Morin, Lisa F.P. Ng, Laurent Nicod, Denis Noble, Laurent Nottale, Helga Nowotny, Theresa Ochoa, Iruna Okeke, Tolu Oni, Peter Openshaw, Mehmet Oztürk, Susanna Palkonen, Janusz Paweska, Christophe Pison, Mihael Polymeropoulos, Christian Pristipino, Ulrike Protzer, Josep Roca, Damjana Rozman, Marc Santolini, Ferran Sanz, Giovanni Scambia, Eran Segal, Ismail Serageldin, Marcelo Bento Soares, Peter Sterk, Sumio Sugano, Giulio Superti-Furga, David Supple, Jesper Tegnér, Mathias Uhlen, Andrea Urbani, Alfonso Valencia, Vincenzo Valentini, Sylvie van der Werf, Manlio Vinciguerra, Olaf Wolkenhauer, Emiel Wouters (2020):
COVID-19 and Beyond: A Call for Action and Audacious Solidarity to All the Citizens and Nations, It Is Humanity’s Fight.
SSRN Electronic Journal
https://doi.org/10.2139/ssrn.3630412

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

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

Annika Jacobsen, Ricardo de Miranda Azevedo, Nick Juty, Dominique Batista, Simon Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. Evelo, Carole Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina Hettne, Jaap Heringa, Rob W.W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes (2020):
FAIR Principles: Interpretations and Implementation Considerations.
Data Intelligence 2(1):10–29
https://doi.org/10.1162/dint_r_00024

Anna-Lena Lamprecht, Leyla Garcia, Mateusz Kuzak, Carlos Martinez, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie Van De Sandt, Jon Ison, Paula Andrea Martinez, Peter Mcquilton, Alfonso Valencia, Jennifer Harrow, Fotis Psomopoulos, Josep Ll. Gelpi, Neil Chue Hong, Carole Goble, Salvador Capella-Gutierrez (2020):
Towards FAIR principles for research software.
Data Science 3(1) pp. 37–59.
https://doi.org/10.3233/DS-190026

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

Raja Mazumder, Vahan Simonyan (eds), IEEE P2791 BioCompute Working Group (BCOWG) (2020):
IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication.
IEEE Std 2791-2020. IEEE SA Standards Board.
https://doi.org/10.1109/IEEESTD.2020.9094416

2019

Carole Goble, Raul Palma, Stian Soiland-Reyes, Daniel Garijo (eds.) (2019):
Proceedings of Workshop on Research Objects (RO2019).
IEEE eScience 2019, San Diego, CA, USA, 2019-09-24.

Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate: A lightweight approach to research object data packaging.
RO-15 at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA.
https://doi.org/10.5281/zenodo.3337883

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

Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi (2019):
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Scientific Data 6:169
https://doi.org/10.1038/s41597-019-0177-4

Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael Jimenez, Arlindo Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen, Søren Brunak (2019):
The bio.tools registry of software tools and data resources for the life sciences.
Genome Biology 20:164
https://doi.org/10.1186/s13059-019-1772-6

John Van Horn, Sumiko Abe, José Luis Ambite, Teresa K. Attwood, Niall Beard, Louisa Bellis, Avnish Bhattrai, Alex Bui, Gully Burns, Lily Fierro, Jonathan Gordon, Jeffrey Grethe, Jeana Kamdar, Xiaoyu Lei, Kristina Lerman, Annette McGrath, Nicola Mulder, Caroline O’Driscoll, Crystal Stewart, Sonika Tyagi (2019):
Advancing the international data science workforce through shared training and education.
[version 1; peer review: 1 approved, 1 approved with reservations].
F1000Research 8:251
https://doi.org/10.12688/f1000research.18357.1

2018

Carole Goble, Raul Palma, Stian Soiland-Reyes, Cees Hoof (eds.) (2018):
Proceedings of Workshop on Research Objects (RO2018). IEEE eScience 2018, Amsterdam, The Netherlands, 2018-10-29

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 [html] [pdf] [preprint server] [arXiv:1809.06935] [slides]

Stian Soiland-Reyes, Farah Zaib Khan, Richard O. Sinnott, Andrew Lonie, Michael R Crusoe, Carole Goble (2018):
Capturing interoperable reproducible workflows with Common Workflow Language.
Workshop on Research Objects (RO 2018), 29 Oct 2018, Amsterdam, Netherlands.
https://doi.org/10.5281/zenodo.1312623 [slides]

Carole Goble, Stian Soiland-Reyes, Sean Bechhofer (2018):
Research Object Community Update.
Workshop on Research Objects (RO 2018), 29 Oct 2018, Amsterdam, Netherlands.
https://doi.org/10.5281/zenodo.1313066 [slides]

Natalie J Stanford, Finn Bacall, Fatemeh Zamanzad Ghavidel, Martin Golebiewski, Inge Jonassen, Rune Kleppe, Olga Krebs, Hadas Leonov, Stuart Owen, Kjell Petersen, Maja Rey, Stian Soiland-Reyes, Kidane Tekle, Andreas Weidemann, Alan Williams, Ulrike Wittig, Katy Wolstencroft, Anders Goksøyr, Jacky L. Snoep, Jon Olav Vik, Wolfgang Müller, Carole Goble (2018):
FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative.
NETTAB 2018 Network Tools and Applications in Biology
[preprint] [preprint server]

Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael Jimenez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim Clark (2018):
Uniform resolution of compact identifiers for biomedical data.
Scientific Data 5 180029
https://doi.org/10.1038/sdata.2018.29

Pinar Alper, Khalid Belhajjame, Vasa Curcin, Carole A. Goble (2018):
LabelFlow Framework for Annotating Workflow Provenance.
Informatics 5(1):11
https://doi.org/10.3390/informatics5010011

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, Jonathon Keeney, KanakaDurga Addepalli, 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)

Shoaib A Sufi, Caroline Jay (2018):
Raising the status of software in research: A survey-based evaluation of the Software Sustainability Institute Fellowship Programme.
[version 1; referees: 1 approved with reservations].
F1000Research 2018, 7:1599
https://doi.org/10.12688/f1000research.16231.1

Shoaib Sufi, Aleksandra Nenadic, Raniere Silva, Beth Duckles, Iveta Simera, Jennifer A. de Beyer, Caroline Struthers, Terhi Nurmikko-Fuller, Louisa Bellis, Wadud Miah, Adriana Wilde, Iain Emsley, Olivier Philippe, Melissa Balzano, Sara Coelho, Heather Ford, Catherine Jones, Vanessa Higgins (2018):
Ten simple rules for measuring the impact of workshops.
PLOS Computational Biology 14(8):e1006191
https://doi.org/10.1371/journal.pcbi.1006191

Pablo Carbonell, Adrian J. Jervis, Christopher J. Robinson, Cunyu Yan, Mark Dunstan, Neil Swainston, Maria Vinaixa, Katherine A. Hollywood, Andrew Currin, Nicholas J. W. Rattray, Sandra Taylor, Reynard Spiess, Rehana Sung, Alan R. Williams, Donal Fellows, Natalie J. Stanford, Paul Mulherin, Rosalind Le Feuvre, Perdita Barran, Royston Goodacre, Nicholas J. Turner, Carole Goble, George Guoqiang Chen, Douglas B. Kell, Jason Micklefield, Rainer Breitling, Eriko Takano, Jean-Loup Faulon, Nigel S. Scrutton (2018):
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals.
Communications Biology 1:66
https://doi.org/10.1038/s42003-018-0076-9

Raniere Gaia Costa da Silva, Shoaib Ahmed Sufi, Selina Aragon Camarasa (2018):
Collaborations Workshop 2018 (CW18) Report – Culture Change, Productivity and Sustainability.
Research Ideas and Outcomes 5:e30250
https://doi.org/10.3897/rio.5.e30250

2017

Neil Chue Hong, Stephan Druskat, Robert Haines, Caroline Jay, Daniel S Katz, Shoaib Sufi (eds.) (2017):
Proceedings of the Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE5.1).
Figshare (collection)
https://doi.org/10.6084/m9.figshare.c.3869782

Francisco Queiroz, Raniere Silva, Jonah Miller, Sandor Brockhauser, Hans Fangohr (2007):
Good Usability Practices in Scientific Software Development.
Proceedings of the Workshop on Sustainable Software for Science
https://doi.org/10.6084/m9.figshare.5331814.v3

Shoaib Sufi, Robin Dasler, Chris Edsall (2017):
The Research Software Project Manager.
WSSSPE5.1 speed blogging series
https://www.software.ac.uk/blog/2017-12-04-research-software-project-manager

Kristian Garza Gutierrez (2017):
Facilitating data sharing: a design approach to incorporate context into the research data repository.
PhD thesis, The University of Manchester uk.bl.ethos.728225
http://isni.org/isni/0000000464990066

Stephen J Eglen, Ben Marwick, Yaroslav O Halchenko, Michael Hanke, Shoaib Sufi, Padraig Gleeson, R Angus Silver, Andrew P Davison, Linda Lanyon, Mathew Abrams, Thomas Wachtler, David J Willshaw, Christophe Pouzat, Jean-Baptiste Poline (2017):
Toward standard practices for sharing computer code and programs in neuroscience.
Nature Neuroscience 20, 770–773.
https://doi.org/10.1038/nn.4550 [bioRxiv preprint]

Lee Larcombe, Rita Hendricusdottir, Teresa K. Attwood, Finn Bacall, Niall Beard, Louisa J. Bellis, Warwick B. Dunn, John M. Hancock, Aleksandra Nenadic, Christine Orengo, Bert Overduin, Susanna-Assunta Sansone, Milo Thurston, Mark R. Viant, Catherine L. Winder, Carole A. Goble, Chris P. Ponting, Gabriella Rustici (2017):
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
[version 1; peer review: 4 approved, 1 approved with reservations]
F1000Research 6:952
https://doi.org/10.12688/f1000research.11837.1

Steffen Möller, Stuart W. Prescott, Lars Wirzenius; Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe (2017):
Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis..
Data Science and Engineering 2:232 pp 232–244.
https://doi.org/10.1007/s41019-017-0050-4

Pinar Alper, Khalid Belhajjame, Carole A.Goble (2017):
Static analysis of Taverna workflows to predict provenance patterns.
Future Generation Computer Systems 75 pp 310-329
https://doi.org/10.1016/j.future.2017.01.004 [preprint] [preprint server]

Aleksandra Pawlik, Celia W.G. van Gelder, Aleksandra Nenadic, Patricia M. Palagi, Eija Korpelainen, Philip Lijnzaad, Diana Marek, Susanna-Assunta Sansone, John Hancock, Carole Goble (2017):
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. [version 1; peer review: 3 approved]
F1000Research 2017 6:1020 ELIXIR-1040.
https://doi.org/10.12688/f1000research.11718.1

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, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, 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, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L Snoep, Stian Soiland-Reyes, Natalie J Stanford, Neil Swainston, Nicole Washington, Alan R Williams, Sarala M Wimalaratne, Lilly M Winfree, Katherine Wolstencroft, Carole Goble, Cristopher J Mungall, Melissa A Haendel, Helen Parkinson (2017):
Identifiers for the 21st century: How to design, provision, and reuse identifiers to maximize utility and impact of life science data.
PLOS Biology 15(6):e2001414
https://doi.org/10.1371/journal.pbio.2001414 [pdf]

Matthias Obst, Saverio Vicario, Kennet Lundin, Matz Berggren, Anna Karlsson, Robert Haines, Alan Williams, Carole Goble, Cherian Mathew, Anton Güntsch (2017):
Marine long-term biodiversity assessment suggests loss of rare species in the Skagerrak and Kattegat region.
Marine Biodiversity pp 1–12.
https://doi.org/10.1007/s12526-017-0749-5

John M Hancock, Alf Game, Chris P Ponting, Carole Anne Goble (2017):
An open and transparent process to select ELIXIR Node Services as implemented by ELIXIR-UK
[version 2; peer review: 2 approved, 1 approved with reservations]
F1000Research 2017, 5(ELIXIR):2894
https://doi.org/10.12688/f1000research.10473.2

Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez X, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí,, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková,, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch (2017):
Four simple recommendations to encourage best practices in research software
[version 1; peer review: 3 approved]
F1000Research 2017, 6:876
https://doi.org/10.12688/f1000research.11407.1

2016

Pinar Alper (2016):
Towards harnessing computational workflow provenance for experiment reporting.
PhD thesis, The University of Manchester. uk.bl.ethos.686781
http://isni.org/isni/0000000459201915

Renato De Giovanni, Alan R. Williams, Vera Hernández Ernst, Robert Kulawik, Francisco Quevedo Fernandez, Alex R. Hardisty (2016):
ENM Components: a new set of web service‐based workflow components for ecological niche modelling.
Ecography 39 pp 376–383
https://doi.org/10.1111/ecog.01552

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

Natalie Stanford, Finn Bacall, Martin Golebiewski, Olga Krebs, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, {van Niekerk}, Dawie, Alan Williams, Katherine Wolstencroft, Lars Malmström, Bernd Rinn, Jacky Snoep, Wolfgang Müller, Carole Goble (2016):
FAIRDOM: Reproducible Systems Biology through FAIR Asset Management.
Reproducibility, standards and SOP in bioinformatics (NETTAB), Rome, Italy 2016-10-25.
[preprint] [pdf]

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 5 December 2016. [preprint]
https://doi.org/10.1109/BigData.2016.7840618 [pdf] [zenodo] [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
Proceedings of the Workshop on Benchmarking Linked Data (BLINK 2016), co-located with the 15th International Semantic Web Conference (ISWC) CEUR Workshop Proceedings 1700(04)
https://doi.org/10.5281/zenodo.159568 [pdf] [zenodo] [preprint]

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 [preprint]

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
https://doi.org/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] [slides]

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)
https://doi.org/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
https://doi.org/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 https://doi.org/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.
https://doi.org/10.1098/rsfs.2015.0103 [pdf]

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(15) http://ceur-ws.org/Vol-1686/WSSSPE4_paper_15.pdf

Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic (2016):
Common Workflow Language, v1.0
Specification, Common Workflow Language working group.
https://w3id.org/cwl/v1.0/ https://doi.org/10.6084/m9.figshare.3115156.v2

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
https://doi.org/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
https://doi.org/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
https://doi.org/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.
https://doi.org/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)
https://doi.org/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
https://doi.org/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 Løngreen and Søren Brunak (2015):
Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Research 44(D1)
https://doi.org/10.1093/nar/gkv1116

2014

Timothy Clark (2014):
Sociotechnical Architecture for Biomedical Communication on the Web of Argument and Data.
PhD Thesis, The University of Manchester uk.bl.ethos.607428 https://isni.org/isni/0000000453641987

Matthew Philip Gamble (2014):
Modelling and computing the quality of scientific information on the Web of Data.
PhD Thesis, The University of Manchester uk.bl.ethos.617974 http://isni.org/isni/0000000453526516

Carole Goble (2014):
Better Software, Better Research.
IEEE Internet Computing 18(5)
https://doi.org/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 Workshop Proeedings 1272:33
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
https://doi.org/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
https://doi.org/10.1016/j.websem.2014.03.003 [preprint]

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.
https://doi.org/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.
https://doi.org/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)
https://doi.org/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
https://doi.org/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
https://doi.org/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
https://doi.org/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
https://doi.org/10.3897/BDJ.2.e1125

Kevin R. Page, Raul Palma, Piotr Hołubowicz, Graham Klyne, Stian Soiland-Reyes, Daniel Garijo, Khalid Belhajjame, and Rudolf Mayer (2014):
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
https://doi.org/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)
https://doi.org/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
https://doi.org/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.
https://doi.org/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
https://doi.org/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.
https://doi.org/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.
https://doi.org/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
https://doi.org/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.
https://doi.org/10.3233/SW-2012-0088 [pdf]

Joseline Ratnam , Barbara Zdrazil, Daniela Digles, Emiliano Cuadrado-Rodriguez, Jean-Marc Neefs, Hannah Tipney, Ronald Siebes, Andra Waagmeester, Glyn Bradley, Chau Han Chau, Lars Richter, Jose Brea, Chris T. Evelo, Edgar Jacoby, Stefan Senger, Maria Isabel Loza, Gerhard F. Ecker, Christine Chichester (2014):
The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research.
PLOS ONE 9(12): e115460.
https://doi.org/10.1371/journal.pone.0115460

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.
https://doi.org/10.1093/nar/gkt328

Hyde Zhang, Stian Soiland-Reyes, Carole Goble (2013):
Taverna Mobile: Taverna workflows on Android.
EMBnet.journal 19(B).
https://doi.org/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 17(6) pp 71-75.
https://doi.org/10.1109/MIC.2013.123 [html] [preprint] 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. https://doi.org/10.1007/978-3-642-41338-4_14

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)
https://doi.org/10.1016/j.future.2011.08.004 [preprint] [preprint server] [pdf]

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.
https://doi.org/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.
https://doi.org/10.1016/j.future.2013.09.018 [preprint]

Carole Goble, David De Roure, Sean Bechhofer (2013):
Accelerating Scientists’ Knowledge Turns.
Knowledge Discovery, Knowledge Engineering and Knowledge Management.
Communications in Computer and Information Science 348
https://doi.org/10.1007/978-3-642-37186-8_1 [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
https://doi.org/10.1145/2457317.2457376 [preprint] [dataset] [GitHub]

Colin Batchelor, Christian Y. A. Brenninkmeijer, Christine Chichester, Mark Davies, Daniela Digles, Ian Dunlop, Chris T. Evelo, Anna Gaulton, Carole Goble, Alasdair J. G. Gray, Paul Groth, Lee Harland, Karen Karapetyan, Antonis Loizou, John P. Overington (2014):
Scientific Lenses to Support Multiple Views over Linked Chemistry Data.
Proceedings of 13th International Semantic Web Conference, Part 1, (ISWC 2014) Riva del Garda, Italy, October 19-23, 2014. Lecture Notes in Computer Science 8796.
https://doi.org/10.1007/978-3-319-11964-9_7 [preprint]

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.
Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data (LISC 2012). In conjunction with the International Semantic Web Conference (ISWC2012). CEUR Workshop Proeedings 951:5
http://ceur-ws.org/Vol-951/paper5.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
https://doi.org/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 Workshop Proeedings 1114:4
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
https://doi.org/10.1109/BigData.Congress.2013.49 [preprint] [slides]

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
https://doi.org/10.1145/2457317.2457370 [preprint]

Anja Le Blanc, John Brooke, Donal Fellows, Marco Soldati, David Pérez-Suárez, Alessandro Marassi & Andrej Santin (2013):
Workflows for Heliophysics.
Journal of Grid Computing 11(3)
https://doi.org/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)
https://doi.org/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
https://doi.org/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.
https://doi.org/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 ([researchgate]). [slides]

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]

Kamal Azzaoui, Edgar Jacoby, Stefan Senger, Emiliano Cuadrado Rodríguez3, Mabel Loza, Barbara Zdrazil, Marta Pinto, Antony J. Williams, Victor de la Torre, Jordi Mestres, Manuel Pastor, Olivier Taboureau, Matthias Rarey, Christine Chichester, Steve Pettifer, Niklas Blomberg, Lee Harland, Bryn Williams-Jones, Gerhard F. Ecker (2013):
Scientific competency questions as the basis for semantically enriched open pharmacological space development.
Drug Discovery Today 18 (17-18) pp 843–852.
https://doi.org/10.1016/j.drudis.2013.05.008

Antony J. Williams, Lee Harland, Paul Groth, Stephen Pettifer, Christine Chichester, Egon L. Willighagen, Chris T. Evelo, Niklas Blomberg, Gerhard Ecker, Carole Goble, Barend Mons (2012):
Open PHACTS: semantic interoperability for drug discovery.
Drug Discovery Today 17(21-22) pp 1188 - 1198.
https://doi.org/10.1016/j.drudis.2012.05.016

2002-2012

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