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FDO PID profiles & attributes
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[Anders 2023] Ivonne Anders, Christophe Blanchi, Daan Broder, Maggie Hellström, Sharif Islam, Thomas Jejkal, Larry Lannom, Karsten Peters-von Gehlen, Robert Quick, Alexander Schlemmer, Ulrich Schwardmann, Stian Soiland-Reyes, George Strawn, Dieter van Uytvanck, Claus Weiland, Peter Wittenburg, Carlo Zwölf (2023):
FAIR Digital Objects Forum FDO requirement specifications. Version 3.0.
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FAIR Digital Objects Forum
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BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Scientific Data 6:169
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[Arend 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
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[Arfaoui 2020] Ghaith Arfaoui, Maroua Jaoua (2020):
RO-Crate RDA maDMP Mapper.
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[Arkisto 2022] Arkisto (2022):
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https://arkisto-platform.github.io/tools/portal/

[Atkinson 2017] Malcolm Atkinson, Sandra Gesing, Johan Montagnat, Ian Taylor (2017):
Scientific workflows: Past, present and future.
Future Generation Computer Systems 75
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[Atkinson 2019] Rob Atkinson, Nicholas J. Car (2019):
The Profiles Vocabulary.
W3C Working Group Note
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[Ayris 2016] Paul Ayris, Jean-Yves Berthou, Rachel Bruce, Stefanie Lindstaedt, Anna Monreale, Barend Mons, Yasuhiro Murayama, Caj Södergård, Klaus Tochtermann, Ross Wilkinson (2016):
Realising the European Open Science Cloud. First report and recommendations of the Commission High Level Expert Group of the European Open Science Cloud.
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[Azeroual 2022] Otmane Azeroual, Joachim Schöpfel, Janne Pölönen, Anastasija Nikiforova (2022):
Putting FAIR Principles in the Context of Research Information: FAIRness for CRIS and CRIS for FAIRness.
International Conference on Knowledge Discovery and Information Retrieval
https://hdl.handle.net/11366/2243

[Bacall 2019] Finn Bacall, Stian Soiland-Reyes, Marina Soares e Silva (2019):
eScienceLab: RO-Composer.
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[Bacall 2022] Finn Bacall, Alan R. Williams, Stuart Owen, Stian Soiland-Reyes (2022):
Workflow RO-Crate Profile 1.0.
WorkflowHub community
https://w3id.org/workflowhub/workflow-ro-crate/1.0

[Bacall 2022b] Finn Bacall, Martyn Whitwell (2022):
GitHub – ResearchObject/ro-crate-ruby: A Ruby gem for creating, manipulating and reading RO-Crates.
https://github.com/ResearchObject/ro-crate-ruby

[Bahra 2011] Avi Bahra (2011):
Managing work flows with ecFlow.
ECMWF Newsletter 129
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[Bahui 2020] Christophe Bahim, Carlos Casorrán-Amilburu, Makx Dekkers, Edit Herczog, Nicolas Loozen, Konstantinos Repanas, Keith Russell, Shelley Stall (2020):
The FAIR data maturity model: An approach to harmonise FAIR assessments.
Data Science Journal 19(1)
https://doi.org/10.5334/dsj-2020-041

[Baker 2013] Thomas Baker, Sean Bechhofer, Antoine Isaacc, Alistair Miles, Guus Schreiber, Ed Summers (2013):
Key choices in the design of Simple Knowledge Organization System (SKOS).
Journal of Web Semantics 20
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[Baker 2016] Monya Baker (2016):
1,500 scientists lift the lid on reproducibility.
Nature 533
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[Baker 2019] Thomas Baker, Eric Prud’hommeaux (2019):
Shape Expressions (ShEx) 2.1 Primer.
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[Baker 2020] Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver (2020):
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics.
PLOS Pathogens 16(8):e1008643
https://doi.org/10.1371/journal.ppat.1008643

[Barker 2019] Michelle Barker, Ross Wilkinson, Andrew Treloar (2019):
The Australian Research Data Commons.
Data Science Journal 18(1)
https://doi.org/10.5334/dsj-2019-044

[Barker 2022] Michelle Barker, Neil P. Chue Hong, Daniel S. Katz, Anna-Lena Lamprecht, Carlos Martinez-Ortiz, Fotis Psomopoulos, Jennifer Harrow, Leyla Jael Castro, Morane Gruenpeter, Paula Andrea Martinez, Tom Honeyman (2022):
Introducing the FAIR Principles for research software.
Scientific Data 9:622
https://doi.org/10.1038/s41597-022-01710-x

[Batista 2022] Dominique Batista, Alejandra Gonzalez-Beltran, Susanna-Assunta Sansone, Philippe Rocca-Serra (2022):
Machine actionable metadata models.
Scientific Data 9:592
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[Baxter 2012] Robert Baxter, Neil Chue Hong, Dirk Gorissen, James Hetherington, Ilian Todorov (2012):
The Research Software Engineer.
Digital Research 2012, 2012-09-10/–12, Oxford, UK
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[Bayarri 2021a] Genís Bayarri, Robin Long (2021):
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in CWL.
WorkflowHub. Workflow (CWL).
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[Bayarri 2021b] Genís Bayarri, Adam Hospital, Douglas Lowe (2021):
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Jupyter Notebook.
WorkflowHub. Workflow (Jupyter Notebook).
https://doi.org/10.48546/workflowhub.workflow.120.2

[Bayarri 2022] Genís Bayarri, Adam Hospital (2022):
CWL GMX Automatic Ligand Parameterization tutorial.
Workflow Hub (Common Workflow Language)
https://doi.org/10.48546/workflowhub.workflow.255.1

[Bechhofer 2013] 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) pp. 599–611.
https://doi.org/10.1016/j.future.2011.08.004

[Beg 2021] Marijan Beg, Juliette Taka, Thomas Kluyver, Alexander Konovalov, Min Ragan-Kelley, Nicolas M. Thiery, Hans Fangohr (2021):
Using Jupyter for Reproducible Scientific Workflows.
Computing in Science & Engineering 23(2) pp 36–46.
https://doi.org/10.1109/MCSE.2021.3052101

[Beier 2024] 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

[Belchev 2021] Kostadin Belchev (2021):
KockataEPich/CheckMyCrate: A command line application for validating a RO-Crate object against a JSON profile.
GitHub
https://github.com/KockataEPich/CheckMyCrate

[Belhajjame 2015] 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 32 pp. 16–42.
https://doi.org/10.1016/j.websem.2015.01.003

[Belshe 2022] Mike Belshe, Roberto Peon, Martin Thomson (2015):
Hypertext Transfer Protocol Version 2 (HTTP/2).
RFC Editor, RFC 7540
https://doi.org/10.17487/rfc7540

[Beltrán 2023] Daniel Beltrán Mora, Miguel Castrillo, Manuel G. Marciani, Bruno P. Kinoshita, Luiggi Tenorio Ku, Aina Gaya-Àvila, Francesc Roura Adserias, Pierre-Antoine Bretonnière, Oriol Mula Valls, Pablo Goitia, Julian Rodrigo Berlin, Miguel Andrés-Martínez, Kim Serradell, Wilmer Uruchi Ticona, Domingo Manubens-Gil, Larissa Batista Leite, Isabel Andreu-Burillo, Javier Vegas-Regidor, Hui Du, Danila Volpi, Fabian Lienert, Joan Giralt, Joan Lopez, Muhammad Asif, Virginie Guemas, Xavier Abellan Ecija (2023):
Autosubmit v4.0.100.
Zenodo
https://doi.org/10.5281/zenodo.10199020

[Benureau 2017] Fabien C. Y. Benureau, Nicolas P. Rougier (2017):
Re-run, repeat, reproduce, reuse, replicate: Transforming code into scientific contributions.
Frontiers in Neuroinformatics 11:69.
https://doi.org/10.3389/fninf.2017.00069

[Berman 2007] Helen Berman, Kim Henrick, Haruki Nakamura, John L Markley (2007):
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data.
Nucleic Acids Research 35(Database issue), D301–D303.
https://doi.org/10.1093/nar/gkl971

[Berners-Lee 1998] Tim Berners-Lee (1998):
Cool URIs don’t change.
Style Guide for online hypertext, W3C
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[Berners-Lee 1999] Tim Berners-Lee, Mark Fischetti (1999):
Weaving the Web: The original design and ultimate destiny of the World Wide Web by its inventor.
ISBN 978-0-06-251586-5

[Berners-Lee 2000] Tim Berners-Lee (2000):
Semantic Web on XML.
XML 2000, Washington DC, 2000-12-06.
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[Berners-Lee 2005] Tim Berners-Lee, Roy T. Fielding, Larry M. Masinter (2005):
Uniform Resource Identifier (URI): Generic Syntax.
RFC Editor, RFC 3986
https://doi.org/10.17487/rfc3986

[Berners-Lee 2006] Tim Berners-Lee (2006):
Linked Data
Design Issues, W3C
https://www.w3.org/DesignIssues/LinkedData.html

[Bernstein 2016] Abraham Bernstein, James Hendler, Natalya Noy (2016):
A new look at the semantic web.
Communications of the ACM 59(9)
https://doi.org/10.1145/2890489

[Bietrix 2021] Florence Bietrix, José Maria Carazo, Salvador Capella-Gutierrez, Frederik Coppens, Maria Luisa Chiusano, Romain David, Jose Maria Fernandez, Maddalena Fratelli, Jean-Karim Heriche, Carole Goble, Philip Gribbon, Petr Holub, Robbie Joosten, Simone Leo, Stuart Owen, Helen Parkinson, Roland Pieruschka, Luca Pireddu, Luca Porcu, Michael Raess, Laura Rodriguez-Navas, Andreas Scherer, Stian Soiland-Reyes, Jing Tang (2021):
EOSC-Life methodology framework to enhance reproducibility within EOSC Life.
Zenodo
https://doi.org/10.5281/zenodo.4705078

[BioMoby 2008] The BioMoby Consortium (2008):
Interoperability with Moby 1.0—It’s better than sharing your toothbrush!
Briefings in Bioinformatics 9(3) pp 220–231.
https://doi.org/10.1093/bib/bbn003

[Bishop 2022] Mike Bishop (2022):
HTTP/3
RFC Editor, RFC 9114
https://doi.org/10.17487/rfc9114

[Bisol 2014] Giovanni Destro Bisol, Paolo Anagnostou, Marco Capocasa, Silvia Bencivelli, Andrea Cerroni, Jorge Contreras, Neela Enke, Bernardino Fantini, Pietro Greco, Catherine Heeney, Daniela Luzi, Paolo Manghi, Deborah Mascalzoni, Jennifer C. Molloy, Fabio Parenti, Jelte M Wicherts, Geoffrey Boulton (2014):
Perspectives on Open Science and Scientific Data Sharing: An Interdisciplinary Workshop.
Journal of Anthropological Sciences 92
https://www.isita-org.com/jass/Contents/2014vol92/Destro/25020017.pdf
https://doi.org/10.4436/JASS.92006

[Bizer 2009] Christian Bizer, Tom Heath, Tim Berners-Lee (2009):
Linked Data - The Story So Far.
International Journal on Semantic Web and Information Systems 5(3)
https://doi.org/10.4018/jswis.2009081901

[Bizer 2011] Christian Bizer, Tom Heath, Tim Berners-Lee (2011):
Linked data: The story so far.
In Semantic Services, Interoperability and Web Applications: Emerging Concepts, Amit Sheth (ed.) ISBN 9781609605933
https://doi.org/10.4018/978-1-60960-593-3.ch008

[Blanchi 2022] Christophe Blanchi, Daan Broeder, Thomas Jejkal, Islam Sharif, Alexander Schlemmer, Dieter van Uytvanck, Peter Wittenburg (2022):
FDO – upload of FDO.
FDO Specification Documents PEN-FDO-Upload-1.1-20221017
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7825549

[Blanchi 2023] Christophe Blanchi, Maggie Hellström, Larry Lannom, Andreas Pfeil, Ulrich Schwardmann, Peter Wittenburg (2022):
Implementation of attributes, types, profiles and registries.
FDO Specification Documents WD-Implementation-of-Attributes-0.4-20230314
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7825572

[Blankenberg 2014] Daniel Blankenberg, Gregory Von Kuster, Emil Bouvier, Dannon Baker, Enis Afgan, Nicholas Stoler, James Taylor, Anton Nekrutenko, the Galaxy Team (2014):
Dissemination of scientific software with Galaxy ToolShed.
Genome Biology 15:403
https://doi.org/10.1186/gb4161

[Blomquist 2009] Eva Blomqvist, Aldo Gangemi, Valentina Presutti (2009):
Experiments on pattern-based ontology design.
K-CAP ‘09: Proceedings of the fifth international conference on Knowledge capture
https://doi.org/10.1145/1597735.1597743

[Bonino 2016] Luiz Olavo Bonino Da Silva Santos, Mark D. Wilkinson, Arnold Kuzniar, Rajaram Kaliyaperumal, Mark Thompson, Michel Dumontier, Kees Burger  (2016):
FAIR Data points supporting big data interoperability.
Enterprise interoperability in the digitized and networked factory of the future, Martin Zelm, Guy Doumeingts, Joao Pedro Mendonça (eds.).
iSTE Press.
ISBN 978-1-84704-044-2
Preprint: https://www.researchgate.net/publication/309468587_FAIR_Data_Points_Supporting_Big_Data_Interoperability

[Bonino 2019] Luiz Bonino, Peter Wittenburg, Bonnie Carroll, Alex Hardisty, Mark Leggott, Carlo Zwölf (2019):
FAIR digital object framework v1.02.
FDOF technical implementation guideline.
Group of European Data Experts in RDA (GEDE-RDA)
https://github.com/GEDE-RDA-Europe/GEDE/blob/master/FAIR%20Digital%20Objects/FDOF/FAIR%20Digital%20Object%20Framework-v1-02.docx

[Bonino 2020] Luiz Olavo Bonino da Silva Santos, Giancarlo Guizzardi, Tiago Prince Sales (2022):
FAIR Digital Object Framework Documentation.
27 October 2022
https://fairdigitalobjectframework.org/

[Bouyssié 2023] David Bouyssié, Pınar Altıner, Salvador Capella-Gutierrez, José M. Fernández, Yanick Paco Hagemeijer, Peter Horvatovich, Martin Hubálek, Fredrik Levander, Pierluigi Mauri, Magnus Palmblad, Wolfgang Raffelsberger, Laura Rodríguez-Navas, Dario Di Silvestre, Balázs Tibor Kunkli, Julian Uszkoreit, Yves Vandenbrouck, Juan Antonio Vizcaíno, Dirk Winkelhardt, Veit Schwämmle (2023):
WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.
bioRxiv 2023.10.02.560412
https://doi.org/10.1101/2023.10.02.560412

[Brack 2022a] Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Phil 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
https://s11.no/2022/phd/10-simple-rules-for-workflow-tools/ (Supplement 1)

[Brack 2022b] Paul Brack, Oliver Woolland, Laurence Livermore (2022):
De novo digitisation. (Galaxy workflow)
WorkflowHub
https://doi.org/10.48546/workflowhub.workflow.373.1

[Brand 2015] Amy Brand, Liz Allen, Micah Altman, Marjorie Hlava, Jo Scott (2015):
Beyond authorship: Attribution, contribution, collaboration, and credit.
Learned Publishing 28(2) pp. 151–155.
https://doi.org/10.1087/20150211

[Bray 2017] Tim Bray (2017):
The JavaScript Object Notation (JSON) Data Interchange Format.
STD 90, RFC 8259
RFC Editor, Internet Engineering Task Force.
https://doi.org/10.17487/rfc8259

[Brenner 2020] Gabriel Brenner (2020):
BrennerG/Ro-Crate_2_ma-DMP: v1.0.0.
https://github.com/BrennerG/Ro-Crate_2_ma-DMP
https://doi.org/10.5281/zenodo.3903463

[Brickley 2014] Dan Brickley, Libby Miller (2014):
FOAF Vocabulary Specification.
http://xmlns.com/foaf/spec/ (accessed 26 May 2022)

[Broeder 2022] Daan Broeder, Peter Wittenburg (2022):
FDO glossary november 2022.
FDO Specification Documents (internal draft)
FAIR Digital Objects Forum
https://drive.google.com/file/d/1KJ9l0p96naKi_2HPJ_MPqPTwS_zlP92G (accessed 2 February 2023)

[Buck 2022] Justin Buck, Deb Agarwal, James Ayliffe, Chris Erdmann, Carole Goble, Ugis Sarkans, Daniel Noesgaard, Uwe Schindler, Shelley Stall, Martin Fenner, Martina Stockhause, Paolo Manghi (2022):
AGU data citation community of practice - Credit for creators of data within collections using the concept of a reliquary.
ESS Open Archive
https://doi.org/10.1002/essoar.10509966.1

[Capadisli 2017] Sarven Capadisli, Amy Guy, eds. (2017):
Linked Data Notifications.
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[Ferreira da Silva] 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.
Technical Report, ORNL/TM-2023/2885
arXiv:2304.00019
https://doi.org/10.48550/arXiv.2304.00019

[Fielding 1999] Roy T. Fielding, Jim Gettys, Jeffrey Mogul, Henrik Frystyk Nielsen, Larry M Masinter, Paul J. Leach, Tim Berners-Lee (1999):
Hypertext Transfer Protocol – HTTP/1.1.
RFC Editor, RFC 2616
https://doi.org/10.17487/rfc2616

[Fielding 2000] Roy Thomas Fielding (2000):
Architectural styles and the design of network-based software architectures
Doctoral Thesis, University of California, Irvine.
https://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm (accessed 28 June 2022)

[Fielding 2014a] Roy T. Fielding, Julian Reschke (2014):
Hypertext Transfer Protocol (HTTP/1.1): Message Syntax and Routing
RFC Editor, RFC 7230
https://doi.org/10.17487/rfc7230

[Fielding 2014b] Roy T. Fielding, Julian Reschke (2014):
Hypertext Transfer Protocol (HTTP/1.1): Semantics and Content
RFC Editor, RFC 7231
https://doi.org/10.17487/rfc7231

[Fielding 2017] Roy T. Fielding, Richard N. Taylor, Justin R. Erenkrantz, Michael M. Gorlick, Jim Whitehead, Rohit Khare, Peyman Oreizy (2017):
Reflections on the REST architectural style and "principled design of the modern web architecture" (impact paper award).
Proceedings of the 2017 11th joint meeting on foundations of software engineering - ESEC/FSE 2017, New York, New York, USA.
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[Fielding 2022] Roy T. Fielding, Mark Nottingham, Julian Reschke (2022):
HTTP Semantics.
RFC Editor, RFC 9110
https://doi.org/10.17487/rfc9110

[Fillbrunn 2017] Alexander Fillbrunn, Christian Dietz, Julianus Pfeuffer, René Rahn, Gregory A. Landrum, Michael R. Berthold (2017):
KNIME for reproducible cross-domain analysis of life science data.
Journal of Biotechnology 261
https://doi.org/10.1016/j.jbiotec.2017.07.028

[Fouilloux 2023] Anne Fouilloux, Elisa Trasatti, Federica Foglini, Alejandro Coca-Castro, Jean Iaquinta (2023):
FAIR Research Objects for realizing Open Science with RELIANCE EOSC project.
Research Ideas and Outcomes 9:e108765
https://doi.org/10.3897/rio.9.e108765

[Freire 2008] Juliana Freire, David Koop, Emanuele Santos, Cl Silva (2008):
Provenance for Computational Tasks: A Survey.
Computing in Science & Engineering 10(3)
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[Galaxy 2022] The Galaxy Community (E. Afgan, A. Nekrutenko, B. A. Grüning, D. Blankenberg, J. Goecks, M. C. Schatz, A. E. Ostrovsky, A. Mahmoud, A. J. Lonie, A. Syme, A. Fouilloux, A. Bretaudeau, A. Nekrutenko, A. Kumar, A. C. Eschenlauer, A. D. DeSanto, A. Guerler, B. Serrano-Solano, B. Batut, B. A. Grüning, B. W. Langhorst, B. Carr, B. A. Raubenolt, C. J. Hyde, C. J. Bromhead, C. B. Barnett, C. Royaux, C. Gallardo, D. Blankenberg, D. J. Fornika, D. Baker, D. Bouvier, D. Clements, D. A. de Lima Morais, D. L. Tabernero, D. Lariviere, E. Nasr, E. Afgan, F. Zambelli, F. Heyl, F. Psomopoulos, F. Coppens, G. R. Price, G. Cuccuru, G. L. Corguillé, G. Von Kuster, G. G. Akbulut, H. Rasche, H. Hans-Rudolf, I. Eguinoa, I. Makunin, I. J. Ranawaka, J. P. Taylor, J. Joshi, J. Hillman-Jackson, J. Goecks, J. M. Chilton, K. Kamali, K. Suderman, K. Poterlowicz, L. B. Yvan, L. Lopez-Delisle, L. Sargent, M. E. Bassetti, M. A. Tangaro, M. van den Beek, M. Čech, M. Bernt, M. Fahrner, M. Tekman, M. C. Föll, M. C. Schatz, M. R. Crusoe, M. Roncoroni, N. Kucher, N. Coraor, N. Stoler, N. Rhodes, N. Soranzo, N. Pinter, N. A. Goonasekera, P. A. Moreno, P. Videm, P. Melanie, P. Mandreoli, P. D. Jagtap, Q. Gu, R. J. M. Weber, R. Lazarus, R. H. P. Vorderman, S. Hiltemann, S. Golitsynskiy, S. Garg, S. A. Bray, S. L. Gladman, S. Leo, S. P. Mehta, T. J. Griffin, V. Jalili, V. Yves, V. Wen, V. K. Nagampalli, W. A. Bacon, W. de Koning, W. Maier, P. J. Briggs) (2022):
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.
Nucleic Acids Research 50
https://doi.org/10.1093/nar/gkac247

[Gamma 1995] Erich Gamma, Richard Helm, Ralph Johnson, John Vlissides (1994):
Design Patterns: Elements of Reusable Object-Oriented Software.
Addison Wesley
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[Garcia 2020] Leyla Garcia, Erick Antezana, Alexander Garcia, Evan Bolton, Rafael Jimenez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama (2020):
Ten simple rules to run a successful BioHackathon.
PLOS Computational Biology 16(5):e1007808.
https://doi.org/10.1371/journal.pcbi.1007808

[Garcia 2020a] Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez del Angel, Michel Dumontier, Kim T. Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L. Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W. G. van Gelder, Patricia M. Palagi (2020):
Ten simple rules for making training materials FAIR.
PLOS Computational Biology 16(5):e1007854
https://doi.org/10.1371/journal.pcbi.1007854

[Garcia-Silva 2019] Andres Garcia-Silva, Jose Manuel Gomez-Perez, Raul Palma, Marcin Krystek, Simone Mantovani, Federica Foglini, Valentina Grande, Francesco De Leo, Stefano Salvi, Elisa Trasatti, Vito Romaniello, Mirko Albani, Cristiano Silvagni, Rosemarie Leone, Fulvio Marelli, Sergio Albani, Michele Lazzarini, Hazel J. Napier, Helen M. Glaves, Timothy Aldridge, Charles Meertens, Fran Boler, Henry W. Loescher, Christine Laney, Melissa A. Genazzio, Daniel Crawl, Ilkay Altintas (2019):
Enabling FAIR research in Earth science through research objects.
Future Generation Computer Systems 98
arXiv:1809.10617
https://doi.org/10.1016/j.future.2019.03.046

[Garijo 2011] Daniel Garijo, Yolanda Gil (2011):
A New Approach for Publishing Workflows.
Proceedings of the 6th Workshop on Workflows in Support of Large-Scale Science - WORKS ‘11.
https://doi.org/10.1145/2110497.2110504

[Garijo 2012] Daniel Garijo, Yolanda Gil (2012):
Augmenting PROV with Plans in P-PLAN: Scientific Processes as Linked Data.
Proceedings of the Second International Workshop on Linked Science 2012 - Tackling Big Data. (LISC 2021)
CEUR Workshop Proceedings 951
https://ceur-ws.org/Vol-951/paper6.pdf

[Garijo 2014a] Daniel Garijo, Pinar Alper, Khalid Belhajjame, Oscar Corcho, Yolanda Gil, Carole Goble (2014):
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

[Garijo 2014b] Daniel Garijo, Yolanda Gil, Oscar Corcho (2014):
Towards Workflow Ecosystems through Semantic and Standard Representations.
9th Workshop on Workflows in Support of Large-Scale Science (WORKS 2014)
https://doi.org/10.1109/works.2014.13

[Gauthier 2019] Jeff Gauthier, Antony T Vincent, Steve J Charette, Nicolas Derome (2019):
A brief history of bioinformatics.
Briefings in Bioinformatics 20(6)
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[GBIF 2021] GBIF Secretariat. (2021):
GBIF Science Review 2020.
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[Gewirtz 1996] Paul Gewirtz (1996):
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Yale Law Journal 105(4)
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[Gil 2011] Yolanda Gil, Varun Ratnakar, Jihie Kim, Pedro Gonzalez-Calero, Paul Groth, Joshua Moody, Ewa Deelman (2011):
Wings: Intelligent Workflow-Based Design of Computational Experiments.
IEEE Intelligent Systems 26(1)
https://doi.org/10.1109/MIS.2010.9

[Giles 2023] Thomas Giles, Stian Soiland-Reyes, Jonathan Couldridge, Stuart Wheater, Blaise Thomson, Jillian Beggs, Suzy Gallier, Sam Cox, Daniel Lea, Justin Biddle, Rima Doal, Naaman Tammuz, Becca Wilson, Christian Cole, Elizabeth Sapey, Simon Thompson, Professor Emily Jefferson, Phillip Quinlan, Carole Goble (2023):
TRE-FX: Delivering a federated network of trusted research environments to enable safe data analytics.
Zenodo / DARE UK
https://doi.org/10.5281/zenodo.10055354

[GitHub 2021] GitHub (2021):
Managing large files – GitHub Docs.
https://docs.github.com/en/repositories/working-with-files/managing-large-files

[Goble 2008] Carole Goble, Robert Stevens (2008):
State of the nation in data integration for bioinformatics.
Journal of Biomedical Informatics 41(5)
https://doi.org/10.1016/j.jbi.2008.01.008

[Goble 2010] Carole A Goble, Jiten Bhagat, Sergejs Aleksejevs, Don Cruickshank, Danius Michaelides, David Newman, Mark Borkum, Sean Bechhofer, Marco Roos, Peter Li, David De Roure (2010):
myExperiment: A repository and social network for the sharing of bioinformatics workflows.
Nucleic Acids Research 38(Web Server issue) W677–W682.
https://doi.org/10.1093/nar/gkq429

[Goble 2016] Carole Goble (2016):
What Is Reproducibility? The R* Brouhaha.
SciRepro Workshop, TPDL, Hannover, Germany, 2016.
http://repscience2016.research-infrastructures.eu/img/CaroleGoble-ReproScience2016v2.pdf

[Goble 2018] 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

[Goble 2020] 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(1–2) pp 108–121.
https://doi.org/10.1162/dint_a_00033

[Goble 2021] Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodríguez-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
https://s11.no/2021/phd/workflow-collaboratory/ (Supplement 3)

[Goble 2022] Carole Goble, Stian Soiland-Reyes, Nick Juty (2022):
FAIR-IMPACT: T3.2.1 PIDs in data production workflows.
FAIR-IMPACT, meeting on T3.2 Integration of PID practices into FAIR data management, 2022-10-06.
Zenodo
https://doi.org/10.5281/zenodo.7157647

[González 2022] Esteban González, Alejandro Benítez, Daniel Garijo (2022):
FAIROs: Towards FAIR Assessment in Research Objects.
TPDL 2022: Linking Theory and Practice of Digital Libraries
https://dgarijo.com/papers/TPDL2022_gonzalez.pdf
https://doi.org/10.1007/978-3-031-16802-4_6

[Gray 2017] Alasdair Gray, Carole Goble, Rafael Jimenez, Bioschemas Community (2017):
Bioschemas: From Potato Salad to Protein Annotation.
Proceedings of the ISWC 2017 posters & demonstrations and industry tracks co-located with 16th international semantic web conference (ISWC 2017), Vienna, Austria.
CEUR Workshop Proceedings 1963
https://iswc2017.semanticweb.org/paper-579/
https://ceur-ws.org/Vol-1963/paper579.pdf

[Gregorio 2007] Joe Gregorio, Bill de hÓra (2007):
The Atom Publishing Protocol.
RFC Editor, RFC 5023
https://doi.org/10.17487/rfc5023

[Gregorio 2012] Joe Gregorio, Roy T. Fielding, Marc Hadley, Mark Nottingham, David Orchard (2012):
URI Template.
RFC Editor, RFC 6570
https://doi.org/10.17487/rfc6570

[Groom 2020] Quentin Groom, Anton Güntsch, Pieter Huybrechts, Nicole Kearney, Siobhan Leachman, Nicky Nicolson, Roderic D M Page, David P Shorthouse, Anne E Thessen, Elspeth Haston (2020):
People are essential to linking biodiversity data.
Database 2020
https://doi.org/10.1093/database/baaa072

[Grossman 2016] Robert L Grossman, Allison Heath, Mark Murphy, Maria Patterson, Walt Wells (2016):
A case for data commons: Toward data science as a service.
Computing in Science & Engineering 18(5)
https://doi.org/10.1109/MCSE.2016.92

[Groth 2014] 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.
Journal of Web Semantics 29
https://doi.org/10.1016/j.websem.2014.03.003

[Grüning 2018a] Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda Team, Johannes Köster (2018):
Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences.
Nature Methods 15 pp 475–476.
https://doi.org/10.1038/s41592-018-0046-7

[Grüning 2018b] Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor (2018):
Practical Computational Reproducibility in the Life Sciences. Cell Systems 6(6)
https://doi.org/10.1016/j.cels.2018.03.014

[Gruenpeter 2021] Morane Gruenpeter, Daniel S. Katz, Anna-Lena Lamprecht, Tom Honeyman, Daniel Garijo, Alexander Struck, Anna Niehues, Paula Andrea Martinez, Leyla Jael Castro, Tovo Rabemanantsoa, Neil P. Chue Hong, Carlos Martinez-Ortiz, Laurents Sesink, Matthias Liffers, Anne Claire Fouilloux, Chris Erdmann, Silvio Peroni, Paula Martinez Lavanchy, Ilian Todorov, Manodeep Sinha (2021):
Defining Research Software: A Controversial Discussion.
FAIR for Research Software (FAIR4RS) / Zenodo
https://doi.org/10.5281/zenodo.5504016

[Guha 2014] Ramanathan Guha, Dan Brickley (2014):
RDF Schema 1.1.
W3C Recommendation
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[Guha 2015] Ramanathan V Guha, Dan Brickley, Steve Macbeth (2015):
Schema.org: Evolution of Structured Data on the Web: Big data makes common schemas even more necessary.
Queue 13(9) pp. 10–37.
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[Guha 2016] Ramanathan V Guha, Dan Brickley, Steve Macbeth (2016):
Schema.org: evolution of structured data on the web.
Communications of the ACM 59(2)
https://doi.org/10.1145/2844544

[Gurevich 1995] Yuri Gurevich (1995):
Evolving Algebras 1993: Lipari Guide.
Specification and Validation Methods
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[Handle] CNRI (2022):
Handle.Net Software.
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[Hardisty 2016] 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(1)
https://doi.org/10.1186/s12898-016-0103-y

[Hardisty 2019a] Alex R Hardisty, Keping Ma, Gil Nelson, Jose Fortes (2019):
‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types.
Biodiversity Information Science and Standards 3:e37033
https://doi.org/10.3897/biss.3.37033

[Hardisty 2019b] Alex Hardisty (2019):
Provisional Data Management Plan for DiSSCo infrastructure.
Zenodo, DiSSCo Deliverable D6.6
https://doi.org/10.5281/zenodo.3532937

[Hardisty 2020] Alex Hardisty, Hannu Saarenmaa, Ana Casino, Mathias Dillen, Karsten Gödderz, Quentin Groom, Helen Hardy, Dimitris Koureas, Abraham Nieva de la Hidalga, Deborah Paul, Veljo Runnel, Xavier Vermeersch, Myriam van Walsum, Luc Willemse (2020):
Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1.
Research Ideas and Outcomes 6:e54280.
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[Hardisty 2022] 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
https://s11.no/2022/phd/specimen-data-refinery/ (section [ch8:the-specimen-data-refinery]{reference-type=“ref+page” reference=“ch8:the-specimen-data-refinery”})

[Harrow 2021] 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 40(6):e107409
https://doi.org/10.15252/embj.2020107409

[Harrow 2022] Jennifer Harrow, Rachel Drysdale, Andrew Smith, Susanna Repo, Jerry Lanfaear, Niklas Blomberg (2022):
ELIXIR: providing a sustainable infrastructure for life science data at European scale.
Bioinformatics 37(16)
https://doi.org/10.1093/bioinformatics/btab481

[Hashem 2015] Ibrahim Abaker Targio Hashem, Ibrar Yaqoob, Nor Badrul Anuar, Salimah Mokhtar, Abdullah Gani, Samee Ullah Khan (2015):
The rise of “big data” on cloud computing: Review and open research issues
Information Systems 47
https://doi.org/10.1016/j.is.2014.07.006

[Hasnain 2018] Ali Hasnain, Dietrich Rebholz-Schuhmann (2019):
Assessing FAIR Data Principles Against the 5-Star Open Data Principles.
ESWC 2018: The Semantic Web: ESWC 2018 Satellite Events,
Lecture Notes in Computer Science 11155
https://doi.org/10.1007/978-3-319-98192-5_60

[Hausenblas 2012] Michael Hausenblas, James G Kim. (2012):
5-star Open Data.
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[Heath 2011] Tom Heath, Christian Bizer (2011):
Linked Data: Evolving the Web into a Global Data Space.
Synthesis Lectures on the Semantic Web: Theory and Technology 1
https://doi.org/10.2200/S00334ED1V01Y201102WBE001

[Heberling 2019] J Mason Heberling, L Alan Prather, Stephen J Tonsor (2019):
The Changing Uses of Herbarium Data in an Era of Global Change: An Overview Using Automated Content Analysis.
BioScience 69(10)
https://doi.org/10.1093/biosci/biz094

[Heberling 2021] J Mason Heberling, Joseph T Miller, Daniel Noesgaard, Scott B Weingart, Dmitry Schigel (2021):
Data integration enables global biodiversity synthesis.
Proceedings of the National Academy of Sciences 118(6)
https://doi.org/10.1073/pnas.2018093118

[Hellström 2022] Maggie Hellström, Carlo Zwölf, Peter Wittenburg (2022):
FDO – granularity, versioning, mutability.
FDO Specification Documents PR-Granularity-2.2-20221017
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7825686

[Hereld 2019] Mark Hereld, Nicola Ferrier (2019):
LightningBug ONE: An experiment in high-throughput digitization of pinned insects.
Biodiversity Information Science and Standards 3:e37228.
https://doi.org/10.3897/biss.3.37228

[Herschel 2017] Melanie Herschel, Ralf Diestelkämper, Houssem Ben Lahmar (2017):
A survey on provenance: What for? What form? What from?
The VLDB Journal 26
https://doi.org/10.1007/s00778-017-0486-1

[Himanen 2019] Lauri Himanen, Amber Geurts, Adam Stuart Foster, Patrick Rinke (2019):
Data-Driven Materials Science: Status, Challenges, and Perspectives.
Advanced Science 6(21):1900808
https://doi.org/10.1002/advs.201900808

[Hitzler 2016] Pascal Hitzler, Aldo Gengami, Krzysztof Janowicz, Adila Krisnadhi, Valentina Presutti (eds.) 2016:
Ontology engineering with ontology design patterns: Foundations and Applications.
Studies on the Semantic Web 25
ISBN 978-1-61499-676-7

[Holland 2014] Vicki Tardif Holland, Jason Johnson (2014):
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The Semantic Web — ISWC 2002
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[Hospital 2020] Adam Hospital, Genís Bayarri, Stian Soiland-Reyes, Jose Lluis Gelpi, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier, Rosa Maria Badia, Rodrigo Vargas, Alexandre Bonvin (2020):
BioExcel-2 Deliverable 2.3 – First release of demonstration workflows.
Project deliverable, Zenodo
https://doi.org/10.5281/zenodo.4540432

[Hospital 2021a] Adam Hospital, Pau Andrio (2021):
Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs.
WorkflowHub. Workflow (PyCOMPSs)
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[Hospital 2021b] Adam Hospital (2021):
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in KNIME.
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[Hu 2011] Wei Hu, Jianfeng Chen, Hang Zhang, Yuzhong Qu (2011):
How matchable are four thousand ontologies on the semantic web.
In Grigoris Antoniou, Marko Grobelnik, Elena Simperl, Bijan Parsia, Dimitris Plexousakis, Pieter De Leenheer, Jeff Pan,eds., The semantic web: Research and applications, pp. 290–304
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[Hui 2012] Yuk Hui (2012):
What is a Digital Object?
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FAIR digital objects, persistent identifiers and machine actionability.
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Knowledge enhanced digital objects.
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Seamless management of ensemble climate prediction experiments on HPC platforms.
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Semantic interoperability in health records standards: a systematic literature review.
Health and Technology 12
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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
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Why and how to engage expert stakeholders in ontology development: Insights from social and behavioural sciences.
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25 years development of knowledge graph theory: the results and the challenge.
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A lightweight approach to research object data packaging.
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RO-Crate: A lightweight approach to research object data packaging.
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Example of Workflow Run RO-Crate Output in Sapporo
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Ya2ro: A tool for creating Research Objects from minimum metadata.
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BackTrackBB: Multi-band array detection and location of seismic sources (PyCOMPSs implementation).
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A more decentralized vision for linked data.
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[RO-Crate 1.0] Peter Sefton, Eoghan Ó Carragáin, Stian Soiland-Reyes, Oscar Corcho, Daniel Garijo, Raul Palma, Frederik Coppens, Carole Goble, José María Fernández, Kyle Chard, Jose Manuel Gomez-Perez, Michael R Crusoe, Ignacio Eguinoa, Nick Juty, Kristi Holmes, Jason A. Clark, Salvador Capella-Gutierrez, Alasdair J. G. Gray, Stuart Owen, Alan R. Williams, Giacomo Tartari, Finn Bacall, Thomas Thelen (2019):
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ResearchObject.org / Zenodo
https://doi.org/10.5281/zenodo.4031327
https://w3id.org/ro/crate/1.1

[RO-Crate 1.1.3] Peter Sefton, Eoghan Ó Carragáin, Stian Soiland-Reyes, Oscar Corcho, Daniel Garijo, Raul Palma, Frederik Coppens, Carole Goble, José María Fernández, Kyle Chard, Jose Manuel Gomez-Perez, Michael R Crusoe, Ignacio Eguinoa, Nick Juty, Kristi Holmes, Jason A. Clark, Salvador Capella-Gutierrez, Alasdair J. G. Gray, Stuart Owen, Alan R. Williams, Giacomo Tartari, Finn Bacall, Thomas Thelen, Hervé Ménager, Laura Rodríguez-Navas, Paul Walk, brandon whitehead, Mark Wilkinson, Paul Groth, Erich Bremer, LJ Garcia Castro, Karl Sebby, Alexander Kanitz, Ana Trisovic, Gavin Kennedy, Mark Graves, Jasper Koehorst, Simone Leo, Marc Portier, Paul Brack, Milan Ojsteršek, Bert Droesbeke, Chenxu Niu, Kosuke Tanabe, Tomasz Miksa, Marco La Rosa, Cedric Decruw, Andreas Czerniak, Jeremy Jay, Sergio Serra, Ronald Siebes, Shaun de Witt, Shady El Damaty, Douglas Lowe, Xuanqi Li, Sveinung Gundersen, Muhammad Radifar (2023):
RO-Crate Metadata Specification 1.1.3.
ResearchObject.org / Zenodo
https://doi.org/10.5281/zenodo.7867028
https://w3id.org/ro/crate/1.1

[RO-Crate 1.2] Peter Sefton, Eoghan Ó Carragáin, Stian Soiland-Reyes, Oscar Corcho, Daniel Garijo, Raul Palma, Frederik Coppens, Carole Goble, José María Fernández, Kyle Chard, Jose Manuel Gomez-Perez, Michael R Crusoe, Ignacio Eguinoa, Nick Juty, Kristi Holmes, Jason A. Clark, Salvador Capella-Gutierrez, Alasdair J. G. Gray, Stuart Owen, Alan R. Williams, Giacomo Tartari, Finn Bacall, Thomas Thelen, Hervé Ménager, Laura Rodríguez-Navas, Paul Walk, brandon whitehead, Mark Wilkinson, Paul Groth, Erich Bremer, LJ Garcia Castro, Karl Sebby, Alexander Kanitz, Ana Trisovic, Gavin Kennedy, Mark Graves, Jasper Koehorst, Simone Leo, Marc Portier, Paul Brack, Milan Ojsteršek, Bert Droesbeke, Chenxu Niu, Kosuke Tanabe, Tomasz Miksa, Marco La Rosa, Cedric Decruw, Andreas Czerniak, Jeremy Jay, Sergio Serra, Ronald Siebes, Shaun de Witt, Shady El Damaty, Douglas Lowe, Xuanqi Li, Sveinung Gundersen, Muhammad Radifar, Rudolf Wittner, Oliver Woolland, Paul De Geest, Douglas Fils, Florian Wetzels, Raül Sirvent, Abigail Miller, Jake Emerson, Davide Fucci, Bruno P. Kinoshita, Maciek Bąk, Jens Hollunder, Martin Weise (2024):
RO-Crate Metadata Specification 1.2.0.
(in preparation https://www.researchobject.org/ro-crate/1.2-DRAFT/)
https://doi.org/10.5281/zenodo.8255842
https://w3id.org/ro/crate/1.2

[ro-crate-html-js] npm:
ro-crate-html-js
https://www.npmjs.com/package/ro-crate-html-js

[Robinson 2017] Mark Robinson, Stian Soiland-Reyes, Michael R. Crusoe, Carole Goble (2017):
CWL Viewer: The Common Workflow Language viewer.
F1000Research 6(ISCB Comm J):1075 (poster)
https://doi.org/10.7490/f1000research.1114375.1

[Robinson 2023] Mark Robinson, Stian Soiland-Reyes, Michael R. Crusoe, Bruno P. Kinoshita, Osakpolor Obaseki, Peter Amstutz, Iacopo Colonnelli, etzanis, Snyk bot, Anushka Shukla, Charles Overbeck, Ward Vandewege, Imgbot, Finn Bacall, Jonathan Leitschuh, yichiehc (2023):
common-workflow-language/cwlviewer: v1.4.7.
Common Workflow Language, GitHub/Zenodo
https://github.com/common-workflow-language/cwlviewer
https://doi.org/10.5281/zenodo.7589709

[Rocca-Serra 2023] Philippe Rocca-Serra, Wei Gu, Vassilios Ioannidis, Tooba Abbassi-Daloii, Salvador Capella-Gutierrez, Ishwar Chandramouliswaran, Andrea Splendiani, Tony Burdett, Robert T. Giessmann, David Henderson, Dominique Batista, Ibrahim Emam, Yojana Gadiya, Lucas Giovanni, Egon Willighagen, Chris Evelo, Alasdair J. G. Gray, Philip Gribbon, Nick Juty, Danielle Welter, Karsten Quast, Paul Peeters, Tom Plasterer, Colin Wood, Eelke van der Horst, Dorothy Reilly, Herman van Vlijmen, Serena Scollen, Allyson Lister, Milo Thurston, Ramon Granell, Gabriel Backianathan, Sebastian Baier, Anne Cambon Thomsen, Martin Cook, Melanie Courtot, Mike d’Arcy, Kurt Dauth, Eva Marin del Piico, Leyla Garcia, Ulrich Goldmann, Valentin Grouès, Daniel J. B. Clarke, Erwan Lefloch, Isuru Liyanage, Petros Papadopoulos, Cyril Pommier, Emiliano Reynares, Francesco Ronzano, Alejandra Delfin-Rossaro, Venkata Sagatopam, Ashni Sedani, Vitaly Sedlyarov, Liubov Shilova, Sukhi Singh, Jolanda Strubel, Kees van Bochove, Zachary Warnes, Peter Woollard, Fuqi Xu, Andrea Zaliani, Susanna-Assunta Sansonem, the FAIR Cookbook Contributors (2023):
The FAIR cookbook - the essential resource for and by FAIR doers.
Scientific Data 10(10)
https://doi.org/10.1038/s41597-023-02166-3

[Saltz 2006] Joel Saltz, Scott Oster, Shannon Hastings, Stephen Langella, Tahsin Kurc, William Sanchez, Manav Kher, Arumani Manisundaram, Krishnakant Shanbhag, Peter Covitz (2006):
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.
Bioinformatics 22(15)
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End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach.
Journal of Biomedical Semantics 13:1
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Ten simple rules for reproducible computational research.
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[Sansone 2019] Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson L. Lister, Milo Thurston, the FAIRsharing Community (2019):
FAIRsharing as a community approach to standards, repositories and policies.
Nature Biotechnology 37
https://doi.org/10.1038/s41587-019-0080

[Sauermann 2008] Leo Sauermann, Richard Cyganiak, Danny Ayers, Max Völkel (2008):
Cool URIs for the semantic web.
W3C Interest Group Note
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[Scheidegger 2008] Carlos E. Scheidegger, Huy T. Vo, David Koop, Juliana Freire, Claudio T. Silva (2008):
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[Schouppe 2018] Michel Schouppe, Jean-Claude Burgelman (2018):
Relevance of EOSC and FAIR in the Realm of Open Science and Phases of Implementing the EOSC.
Data Analytics and Management in Data Intensive Domains (DAMDID/RCDL 2018)
CEUR Workshop Proceedings 2277 https://ceur-ws.org/Vol-2277/paper01.pdf

[Schreiber 2014] Guus Schreiber, Yves Raimond (2014):
RDF 1.1 Primer.
W3C Note
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[Schriml 2020] Lynn M. Schriml, Maria Chuvochina, Neil Davies, Emiley A. Eloe-Fadrosh, Robert D. Finn, Philip Hugenholtz, Christopher I. Hunter, Bonnie L. Hurwitz, Nikos C. Kyrpides, Folker Meyer, Ilene Karsch Mizrachi, Susanna-Assunta Sansone, Granger Sutton, Scott Tighe, Ramona Walls (2020):
COVID-19 pandemic reveals the peril of ignoring metadata standards.
Scientific Data 7(1):188
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[Schröder 2022] Max Schröder, Susanne Staehlke, Paul Groth, J. Barbara Nebe, Sascha Spors, Frank Krüger (2022):
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation.
Journal of Biomedical Semantics 13:4
https://doi.org/10.1186/s13326-021-00257-x

[Schultes 2019] Erik Schultes, Peter Wittenburg (2019):
FAIR principles and digital objects: Accelerating convergence on a data infrastructure.
Data analytics and management in data intensive domains: 20th international conference (DAMDID/RCDL 2018)
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[Schultes 2020] Erik Schultes, Barbara Magagna, Kristina Maria Hettne, Robert Pergl, Marek Suchánek, Tobias Kuhn (2020):
Reusable FAIR implementation profiles as accelerators of FAIR convergence.
International Conference on Conceptual Modeling, ER 2020: Advances in Conceptual Modeling, 2022-11-03/–06, Vienna, Austria.
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[Schultes 2022] Erik Schultes, Marco Roos, Luiz Olavo Bonino da Silva Santos, Giancarlo Guizzardi, Jildau Bouwman, Thomas Hankemeier, Arie Baak, Barend Mons (2022):
FAIR Digital Twins for Data-Intensive Research.
Frontiers in Big Data 5
https://doi.org/10.3389/data.2022.883341

[Schwardmann 2022a] Ulrich Schwardmann, George Strawn, Robert Quick, Peter Wittenburg (2022):
DOIP endorsement request.
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FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7824796

[Schwardmann 2022b] Ulrich Schwardmann, Tibor Kálmán (2022):
Two Examples on How FDO Types can Support Machine and Human Readability.
Research Ideas and Outcomes 8:e96014
https://doi.org/10.3897/rio.8.e96014

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The Survey Ontology: Packaging Survey Research as Research Objects.
2nd Workshop on Data and Research Objects Management for Linked Open Science
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[Sefton 2018] Peter Sefton, Gerard Devine, Christian Evenhuis, Michael Lynch, Sharyn Wise, Michael Lake, Duncan Loxton (2018):
DataCrate: a method of packaging, distributing, displaying and archiving Research Objects.
Workshop on Research Objects (RO 2018), 29 Oct 2018 at IEEE eScience 2018, Amsterdam, Netherland.
Zenodo
https://doi.org/10.5281/zenodo.1445817

[Sefton 2021] Peter Sefton, Mike Lynch, Stian Soiland-Reyes (2021):
GitHub – UTS-eResearch/ro-crate-js: Research Object Crate (RO-Crate) utilities.
https://github.com/UTS-eResearch/ro-crate-js

[Sefton 2021] Peter Sefton (2021):
FAIR Data Management; It’s a lifestyle not a lifecycle.
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[Semmler 2022] Tido Semmler, Sergey Danilov, Thomas Rackow, Dmitry Sidorenko, Dirk Barbi, Jan Hegewald, Dmitri Sein, Qiang Wang, Thomas Jung (2022):
IPCC DDC: AWI AWI-CM1.1MR model output prepared for CMIP6 CMIP historical.
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Open data sharing and the Global South—Who benefits?
Science 359(6376)
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[Shanahan 2021] Hugh Shanahan, Nancy Hoebelheinrich, Angus Whyte (2021):
Progress toward a comprehensive teaching approach to the FAIR data principles.
Patterns 2(10)
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Introducing the knowledge graph: Things, not strings.
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Automatic, Efficient, and Scalable Provenance Registration for FAIR HPC Workflows.
2022 IEEE/ACM Workshop on Workflows in Support of Large-Scale Science (WORKS)
https://doi.org/10.1109/works56498.2022.00006
https://hdl.handle.net/2117/384589

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Current Opinion in Structural Biology 48
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The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration.
Nature Biotechnology 25(11)
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PeerJ Computer Science 2:e86
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Integrating Our Community. Year 1
Health Data Research UK (report)
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Research Object Bundle 1.0.
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[Soiland-Reyes 2016] Stian Soiland-Reyes, Pinar Alper, Carole Goble (2016):
Tracking Workflow Execution With TavernaPROV, ProvenanceWeek 2016, session “PROV: Three Years Later”
https://s11.no/2016/provweek-tavernaprov/
https://doi.org/10.5281/zenodo.51314

[Soiland-Reyes 2018] Stian Soiland-Reyes, Farah Zaib Khan, Michael R Crusoe (2018):
common-workflow-language/cwlprov: CWLProv 0.6.0.
Zenodo
https://doi.org/10.5281/zenodo.1471585

[Soiland-Reyes 2020a] Stian Soiland-Reyes (2020):
I am looking for which bioinformatics journals encourage authors to submit their code/pipeline/workflow supporting data analysis, Twitter
https://twitter.com/soilandreyes/status/1250721245622079488 (archived 2022-12-25 https://web.archive.org/web/20221225100843/https://twitter.com/soilandreyes/status/1250721245622079488)

[Soiland-Reyes 2021] Stian Soiland-Reyes (2021):
Describing and packaging workflows using RO-Crate and BioCompute Objects.
Webinar for U.S. Food and Drug Administration (FDA), 2021-05-12
Zenodo
https://doi.org/10.5281/zenodo.4633732

[Soiland-Reyes 2022a] 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
https://s11.no/2022/phd/ro-crate/ (sections [ch5:packaging-research-artefacts-with-ro-crate]{reference-type=“ref+page” reference=“ch5:packaging-research-artefacts-with-ro-crate”} and [ch5:formaldefinition]{reference-type=“ref+page” reference=“ch5:formaldefinition”})

[Soiland-Reyes 2022b] 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
https://s11.no/2022/phd/canonical-workflow-building-blocks/ (section [ch6:making-canonical-workflow-building-blocks-interoperable-across-workflow-languages]{reference-type=“ref+page” reference=“ch6:making-canonical-workflow-building-blocks-interoperable-across-workflow-languages”})

[Soiland-Reyes 2022c] 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.
Research Ideas and Outcomes 8:e93937
https://doi.org/10.3897/rio.8.e93937
https://s11.no/2022/phd/fdo-with-ro-crate/ (section [ch4:lightweight-fdo]{reference-type=“ref+page” reference=“ch4:lightweight-fdo”})

[Soiland-Reyes 2022d] Stian Soiland-Reyes, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, Paul Groth (2022):
Updating Linked Data practices for FAIR Digital Object principles.
Research Ideas and Outcomes 8
https://doi.org/10.3897/rio.8.e94501
https://s11.no/2022/phd/updating-ld-for-fdo/ (section [ch2:updating-linked-data-practices-for-fair-digital-object-principles]{reference-type=“ref+page” reference=“ch2:updating-linked-data-practices-for-fair-digital-object-principles”})

[Soiland-Reyes 2022e] Stian Soiland-Reyes,Bruno P. Kinoshita (2022):
stain/signposting: Signposting v0.9.0.
Zenodo
https://doi.org/10.5281/zenodo.7256713

[Soiland-Reyes 2022f] Stian Soiland-Reyes, Carole Goble (2022):
EuroScienceGateway: WP2 introduction.
EuroScienceGateway kickoff 2022-10-06
https://doi.org/10.5281/zenodo.7152762

[Soiland-Reyes 2022g] 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.
RO-Crate
Zenodo
https://w3id.org/ro/doi/10.5281/zenodo.5146227
https://doi.org/10.5281/zenodo.5833456

[Soiland-Reyes 2023a] Stian Soiland-Reyes (2023):
Comparison tables for evaluating FAIR Digital Object and Linked Data.
RO-Crate.
Zenodo
https://w3id.org/ro/doi/10.5281/zenodo.8075229
https://doi.org/10.5281/zenodo.8075229

[Soiland-Reyes 2023b] Stian Soiland-Reyes, Herbert Van de Sompel (2023):
Enabling FAIR Signposting and RO-Crate for content/metadata discovery and consumption.
Webinar: FAIR-IMPACT Open Call for Support, 2023-03-27
Zenodo
https://doi.org/10.5281/zenodo.7774582

[Soiland-Reyes 2023d] Stian Soiland-Reyes, Carole Goble (2023):
Building diverse FDO Collections using RO-Crate.
FAIR Digital Object Forum, workshop "Defining FDO Collections", 2023-04-14.
https://doi.org/10.5281/zenodo.7828632

[Soiland-Reyes 2023e] Stian Soiland-Reyes, Stuart Wheater (2023):
Five Safes RO-Crate profile, version 0.4.
TRE-FX Candidate Recommendation
https://w3id.org/5s-crate/0.4

[Soiland-Reyes 2023f] Stian Soiland-Reyes, Stuart Wheater, Thomas Giles, Carole Goble, Philip Quinlan (2023):
TRE-FX Technical Documentation - Five Safes RO-crate.
Zenodo
https://doi.org/10.5281/zenodo.10376350

[Soiland-Reyes 2024] 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

[Soiland-Reyes 2024b] Stian Soiland-Reyes, Carole Goble, Paul Groth (2024):
Evaluating FAIR Digital Object and Linked Data as distributed object systems.
PeerJ Computer Science 10:e1781
arXiv 2306.07436 [cs.DC]
https://doi.org/10.7717/peerj-cs.1781
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[Soiland-Reyes 2024c] 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.
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JSON-LD 1.0: A JSON-based Serialization for Linked Data.
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RDFa 1.1 Primer - Third Edition.
W3C Working Group Note 17 March 2015
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[Sporny 2020] Manu Sporny, Dave Longley, Gregg Kellogg, Markus Lanthaler, Pierre-Antoine Champin, Niklas Lindström (2020):
JSON-LD 1.1: A JSON-based Serialization for Linked Data.
W3C Recommendation 16 July 2020
https://www.w3.org/TR/2020/REC-json-ld11-20200716/

[Sporny 2023] Manu Sporny, Amy Guy (2023):
Media Types with Multiple Suffixes.
Internet Engineering Task Force
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Process modelling for information system description.
The Open University
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To develop or to reuse? Two perspectives on external reuse in software projects.
International Conference of Software Business (ICSOB 2015), Braga, Portugal, 2015-06-10/–12.
ICSOB 2015: Software business
http://doi.org/10.1007/978-3-319-19593-3_18

[Stefi 2015b] Anisa Stefi (2015):
Do Developers Make Unbiased Decisions? - The Effect of Mindfulness and Not-Invented-Here Bias on the Adoption of Software Components.
European Conference on Information Systems (ECIS 2015), Münster, Germany, 2015-05-26/–29
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[Stodden 2016] Victoria Stodden, Marcia McNutt, David H. Bailey, Ewa Deelman, Yolanda Gil, Brooks Hanson, Michael A. Heroux, John P.A. Ioannidis, Michela Taufer (2016):
Enhancing reproducibility for computational methods.
Science 354(6317)
https://doi.org/10.1126/science.aah6168

[Suetake 2022] Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita, Takeshi Fujino, Tsuyoshi Hachiya, Yuichi Kodama, Takatomo Fujisawa, Osamu Ogasawara, Atsushi Shimizu, Masanori Arita, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2022):
Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics [version 1; peer review: 2 approved with reservations].
F1000Research 11:889
https://doi.org/10.12688/f1000research.122924.1

[Suetake 2023a] Hirotaka Suetake, Tsukasa Fukusato, Takeo Igarashi, Tazro Ohta (2023):
A workflow reproducibility scale for automatic validation of biological interpretation results.
GigaScience 12:iad031
https://doi.org/10.1093/gigascience/giad031

[Suetake 2023b] Hirotaka Suetake, Tazro Inutano Ohta, Tomoya Tanjo, Manabu ISHII, Bruno P. Kinoshita, DrYak (2023):
sapporo-wes/sapporo-service: 1.5.1
Zenodo
https://doi.org/10.5281/zenodo.10134452

[Sun 2003a] Sam Sun, Larry Lannom, Brian P. Boesch (2003):
Handle System Overview.
RFC Editor, RFC 3650
https://doi.org/10.17487/rfc3650

[Sun 2003b] Sam Sun, Sean Reilly, Larry Lannom, Jason Petrone (2003):
Handle System Protocol (ver 2.1) Specification.
RFC Editor, RFC 3652
https://doi.org/10.17487/rfc3652

[Sweeney 2018] Patrick W. Sweeney, Binil Starly, Paul J. Morris, Yiming Xu, Aimee Jones, Sridhar Radhakrishnan, Christopher J. Grassa, Charles C. Davis (2018):
Large-scale digitization of herbarium specimens: Development and usage of an automated, high-throughput conveyor system.
Taxon 67(1)
https://doi.org/10.12705/671.10

[Taschuk 2017] Morgan Taschuk, Greg Wilson (2017):
Ten simple rules for making research software more robust.
PLOS Computational Biology 13(4):e1005412
https://doi.org/10.1371/journal.pcbi.1005412

[Taivalsaari 2021] Antero Taivalsaari, Tommi Mikkonen, Cesare Pautasso, Kari Systä (2021):
Full Stack Is Not What It Used to Be. Web Engineering (ICWE 2021)
Lecture Notes in Computer Science 12706
https://doi.org/10.1007/978-3-030-74296-6_28

[Tegelberg 2017] Riitta Tegelberg, Jere Kahanpaa, Janne Karppinen, Tero Mononen, Zhenzhe Wu, Hannu Saarenmaa (2017):
Mass Digitization of Individual Pinned Insects Using Conveyor-Driven Imaging.
2017 IEEE 13th International Conference on E-Science (e-Science)
https://doi.org/10.1109/eScience.2017.85

[Tejedor 2017] Enric Tejedor, Yolanda Becerra, Guillem Alomar, Anna Queralt, Rosa M. Badia, Jordi Torres, Toni Cortes, Jesús Labarta (2017):
PyCOMPSs: Parallel computational workflows in Python.
The International Journal of High Performance Computing Applications 31(1)
https://doi.org/10.1177/1094342015594678

[Thieberger 2012] N. Thieberger, L. Barwick (2012):
Keeping records of language diversity in melanesia: The Pacific and regional archive for digital sources in endangered cultures (PARADISEC).
Melanesian Languages on the Edge of Asia: Challenges for the 21st Century, N. Evans and M. Klamer (eds.)
Language Documentation & Conservation Special Publication SP05
https://hdl.handle.net/10125/4567

[Thiers 2016] Barbara M. Thiers, Melissa C. Tulig, Kimberly A. Watson (2016):
Digitization of the New York Botanical Garden herbarium.
Brittonia 68(3)
https://doi.org/10.1007/s12228-016-9423-7

[Thompson 2012] Henry Thompson, Sandy Gao, David Beech, Murray Maloney, Noah Mendelsohn, Michael Sperberg-McQueen (2012):
W3C XML Schema Definition Language (XSD) 1.1 Part 1: Structures.
W3C Recommendation 5 April 2012
https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/

[Thompson 2020] Mark Thompson, Kees Burger, Rajaram Kaliyaperumal, Marco Roos, Luiz Olavo Bonino da Silva Santos (2020):
Making FAIR Easy with FAIR Tools: From Creolization to Convergence.
Data Intelligence 2(1-2)
https://doi.org/10.1162/dint_a_00031

[Thornton 2019] Katherine Thornton, Harold Solbrig, Gregory S. Stupp, Jose Emilio Labra Gayo, Daniel Mietchen, Eric Prud, Andra Waagmeester (2019):
Using shape expressions (ShEx) to share RDF data models and to guide curation with rigorous validation.
The Semantic Web: 16th international conference, (ESWC 2019), Portorož, Slovenia, 2019-06-02/–06
https://doi.org/10.1007/978-3-030-21348-0_39

[Tirmizi 2011] Syed Tirmizi, Stuart Aitken, Dilvan A. Moreira, Chris Mungall, Juan Sequeda, Nigam H. Shah, Daniel P. Miranker (2011):
Mapping between the OBO and OWL ontology languages.
Journal of Biomedical Semantics 2:S3
https://doi.org/10.1186/2041-1480-2-s1-s3

[Tran 2014] Linked Data Mashups: A Review on Technologies, Applications and Challenges Intelligent Information and Database Systems. ACIIDS 2014. Ngoc Thanh Nguyen, Boonwat Attachoo, Bogdan Trawiński, Kulwadee Somboonviwat (eds.)
Lecture Notes in Computer Science 8398
https://doi.org/10.1007/978-3-319-05458-2_27

[Trautwein 2022] Dennis Trautwein, Aravindh Raman, Gareth Tyson, Ignacio Castro, Will Scott, Moritz Schubotz, Bela Gipp, Yiannis Psaras (2022):
Design and Evaluation of IPFS: A Storage Layer for the Decentralized Web.
Proceedings of the ACM SIGCOMM 2022 Conference
https://doi.org/10.48550/arXiv.2208.05877
https://doi.org/10.1145/3544216.3544232

[Triki 2020] Abdelaziz Triki, Bassem Bouaziz, Walid Mahdi, Jitendra Gaikwad (2020):
Objects Detection from Digitized Herbarium Specimen based on Improved YOLO V3.
Proceedings of the 15th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications 4
https://doi.org/10.5220/0009170005230529

[Troncy 2010] Raphaël Troncy, Werner Bailer, Martin Höffernig, Michael Hausenblas (2010):
VAMP: A service for validating MPEG-7 descriptions w.r.t. to formal profile definitions.
Multimedia tools and applications 46(2–3)
https://www.persistent-identifier.nl/urn:nbn:nl:ui:18-14511
https://doi.org/10.1007/s11042-009-0397-2

[Tudorache 2020] Tania Tudorache (2020):
Ontology engineering: Current state, challenges, and future directions.
Semantic Web 11(1)
https://doi.org/10.3233/SW-190382

[Tupelo-Scheck 2022] Robert Tupelo-Schneck, Larry Lannom (2022):
Brief Introduction to Cordra & DOIP.
RDA FAIR DO Fabric, 2022-03-22
https://www.rd-alliance.org/sites/default/files/Cordra.2022.pdf

[Turcoane 2014] Ovidiu Turcoane (2014):
Linked data, JSON-LD and the semantics of cultural and scientific heritage.
Digital Presentation and Preservation of Cultural and Scientific Heritage 4
https://doi.org/10.55630/dipp.2014.4.11

[Unger 2016] Jakob Unger, Dorit Merhof, Susanne Renner (2016):
Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification
. BMC Evolutionary Biology 16(1)
https://doi.org/10.1186/s12862-016-0827-5

[Van de Sompel 2007] Herbert Van de Sompel, Carl Lagoze (2007):
Interoperability for the discovery, use, and re-use of units of scholarly communication.
CTWatch Quarterly 3(3)
http://icl.utk.edu/ctwatch/quarterly/articles/2007/08/interoperability-for-the-discovery-use-and-re-use-of-units-of-scholarly-communication/

[Van de Sompel 2013] Herbert Van de Sompel, Michael Nelson, Robert Sanderson (2013):
HTTP Framework for Time-Based Access to Resource States – Memento.
RFC Editor, RFC 7089
https://doi.org/10.17487/rfc7089

[Van de Sompel 2015] Herbert Van de Sompel, Michael L. Nelson (2015):
Reminiscing About 15 Years of Interoperability Efforts.
D-Lib Magazine 21(11/12)
https://doi.org/10.1045/november2015-vandesompel

[Van de Sompel 2022] Herbert Van de Sompel, Martin Klein, Shawn Jones, Michael L. Nelson, Simeon Warner, Anusuriya Devaraju, Robert Huber, Wilko Steinhoff, Vyacheslav Tykhonov, Luc Boruta, Enno Meijers, Stian Soiland-Reyes, Mark Wilkinson (2022):
FAIR Signposting Profile. (version 20220727)
https://signposting.org/FAIR/

[Van de Sompel 2023] Herbert van de Sompel (2023):
FAIR Digital Objects and FAIR Signposting.
FAIR Digital Object forum webinar.
https://doi.org/10.5281/zenodo.7977333

[Verborgh 2018] Ruben Verborgh (2018):
Designing a Linked Data developer experience.
https://ruben.verborgh.org/blog/2018/12/28/designing-a-linked-data-developer-experience/ (accessed 26 May 2022)

[Verborgh 2020] Ruben Verborgh, Miel Vander Sande (2020):
The semantic web identity crisis: In search of the trivialities that never were.
Semantic Web 11(1)
https://doi.org/10.3233/SW-190372

[Verburg 2023] Maaike Verburg, Robert Huber, Clement Jonquet, Daniel Garijo (2023): FAIR-IMPACT project response to "FAIR Assessment Tools: Towards an "Apples to Apples" Comparisons".
Zenodo
https://doi.org/10.5281/zenodo.7848102

[Vergoulis 2021] Thanasis Vergoulis (2021): Use of RO-Crates in SCHeMa.
RO-Crate community call, 2021-04-08
https://doi.org/10.5281/zenodo.4671709

[Vergoulis 2022] Thanasis Vergoulis, Konstantinos Zagganas, Loukas Kavouras, Martin Reczko, Stelios Sartzetakis, Theodore Dalamagas (2022):
SCHeMa: Scheduling Scientific Containers on a Cluster of Heterogeneous Machines.
SSDBM 2021: 33rd International Conference on Scientific and Statistical Database Management
arXiv:2103.13138
https://doi.org/10.1145/3468791.3468813

[de Visser 2023] Casper de Visser, Lennart F. Johansson, Purva Kulkarni, Hailiang Mei, Pieter Neerincx, K. Joeri van der Velde, Péter Horvatovich, Alain J. van Gool, Morris A. Swertz, Peter A. C. ’t Hoen, Anna Niehues (2023):
Ten quick tips for building FAIR workflows.
PLOS Computational Biology 19(9): e1011369
https://doi.org/10.1371/journal.pcbi.1011369

[Vivian 2017] John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian, Alden D Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O’Connor, Megan Hanna, Chet Birger, W James Kent, David A Patterson, Anthony D Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler & Benedict Paten (2017):
Toil enables reproducible, open source, big biomedical data analyses.
Nature Biotechnology 35(4)
https://doi.org/10.1038/nbt.3772

[Volk 2014] Carol J. Volk, Yasmin Lucero, Katie Barnas (2014):
Why is data sharing in collaborative natural resource efforts so hard and what can we do to improve it?
Environmental Management x53(5)
https://doi.org/10.1007/s00267-014-0258-2

[W3C 2007] W3C Technical Architecture Group (2007):
Dereferencing HTTP URIs.
Draft Tag Finding.
https://www.w3.org/2001/tag/doc/httpRange-14/2007-08-31/HttpRange-14.html

[W3C 2012] W3C OWL Working Group (2012):
OWL 2 Web Ontology Language Document Overview (Second Edition).
W3C Recommendation 11 December 2012
https://www.w3.org/TR/2012/REC-owl2-overview-20121211

[W3C 2013] The W3C SPARQL Working Group (2013):
SPARQL 1.1 Overview.
W3C Recommendation 21 March 2013
https://www.w3.org/TR/2013/REC-sparql11-overview-20130321/ (accessed 26 May 2022)

[W3C 2015] W3C (2015):
Linked Data.
https://www.w3.org/standards/semanticweb/data (accessed 26 May 2022)

[W3Techs 2023] W3Techs 2023:
Usage Statistics of JSON-LD for Websites. 2023-05.
W3Techs - World Wide Web Technology Surveys, Q-Success.
https://w3techs.com/technologies/details/da-jsonld (accessed 18 May 2023)

[Walton 2020a] Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia Santos, Ben Scott, Alan 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

[Walton 2020b] Stephanie Walton, Laurence Livermore, Mathias Dillen, Sofie De Smedt, Quentin Groom, Anne Koivunen, Sarah Phillips (2020):
A cost analysis of transcription systems.
Research Ideas and Outcomes 6:e56211.
https://doi.org/10.3897/rio.6.e56211

[Watanabe 2019] Myrna E Watanabe (2019):
The Evolution of Natural History Collections: New research tools move specimens, data to center stage.
BioScience 69(3)
https://doi.org/10.1093/biosci/biy163

[WHATWG 2023] WHATWG (2023):
Microdata.
HTML Living Standard
https://html.spec.whatwg.org/multipage/microdata.html (accessed 13 June 2023)

[Weigel 2018] Tobias Weigel, Beth Plale, Mark Parsons, Gabriel Zhou, Yu Luo, Ulrich Schwardmann, Robert Quick, Margareta Hellström, Kei Kurakawa (2018):
RDA Recommendation on PID Kernel Information
Research Data Alliance
https://doi.org/10.15497/rda00031

[Weigel 2022] Daan Broeder, Peter Wittenburg, Ivonne Anders, Karsten Peters-von Gehlen (2022):
FDO – kernel attributes & metadata.
FDO Specification Documents PR-FDO-KernelAttributesAndMetadata-2.0-20221017
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7825693

[Weiland 2022a] C. Weiland, U. Schwardmann, P. Wittenburg, C. Kirkpatrick, R. Hanisch, Z. Trautt, C. Weiland, U. Schwardmann, P. Wittenburg (2022):
FAIR Digital Objects Forum Document Standards WD-DocProcessStd-1.1-20220129
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.10943371

[Weiland 2022b] Claus Weiland, Sharif Islam, Daan Broder, Ivonne Anders, Peter Wittenburg (2022):
FDO machine actionability. Version 2.2
FAIR Digital Objects Forum Document Standards PR-MachineActionDef-2.2-20221119
FAIR Digital Objects Forum
https://doi.org/10.5281/zenodo.7825650

[Whetzel 2011] Patricia L Whetzel, Natalya F Noy, Nigam H Shah, Paul R Alexander, Csongor Nyulas, Tania Tudorache, Mark A Musen (2011):
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.
Nucleic Acids Research 39(Web Server issue):W541-5
https://doi.org/10.1093/nar/gkr469

[de Wit 2022] Renske de Wit (2022):
A Non-Intimidating Approach to Workflow Reproducibility in Bioinformatics: Adding Metadata to Research Objects through the Design and Evaluation of Use-Focused Extensions to CWLProv.
Zenodo
https://doi.org/10.5281/zenodo.7113250

[de Wit 2023] Renske de Wit, Michael R Crusoe (2023):
Analysis of runcrate.
Zenodo
https://doi.org/10.5281/zenodo.10251812

[Wieczorek 2012] John Wieczorek, David Bloom, Robert Guralnick, Stan Blum, Markus Döring, Renato Giovanni, Tim Robertson, David Vieglais (2012):
Darwin Core: An Evolving Community-Developed Biodiversity Data Standard.
PLOS ONE 7(1):e29715
https://doi.org/10.1371/journal.pone.0029715

[Wilde 2013] Erik Wilde (2013):
The ‘profile’ Link Relation Type.
RFC Editor, RFC 6906
https://doi.org/10.17487/rfc6906

[Wilde 2020] Erik Wilde, Herbert Van de Sompel (2022):
Linkset: Media Types and a Link Relation Type for Link Sets.
RFC Editor, RFC 9264
https://doi.org/10.17487/rfc9264

[Wilkinson 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(1):160018
https://doi.org/10.1038/sdata.2016.18

[Wilkinson 2018] Mark D. Wilkinson, Susanna-Assunta Sansone, Erik Schultes, Peter Doorn, Luiz Olavo Bonino da Silva Santos, Michel Dumontier (2018):
A design framework and exemplar metrics for FAIRness.
Scientific Data 5:180118
https://doi.org/10.1038/sdata.2018.118

[Wilkinson 2022a] Mark D. Wilkinson, Susanna-Assunta Sansone, Grootveld Marjan, Josefine Nordling, Richard Dennis, David Hecker (2022):
FAIR Assessment Tools: Towards an “Apples to Apples” Comparisons.
EOSC FAIR Metrics and Data Quality Task Force
EOSC Association / Zenodo
https://doi.org/10.5281/zenodo.7463421

[Wilkinson 2022b] Sean R. Wilkinson, Greg Eisenhauer, Anuj J. Kapadia, Kathryn Knight, Jeremy Logan, Patrick Widener, Matthew Wolf (2022):
F*** workflows: When parts of FAIR are missing.
arXiv 2209.09022 [cs.DL]
https://doi.org/10.48550/arxiv.2209.09022 IEEE 18th International Conference on e-Science (e-Science 2022)
\href{https://doi.org/10.48550/arXiv.2209.09022}{arXiv:2209.09022}
https://doi.org/10.1109/eScience55777.2022.00090

[Wilkinson 2023a] Mark D. Wilkinson, Susanna-Assunta Sansone, Eva Méndez, Romain David, Richard Dennis, David Hecker, Mari Kleemola, Carlo Lacagnina, Anastasija Nikiforova, Leyla Jael Castro (2023):
Community-driven governance of FAIRness assessment: an open issue, an open discussion.
Open Research Europe 2
https://doi.org/10.12688/openreseurope.15364.2

[Wilkinson 2024] 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 (Supplement 21)

[Williams 2012] 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)
https://doi.org/10.1016/j.drudis.2012.05.016

[Wittenburg 2019] Peter Wittenburg, George Strawn, Barend Mons, Luiz Bonino, Erik Schultes (2019):
Digital objects as drivers towards convergence in data infrastructures.
B2Share
https://doi.org/10.23728/b2share.b605d85809ca45679b110719b6c6cb11

[Wittenburg 2022a] 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 Sanden, Ulrich Schwardmann, Stian Soiland-Reyes, Rainer Stotzka, Zachary Trautt, Dieter Van Uytvanck, Claus Weiland, Philipp Wieder (2022):
FAIR digital object demonstrators 2021.
Zenodo
https://doi.org/10.5281/zenodo.5872645

[Wittenburg 2022b] Peter Wittenburg, Alex Hardisty, Yann Le Franc, Amirpasha Mozaffari, Limor Peer, Nikolay A. Skvortsov, Zhiming Zhao, Alessandro Spinuso (2022):
Canonical Workflows to Make Data FAIR.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00132

[Wittenburg 2023a] Peter Wittenburg, Ulrich Schwardmann, Christophe Blanchi, Claus Weiland (2023):
FDOs to Enable Cross-Silo Work.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.263

[Wittenburg 2023b] Peter Wittenburg, Dimitris Koureas (2023):
FDO to Structure the Domain of Knowledge.
Proceedings of the Conference on Research Data Infrastructure 1
https://doi.org/10.52825/cordi.v1i.374

[Wittner 2020] Rudolf Wittner, Petr Holub, Heimo Müller, Joerg Geiger, Carole Goble, Stian Soiland-Reyes, Luca Pireddu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio, David Grunwald, Hiroki Nakae (2020):
ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data. In: Glavic B., Braganholo V., Koop D. (eds) Provenance and Annotation of Data and Processes (IPAW 2020/2021).
Lecture Notes in Computer Science 12839
https://doi.org/10.1007/978-3-030-80960-7_16
https://s11.no/2021/phd/iso-23494-provenance/ (Supplement 7)

[Wittner 2022] Rudolf Wittner, Cecilia Mascia, Matej Gallo, Francesca Frexia, Heimo Müller, Markus Plass, Jörg Geiger, Petr Holub (2022):
Lightweight Distributed Provenance Model for Complex Real–world Environments.
Scientific Data 9:503
https://doi.org/10.1038/s41597-022-01537-6

[Wittner 2023a] 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):
Toward a common standard for data and specimen provenance in life sciences.
Learning Health Systems :e10365
https://doi.org/10.1002/lrh2.10365

[Wittner 2023b] 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 (PeerJ Computer Science)
https://s11.no/2023/phd/linking-provenance/ (Supplement 17)

[Wittner 2023c] Rudolf Wittner, Matej Rudolf, Simone Leo, Stian Soiland-Reyes (2023):
Packing provenance using CPM RO-Crate profile (Version 1.1)
Data set.
Zenodo
https://doi.org/10.5281/zenodo.8095888

[Wolstencroft 2011] Katy Wolstencroft, Stuart Owen, Matthew Horridge, Olga Krebs, Wolfgang Mueller, Jacky L. Snoep, Franco du Preez, Carole Goble (2011):
RightField: Embedding ontology annotation in spreadsheets.
Bioinformatics 27(14)
https://doi.org/10.1093/bioinformatics/btr312

[Wolstencroft 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)
https://doi.org/10.1093/nar/gkt328

[Wood 2014] David Wood, Richard Cyganiak, Markus Lanthaler (2014):
RDF 1.1 Concepts and Abstract Syntax.
W3C Recommendation 25 February 2014
https://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/

[Woolland 2022] 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
https://s11.no/2022/phd/incrementally-building-fdos/
(see section [ch7:incrementally-building-fair-digital-objects-with-specimen-data-refinery-workflows]{reference-type=“ref+page” reference=“ch7:incrementally-building-fair-digital-objects-with-specimen-data-refinery-workflows”})

[WorkflowHub 2023] WorkflowHub (2023):
 WorkflowHub project: Project pages for developing and running the WorkflowHub, a registry of scientific workflows.
https://w3id.org/workflowhub/

[Wright 2022] Austin Wright, Henry Andrews, Ben Hutton, Greg Dennis (2022):
JSON schema: A media type for describing JSON documents.
Internet Engineering Task Force
https://datatracker.ietf.org/doc/draft-bhutton-json-schema/01/

[WRROC 2023a] Workflow Run RO-Crate working group (2023):
Process Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/process/0.4
https://doi.org/10.5281/zenodo.10203944

[WRROC 2023b] Workflow Run RO-Crate working group (2023):
Workflow Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/workflow/0.4
https://doi.org/10.5281/zenodo.10203971

[WRROC 2023c] Workflow Run RO-Crate working group (2023):
Provenance Run Crate specification. Version 0.4
Zenodo
https://w3id.org/ro/wfrun/provenance/0.4
https://doi.org/10.5281/zenodo.10203978

[Yoo 2003] Andy B. Yoo, Morris A. Jette, Mark Grondona (2003):
SLURM: Simple Linux Utility for Resource Management.
Job Scheduling Strategies for Parallel Processing (JSSPP 2003)
Lecture Notes in Computer Science 2862
https://doi.org/10.1007/10968987_3

[Yuen 2021] Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen, Elizabeth Sheets, Ash O’Farrell, Kim Cullion, Brian D O’Connor, Benedict Paten, Lincoln Stein (2021):
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
Nucleic Acids Research 49(W1)
https://doi.org/10.1093/nar/gkab346

[Zarras 2004] Apostolos Zarras (2004):
A Comparison Framework for Middleware Infrastructures.
The Journal of Object Technology 3(5)
https://doi.org/10.5381/jot.2004.3.5.a2

[Zerouali 2023] Ahmed Zerouali, Ruben Opdebeeck, Coen De Roover (2023):
Helm Charts for Kubernetes Applications: Evolution, Outdatedness and Security Risks.
IEEE/ACM 20th International Conference on Mining Software Repositories (MSR), Melbourne, Australia
https://doi.org/10.1109/MSR59073.2023.00078

[Zhao 2012] Jun Zhao, Jose Manuel Gomez-Perezy, Khalid Belhajjame, Graham Klyne, Esteban Garcia-Cuestay, Aleix Garridoy, Kristina Hettne, Marco Roos, David De Roure, Carole Goble (2012):
Why workflows break – understanding and combating decay in taverna workflows.
IEEE 8th International Conference on e-Science (eScience 2012)
https://research.manchester.ac.uk/en/publications/cba81ca4-e92c-408e-8442-383d1f15fcdf
https://doi.org/10.1109/eScience.2012.6404482

[Zoubek 2021] Filip Zoubek, Martin Winkler (2021):
RO Crates and Excel.
https://github.com/e11938258/RO-Crates-and-Excel
https://doi.org/10.5281/zenodo.5068950

[Žumer 2009] Maja Žumer (ed.) (2009):
National Bibliographies in the Digital Age: Guidance and New Directions.
IFLA Series on Bibliographic Control, IFLA Working Group on Guidelines for National Bibliographies
https://doi.org/10.1515/9783598441844

[Åkerström 2024] Wolmar Nyberg Åkerström, Kurt Baumann, Oscar Corcho, Romain David, Yann Le Franc, Bénédicte Madon, Barbara Magagna, András Micsik, Marco Molinaro, Milan Ojsteršek, Silvio Peroni, Andrea Scharnhorst, Lars Vogt, Heinrich Widmann (2024):
Developing and implementing the semantic interoperability recommendations of the EOSC Interoperability Framework.
Zenodo, EOSC-A Semantic Interoperability Task Force
https://doi.org/10.5281/zenodo.10843882