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ELIXIR Software Management Plan for Life Sciences.
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[Anders 2022] Ivonne Anders, Maggie Hellström, Sharif Islam, Thomas Jejkal, Larry Lannom, Ulrich Schwardmann, Peter Wittenburg (2022):
FDO PID profiles & attributes
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FAIR Digital Objects Forum
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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.
George Strawn, Peter Wittenburg (eds.)
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FAIR Digital Objects Forum
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[Andrio 2019] 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
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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.
Zenodo
https://github.com/GhaithArf/ro-crate-rda-madmp-mapper
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[Arkisto 2022] Arkisto (2022):
 Tools: Data Portal & Discovery.
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.
https://esciencelab.org.uk/projects/ro-composer/
https://github.com/ResearchObject/research-object-composer

[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 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
https://doi.org/10.1038/s41597-022-01707-6

[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).
https://doi.org/10.48546/workflowhub.workflow.29.3

[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.
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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

[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.
W3C Recommendation 2 May 2017
https://www.w3.org/TR/2017/REC-ldn-20170502/

[Cardoso 2020a] João Cardoso, Diogo Proença, José Borbinha (2020):
Machine-actionable data management plans: A knowledge retrieval approach to automate the assessment of funders’ requirements.
ECIR 2020: Advances in Information Retrieval
ISBN 978-3-030-45442-5.
https://doi.org/10.1007/978-3-030-45442-5_15

[Cardoso 2020b] João Cardoso, Leyla Jael Garcia Castro, Fajar Ekaputra, Marie-Christine Jacquemot-Perbal, Tomasz Miksa, José Borbinha (2020):
Towards Semantic Representation of Machine-Actionable Data Management Plans.
PUBLISSO
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Hypertext Transfer Protocol (HTTP/1.1): Message Syntax and Routing
RFC Editor, RFC 7230
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[Fielding 2014b] Roy T. Fielding, Julian Reschke (2014):
Hypertext Transfer Protocol (HTTP/1.1): Semantics and Content
RFC Editor, RFC 7231
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FAIR Research Objects for realizing Open Science with RELIANCE EOSC project.
Research Ideas and Outcomes 9:e108765
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.
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Wings: Intelligent Workflow-Based Design of Computational Experiments.
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TRE-FX: Delivering a federated network of trusted research environments to enable safe data analytics.
Zenodo / DARE UK
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State of the nation in data integration for bioinformatics.
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[Goble 2022] Carole Goble, Stian Soiland-Reyes, Nick Juty (2022):
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The Specimen Data Refinery: A canonical workflow framework and FAIR Digital Object approach to speeding up digital mobilisation of natural history collections.
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FDO – granularity, versioning, mutability.
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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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[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):
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[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):
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[ro-crate-html-js] npm:
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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
https://doi.org/10.1038/s41597-020-0524-5

[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)
Data analytics and management in data intensive domains: 20th international conference, DAMDID/RCDL 2018, Moscow, Russia, 2018-10-09/–12.
https://doi.org/10.1007/978-3-030-23584-0_1 Preprint: https://doi.org/10.23728/B2SHARE.166A074BFF614A31B05E9DF5BFD9809D

[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.
Lecture notes in Computer Science 12584
https://doi.org/10.1007/978-3-030-65847-2_13

[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.
FDO Specification Documents PED-DOIPEndorsement-1.1-20221017
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
https://doi.org/10.3897/rio.8.e96014

[Scrocca 2021] Mario Scrocca, Damiano Scandolari, Gloria Re Calegari, Ilaria Baroni, Irene Celino (2021):
The Survey Ontology: Packaging Survey Research as Research Objects.
2nd Workshop on Data and Research Objects Management for Linked Open Science
https://doi.org/10.4126/frl01-006429412

[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.
ptsefton.com. http://ptsefton.com/2021/04/07/rdmpic/

[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.
https://www.wdc-climate.de/ui/entry?acronym=C6CMAWAWMhi
https://hdl.handle.net/21.14100/2fcf49d3-0608-3373-a47f-0e721b7eaa87

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Introducing the knowledge graph: Things, not strings.
https://blog.google/products/search/introducing-knowledge-graph-things-not/ (accessed 18 May 2023)

[Sirvent 2022] Raul Sirvent, Javier Conejero, Francesc Lordan, Jorge Ejarque, Laura Rodriguez-Navas, Jose M. Fernandez, Salvador Capella-Gutierrez, Rosa M. Badia (2022):
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

[Smith 2007] Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel, Suzanna Lewis (2007):
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration.
Nature Biotechnology 25(11)
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Software citation principles.
PeerJ Computer Science 2:e86
https://doi.org/10.7717/peerj-cs.86

[Smith 2022] River Tae Smith, Louisa Willoughby, Trevor Johnston (2022):
Integrating Auslan Resources into the Language Data Commons of Australia.
Proceedings of the LREC2022 10th Workshop on the Representation and Processing of Sign Languages: Multilingual Sign Language Resources.
https://aclanthology.org/2022.signlang-1.28

[Snowley 2023] Kay Snowley, Lara Edwards, Ben Crosby, Helen Tatlow (2023):
Integrating Our Community. Year 1
Health Data Research UK (report)
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[Soiland-Reyes 2014] Stian Soiland-Reyes, Matthew Gamble, Robert Haines (2014):
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
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[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 10(8)
https://doi.org/10.3897/rio.8.e93937
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[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 10(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
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[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
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[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 2023c] Stian Soiland-Reyes, Carole Goble, Paul Groth (2023):
Evaluating FAIR Digital Object and Linked Data as distributed object systems.
PeerJ Computer Science (accepted) arXiv 2306.07436 [cs.DC] https://doi.org/10.48550/arXiv.2306.07436
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[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.
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JSON-LD 1.1: A JSON-based Serialization for Linked Data.
W3C Recommendation 16 July 2020
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[Sporny 2023] Manu Sporny, Amy Guy (2023):
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[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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[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):
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Objects Detection from Digitized Herbarium Specimen based on Improved YOLO V3.
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Semantic Web 11(1)
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Linked data, JSON-LD and the semantics of cultural and scientific heritage.
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[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):
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FAIR Digital Objects and FAIR Signposting.
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The semantic web identity crisis: In search of the trivialities that never were.
Semantic Web 11(1)
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[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
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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 (internal draft)
FAIR Digital Objects Forum
https://drive.google.com/file/d/1lPNBBROjEoZ6fTfrtdqcMa3Q2G27PoC_ (accessed 30 November 2022)

[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

[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

[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

[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) (2012)
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.
2012 IEEE 8th International Conference on e-Science
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