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Kyle Chard, Niall Gaffney, Mihael Hategan, Kacper Kowalik, Bertram Ludäscher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis (2020):
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities.
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Oscar Corcho, Fajar J. Ekaputra, Ivan Heibi, Clement Jonquet, Andras Micsik, Silvio Peroni, Emanuele Storti (2023):
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Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2022):
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DCMI Recommendation
https://www.dublincore.org/specifications/dublin-core/dcmi-terms/2020-01-20/

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

Paul De Geest, Bert Droesbeke, Ignacio Eguinoa, Alban Gaignard, Sebastiaan Huber, Bruno Kinoshita, Simone Leo, Luca Pireddu, Laura Rodríguez-Navas, Raül Sirvent, Stian Soiland-Reyes (2022):
GitHub – ResearchObject/ro-crate-py: Python library for RO-Crate, version 0.8.0.
https://github.com/researchobject/ro-crate-py
https://doi.org/10.5281/zenodo.8005944

Renato De Giovanni, Alan R. Williams, Vera Hernández Ernst, Robert Kulawik, Francisco Quevedo Fernandez, Alex R. Hardisty (2016):
ENM Components: a new set of web service‐based workflow components for ecological niche modelling.
Ecography 39(4) pp 376–383.
https://doi.org/10.1111/ecog.01552

Blanda Helena de Mello, Sandro José Rigo, Cristiano André da Costa, Rodrigo da Rosa Righi, Bruna Donida, Marta Rosecler Bez, Luana Carina Schunke (2022):
Semantic interoperability in health records standards: a systematic literature review.
Health and Technology 12
https://doi.org/10.1007/s12553-022-00639-w

David De Roure, Carole Goble (2010):
Anchors in shifting sand: the primacy of method in the web of data.
Proceedings of the WebSci10: Extending the Frontiers of Society On-Line, at Web Science Conference 2010 Raleigh, NC: US 2010-04-26/–27
https://web.archive.org/web/20140828142306/http://journal.webscience.org/325/
http://eprints.soton.ac.uk/id/eprint/270817

Koenraad De Smedt, Dimitris Koureas, Peter Wittenburg (2020):
FAIR Digital Objects for Science: From Data Pieces to Actionable Knowledge Units.
Publications 8(2):21
https://doi.org/10.3390/publications8020021

José Carlos Martins Delgado (2016):
An Interoperability Framework and Distributed Platform for Fast Data Applications.
Data Science and Big Data Computing
https://doi.org/10.1007/978-3-319-31861-5_1

Anusuriya Devaraju, Mustapha Mokrane, Linas Cepinskas, Robert Huber, Patricia Herterich, Jerry de Vries, Vesa Akerman, Hervé L’Hours, Joy Davidson, Michael Diepenbroek (2021):
From conceptualization to implementation: FAIR assessment of research data objects.
Data Science Journal 20 (2021).
https://doi.org/10.5334/dsj-2021-004

Mathias Dillen, Quentin Groom, Donat Agosti, Lars Nielsen (2019):
Zenodo, an archive and publishing repository: A tale of two herbarium specimen pilot projects.
Biodiversity Information Science and Standards 3:e37080
https://doi.org/10.3897/biss.3.37080

Mathias Dillen, Quentin Groom, Simon Chagnoux, Anton Güntsch, Alex Hardisty, Elspeth Haston, Laurence Livermore, Veljo Runnel, Leif Schulman, Luc Willemse, Zhengzhe Wu, Sarah Phillips (2019):
A benchmark dataset of herbarium specimen imagfes with label data.
Biodiversity Data Journal 7:e31817.
https://doi.org/10.3897/BDJ.7.e31817

Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, Cedric Notredame (2017):
Nextflow enables reproducible computational workflows.
Nature Biotechnology 35(4)
https://doi.org/10.1038/nbt.3820

DOI (2019):
DOI Handbook - Resolution.
DOI Handbook
DOI Foundation
https://doi.org/10.1000/182
https://www.doi.org/doi_handbook/3_Resolution.html

DONA Foundation (2018):
Digital Object Interface Protocol specification, version 2.0.
DONA Foundation
https://hdl.handle.net/0.DOIP/DOIPV2.0

DONA Foundation (2021):
Digital Object Architecture.
https://www.dona.net/node/88 (accessed 2021-08-10)

Lisa M. Dusseault (2007):
HTTP Extensions for Web Distributed Authoring and Versioning (WebDAV).
RFC Editor, RFC 4918.
https://doi.org/10.17487/rfc4918

Martin J. Dürst, Michel Suignard (2005):
Internationalized resource identifiers (IRIs).
RFC 3987, Internet Requests for Comments, RFC Editor
https://doi.org/10.17487/rfc3987

Ignacio Eguinoa, Stian Soiland-Reyes, Bert Droesbeke, Michael R. Crusoe (2020):
GitHub workflowhub-eu/galaxy2cwl: Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.
https://github.com/workflowhub-eu/galaxy2cwl

Martin Ekuan, Mick Alberts, Tim Sherer, Udi Dahan, Mike Kistler et al. (2023):
Web API design best practices.
Azure Architecture Center
https://learn.microsoft.com/en-us/azure/architecture/best-practices/api-design (accessed 24 January 2023)

EMBL-EBI Microbiome Informatics Team (2019):
FTP index of /pub/databases/metagenomics/umgs_analyses/.
http://ftp.ebi.ac.uk/pub/databases/metagenomics/umgs_analyses/

EMBL-EBI Microbiome Informatics Team (2020):
GitHub – Finn-Lab/MGS-gut: Analysing Metagenomic Species (MGS).
https://github.com/Finn-Lab/MGS-gut

European Commission, Directorate-General for Research & Innovation (2016):
Guidelines on FAIR Data Management in Horizon 2020. Version 3.0
H2020 Programme.
https://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-data-mgt_en.pdf

Philip A Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen (2020):
The nf-core framework for community-curated bioinformatics pipelines.
Nature Biotechnology 38(3), 276–278.
https://doi.org/10.1038/s41587-020-0439-x

FAIR Data Maturity Model Working Group (2020):
FAIR data maturity model: Specification and guidelines.
Research Data Alliance
https://doi.org/10.15497/rda00050

Sharon Farnel, Ali Shiri (2014):
Metadata for research data: Current practices and trends.
2014 Proceedings of the International Conference on Dublin Core and Metadata Applications
ISSN 1939-1366.
https://dcpapers.dublincore.org/pubs/article/view/3714

FAIR Digital Objects Forum
https://fairdo.org/ (accessed 26 May 2022)

FDO (2022):
FDO Specification Documents - November 2022 FAIR Digital Objects Forum https://hdl.handle.net/20.500.14132/fdo-spec-docs
https://fairdo.org/specifications/ (accessed 2 February 2023)

Martin Fenner, Amir Aryani (2019):
Introducing the PID graph.
DataCite Blog
https://doi.org/10.5438/jwvf-8a66

Dieter Fensel, Federico Michele Facca, Elena Simperl, Ioan Toma (2011):
Semantic Web Services
https://doi.org/10.1007/978-3-642-19193-0

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

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

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)

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

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

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.
https://doi.org/10.1145/3106237.3121282

Roy T. Fielding, Mark Nottingham, Julian Reschke (2022):
HTTP Semantics
RFC Editor, RFC 9110
https://doi.org/10.17487/rfc9110

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

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

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

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
https://arxiv.org/abs/1809.10617
https://doi.org/10.1016/j.future.2019.03.046

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

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

GBIF Secretariat. (2021):
GBIF Science Review 2020.
https://doi.org/10.35035/bezp-jj23

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

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

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

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

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

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

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

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

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

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

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

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) pp. 10–20.
https://doi.org/10.1109/MCSE.2016.92

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

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

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

Ramanathan Guha, Dan Brickley (2014):
RDF Schema 1.1.
W3C Recommendation
http://www.w3.org/TR/rdf-schema/

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.
https://doi.org/10.1145/2857274.2857276

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

CNRI (2022):
Handle.Net Software.
https://www.handle.net/download_hnr.html (accessed 24 January 2023)

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

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

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

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

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
(section [ch8:the-specimen-data-refinery]{reference-type=“ref+page” reference=“ch8:the-specimen-data-refinery”})

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

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

Michael Hausenblas et al. (2012):
5-star Open Data.
http://5stardata.info/ (accessed 24 January 2023)

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

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

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

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

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

Vicki Tardif Holland, Jason Johnson (2014):
Introducing ‘Role’.
schema blog
http://blog.schema.org/2014/06/introducing-role.html

Ian Horrocks, James Hendler, eds. (2002):
The Semantic Web — ISWC 2002
First International Semantic Web Conference, Sardinia, Italy, June 9-12, 2002
https://doi.org/10.1007/3-540-48005-6

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

Adam Hospital (2021):
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in KNIME.
WorkflowHub. Workflow (KNIME).
https://doi.org/10.48546/workflowhub.workflow.201.1

Adam Hospital, Pau Andrio (2021):
Protein MD Setup HPC tutorial using BioExcel Building Blocks (biobb) in PyCOMPSs.
WorkflowHub. Workflow (PyCOMPSs)
https://doi.org/10.48546/workflowhub.workflow.200.1

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
ISBN 978-3-642-21033-4

Yuk Hui (2012):
What is a Digital Object?
Metaphilosophy 43(4)
https://doi.org/10.1111/j.1467-9973.2012.01761.x

Burhan Rashid Hussein, Owais Ahmed Malik, Wee-Hong Ong, Johan Willem Frederik Slik (2021):
Application of Computer Vision and Machine Learning for Digitized Herbarium Specimens: A Systematic Literature Review.
arXiv 2104.08732v1
https://doi.org/10.48550/arXiv.2104.08732

Raja Mazumder, Vahan Simonyan (eds.) (2020):
IEEE Standard for Bioinformatics Analyses Generated by High-Throughput Sequencing (HTS) to Facilitate Communication (2020).
IEEE Std 2791-2020.
ISBN 978-1-5044-6466-6.
https://research.manchester.ac.uk/en/publications/936de52b-ac53-4f0e-9927-77fd7073e88d
https://doi.org/10.1109/ieeestd.2020.9094416

Sharif Islam, Alex Hardisty, Wouter Addink, Claus Weiland, Falko Glöckler (2020):
Incorporating RDA Outputs in the Design of a European Research Infrastructure for natural history Collections.
Data Science Journal 19:50
https://doi.org/10.5334/dsj-2020-050

Antoine Isaac, Ed Summers (2009):
SKOS Simple Knowledge Organization System Primer.
W3C Note
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/

Sharif Islam (2023):
FAIR digital objects, persistent identifiers and machine actionability.
FAIR Connect 1(1)
https://doi.org/10.3233/FC-230001

ISO (2019):
ISO 16684-1:2019 — graphic technology — extensible metadata platform (XMP) — part 1: Data model, serialization and core properties.
ISO standard
https://www.iso.org/standard/75163.html

ISO/IEC (2022):
ISO/IEC 23009-1:2022 — information technology — dynamic adaptive streaming over HTTP (DASH) — part 1: Media presentation description and segment formats.
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Stian Soiland-Reyes, Peter Sefton, Leyla Jael Castro, Frederik Coppens, Daniel Garijo, Simone Leo, Marc Portier, Paul Groth (2022):
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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
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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
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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

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
https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/

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

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.
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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

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    Lecture Notes in Computer Science 8398
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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
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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

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) pp. 307–329.
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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

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

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.
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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/

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

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

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/

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

Ruben Verborgh (2018):
Designing a Linked Data developer experience.
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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

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

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

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
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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) pp. 883–893.
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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
https://doi.org/10.1038/nbt.3772

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

W3C (2015):
Linked Data
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W3C OWL Working Group (2012):
OWL 2 Web Ontology Language Document Overview (Second Edition).
W3C Recommendation
https://www.w3.org/TR/2012/REC-owl2-overview-20121211

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

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)

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

Myrna E Watanabe (2019):
The Evolution of Natural History Collections: New research tools move specimens, data to center stage.
BioScience 69(3)
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WHATWG (2023):
Microdata.
HTML Living Standard
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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

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

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
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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

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

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

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

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

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

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
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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

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

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

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

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

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 Preprint: https://doi.org/10.5281/zenodo.3901011

Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, Mélanie Courtot, Vasa Curcin, Johann Eder, Mark Elliot, Katrina Exter, Carole Goble, Martin Golebiewski, Bron Kisler, Andreas Kremer, Simone Leo, Sheng Lin-Gibson, Anna Marsano, Marco Mattavelli, Josh Moore, Hiroki Nakae, Isabelle Perseil, Ayat Salman, James Sluka, Stian Soiland-Reyes, Caterina Strambio-De-Castillia, Michael Sussman, Jason R. Swedlow, Kurt Zatloukal, Jörg Geiger (2023):
Towards a common standard for data and specimen provenance in life sciences.
Learning Health Systems :e10365
https://doi.org/10.1002/lrh2.10365

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

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

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

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

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/

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

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

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

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