Options
FAIR Research Objects for realizing Open Science with RELIANCE EOSC project
Author(s)
Language
English
Obiettivo Specifico
5IT. Osservazioni satellitari
Status
Published
JCR Journal
N/A or not JCR
Peer review journal
Yes
Title of the book
Issue/vol(year)
/9 (2023)
Electronic ISSN
2367-7163
Publisher
Pensoft
Pages (printed)
e108765
Issued date
June 30, 2023
Last version
https://doi.org/10.3897/arphapreprints.e108817
Subjects
Abstract
The numerous benefits of Open Science (OS) and of the four FAIR foundational principles
-Findable, Accessible, Interoperable and Reusable- are increasingly valued in academia,
although what OS and FAIR entail is still largely misunderstood. In such conditions putting
in practice OS and applying the FAIR principles is challenging and underrated. However,
realising OS is perfectly within grasp provided that an infrastructure supporting the
management of the research lifecycle is available. RoHub is precisely a Research
Object (RO) management platform implementing three complementary technologies:
Research Objects, Data Cubes and Artificial Intelligence-based Text Mining services.
RoHub enables researchers to collaboratively manage, share and preserve their research
while they are still working on it (rather than after the work is finished). In this paper, three
communities from Earth Sciences, namely Geohazards, Sea Monitoring and Climate
Change, demonstrate how RoHub helped them to understand each other and to work
openly, and more importantly how communities of practice play an important role in
facilitating reuse and interdisciplinary collaboration. These findings are illustrated with
several use cases from these various communities.
-Findable, Accessible, Interoperable and Reusable- are increasingly valued in academia,
although what OS and FAIR entail is still largely misunderstood. In such conditions putting
in practice OS and applying the FAIR principles is challenging and underrated. However,
realising OS is perfectly within grasp provided that an infrastructure supporting the
management of the research lifecycle is available. RoHub is precisely a Research
Object (RO) management platform implementing three complementary technologies:
Research Objects, Data Cubes and Artificial Intelligence-based Text Mining services.
RoHub enables researchers to collaboratively manage, share and preserve their research
while they are still working on it (rather than after the work is finished). In this paper, three
communities from Earth Sciences, namely Geohazards, Sea Monitoring and Climate
Change, demonstrate how RoHub helped them to understand each other and to work
openly, and more importantly how communities of practice play an important role in
facilitating reuse and interdisciplinary collaboration. These findings are illustrated with
several use cases from these various communities.
References
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forecasting with probabilistic deep learning. Nat Commun 12: 5124. https://doi.org/
10.1038/s41467-021-25257-4
• Bechhofer S, Buchan I, Roure DD, Missier P, Ainsworth J, Bhagat J, Couch P,
Cruickshank D, Delderfield M, Dunlop I, Gamble M, Michaelides D, Owen S, Newman
D, Sufi S, Goble C (2013) Why linked data is not enough for scientists. In this paper we
make the case for a scientific data publication model on top of linked data and introduce
the notion of Research Objects 29 https://doi.org/10.1016/j.future.2011.08.004.
• Belgacem M, Chiggiato J, Bastianini M (2021) Snapshot 2021 study case: Lockdown
impacts on the Northern Adriatic Sea at selected site: AcquaAlta Platform Water quality.
ROHub URL: https://w3id.org/ro-id/0869e396-3733-4aff-8fb2-94c8937b28aa
• Book Community EDS, Coca-Castro A, Iaquinta J, Andersson T, Barlow N, Hosking .S,
Fouilloux A (2022) AGU 2022 - Environmental Data Science Book: a community-driven
resource showcasing open-source Environmental science - archive. Simula Research
Laboratory https://doi.org/10.24424/ch0e-b129
• Carragáin EÓ, Goble C, Sefton P, Soiland-Reyes S (2019) A lightweight approach to
research object data packaging. A lightweight approach to research object data
packaging. Bioinformatics Open Source Conference (BOSC2019). . Zenodo https://
doi.org/10.5281/zenodo.3250687
• Coca-Castro A, Environmental Data Science Community (2022) Environmental Data
Science Book: A community-driven online resource to showcase and support a
collaborative, reproducible and transparent Environmental Data Science. 0.0.1. Zenodo.
Release date: 2022-1-29. URL: https://doi.org/10.5281/zenodo.5918932
• Coca-Castro A, Andersson T, Barlow N (2022a) Sea ice forecasting using IceNet
(Jupyter Notebook) published in the Environmental Data Science book. ROHub URL:
https://w3id.org/ro-id/ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef
14
Author-formatted, not peer-reviewed document posted on 30/06/2023. DOI:
https://doi.org/10.3897/arphapreprints.e108817
• Coca-Castro A, Fouilloux A, Iaquinta J (2022b) Sea ice forecasting using IceNet
(Jupyter Notebook) forked from the Environmental Data Science book. https://w3id.org/
ro-id/18269477-c1b8-4aa8-9b0e-372c7bb6b65c. Accessed on: 2023-1-17.
• Fouilloux A (2021a) Investigation of lockdown effect on air quality between January
2019 to May 2021. 1. WorkflowHub. Release date: 2021-12-20. URL: https://doi.org/
10.48546/WORKFLOWHUB.WORKFLOW.251.1
• Fouilloux A (2021b) 5 years CLM-FATES simulation for Nordic site ALP1. ROHub URL:
https://w3id.org/ro-id/4086e5b7-284e-4551-a156-e3453ddcee58
• Fouilloux A, Iaquinta J, Mantovani S (2021) Impact of the Covid-19 Lockdown on Air
quality over Europe. ROHub URL: https://w3id.org/ro-id/53aa90bf-c593-4e6d-923fd4711ac4b0e1
• Fouilloux A, Iaquinta J (2022) Galaxy CESM Tool Example. ROHub. Release date:
2022-6-12. URL: https://w3id.org/ro-id/f99a5c78-6e3d-44a6-a283-3a61e46e249b.
• Fouilloux A, Coca-Castro A, Iaquinta J, Andersson T, Barlow N, Hosking S, Book
Community, Environmental Data Science (2022) AGU 2022 - Environmental Data
Science Book: a community-driven resource showcasing open-source Environmental
science - archive. Simula Research Laboratory https://doi.org/10.24424/ch0e-b129
• Fouilloux A, Foglini F, Castellan G, Belgacem M, Iaquinta J, Mantovani S (2023)
Changes in air and water quality during the Covid-19 Lockdown in the Venice Lagoon.
1.0. ROHub. Release date: 2023-1-08. URL: https://w3id.org/ro-id/
998dccd6-7192-4d88-af39-6018c71e6bdf.
• Garcia-Silva A, Gomez-Perez JM, Palma R, Krystek M, Mantovani S, Foglini F, Grande
V, Leo FD, Salvi S, Trasatti E, Romaniello V, Albani M, Silvagni C, Leone R, Marelli F,
Albani S, Lazzarini M, Napier H, Glaves H, Aldridge T, Meertens C, Boler F, Loescher H,
Laney C, Genazzio M (2019) Enabling FAIR research in Earth Science through
research objects. Enabling FAIR research in Earth Science through research objects,
Future Generation Computer Systems 98 https://doi.org/10.1016/j.future.2019.03.046.
• Goble C, Soiland-Reyes S, Bacall F, Owen S, Williams A, Eguinoa I, Droesbeke B, Leo
S, Pireddu L, Rodríguez-Navas L, Fernández J, Capella-Gutierrez S, ndez SC,
Ménager H, Grüning B, Serrano-Solano B, Ewels P, Coppens F, et al. (2021)
Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. In: Zenodo
(Ed.) WokflowHub. Zenod https://doi.org/10.5281/zenodo.4605654
• Iaquinta J, Fouilloux A (2021) Galaxy workflow and Galaxy histories for air quality
analysis. ROHub URL: https://w3id.org/ro-id/67edd16f-c3d8-4879-a3a5-2d223e7dce6d
• Mantovani S, Natali S, Folegani M, Cavicchi M, Barboni D, Ferraresi S (2020) The
ADAM platform. EGU conferenc https://doi.org/10.5194/egusphere-egu2020-17707
• Mantovani S (2021) D4.4 FAIR Data Cubes -Release I. Zenodo https://doi.org/10.5281/
zenodo.5153210
• Marin AM, Chis A, Bogdan C, Glăvan E, et al. (2022) EU FAR - EU Funds by Area
Results. ROHub URL: https://w3id.org/ro-id/941ecf90-82ba-4c56-961b-2f727da5df78
• Norwegian Climate Centre (2022) NorESM1-M CMIP5 historical (3.2) r2 raw output.
ROHub URL: https://w3id.org/ro-id/707ef635-5f5a-448f-8ae4-1371fd367d77.
• Rapa M, Cecchi T, Poletto D, Castellan G (2022) Microplastics monitoring methodology
in seawaters. ROHub URL: https://w3id.org/ro-id/a1fe8d87-7ca4-4846-
ab84-869b9d8a2b57
• Sefton P, Ó Carragáin E, Soiland-Reyes S, Corcho O, Garijo D, Palma R, Coppens F,
Goble C, Fernández J, Chard K, Gomez-Perez JM, Crusoe M, Eguinoa I, Juty N,
15
Author-formatted, not peer-reviewed document posted on 30/06/2023. DOI:
https://doi.org/10.3897/arphapreprints.e108817
*1
*2
*3
Holmes K, Clark J, Capella-Gutierrez S, Gray AG, Owen S, Williams A, Tartari G, Bacall
F, Thelen T, Ménager H, Rodríguez-Navas L, Walk P, whitehead b, Wilkinson M, Groth
P, Bremer E, Castro LJ, Sebby K, Kanitz A, Trisovic A, Kennedy G, Graves M, Koehorst
J, Leo S, Portier M, Brack P, Ojsteršek M, Droesbeke B, Niu C, Tanabe K, Miksa T, La
Rosa M, Decruw C, Czerniak A, Jay J, Serra S, Siebes R, de Witt S, El Damaty S, Lowe
D, Li X, Gundersen S, Radifar M (2022) RO-Crate Metadata Specification 1.1.2. Zenodo
https://doi.org/10.5281/zenodo.3406497
• Serrano-Solano B, Fouilloux A, Eguinoa I, Kalaš M, Grüning B, Coppens F (2022)
Galaxy: A Decade of Realising CWFR Concepts. Data Intelligence 4 (2): 358‑371.
https://doi.org/10.1162/dint_a_00136
• The Galaxy Community, Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J,
Schatz MC, Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A,
Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B,
Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ, Bromhead CJ,
Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D, Bouvier D,
Clements D, de Lima Morais DA, Tabernero DL, Lariviere D, Nasr E, Afgan E, Zambelli
F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Corguillé GL, Von Kuster
G, Akbulut GG, Rasche H, Hotz H, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi
J, Hillman-Jackson J, Goecks J, Chilton JM, Kamali K, Suderman K, Poterlowicz K,
Yvan LB, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech
M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M,
Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA,
Moreno PA, Videm P, Melanie P, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus
R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S,
Mehta SP, Griffin TJ, Jalili V, Yves V, Wen V, Nagampalli VK, Bacon WA, de Koning W,
Maier W, Briggs PJ (2022) The Galaxy platform for accessible, reproducible and
collaborative biomedical analyses: 2022 update. Nucleic Acids Research 50 (W1).
https://doi.org/10.1093/nar/gkac247
• Trasatti E (2022) Volcanic and Seismic source Modelling (VSM). The Python toolkit for
modelling geodetic data. ROHub https://doi.org/10.24424/t83f-5t97.
• United Nations Educational, Scientific and Cultural Organization (2021) UNESCO
recommendation on open science. SC-PCB-SPP/2021/OS/UROS. URL: https://
unesdoc.unesco.org/ark:/48223/pf0000379949.locale=en
• Wilkinson M, Dumontier M, Aalbersberg I, Appleton G (2016) The FAIR Guiding
Principles for scientific data management and stewardship. Sci Data 3: 160018. https://
doi.org/10.1038/sdata.2016.18
• Wittner R, Gallo M, Leo S, Soiland-Reyes S (2023) Packing provenance using CPM
RO-Crate profile. Zenodo https://doi.org/10.5281/zenodo.7676923
forecasting with probabilistic deep learning. Nat Commun 12: 5124. https://doi.org/
10.1038/s41467-021-25257-4
• Bechhofer S, Buchan I, Roure DD, Missier P, Ainsworth J, Bhagat J, Couch P,
Cruickshank D, Delderfield M, Dunlop I, Gamble M, Michaelides D, Owen S, Newman
D, Sufi S, Goble C (2013) Why linked data is not enough for scientists. In this paper we
make the case for a scientific data publication model on top of linked data and introduce
the notion of Research Objects 29 https://doi.org/10.1016/j.future.2011.08.004.
• Belgacem M, Chiggiato J, Bastianini M (2021) Snapshot 2021 study case: Lockdown
impacts on the Northern Adriatic Sea at selected site: AcquaAlta Platform Water quality.
ROHub URL: https://w3id.org/ro-id/0869e396-3733-4aff-8fb2-94c8937b28aa
• Book Community EDS, Coca-Castro A, Iaquinta J, Andersson T, Barlow N, Hosking .S,
Fouilloux A (2022) AGU 2022 - Environmental Data Science Book: a community-driven
resource showcasing open-source Environmental science - archive. Simula Research
Laboratory https://doi.org/10.24424/ch0e-b129
• Carragáin EÓ, Goble C, Sefton P, Soiland-Reyes S (2019) A lightweight approach to
research object data packaging. A lightweight approach to research object data
packaging. Bioinformatics Open Source Conference (BOSC2019). . Zenodo https://
doi.org/10.5281/zenodo.3250687
• Coca-Castro A, Environmental Data Science Community (2022) Environmental Data
Science Book: A community-driven online resource to showcase and support a
collaborative, reproducible and transparent Environmental Data Science. 0.0.1. Zenodo.
Release date: 2022-1-29. URL: https://doi.org/10.5281/zenodo.5918932
• Coca-Castro A, Andersson T, Barlow N (2022a) Sea ice forecasting using IceNet
(Jupyter Notebook) published in the Environmental Data Science book. ROHub URL:
https://w3id.org/ro-id/ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef
14
Author-formatted, not peer-reviewed document posted on 30/06/2023. DOI:
https://doi.org/10.3897/arphapreprints.e108817
• Coca-Castro A, Fouilloux A, Iaquinta J (2022b) Sea ice forecasting using IceNet
(Jupyter Notebook) forked from the Environmental Data Science book. https://w3id.org/
ro-id/18269477-c1b8-4aa8-9b0e-372c7bb6b65c. Accessed on: 2023-1-17.
• Fouilloux A (2021a) Investigation of lockdown effect on air quality between January
2019 to May 2021. 1. WorkflowHub. Release date: 2021-12-20. URL: https://doi.org/
10.48546/WORKFLOWHUB.WORKFLOW.251.1
• Fouilloux A (2021b) 5 years CLM-FATES simulation for Nordic site ALP1. ROHub URL:
https://w3id.org/ro-id/4086e5b7-284e-4551-a156-e3453ddcee58
• Fouilloux A, Iaquinta J, Mantovani S (2021) Impact of the Covid-19 Lockdown on Air
quality over Europe. ROHub URL: https://w3id.org/ro-id/53aa90bf-c593-4e6d-923fd4711ac4b0e1
• Fouilloux A, Iaquinta J (2022) Galaxy CESM Tool Example. ROHub. Release date:
2022-6-12. URL: https://w3id.org/ro-id/f99a5c78-6e3d-44a6-a283-3a61e46e249b.
• Fouilloux A, Coca-Castro A, Iaquinta J, Andersson T, Barlow N, Hosking S, Book
Community, Environmental Data Science (2022) AGU 2022 - Environmental Data
Science Book: a community-driven resource showcasing open-source Environmental
science - archive. Simula Research Laboratory https://doi.org/10.24424/ch0e-b129
• Fouilloux A, Foglini F, Castellan G, Belgacem M, Iaquinta J, Mantovani S (2023)
Changes in air and water quality during the Covid-19 Lockdown in the Venice Lagoon.
1.0. ROHub. Release date: 2023-1-08. URL: https://w3id.org/ro-id/
998dccd6-7192-4d88-af39-6018c71e6bdf.
• Garcia-Silva A, Gomez-Perez JM, Palma R, Krystek M, Mantovani S, Foglini F, Grande
V, Leo FD, Salvi S, Trasatti E, Romaniello V, Albani M, Silvagni C, Leone R, Marelli F,
Albani S, Lazzarini M, Napier H, Glaves H, Aldridge T, Meertens C, Boler F, Loescher H,
Laney C, Genazzio M (2019) Enabling FAIR research in Earth Science through
research objects. Enabling FAIR research in Earth Science through research objects,
Future Generation Computer Systems 98 https://doi.org/10.1016/j.future.2019.03.046.
• Goble C, Soiland-Reyes S, Bacall F, Owen S, Williams A, Eguinoa I, Droesbeke B, Leo
S, Pireddu L, Rodríguez-Navas L, Fernández J, Capella-Gutierrez S, ndez SC,
Ménager H, Grüning B, Serrano-Solano B, Ewels P, Coppens F, et al. (2021)
Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. In: Zenodo
(Ed.) WokflowHub. Zenod https://doi.org/10.5281/zenodo.4605654
• Iaquinta J, Fouilloux A (2021) Galaxy workflow and Galaxy histories for air quality
analysis. ROHub URL: https://w3id.org/ro-id/67edd16f-c3d8-4879-a3a5-2d223e7dce6d
• Mantovani S, Natali S, Folegani M, Cavicchi M, Barboni D, Ferraresi S (2020) The
ADAM platform. EGU conferenc https://doi.org/10.5194/egusphere-egu2020-17707
• Mantovani S (2021) D4.4 FAIR Data Cubes -Release I. Zenodo https://doi.org/10.5281/
zenodo.5153210
• Marin AM, Chis A, Bogdan C, Glăvan E, et al. (2022) EU FAR - EU Funds by Area
Results. ROHub URL: https://w3id.org/ro-id/941ecf90-82ba-4c56-961b-2f727da5df78
• Norwegian Climate Centre (2022) NorESM1-M CMIP5 historical (3.2) r2 raw output.
ROHub URL: https://w3id.org/ro-id/707ef635-5f5a-448f-8ae4-1371fd367d77.
• Rapa M, Cecchi T, Poletto D, Castellan G (2022) Microplastics monitoring methodology
in seawaters. ROHub URL: https://w3id.org/ro-id/a1fe8d87-7ca4-4846-
ab84-869b9d8a2b57
• Sefton P, Ó Carragáin E, Soiland-Reyes S, Corcho O, Garijo D, Palma R, Coppens F,
Goble C, Fernández J, Chard K, Gomez-Perez JM, Crusoe M, Eguinoa I, Juty N,
15
Author-formatted, not peer-reviewed document posted on 30/06/2023. DOI:
https://doi.org/10.3897/arphapreprints.e108817
*1
*2
*3
Holmes K, Clark J, Capella-Gutierrez S, Gray AG, Owen S, Williams A, Tartari G, Bacall
F, Thelen T, Ménager H, Rodríguez-Navas L, Walk P, whitehead b, Wilkinson M, Groth
P, Bremer E, Castro LJ, Sebby K, Kanitz A, Trisovic A, Kennedy G, Graves M, Koehorst
J, Leo S, Portier M, Brack P, Ojsteršek M, Droesbeke B, Niu C, Tanabe K, Miksa T, La
Rosa M, Decruw C, Czerniak A, Jay J, Serra S, Siebes R, de Witt S, El Damaty S, Lowe
D, Li X, Gundersen S, Radifar M (2022) RO-Crate Metadata Specification 1.1.2. Zenodo
https://doi.org/10.5281/zenodo.3406497
• Serrano-Solano B, Fouilloux A, Eguinoa I, Kalaš M, Grüning B, Coppens F (2022)
Galaxy: A Decade of Realising CWFR Concepts. Data Intelligence 4 (2): 358‑371.
https://doi.org/10.1162/dint_a_00136
• The Galaxy Community, Afgan E, Nekrutenko A, Grüning BA, Blankenberg D, Goecks J,
Schatz MC, Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A,
Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B,
Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ, Bromhead CJ,
Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D, Bouvier D,
Clements D, de Lima Morais DA, Tabernero DL, Lariviere D, Nasr E, Afgan E, Zambelli
F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Corguillé GL, Von Kuster
G, Akbulut GG, Rasche H, Hotz H, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi
J, Hillman-Jackson J, Goecks J, Chilton JM, Kamali K, Suderman K, Poterlowicz K,
Yvan LB, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech
M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M,
Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA,
Moreno PA, Videm P, Melanie P, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus
R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S,
Mehta SP, Griffin TJ, Jalili V, Yves V, Wen V, Nagampalli VK, Bacon WA, de Koning W,
Maier W, Briggs PJ (2022) The Galaxy platform for accessible, reproducible and
collaborative biomedical analyses: 2022 update. Nucleic Acids Research 50 (W1).
https://doi.org/10.1093/nar/gkac247
• Trasatti E (2022) Volcanic and Seismic source Modelling (VSM). The Python toolkit for
modelling geodetic data. ROHub https://doi.org/10.24424/t83f-5t97.
• United Nations Educational, Scientific and Cultural Organization (2021) UNESCO
recommendation on open science. SC-PCB-SPP/2021/OS/UROS. URL: https://
unesdoc.unesco.org/ark:/48223/pf0000379949.locale=en
• Wilkinson M, Dumontier M, Aalbersberg I, Appleton G (2016) The FAIR Guiding
Principles for scientific data management and stewardship. Sci Data 3: 160018. https://
doi.org/10.1038/sdata.2016.18
• Wittner R, Gallo M, Leo S, Soiland-Reyes S (2023) Packing provenance using CPM
RO-Crate profile. Zenodo https://doi.org/10.5281/zenodo.7676923
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article
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