WP2 updates
Stimulate FAIR and reusable research
Stian Soiland-Reyes�The University of Manchester
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This work is licensed under a �Creative Commons Attribution 4.0 International License.
2023-10-06 by Stian Soiland-Reyes�European Galaxy Days 2023, Freiburg
Grant agreement 101057388
WP2 Objectives
O2.1 Bringing FAIR workflows into EOSC through the EuroScienceGateway
O2.2 Support reusable and reproducible workflows
O2.3 Establish FAIR Digital Objects as citable exchange format for workflows for all EOSC services
O2.4 Establish FAIR Workflow Digital Objects as publishable scholarly objects
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
WP2 Aims
Support FAIR practices for and by workflows.
Realize FAIR Digital Objects (FDOs) as RO-Crates
Exchanging, publishing, archiving and citing workflows and their companion data, provenance logs and associated resources
Publish FDOs in EOSC catalogues (e.g. OpenAIRE)
Mature WorkflowHub to TRL-9 status EOSC service
Promote WorkflowHub as registry of choice for all workflow system types and for all disciplines in EOSC
Reach out to computational researcher communities and publishers
Align with EOSC’s PID and metadata schema frameworks
…in collaboration with FAIR-IMPACT
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of EuroScienceGateway in EOSC
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of EuroScienceGateway in EOSC
Register in EOSC catalogues/aggregators
WorkflowHub is registered as a Data Source in EOSC Marketplace.
→ Registering Workflow RO-Crate profiles as EOSC Interoperability Guidelines
→ Investigating EOSC Marketplace APIs�for announcing workflows��Q: Some uncertainty in long term sustainability of the marketplace
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of �EuroScienceGateway in EOSC
Use WorkflowHub as workflow registry in ESG & EOSC → mature to TRL-9 EOSC service
Following Nine best practices for Research Software Registries and Repositories & EOSC portal hints
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of �EuroScienceGateway in EOSC
WorkflowHub - Ask me anything session
Training session was in June 2023�Joint across EuroScienceGateway, BioDT and Biodiversity Genomics Europe
Improved documentation on https://about.workflowhub.eu/docs/ -- �Contributions from Australian BioCommons!
Galaxy Smörgåsbord 2023 – new module on RO-Crate and WorkflowHub
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of �EuroScienceGateway in EOSC
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.1: Integration of EuroScienceGateway in EOSC
→ Integrate workflows in existing EOSC services (Findability, Accessibility)
→ Catalogue of workflows adhering to best practices (MS3, MS4)
Integration from IWC → Mass import but not grouped�← ..from use cases (WP5) and for training (WP1)�→ Milestone MS3 in 6 months
→ WorkflowHub to integrate execution through EuroScienceGateway (T3.4)
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.2: Reproducible and reusable FAIR Digital Objects
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Goal: Mature FAIR Digital Object RO-Crate approach
https://www.researchobject.org/workflow-run-crate/
https://gallantries.github.io/video-library/modules/ro-crate
Mature RO-Crate Profiles: �Workflow Crate Profile. Workflow Run Profile.
(Nextflow. Snakemake)
Electronic Lab Notebook (ELN) format
2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.2: Reproducible and reusable FAIR Digital Objects
Stian Soiland-Reyes, Carole Goble, Paul Groth (2023): Evaluating FAIR Digital Object and Linked Data as distributed object systems. arXiv 2306.07436 [cs.DC] https://s11.no/2023/phd/evaluating-fdo/
Preprint has already made large impact in FDO Forum. Two invited talks, planning two FDO workshops.
RO-Crate topic in several FDO workshops
RO-Crate community invited as partner organization for FDO 2024
FDO & RO-Crate growing in Germany:�NFDI, CORDi, Helmholtz, DIN, �Federal Ministry for Digital and Transport
FAIR-IMPACT support action on Signposting & RO-Crate: Adding support to Dataverse and other repositories
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Goal: Mature FAIR Digital Object RO-Crate approach
Formalize FAIR Digital Object profile using RO-Crate.
2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.2: Reproducible and reusable FAIR Digital Objects
Workflows as first class objects in the �EOSC Interoperability Framework
Harvest metadata from Galaxy and other WMS
ELIXIR Biohackathon 2022 & 2023
Workflow Run Crate paper → PLOS One
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ESG analytics over provenance �→ inform optimisation of meta-scheduling (WP4)
Goal: Mature FAIR Digital Object RO-Crate approach
2022-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes, Carole Goble
Task T2.3: Using and enriching workflow FDOs
Ensure deposition in long term archives (e.g. Zenodo, Software Heritage)
Use & contribute to EOSC scholarly metadata services �..and scholarly aggregation catalogues (e.g. OpenAIRE)
Include in scholarship Knowledge Graphs (KG) (e.g. OpenAIRE Research Graph, DataCite PID graph).
Make EuroScienceGateways metadata suitable for other EOSC services
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Accumulate additional workflow metadata
Explore metadata extraction from publications, use Knowledge Graph services (MS5, MS6)
Provide guidance and workflow discovery for the user communities (WP5)
Inform EuroScienceGateway infrastructure decision making (WP4)
Formally start in M15 (Nov 2023)
2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.4: FAIR workflows as scholarly objects in scientific publishing
Workflows Community Initiative: �Established FAIR Computational Workflows working group�https://workflows.community/groups/fair/ � Gathering FAIR WF guidelines� Drafting paper & book chapter �(in: Workflow Systems for Scientific Data Analysis, eds. Ulf Leser, Marcus Hilbrich, Rafael Ferreira da Silva)
Prototyped extraction of workflow links from LaTeX manuscript → Link to executable paper initiatives
Extracting provenance & RO-Crate from astronomy use case (INTEGRAL)
Developing a Recuperative RO-Crate profile – what is needed in order to later fix the workflow?
Trying LifeMonitor for workflow testing
Working with publishers:
Conversations with DataCite, GigaScience, F1000 Research and other journals – modifying policies to encourage use of WorkflowHub & RO-Crate
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Task T2.4: FAIR workflows as scholarly objects �in scientific publishing
Linking of workflows and their metadata to research publications
Supplement workflow metadata with information on publications
Extract such crosslinks from existing publications
Link publishing services used in research communities (WP5):
rapid communication services �(e.g. Astronomer’s Telegrams) 🡪 T5.2
preprint publishing services (e.g. arXiv.org)
public research output databases such as OpenAIRE
specialist journals for software publications �(e.g. Journal of Open Source Software, GigaByte)
traditional publishers and their services.
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Establish WorkflowHub as a registry authority
Encourage workflow citations (e.g. DOI to WorkflowHub, DockStore, Zenodo) in journal articles
Extend research software citation practices and initiatives (e.g. RDA FAIR4RS, Workflows Community Initiative)
Establish peer review assessment of workflows
Collaborate w/ FAIR-IMPACT (INFRA-2021-EOSC-01-05)
2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Next deliverables and milestones
D2.1 Reproducible FAIR Digital Objects for workflows�(lead: UNIMAN) M24
Report: FAIR Digital Objects (FDOs), for exchanging, publishing, archiving and citing workflows and their companion data, provenance logs and associated resources, will be realized as RO-Crates.
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MS3 Initial EuroScienceGateway workflows registered�(lead: VIB/UNIMAN) M18
Collection in WorkflowHub
MS5 Initial EuroScienceGateway knowledge graph�(lead: VIB/UNIMAN) M24
Zenodo Data Deposit
2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes
Open questions – discuss!
Who will register the EuroScienceGateway workflows in WorkflowHub?
How to engage more of ESG partners in WorkflowHub?
What do we do about EOSC?
Which EOSC services is it realistic to integrate with? AAI, compute, storage, PID
How to establish system for archiving and registering workflow run provenance
FAIR Computational Workflows – how different are they from FAIR Research Software?
Shall we host our own knowledge graph – if so where?
Further journal/publisher contacts that would be friendly to try further integration?
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2023-10-06 EuroScienceGateway WP2 | Stian Soiland-Reyes