Research Data Management

Agenda

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Date: Wednesday - 8th of June 2022

Time: 9.00-10.30 CEST

Introduction

Ulrike Wittig (DE)

ELIXIR-DE and ELIXIR Data Platform ExCo

Heidelberg Institute for Theoretical Studies, Heidelberg, Germany

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Time: 9.00-9.05

Research Data Management

#ELIXIR22

Data Management Systems as ELIXIR Services

Support researchers

to manage their data and make them FAIR

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#ELIXIR22

Supporting FAIR Data in ELIXIR

FAIR Resources & Tools

Registries

Standards, Ontologies & Identifiers

Data Management Platforms

DMP & Stewardship Tools

FAIR Metadata Markup

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Trusted Repositories

Core Data Resources

Deposition Databases & Portals

Scalable Curation

Sustainability

#ELIXIR22

Supporting FAIR Data in ELIXIR

Communities & Focus Groups

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FAIR Expertise & Training

Capability & Skills

Training Events & Material

Data Management Expert Network

RDM Guidelines

FAIR recipes

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#ELIXIR22

Workshop

“ELIXIR FAIR & Research Data Management know-how ecosystem”

Thursday 11:00-12:30

#ELIXIR22

Contributing to EOSC Research Graphs: the role of FAIRsharing and Bioschemas

Susanna-Assunta Sansone (UK)

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ELIXIR-UK and ELIXIR Interoperability Platform ExCo;

Professor of Data Readiness, University of Oxford, UK.

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In collaboration with:

Allyson Lister, FAIRsharing

Alasdair Gray, Bioschemas

Time: 9.05-9.20

#WeAreEOSC - let’s make sure our data resources are visible!

• Ensuring that ELIXIR resources and services, and in particular databases, knowledge bases and repositories are more discoverable in EOSC
• Via the EOSC Research Graph by OpenAIRE

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#ELIXIR22

A 10,000 foot view of the EOSC Research Graph by OpenAIRE

“Open, participatory research graph where products of the research life-cycle (e.g. scientific literature, research data, project, software) are semantically linked to each other and carry information about their access rights (i.e. if they are Open Access, Restricted, Embargoed, or Closed) and the sources from which they have been collected and where they are hosted”

URL: graph.openaire.eu

#ELIXIR22

ELIXIR’s end goals: feed proper info in the graph, and easily

#ELIXIR22

FAIRsharing and Bioschemas as information providers

• Provides rich descriptions of the databases, incl. content types, access conditions, mantainers (ORCiD), organizations (ROR) etc., also interlinked with standards
• And we already have descriptions of many/most ELIXIR and EOSC-Life databases and standards!

• Provides key metadata for discoverability of dataset content
• Many ELIXIR databases’ pages are already marked up

#ELIXIR22

Prototyping the process, unfunded - your role and our work

Mapping

and

harvesting

We are mapping Bioschemas to the Datacite schema (Enrico Ottonello, Andreas Czerniak, Nick Juty, Alasdair J. G. Gray)

We are mapping FAIRsharing model and databases IDs to the openAIRE model (Ramon Granell, Alessia Bardi, Delphine Dauga, Allyson Lister)

*note: this is an unfunded pilot!

#ELIXIR22

Bioschemas - database records: consolidation of concepts

sameAs

#ELIXIR22

FAIRsharing - database as a whole: full curated descriptions

DOI: 10.25504/FAIRsharing.jwra3e

DOI: 10.25504/FAIRsharing.dt9z89

FAIRsharing - database as a whole

DOI: 10.25504/FAIRsharing.dt9z89

License

Maintainer(s)

Standard(s)

Database(s)

API

Life cycle status

Overview information and status

FAIRsharing - database as a whole

DOI: 10.25504/FAIRsharing.dt9z89

Subject classification

Classification is powered by our

Subject Ontology of 436 terms

URL: fairsharing.org/browse/subject

URL: github.com/FAIRsharing/subject-ontology

FAIRsharing - database as a whole

DOI: 10.25504/FAIRsharing.dt9z89

Organizations and publications

FAIRsharing - database as a whole

DOI: 10.25504/FAIRsharing.dt9z89

Standards implemented and related databases

FAIRsharing - database as a whole

DOI: 10.25504/FAIRsharing.dt9z89

Access points and conditions

FAIRsharing - building the EOSC-Life map of resources

These are profiles of the organizations and their RIs, with their data resources and standards

URL: fairsharing.org/graph/3513

FAIRsharing - signposting, surfacing resources to EOSC

Organization pages in

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give an overview of their data resources and standards

A curated EOSC-Life Collection in

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of data resources and their standards

OUTPUT

TASK & OWNER

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RI and organization pages are automatically created

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resource managers

Add or claim, and describe data resources and standards they have developed, and associate them to their organisation(s) and their RI(s)

Descriptions of data resources in

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are accessible in the

EOSC ecosystem

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Create and maintain mappings of the description of data resources

FAIRsharing - working with international communities to create subject-specific collection of resources, e.g.:

FAIRsharing - launching the Community Curation Programme!

https://eoscfuture-grants.eu/node/262

https://fairsharing.org/community_curation

She is the first ELIXIR awardee of the

Domain Ambassador Programme!

Play your part and help us surfacing proper info to EOSC!

Mapping

and

harvesting

Markup your database’s pages

Register or claim your database

Thank you to the Bioschema, FAIRsharing

and OpenAIRE teams!

We do* the rest of the work for you!

*note: this is an unfunded pilot!

#ELIXIR22

RO-Crate for Research Reproducibility & Data Management - Carole Goble

Carole Goble (UK) with Stian Soiland-Reyes (UK)

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Time: 9.20-9.35

Slides: linked here

Highlights of RDM within the ELIXIR Communities:

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1. Rare Disease Community and RDM

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• Plants: Extending Bioschemas to plant biology, experience with real data

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• Community DBs, Aggregator DB for Niche communities

Time: 9.35-10.05

Rare Disease Community and Research Data Management

Nirupama Benis (NL)

Time: 9.35-9.45

Rare disease community and research data management

Nirupama Benis and Marco Roos

EJP RD

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• Create a comprehensive, sustainable ecosystem to circle between research, care and medical innovation​
• Scattered data​
• Benefits from going FAIR

#ELIXIR22

#ELIXIR22

European Reference Networks (ERNs)​

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• 24 ERNs​

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• Set up patient registries​

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• Share patient data responsibly​

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• Perform research to impact patient lives ​

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#ELIXIR22

#ELIXIR22

Research data management​

#ELIXIR22

Rare disease registries

#ELIXIR22

Collect data​

• Common data elements (CDEs)​

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• Proposed by the JRC​

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• For RD registries​

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• Promotes interoperability​

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• Covers key data points​

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• Not perfect but a great start​

#ELIXIR22

Analyse data​

• EJP RD Virtual Platform allows federated queries over several RD resources​

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• Link registry data to information from other resources​

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• New features for data analyses ​

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• Workshop tomorrow​ (11.00 - 12.30 CEST)

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https://vp.ejprarediseases.org/​

#ELIXIR22

Share data​

• Interoperable data​
• CDE semantic model (CDE-in-a-box)​
• Can be connected to the EJP RD VP​
• Share data with other ERNs or interested parties
• Collect information on data sharing from registries​​
• Mappings to widely used data models​
• OMOP​
• CDISC​
• FHIR​

#ELIXIR22

Reuse data​

• Sensitive data​

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• Data use conditions​

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• Informed consent form​

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• Semantic model describing consent​

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• Existing technology​

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#ELIXIR22

#ELIXIR22

Outlook R&D practical FAIRification support​

• Maturation of FAIRification support infrastructure​
• FAIRification tools for stewards (FAIRopoly, RDMkit, DSW, cookbook)​
• FAIR-generating registry software (e.g. CastorEDC, LOVD, MOLGENIS, etc.)​
• ‘FAIR-in-a-box’ to ‘ontologise’ data and metadata at source​
• SaaS FAIR Data Point & model-to-API conversion services​
• Automatically ‘find and use’ FAIR artefacts in FAIR registries (EOSC-Life)​
• Tooling ontology-based data modelling still R&D​
• Models for human sustainable FAIRification services emerging ​
• Analytics examples on (federated) FAIR data AHM workshop!​

#ELIXIR22

Questions or Comments

#ELIXIR22

Plants: Extending Bioschemas to plant biology, experience with real data

Sebastian Beier (DE)

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Time: 9.45-9.55

Bioschemas in a nutshell

• Provides vocabulary of terms → Improve data discoverability and interoperability in the Life Sciences
• Basic idea to annotate webpages with lightweight markup (in Plants: Genes, Phenotypes, Species, Genus, Accession, etc)

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Connect with Plant standards

#ELIXIR22

MIAPPE for Bioschemas

• : Minimal Information about a Plant Phenotyping Experiment
• Set of 94 variables (+48 variables for environment)
• Mapping to Bioschemas (start BioHackathon 2021)→ Meaningful subset

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Papoutsoglou et al. 2020

#ELIXIR22

Use Case #1

#ELIXIR22

Use Case #1

• AgriSchemas: Modelling Agronomy with Bioschemas
• Idea: Use lightweight models for building dataset - not only for web page annotations

#ELIXIR22

Use Case #1

#ELIXIR22

Use Case #2

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• Schema.org and Dublin Core
• Bioschemas ‘Dataset’ and ‘Taxon’ Profiles → Find specific dataset or look for species
• Automatic addition to context pages

• Accepted by Nature Publishing Group & Oxford GigaScience
• Registered in re3data.org, OpenAIRE, FAIRsharing.org and DataCite

#ELIXIR22

Next steps

• BioHackathon 2022 project link and finalise MIAPPE-Bioschemas mapping
• Real data to be converted and integrated in KnetMiner/AgriSchemas endpoint
• Merge with similar projects (e.g. PIPPA)

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#ELIXIR22

Acknowledgements

Marco Brandizi

Daniel Arend

Erik Ralfs

Keywan Hassani-Pak

Cyril Pommier

Alasdair Gray

Appendix: e!DAL PGP Movie

https://edal-pgp.ipk-gatersleben.de/movie/SimpleShow.mp4

#ELIXIR22

Community DBs, Aggregator DB for Niche communities

Damiano Piovesan (IT)

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Time: 9.55-10.05

IDRs – Ubiquitous and functionally important

• 1/3 of the human proteome
• ~100,000 transient, conditional, regulatory interaction modules
• 70% of experimentally validated PTMs

#ELIXIR22

IDP research – experimental

• IDP research spans several experimental fields studying protein structure and function
• Most of the methods used are distinct to the field of IDPs

#ELIXIR22

IDP community goals

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Necci et al. (2018) Database

Monzon et al. (2020) International Journal of Molecular Sciences

https://idpcentral.org/

1. Simplify IDP data access and dissemination
2. Drive the curation of IDP literature
3. Develop a centralised knowledgebase for IDP data
4. Integrate IDP data into ELIXIR Core Data Resources
5. Improve tools for IDP analysis

Former co-leads

Silvio

Tosatto

Norman

Davey

Wim

Vranken

Zsuzsanna

Dosztanyi

Damiano

Piovesan

Current co-leads

IDPcentral Vs IMEX

Mimic the IMEx consortium ???

• Shared curation effort
• Shared export format
• Single dataset
• Single detailed curation model

#ELIXIR22

IDPcentral and Bioschemas

FAIR community registry of Bioschemas metadata

Concept merging

https://idpcentral.org/registry

Bioschemas Markup for IDP

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Red Schema.org

Blue Pending Schema.org

Green Bioschemas

• Protein
• SequenceAnnotation
• SequenceRange
• Taxon
• Dataset
• Scholarly Article

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Not shown

• DataCatalog

BMUSE: Bioschemas Markup Scraper and Extractor

https://app.swaggerhub.com/apis-docs/swel/BMUSE/

• Data harvester
• List of URLs and sitemaps
• Extracts markup
• JSON-LD or RDFa or both
• Static or dynamic
• Returns markup with provenance
• Where
• When
• Tool version
• File per page of harvested markup

Harvested Markup

• Markup harvested through standard API
• HTTP Get requests
• Saves time as common API and model (Bioschemas) for all sites
• Harvested markup is page centric
• Multiple sites represent the same concept
• Sites use their own IDs

No need for custom APIs

Concept merging

IDPcentral as a Knowledge Graph (IDP-KG)

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https://github.com/AlasdairGray/IDP-KG

Querying IDP-KG

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Count by type

Protein information

Annotation count per protein

Annotation information

Annotation count by term code

https://swel.macs.hw.ac.uk/idp/

IDPcentral as a registry

https://idpcentral.org/registry

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The IDPcentral registry is just a (protein-centric) view of the IDP-KG

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The IDP-KG can be expanded to include eternal SPARQL endpoints (ex. UniProt to get PDB data)

Conclusions

Summary

• Markup added to three IDP sources
• Markup harvested using BMUSE
• Standard HTTP Get requests
• Markup transformed into IDP-KG
• Proteins merged from multiple sources
• Analysis queries to explore IDP-KG
• IDPcentral registry prototype

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Next Steps

• Add more IDP sources
• Take IDPcentral to production
• Feed data into OpenAIRE Research Graph

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BioStudies database - filling in gaps in research data publishing

Ugis Sarkans (EMBL-EBI)

Time: 10.05-10.15

BioStudies – aggregating all research study data

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• Facilitate transparency and reproducibility of research, by aggregating all the outputs of a study, the data package, in a single place
• A single study may be associated to a single publication, or may contain data from a unit of work in a larger project.

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#ELIXIR22

BioStudies across the research life cycle

#ELIXIR22

BioStudies usage examples

#ELIXIR22

BioStudies usage examples

#ELIXIR22

BioStudies usage examples

#ELIXIR22

BioStudies usage examples

#ELIXIR22

BioStudies usage examples

#ELIXIR22

BioStudies for a new data type – why it works?

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• Generic underlying data model – files, links, flexible metadata, hierarchies if necessary
• Robust, scalable implementation
• Services typical for a range of life sciences data repositories
• Data file upload and download – FTP, Aspera, Web
• Metadata capture via web forms or via spreadsheets
• Data lifecycle: pre-publication, access for reviewers, warning users about the upcoming release, post-publication modifications etc.
• Integration into the larger scientific ecosystem - ORCIDs, RORs, DOIs etc. (in progress)
• Data access
• “Data collection” concept
• Collection-specific search facets

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#ELIXIR22

Team

Funding

In collaboration with

#ELIXIR22

Community of Practice in training on data management

& data stewardship

Daniel Wibberg

ELIXIR-DE training coordinator, ELIXIR Training Platform and ELIXIR-CONVERGE WP2 member

Forschungszentrum Jülich GmbH, de.NBI, DE.

Time: 10.15-10.25

ELIXIR-CONVERGE

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• The purpose of ELIXIR-CONVERGE is to establish good life-science data management, reproducibility and reuse - infrastructure foundation for Open Science

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• ELIXIR-CONVERGE do this by
• Consolidate good practices, provide a common toolkit
• to develop the national operations and brokering capabilities of the distributed ELIXIR research infrastructure
• Disseminate outcomes to research communities throughout the ERA

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• Thus, ELIXIR-CONVERGE takes the next step to realise a European data federation driven by connected national operations - strategically managed via national research infrastructure roadmaps

#ELIXIR22

WP2 at a glance: Data Management and Stewardship Training by the Nodes for the Nodes

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C0-production model: connected to all other WPs in CONVERGE

#ELIXIR22

The idea: Community of Practice in Data Management and Stewardship

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Node DS/DM

Com.

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DS/DM trainer community of practice

ELIXIR-CONVERGE

Hackathons

Community meeting

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Communities of special interest

• Developing training material
• Developing learning paths
• Developing Tools for DM/DS training
• …

• Experience exchange
• Best practice
• Networking
• Train the Trainer
• …

• DMP Training
• FAIR Training
• Tools Training
• …

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#ELIXIR22

Online Kickoff Meeting – 24 March

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12:00-12:05 | Welcome (Daniel Wibberg, ELIXIR-DE, de.NBI)

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12:05-12:15 | Introduction to ELIXIR-CONVERGE with focus on WP2 (Celia van Gelder, ELIXIR-NL, DTL)

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12:15-12:45 | Examples of national DM/DS communities involved in training

NFDI - Germany (Daniel Tschink, NFDI4Biodiversity, GFBio)

DaSH Project - UK (Robert Andrews, DaSh Project, Cardiff University)

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12:45 - 13:05 | Short introductions to the first community events - Training material hackathons and their topics.

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13:10 - 13:15 | Introduction to CoP (Daniel Wibberg, ELIXIR-DE, de.NBI)

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13:15 - 13:35 | Breakout Room Discussions of important community questions

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13:35 - 14:00 | Result Presentation, Summary and Goodbye

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#ELIXIR22

Online Kickoff Meeting – 24 March – Who was there?

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#ELIXIR22

Online Kickoff Meeting – 24 March – What was discussed?

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#ELIXIR22

First CoP events – Hackathon series for training material

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• DMP (Nils-Christian Lübke, Helena Schnitzer, Daniel Wibberg) – ELIXIR-DE
• 29 March, 1 April, 8 April, 10 May, 3 June
• DM/DS Basics (Ana Melo, Brane Leskosek, Erik Hjerde, Wolmar Akerström, Stephan Nylinder) – ELIXIR-PT, SI, NO & SE
• 8 June, 22 June
• FAIR (Mijke Jetten, Martijn Kersloot, Stephan Nylinder) - ELIXIR-NL & SE
• 29 June
• Reproducibility (Alexia Cardona, Nazeefa Fatima) – ELIXIR-UK & NO
• ?

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#ELIXIR22

Example: DMP Hackathon series for training material

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• In total, we had 25 registration and 20 participants
• Five hackathons day: 29 March, 1 April, 8 April, 10 May, 3 June

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• 3 slide decks
• Introduction
• How write a DMP?
• Recommendations

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#ELIXIR22

CoP next steps: 2nd Event – 21 June

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13:00-13:05 | Welcome (Daniel Wibberg, ELIXIR-DE, de.NBI)

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13:05-13:15 | Results of the discussion round at the kickoff event and next steps (Daniel Wibberg, ELIXIR-DE, de.NBI)

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13:15-13:25 | Current status of the Hackathon series (Helena Schnitzer, ELIXIR-DE, de.NBI)

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13:25-13:40 | FAIRDOM & Training (Ulrike Wittig, ELIXIR-DE, FAIRDOM)

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13:40 - 13:55 | DataPlant & Training (Sebastian Beier, ELIXIR-DE, DataPlant)

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13:55 - 14:00 | Summary and Goodbye

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#ELIXIR22

CoP future plan

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• Discussion on the goals on the CoP on Friday at WP2 Breakout session
• More Hackathons for training material
• Another Online Event in November
• Presentations about famous DM/DS tools and how they are involved in training
• Discussion based on questions by the tool developer
• And more…

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#ELIXIR22

Acknowledgements

Helena Schnitzer

Nils Lübke

Celia van Gelder

Ana Melo

Brane Leskosek

Erik Hjerde

Wolmar Akerström

Stephan Nylinder

Mijke Jetten

Alexia Cardona

Nazeefa Fatimajn

Closing Remarks

Time: 10.25-10.30

Carole Goble (UK) - Chair

Q+A Discussion

Time: if time allows at end

Slido link: Here!

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