FAIR-Bioschemas Training at DTL

The Outcome on Bioschemas SE and improvements on French Resources

Victoria Dominguez Del Angel ELIXIR-FR , Utrecht (7-8 Feb, 2019)

IFB

French National Bioinformatic Infrastructure

ABOUT Elixir-FR

Missions : Performance world-class research in Life-sciences and medecines, thanks to innovative Bioinformatic Services (High Impact Services)
IFB coordinates and leads the field of bioinformatics in France from 32 platforms which belong to the main French research organisations: CNRS, INSERM, CEA, INRA, INRIA
To empower the French Bioinformatic community
Elixir-FR coordinates Elixir Activities to maintain and push the frontieres of knowledge from French bioinformatic communities

European Open Science Cloud

A virtual environment for Europe’s 1.7 million researchers

European Open Science Cloud : FAIR

European Open Science Cloud : DMP

Security and sustainability of data

Services

National Network of Computational Resources (NNCR)
- Compute 21 k vCPU, Storage 9,5 K (TB) and RAM 173 k (Gb)
Software and Data Environment: middleware, tools and workflows
Databases (Data collections)
DMP (new)
Traning : TrR, TrD and TrT (via Elixir)
Catalogue of French resources in bioinformatics

Bioschemas on catalogue of French Resources

To Improve interoperability in our services
To structure information then makes it easier to discover, collate and analyse the distributed information
Tools, Data, Person, Organistions (platforms, labs, companies) and Training (Event and Material)

Bioschemas Tools - Editor

Generate dynamic forms from Bioschemas specifications (adaptive)
User-friendly edition of resource metadata
Display and export the markup code in JSON-LD (linked data)

TeSS advanteges

The schema.org and bioschemas markup
Search Engine optimized
Training material can be easily parsed with JQuery
The TeSS portal fully supports the FAIR principles for scientific data
EDAM Browser

IFB Challenges in the ID’s and URL’s landscape

Typical properties of systems for identifiers:
- Uniqueness, non ambiguity, persistence, abstraction (opacity)
- Gratis: identifiers (millions of objects)
- Integrity: the associated object cannot be changed

Systems of identifiers

Generation => Create a new label

Assignment => Associate label to object

Retrieval => Get object from a label

Verification (opt) => check label and object

Reverse Lookup (opt) => get label from an object

Description (opt) => get metadata of an object

Mechanismes offered in some identifiers

Mech. / System | Handle | DOI | Ark | PURL

Generation | Yes | Yes | Yes | Yes

Assignment | Yes | Yes | Yes | Yes

Retrieval | Yes | Yes | Yes | Yes

Verification | N.A. | N.A. | N.A. | N.A.

Reverse Lookup | N.A. | N.A. | N.A. | N.A.

Description | Yes | Yes | Yes | N.A

“On-going” Discussion

DOI vs IDO
- The term “Digital Object Identifier” is construed as “digital identifier of an object,” rather than “identifier of a digital object”
DIO (Digital Identifier of an Object)
- digital identifiers for (potentially) non digital objects
- epistemic complexity (manifestations, versions, locations, etc.) need an authority to ensure persistence and uniqueness
IDO (Identifier of a Digital Object)
- digital identifiers (only) for digital objects
- can provide both integrity and no middle man
- broadly used in modern software development (git, etc.)

Future Catalogue

ELIXIR Node Capacity Building and Communities and Staff exchanges

Construct and coordinate ELIXIR-wide ‘communities of practice’ that support and develop the professionals who deliver advanced data and bioinformatics services in ELIXIR Nodes
Bioschema Staff-exchanges “how to do guidelines” (covering creation and use of profiles)

GITBOOK (bioschemas.gitbook.io/training-portal/)

Improvements on distributed information system with BioSchemas

F-A of the Breeding API initiative (brapi.org)
Genetic Material, phenotyping experiments, genotyping experiments ..
Aligned on implementation of data satandards: MCPD, MIAPPE (Minimal Information About Plant Phenotyping Experiments)