Faidare

Faidare

Table of Contents

• Documentation
• Pros and Cons
• FAIR Principles
• Example use cases

Documentation

• Technology Description

  • The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories. It is based on the Breeding API (BrAPI) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface. It also provides a standard interface that can be accessed programmatically through web services. It is an extension of the generic Data-Discovery portal, a web portal that allows finding any type of data across several databases through a lightweight keyword based search. FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.

• Learn from an expert

  • A recorded presentation by Cyril Pommier: https://youtu.be/a2Fetp2iZKA

• More Information

  • The Faidare website: https://urgi.versailles.inrae.fr/faidare/

Pros and Cons

• Cost to setup

  • The cost of joining the existing federation greatly depends on the level of technical expertise and resource available. Could be anywhere from one week to 6 months worth of work.
  • Independently setting up the data-discovery software: software is free, setup and maintenance costs unknown.
  • Both options will likely incur costs related to metadata curation.

• Pros

  • increases findability of data;
  • facilitates accessibility as data and metadata need to be accessible to be used in Faidare;
  • use of Brapi schema can help with interoperability and reusability

• Cons

  • Curating/structuring data and metadata to follow the Brapi schema may take time

FAIR Principles

• Findability - Metadata and data should be easy to find for both humans and computers.

  • F1 - (Meta)data are assigned a globally unique and persistent identifier

    Persistent identifiers are up to the providing database

  • F2 - Data are described with rich metadata (defined by R1 below)

    Metadata description is up to the providing database

  • F3 - Metadata clearly and explicitly include the identifier of the data they describe

    URI is associated with the metadata

  • F4 - (Meta)data are registered or indexed in a searchable resource

    joint elasticsearch engine

• Accessibility - Once the user finds the required data, it should be clear how the data can be fully accessed.

  • A1.1 - The protocol is open, free, and universally implementable

    FAIDARE uses a standardized, open, freely available communication protocol

  • A1.2 - The protocol allows for an authentication and authorization procedure, where necessary

    not sure about authorization/authentication mechanism

  • A2 - Metadata are accessible, even when the data are no longer available

    metadata persistence is up to the original data provider

• Interoperability - The data should easily interoperate with other data, as well as applications for analysis, storage, and processing.

  • I1 - (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.

    The language for knowledge representation is JSON

  • I2 - (Meta)data use vocabularies that follow FAIR principles

    not sure whether controlled vocabularies are required for all data

  • I3 - (Meta)data include qualified references to other (meta)data

    not sure how cross-references are implemented (may depend on the original data source)

• Reusability - Metadata and data should be well-described so that they can be replicated and/or combined in different settings.

  • R1 - (Meta)data are richly described with a plurality of accurate and relevant attributes

    metadata description is up to the providing database (I don't think it's required by faidare)

  • R1.1 - (Meta)data are released with a clear and accessible data usage license

    license is likely up to the providing database

  • R1.2 - (Meta)data are associated with detailed provenance

    provenance is available in Faidare but detail is likely up to the providing database

  • R1.3 - (Meta)data meet domain-relevant community standards

    BrAPI requirement could help partially meet domain-specific metadata requirements

Example use cases

• Joining the existing federation

  • A database curating plant genotype, phenotype, germplasm data and metadata wants to make their data more findable by the scientific community.

• Establishing a new federation

  • A group of data repositories with similar data types want to have a system for searching across all resources simultaneously.