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

  • F1: persistent identifiers are up to the providing database;
  • F2: metadata description is up to the providing database;
  • F3: URI is associated with the metadata;
  • F4: joint elasticsearch engine;

• Accessibility

  • A1.1: uses a standardized, open, freely available communication protocol;
  • A1.2: not sure about authorization/authentication mechanism;
  • A2: metadata persistence is up to the original data provider

• Interoperability

  • I1: language for knowledge representation: json;
  • I2: not sure whether controlled vocabularies are required for all data;
  • I3: not sure how cross-references are implemented (may depend on the original data source)

• Reusability

  • R1: metadata description is up to the providing database (I don't think it's required by faidare);
  • R1.1: license is likely up to the providing database;
  • R1.2: provenance is available in Faidare but detail is likely up to the providing database;
  • R1.3: 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.