July 31, 2021

Our FAIR stance on data access and sharing

In 2016 Mark D. Wilkinson and a group of co-authors proposed a set of guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets, they were published as the ‘FAIR Guiding Principles for scientific data management and stewardship‘ and they are also available on-line. The main goal of these guidelines is to facilitate the finding, access, interoperability and reuse of data at a computer-system level. The importance of this schema lies in the fact that most of our access to massive data is through computers, and the more this process is automated the faster and better is the information we retrieve.

The users of T3 data portal greatly benefit from the work we have done to implement the FAIR guidelines. You can follow it in the lines below, where we match every FAIR attribute to its T3 implementation.

The Triticeae Toolbox (T3) FAIR attributes

Findable

  • F1. (Meta)data are assigned a globally unique and persistent identifier
    • Traits use international standard Crop Ontology identifiers (http://www.cropontology.org/)
    • Accessions can include registered accession numbers (GRIN PI, CI, numbers, etc.)
  • F2. Data are described with rich metadata
    • Traits include trait and method descriptions and scale information
    • Trial metadata structures include planting and harvest dates, notes, and field map and management metadata
    • Accession metadata structures include pedigree origin information (country, breeding program) among others
  • F3. Metadata clearly and explicitly include the identifier of the data they describe
    • Crop Ontology identifiers are consistently displayed throughout Breedbase (trait search page, trait detail page, ontology browser)
    • Accession detail pages display registered accession numbers and links to external databases with more information
  • F4. (Meta)data are registered or indexed in a searchable resource 

Accessible

  • A1. (Meta)data are retrievable by their identifier using a standardized communications protocol
    • Data is accessible using the international breeding community standard BrAPI (https://brapi.org/)
      • A1.1 The protocol is open, free, and universally implementable
        • BrAPI meets these requirements
      • A1.2 The protocol allows for an authentication and authorization procedure, where necessary
        • BrAPI supports authentication when necessary
  • A2. Metadata are accessible, even when the data are no longer available
    • The trait ontology is always accessible
    • Accessions are not deleted from the database, but marked as obsolete
    • Trial metadata and observations are completely removed when deleted

Interoperable

  • I1. (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation
    • BrAPI responses are returned in JSON format with documented key:value pairs
  • I2. (Meta)data use vocabularies that follow FAIR principles
    • The BrAPI standard itself is FAIR

Reusable

  • R1. (Meta)data are richly described with a plurality of accurate and relevant attributes
    • R1.1 (Meta)data are released with clear and accessible data usage license
      • T3/Breedbase users agree to the Toronto Agreement when first accessing the website
    • R1.2 (Meta)data are associated with detailed provenance
      • Accessions and trials are associated with a breeding program
      • Accessions and trials display the names of the users who have curated the data
    • R1.3 (Meta)data meet domain-relevant community standards