BioDBcore

BioDBcore is a community-defined, uniform, generic description of the core attributes of biological databases.

The BioDBcore checklist is overseen by the International Society for Biocuration (ISB) and FAIRsharing, a manually curated informative and educational resource on inter-related data standards, databases, and policies in the life, environmental and biomedical sciences.

The BioDBcore guidelines were developed in 2011 in response to the unprecedented growth in biological databases and data repositories seen since the turn of the century. With the annual NAR database issue and the creation of new journals such as DATABASE, dedicated to databases and biocuration, we had a wonderful opportunity to survey the landscape and map the data, domains and standards.

As in any emerging field, standardization, in terms of data standards and formats, was still inadequate. BioDBcore, a community-defined, uniform, generic description of the core attributes of biological databases aims to address this.

The goals of the proposed BioDBcore checklist are to:

  • Gather the necessary information to provide a general overview of the database landscape, and compare and contrast the various resources.
  • Encourage consistency and interoperability between resources.
  • Promote the uptake and use of semantic and syntactic standards.
  • Provide guidance for users when evaluating the scope and relevance of a resource, as well as details of the data access methods supported.
  • Ensure that the collective impact of these resources is maximized.

Proposed core attributes include:

  • Database name
  • Main resource URL
  • Contact information (e-mail; postal mail)
  • Date resource established (year)
  • Conditions of use (Free, or type of license)
  • Scope: data types captured, curation policy, standards used
  • Standards implemented: MIs, Data formats, terminologies
  • Taxonomic coverage
  • Data accessibility/output options
  • Data release frequency
  • Versioning period and access to historical files
  • Documentation available
  • User support options
  • Data submission policy
  • Relevant publications
  • Resource’s Wikipedia URL
  • Tools available

FAIRsharing has implemented a BioDBCore-compliant catalog also using papers submitted to Nucleic Acids Research, see https://www.fairsharing.org/biodbcore. Entries are also linked to related standards and (journal and funder) data policies, where appropriate.

We encourage all database providers to either create or claim your BioDBCore entry in FAIRsharing and update it as appropriate.

You can also record your content standards in FAIRsharing, be they terminologies (controlled vocabularies/ontologies), Models or Formats (such as FASTA, CellML or ISA-Tab), or Reporting Guidelines (such as MIAME, or ARRIVE) and relate them to the databases that use them and the journal and funder data policies that recommend or endorse their use. The FAIRsharing standards registry can be accessed here: https://FAIRsharing.org/standards