International Society for Biocuration

Annoucements

BioDBCore is registered at MIBBI
An annoucement of BioDBCore is published in the 2011 edition of the NAR Database issue: Gaudet et al. 2011 and in the DATABASE journal Gaudet et al. 2011.

Overview

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) (http://biocurator.org/), in collaboration with the BioSharing forum.

Motivation for BioDBCore

The world of public biological databases is constantly evolving, as attested by the ever-growing size of the annual NAR database issue, as well as by the creation of a new journal dedicated to databases and biocuration, DATABASE. As in any emerging field, standardization across the biological databases is still inadequate at many levels. To address this we propose the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, which we will name BioDBCore.

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: 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

Long term vision and potential impact

The BioDBCore implementation will take place in three phases: 1) consultation with interested parties; 2) collaborative development of the minimal information list: to help establish requirements, some examples can be found on the BioDBCore page of the ISB, and moreover the APBioNet's BioDB100 initiative will be used to develop further working examples; and 3) in the longer term, completion of stable guidelines and their implementation as a public submission website that will allow data entry and easy update by database providers, in collaboration with the existing database collections and the BioSharing standards portal to reduce duplication of effort. Many of the members of the BioDBCore working group have experience and expertise in establishing such services.

Relevant resources