- 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.
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
BioSharing has implemented a BioDBCore-compliant catalog also using papers submitted to Nucleic Acids Research, see
http://www.biosharing.org/biodbcore. Entries are also linked to the BioSharing catalog of standards, where those are implemented by the database.
We encourage all of the database providers to either create or claim your BioDBCore entry and update it as appropriate.
We also welcome the submission of standards, including Reporting Guidelines, Terminology Artifacts or Exchange Formats: http://biosharing.org/standards.
We look forward to your contributions ! Please contact email@example.com (BioSharing) or firstname.lastname@example.org (the ISB helpdesk) with any questions or suggestions.
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.
- BioSharing: Contains catalogues of policies and reporting standards
- BioCatalogue (Web resources)
- Bioinformatics Links Directory
- BRO- Biological Resources Ontology
- EDAM ontology
- Integbio Database Catalog
- MIRIAM (EBI)
- NAR Database Issue list of databases
- NIF registry
- W3C HCLS