This is a slightly extended version of the BioDBcore presentation I gave at Biocuration2012 in the Workshop Databases & Journals – How to have a sustainable long term plan for journals and databases?

1. The International Society for Biocuration & BioDBcore:
Promoting data exchange across databases, journals and users
Pascale Gaudet
Scientific Manager
Swiss Institute of Bioinformatics
Chair
International Society for Biocuration

2. The need
• Databases: improve data integration from
published papers
• Journals: link to databases objects
• Researchers: identify resources
• Grant submitters: enforce data sharing plans

3. An information specification
for biological databases
Goals
• Gather information required to provide a general
overview of the database landscape
• Encourage consistency and interoperability
• Promote the use of standards
• Provide guidance for users
• Maximize the collective impact of the resources

4. BioDBcore descriptors
² Database name
² Main resource URL
² Contact information (e-mail; postal mail)
² Date resource established (year)
² Conditions of use (Free, or type of license)
² Scope: data types captured, curation policy,
standards used
² Standards: MIs, Data formats, Terminologies
² Taxonomic coverage

5. Descriptors (cont’d)
² Data accessibility / output options
² Data release frequency
² Versioning policy / access to historical files
² Documentation available
² User support options
² Data submission policy
² Relevant publications
² Resource’s Wikipedia URL
² Tools available

6. Collaborative philosophy
• Many groups/resources have been
providing registries and lists of databases
• Often not funded, not maintained
• BioDBcore seeks to collaborate with all
interested parties to work together to
provide a more permanent solution to
database descriptions

7. NAR Database issue 2012
• More than 300 BioDBcore entries submitted
PROTOTYPE

10. BioDBcore implementation plan
ü Consultation with interested parties
ü Collaborative development of the guidelines
ü Provide examples: NAR 2012 and BioDB100
ü Infrastructure to capture BioDBcore information
q Refine guidelines
q Identify/develop ontologies/vocabularies
q Exchange of data among various groups
q Providing support for users

11. Identifying or developing
semantic support
• Terminologies (BRO, EDAM, others)
• Policies and guidelines (BioSharing)
• Name attribution (identifiers.org)
• Author (orchid)
Identifying resources is better than developing new ones !

12. BioDBcore: Participating groups
² BioDB100
² BioSharing
² BioCatalogue
² Bioinformatics Links Directory
² Biositemaps
² CASIMIR
² MIBBI
² MIRIAM/identifiers.org
² Model Organism Databases
² NIF registry
² ORCHID
² … and your group ! contact the ISB

13. Acknowledgements
Susanna-Assunta Sansone
Philippe Rocca-Serra
Michael Galperin, Editor,
Nucleic Acids Research Database issue
BioDBcore collaborators