Gaudet - BioDBcore

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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?

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Gaudet - BioDBcore

  1. 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. 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. 3. An information specification for biological databasesGoals•  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. 4. BioDBcore descriptors²  Database name²  Main resource URL²  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 used²  Standards: MIs, Data formats, Terminologies²  Taxonomic coverage
  5. 5. Descriptors (cont’d)²  Data accessibility / output options²  Data release frequency²  Versioning policy / access to historical files ²  Documentation available ²  User support options²  Data submission policy ²  Relevant publications ²  Resource’s Wikipedia URL²  Tools available
  6. 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. 7. NAR Database issue 2012•  More than 300 BioDBcore entries submitted PROTOTYPE
  8. 8. BioDBcore implementation planü  Consultation with interested partiesü  Collaborative development of the guidelinesü  Provide examples: NAR 2012 and BioDB100ü  Infrastructure to capture BioDBcore informationq  Refine guidelinesq  Identify/develop ontologies/vocabulariesq  Exchange of data among various groupsq  Providing support for users
  9. 9. 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 !
  10. 10. BioDBcore: Participating groups²  BioDB100²  BioSharing²  BioCatalogue ²  Bioinformatics Links Directory ²  Biositemaps ²  CASIMIR ²  MIBBI²  MIRIAM/identifiers.org²  Model Organism Databases²  NIF registry ²  ORCHID²  … and your group ! contact the ISB
  11. 11. Acknowledgements Susanna-Assunta Sansone Philippe Rocca-Serra Michael Galperin, Editor, Nucleic Acids Research Database issue BioDBcore collaborators

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