Bio db core-mockup-v1
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This document outlines a proposed framework for standardizing the description of biological databases. It includes sections for database identification information, scope, supported data types, formats and standards, curation policies, data access and release policies, and potential users of such standardized descriptions. Database providers would use the framework to enter information about their resources, allowing users, publishers and funders to more easily find, assess and utilize biological databases.
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Solution
1)
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2)
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Bio db core-mockup-v1
- 1. 1. DATABASE IDENTIFICATION Database name / Namespace Main resource URL Contact information Date resources established License Taxonomic coverage (NCBI Taxid) User support options
- 2. 2. DATABASE SCOPE There would be a form where database providers would enter the scope of their database (all datatypes) Those types of could come from some ontology (see EDAM, next slide) – maintained by the EBI (Jon Ison)
- 3. 2. DATABASE SCOPE (here selection is from EDAM ontology) : http://sourceforge.net/projects/edamontology/ http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM x
- 6. Data formats : MIMIx compilant?
- 9. Versioning policy/ access to historical files (only if data is not from secondary parties? )
- 11. Data submission policy (only if data is not from secondary parties)
- 13. Data formats : GFF3, FASTA, etc
- 14. Data accessibility/output options GFF3, FASTA, etc
- 15. Data release frequency (only if data is not from secondary parties? )
- 16. Versioning policy/ access to historical files
- 18. Data submission policy (only if data is not from secondary parties)
- 20. Users: so they can search for specific resources and quickly assess the quality
- 21. Publishers: It would be easier for data transfer (see Adriaan’s message on the Google group)
- 22. Funders : Having standardized descriptions of databases, and also who accepts which data should help funding agencies enforce good data sharing policies.