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.
![Each datatype would have options for MI* standards and dataformatsEXAMPLE 1: protein-protein interaction dataDate the data was first integrated CurationPolicy - Check all that apply[ ] Data integrated without curation from users[ ] Data obtained from an external source[ ] Data manually curated at databaseStandards: MIs, Data formats, Terminologies- For PPI data: MIMIx compilant?](https://image.slidesharecdn.com/biodbcore-mockup-v1-101209121129-phpapp02/85/Bio-db-core-mockup-v1-5-320.jpg)
Bio db core-mockup-v1
- 1. 1. DATABASE IDENTIFICATIONDatabase name / Namespace Main resource URLContact informationDate resources establishedLicenseTaxonomic coverage (NCBI Taxid)User support options
- 2. 2. DATABASE SCOPEThere 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=EDAMx
- 4. SPECS AND FORMATSFrom MIBBI/ BioSharing
- 5. Each datatype would have options for MI* standards and dataformatsEXAMPLE 1: protein-protein interaction dataDate the data was first integrated CurationPolicy - Check all that apply[ ] Data integrated without curation from users[ ] Data obtained from an external source[ ] Data manually curated at databaseStandards: MIs, Data formats, Terminologies- For PPI data: MIMIx compilant?
- 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)
- 12. Tools available (querying, analysis, etc)EXAMPLE 2: genome sequence dataDate the data was first integrated CurationPolicy - Check all that apply[ ] Data integrated without curation from users[ ] Data obtained from an external source[ ] Data manually curated at databaseStandards: MIs, Data formats, TerminologiesMIGS
- 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)
- 19. Tools available (BLAST, etc)POTENTIAL USERSDatabase providers : to be sure we know about all available resources
- 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.