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Category: Forum || Secondary Category: Resources Portal || File ID: 65 || Last changed on: 2009-03-04 18:30:52

Database description framework

As part of the remit of CASIMIR to develop and disseminate standards for mouse informatics, a cross-workpackage discussion in conjunction with the ENFIN project has developed a series of “benchmarks” or “characteristics” for databases which will allow the easy and standardised capture of key technical and scientific information about databases relevant to mouse functional genomics. The aim of this is to provide investigators with a ready summary of the resources associated with the database and informaticians with the key technical information to access the data and come to an informed position on data quality, structure and scope. The aim is not to make “value judgements” on the database. What is useful or relevant for some databases need not be so for others, and each database needs to be assessed in terms of its own remit and user community. The aim of the benchmark stars is to reflect the degree of complexity or sophistication of the operation at a glance. This may be an inappropriate way to “score” databases and we would welcome suggestions as to how we might “score” in a clearly non-judgmental way.
We envisage other uses for a clearly articulated set of benchmarks.

  • Dissemination of good database practice

  • Support of aspiration to improve the services offered

  • Objective criteria which can be used as a measure of database quality against the self-declared aims

All feedback welcome! Please make sure that you leave your name with your comments below. The table itself will not be modified until we have something approaching a consensus, at least within this group.


Quality and Consistency No explicit process for assuring consistencyProcess for assuring consistency, automatic curation onlyProcess for assuring consistency with manual curation
CurrencyClosed legacy databaseUpdates or versions more than once a yearUpdates or versions more than once a month
AccessibilityAccess via browserDatabase reports or database dumpsProgrammatic access. SQL access or web services. Well defined API. Published.
OutputConforms to recognised standard open source syntax; html or similar to browserConforms to recognised standard open source syntax. Sparse standard file format. Eg. FASTAConforms to recognised standard open source syntax Rich standard file format., Eg. XML, SBML.
Technical documentationWritten textFormal structured description, eg automatically generated API eg JavaDoc, schema, UML etcTutorials, demonstrations, plus ** criteria
Data representation standardsData coded by local formalism onlySome Data coded by recognised controlled vocabulary or ontology or use of MIBBIGeneral use of both recognised vocabularies or ontologies, and Minimal standards
Data structure standardsData structured with local modelData structured with formal model eg XML, XML schemaUse of recognised standard model, eg FUGE
User support User documentationEmail/web form help desk functionPersonal contact help desk function/training
Ability to track back through previous versionsNo provisionPrevious version of database available but no tracking of entities between versionsPrevious version of database available AND tracking of entities between versions
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