Hi Junjun,
In an ideal world, everybody would announce changes to their database
schemas beforehand. But in reality, the people maintaining BioMart
databases usually have many other tasks on their hands, so this tends
not to happen. An automated alerting system wouldn't be able to predict
changes to the schema before they were made, obviously, but it would
reliably let users know once something has happened. And this would be
helpful to groups like ours, which only need to access the ENSEMBL
BioMarts every 3 months. For us, it would be sufficient to know about
changes a day or two in advance of actually using the data, and an
automated system would do the job pretty well.
Cheers,
David Croft.
This is interesting. Tool for identifying diff between configurations
exists, it's used by some BioMart data source providers for QC purposes
before releasing a new version of their data. Yes, it would be good if the
diff can be made available to data consumers. At present time, there is no
automated way of doing so. It is encouraged for data providers to announce
those changes via biomart mailing list.
Looking forward, in future BioMart releases, we are considering to support
tracking changes in sophisticated way.
Best regards,
Junjun
On 11-06-10 5:29 AM, "David Croft"<[email protected]> wrote:
Hi,
It occurs to me that the whole issue of informing users about schema
changes in BioMart could be automated. Schema change alerting could be
bundled as part of the standard BioMart package. A user wanting to be
kept informed would register with the BioMart for the relevant database,
providing an email. Once per month, a server would compare the current
schema with the one stored during the previous month. If there are any
differences, these would be mailed to all registered users.
The already-existing BioMart web services make it easy to obtain the
database names, dataset names, attribute names and filter names from a
given host. What would need to be added would be a diff mechanism and
user registration.
For users who don't want to register, BioMart Central could maintain an
automatically generated page, based on the monthly diffs of all member
databases.
Doing things this way would push the onus of keeping informed about
schema changes from the database maintainers to the individual users,
and it might also help to reduce the traffic in the [email protected]
list a bit too!
Cheers,
David Croft.
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