[BioPython] [bip] [OT] Revision control and databases

[Peter]

Giovanni Marco Dall'Olio wrote:
> Bruce Southey wrote:
>> Of course Biopython's BioSQL interface may provide a starting point.
>
> The problem is that BioSQL doesn't support yet Population Genetics record
> (see another thread in biopython mailing list), so I would have to implement
> something like that in BioSQL or wait for the developers to do it.
> Maybe I will do this later, but now I don't have the time.

BioSQL currently focuses on annotated sequences, but they are working
on some phylogenetics support too.  See http://www.biosql.org/ and the
PhyloDB extension module.  If there was enough interest, perhaps a
BioSQL schema for Population Genetics could be devised too.

Giovanni Marco Dall'Olio wrote:
>>> The problem is I don't know if databases do Revision Control.
>>> When I used flat files, I was used to save all the results in a git
>>> repository, and, everytime something was changed or calculated
>>> again, I did commit it.
>>> Do you know how to do this with databases? Does MySQL
>>> provide support for revision control?

As other people have said, databases don't generally "waste" resources
on version control.  If you need this, then it is up to you to design
your schema to record this additional metadata.  For example, the
BioSQL sequences have a "version" field in the "bioentry" table
allowing multiple revisions of the same accession to be held.  When
querying the database, you could request a particular version, or
indeed the latest version.  Essentially AFAIK database version control
is a Do-It-Yourself affair when designing your database tables.

Peter