[Biopython-dev] Active projects list? (BOSC Biopython Project Update)

[Andrea Pierleoni]

> The current functionality is limited to loading and retrieving records
> (and retreiving is done in a lazy or on demand way which saves
> memory and DB access). As a consequence, if you want to edit a
> record in the database you have to either do it directly (bypass our
> BioSQL code) or load a new record.
>
> The BioSQL schema doesn't have any sort of audit trail (unlike CHADO
> if I remember correctly), so for many uses this almost read only setup
> is actually a plus point. Here we use BioSQL essentially as a container
> for NCBI GenBank / RefSeq dumps - although we do add additional
> annotations on top.
>
> I can see advantages in allowing the DBSeqRecord to write back
> to the database - it would need a lots of refactoring through (e.g. most
> of the loader code would get moved). I would start by creating a read
> only proxy for the DBSeqFeature (something I think Leighton Pritchard
> did in some of his code) because editing feature annotations would
> be an important part of this.
>


maybe I'll succeed in the next month in writing some methods to modify
bioentry
directly in the SQL db. we can talk about this later, as soon as we have
some code
to work on. however audit trail will not be possible in the current BioSQL
schema,
unless using separate tables (as I'm actually doing). but I don't think
this will be
easily integrable in biopython. Is there anyone needing user logs?