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

[Peter]

On Wed, Jul 21, 2010 at 4:48 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it> wrote:
>> 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.

Sure - there is no hurry.

> 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?

I agree, and didn't mean to suggest adding audit tables to the BioSQL
schema. I was just pointing out this issue (depending on the intended
usage, this may or may not be a problem).

Peter