[BioSQL-l] Versioning in BioSQL Database

[Peter Cock]

Thanks for clarifying Luke.

If you are hoping for advice from other users, you may be out of luck - my
impression from the mailing list and git questions is that using BioSQL
with Biopyton is quite rare nowadays.

The database schemas for BioSQL itself has been effectively static for
years: the only recent changes were sqlite added 5 years ago, and a tweak
for MySQL8 last year. On the bright side, what it does works fine - and you
are free to experiment and extend your copy.

For your usecase, are you talking about point revisions to published
records (e.g. NCBI or EMBL annotation), where the naming convention is an
accession dot version? Or are you dealing with local revisions to annotated
sequences?

Peter

On Mon, Aug 3, 2020 at 11:46 AM Lsting likebee <lukeswabypetts at gmail.com>
wrote:

> Hi Peter
>
> Yes, where possible I’m using BioSQL—especially BioSeqDatabase—which has
> been perfectly fine for all my scripts (so far just data ingestion and
> output) but am having a particularly difficult time with data replacement.
>
> The goal is to be able to extract some records, modify them, and push them
> back in under the same name with an updated version number and bioentry_id,
> such that whenever those records are next extracted it is the latest
> version that is pulled by default.
>
> I am very new to all of this (just about to start my masters) so this is
> no doubt just a shortcoming in my understanding, but it feels like I must
> be missing something very simple, as this is surely something that most
> users would need!
>
> Can you think of anything that could help?
>
> Very much appreciated
>
> Luke
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
>
> ------------------------------
> *From:* Peter Cock <p.j.a.cock at googlemail.com>
> *Sent:* Monday, August 3, 2020 9:39 am
> *To:* Luke Swaby
> *Cc:* biosql-l at mailman.open-bio.org
> *Subject:* Re: [BioSQL-l] Versioning in BioSQL Database
>
> Hello Luke,
>
> It has been some time since I looked at the tables in BioSQL, but just to
> be clear - you are not using the Biopthon BioSQL wrapper, are you?
>
> https://github.com/biopython/biopython/tree/master/BioSQL/
>
> Peter
>
> On Mon, Aug 3, 2020 at 2:36 AM Luke Swaby <lukeswabypetts at gmail.com>
> wrote:
>
>> Hello
>>
>> I’m currently writing a load of Python scripts to interact with a
>> slightly modified version of your BioSQL database (pretty much identical,
>> with an additional table for metadata), and am having a lot of trouble
>> working out how to implement record versioning in it.
>>
>> Comments in the schema—and the version field in the bioentry
>> table—suggest a particular method of doing this was in mind when the schema
>> was written, but I can’t find any documentation on how this is to be done.
>>
>>
>> In sum, I need it to be able to hold multiple versions of the same record
>> in the same table, and a means of accessing (ideally by default) only the
>> latest version of each record when it is requested. It would ideally also
>> automatically add a new version of a record whenever any change is made to
>> it, either internally by direct MySQL queries or externally by ingestion of
>> newly modified .gb/.csv files. I’ve thought of numerous ways of doing this,
>> including creating a new table which points to the unique
>> bioentry_id/metadata_id of the latest version of each record, but am very
>> stuck on how to do this.
>>
>> Do you have any suggestions? I’m sure there is a relatively basic answer
>> that I am totally missing, but I’m pressed for time now and am finding
>> nothing anywhere!
>>
>> Very much appreciated if so
>>
>> Luke
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at mailman.open-bio.org
>> https://mailman.open-bio.org/mailman/listinfo/biosql-l
>
>
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