[BioSQL-l] SeqFeature scores

[Chris Fields]

On Oct 14, 2008, at 2:14 PM, Mark Johnson wrote:

> On Tue, Oct 14, 2008 at 12:28 PM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>> On Oct 14, 2008, at 11:03 AM, Mark Johnson wrote:
>>
>>> On Mon, Oct 13, 2008 at 3:03 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>>>>
>>>> Hi Mark, this was a known bug at some point. In fact, I can't  
>>>> swear that
>>>> it
>>>> was solved, so if you are running the latest bioperl-db version  
>>>> then I
>>>> think
>>>> it hasn't been. Can you confirm?
>>>>
>>>>     -hilmar
>>>
>>> I just pointed my scriptage to a freshly updated bioperl-live and
>>> bioperl-db (updated via svn a few minutes ago).  I'm seeing the same
>>> problem.  So, unless I'm hallucinating, this is still an issue.   
>>> Shall
>>> I open a new bug in bugzilla, or is there an old one you'd like to
>>> reopen?
>>
>> I think open a new bug so we can track it.  Personally I'm not sure  
>> how we'd
>> store score data in BioSQL.  Is 'score' within the schema?  I  
>> suppose we
>> could add it as a specific tag value but that seems potentially  
>> hackish and
>> prone to naming conflicts.
>>
>> chris
>
> Well, if there is no provision for storing score in the schema, it's
> not a bug, it's an enhancement request.  If it worked in the past or
> is supposed to work, it's a bug.  As to where it ends up in the
> schema, I had been wondering about that.  I presumed it ended up with
> the rest of the tags...and I wonder if that's not the most appropriate
> place for it.  It's an attribute that not all features have.  In fact,
> I don't see score as part of SeqFeatureI.  Bio::SeqFeature::Generic
> has it's own accessor and storage.  Speaking of which, I just tried to
> go browsing the deobfuscator and it seems to be horked (internal
> server error). Is there a better contact other than dag at sonsorol.org
> (server administrator)?   Is there a bugzilla queue for website
> issues?

I would support adding score in as a tag (particularly seeing as it's  
not part of SeqFeatureI) but I think it requires a bit more  
discussion.  I wouldn't be surprised if it was added as a method  
primarily to match GFF-like feature data with score information.   
Hilmar, thoughts?

For the website issues you can submit support issues directly to support at helpdesk.open-bio.org 
  (it will probably be faster).

chris