Re: [GUSDEV] Blast parameters revisited

[<ju...@cs...>]

Chris Stoeckert <sto...@pc...> writes:
>
> AlgorithmInvocation has a comment_string attribute that can be used
> to put your convenient name. AnalysisAlgorithm can be used to tie
> that to Similarity rows through the softlinks table_id, row_id.

Ok, for a set of blast results I can put one row
in Core.AlgorithmInvocation (with the blast parameters)
and Core.AnalysisAlgorithm is the linking table to
multiple lines in DoTS.Similarity.  For this purpose,
one can then just ignore :

    Core.AlgorithmParamKey
    Core.AlgorithmParam
    Core.AlgorithmParamKeyType

I did make it overly complicated.

[...]
> Evidence could
> be use (target = similarity; fact = external database release).

Ok, this could work too.

> We are looking into altering Similarity or adding a table to better
> capture alignments (an attribute to indicate gaps).

Cool;

> We can also
> consider providing a link to external database release as part of
> this if it makes sense.

That's pretty much what I went a head an implemented in
our local installation.

Thanks for taking a look;

Josef



> On Feb 6, 2006, at 12:13 PM, Josef Jurek wrote:
>
> >
> >
> > Any thoughts on this?
> >
> > Does implementing a "SRes.ExternalDatabaseRelease"-like way to group
> > rows in DoTS.Similarity together sound useful to anybody,
> > or do people find the use of Core.AnalysisAlgorithm to accomplish
> > such a thing completely satisfactory?
> >
> > Thanks, Josef
> >
[...]
> >
> > I wrote:
> >>
> >>
> >> In the recent past, some of us needed a way to
> >> distinguish between blast results in DoTS.Similarity by
[...]