Extending the analysisfeature table

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Extending the analysisfeature table

Karl O. Pinc
Hi,

Perhaps I'm mis-understanding, but I'm looking at the
docs on the analsysfeature table and see a problem.

http://gmod.org/wiki/Chado_Companalysis_Module#Table:_analysisfeature

The description of analysisfeature.identify says:
--------------<snip>--------------
Percent identity between the locations compared. Note that these 4
metrics do not cover the full range of scores possible; it would be
undesirable to list every score possible, as this should be kept
extensible. instead, for non-standard scores, use the analysisprop
table.
--------------<snip>--------------

However, the analysisprop table is per-analysis, it extends
the analysis table.  To properly extend the analysisfeature
table there would need to be an analysisfeatureprop table.
Something like:

create table analysisfeatureprop (
   analysisfeatureprop_id serial primary key,
   value text not null,
   analysisfeature_id bigint not null
                      references analysisfeature,
   rank int not null);

create index analysisfeatureprop_value
   on analysisfeatureprop (value);

create index analysisfeatureprop_analysisfeature_id
   on analysisfeatureprop (analysisfeature_id);


Do I have a correct understanding of the problem here
or am I missing something?

Thanks.

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Extending the analysisfeature table

Stephen Ficklin-2
Hi Karl,

I agree that we need an analysisfeature_prop table.  Also, just by way
of information.... because Tripal needs to support properties for
analysisfeature records it adds an analysisfeature_prop table
automatically as a custom table.

Stephen


On 5/30/2014 11:28 AM, Karl O. Pinc wrote:

> Hi,
>
> Perhaps I'm mis-understanding, but I'm looking at the
> docs on the analsysfeature table and see a problem.
>
> http://gmod.org/wiki/Chado_Companalysis_Module#Table:_analysisfeature
>
> The description of analysisfeature.identify says:
> --------------<snip>--------------
> Percent identity between the locations compared. Note that these 4
> metrics do not cover the full range of scores possible; it would be
> undesirable to list every score possible, as this should be kept
> extensible. instead, for non-standard scores, use the analysisprop
> table.
> --------------<snip>--------------
>
> However, the analysisprop table is per-analysis, it extends
> the analysis table.  To properly extend the analysisfeature
> table there would need to be an analysisfeatureprop table.
> Something like:
>
> create table analysisfeatureprop (
>     analysisfeatureprop_id serial primary key,
>     value text not null,
>     analysisfeature_id bigint not null
>                        references analysisfeature,
>     rank int not null);
>
> create index analysisfeatureprop_value
>     on analysisfeatureprop (value);
>
> create index analysisfeatureprop_analysisfeature_id
>     on analysisfeatureprop (analysisfeature_id);
>
>
> Do I have a correct understanding of the problem here
> or am I missing something?
>
> Thanks.
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                   -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> Time is money. Stop wasting it! Get your web API in 5 minutes.
> www.restlet.com/download
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> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


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Re: Extending the analysisfeature table

Karl O. Pinc
Hi Stephan,

On 05/30/2014 10:31:26 AM, Stephen Ficklin wrote:
> I agree that we need an analysisfeature_prop table.  Also, just by
> way
>
> of information.... because Tripal needs to support properties for
> analysisfeature records it adds an analysisfeature_prop table
> automatically as a custom table.
>

As it turns out, there is an analysisfeatureprop table
in chado (SVN head).  But I didn't notice because
there's no docs.



Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: Extending the analysisfeature table

Scott Cain
I expect analysisfeatureprop to be in the next Chado release.


On Mon, Jun 2, 2014 at 2:45 PM, Karl O. Pinc <[hidden email]> wrote:
Hi Stephan,

On 05/30/2014 10:31:26 AM, Stephen Ficklin wrote:
> I agree that we need an analysisfeature_prop table.  Also, just by
> way
>
> of information.... because Tripal needs to support properties for
> analysisfeature records it adds an analysisfeature_prop table
> automatically as a custom table.
>

As it turns out, there is an analysisfeatureprop table
in chado (SVN head).  But I didn't notice because
there's no docs.



Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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