tripal feature accession

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tripal feature accession

P. Ziarsolo
Hi!
        I am new to tripal(awesome project). I have found that the accession
used in tripal is a sum of a site specific prefix and chado feature_id.
Is it possible to use the chado's feature's uniquename as accession of
tripal?

        This is useful when you try to access a tripal feature page from an
external application without access to chado database.
        I thing is not a good idea to use feature_id as accession because
feature_id is an internal id of chado and it could change in a database
regeneration. Showing this data to users could confuse them if

Maybe I haven't understand tripal, so I someone could clarify me...

Thanks in advance
p.



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Re: tripal feature accession

Stephen Ficklin
Hi P?,

We appreciate your feedback!

Yes, you are correct about the accession number being a combination of a site specific prefix and the feature_id.  We agree that this should be fixed.

In designing Tripal we wanted each feature to have its own site-specific accession.  To accomplish this, rather than use the feature_id, as you point out, we really should have a db table entry for the site and assign site-specific accessions by way of the dbxref table and dbxref_id foreign key in the feature table.  

However, it sounds like you would like to use external accessions and have those be used as links into the site.  I can see that in some cases folks may want unique site-specific accessions but in other cases would prefer to use external accessions.   So, I think what we should do to fix this is the following:

1. Correct the use of feature_ids as a component of the site-specific accession.
2. Make the use of site-specific accessions optional and require users to manually generate accessions for features with a NULL dbxref_id rather than have this occur automatically.
3. Use the accession provided by the dbxref_id in the feature table as the true accession that get's linked into the site.

This way, users can have a site-specific accession if they want, or they can have external accessions, or none at all.

I welcome comments from anyone about this idea.  But I'll put it on our task list of things to fix.

Stephen


-----Original Message-----
From: P. Ziarsolo [mailto:[hidden email]]
Sent: Friday, June 11, 2010 5:27 AM
To: [hidden email]
Subject: [Gmod-tripal] tripal feature accession

Hi!
        I am new to tripal(awesome project). I have found that the accession
used in tripal is a sum of a site specific prefix and chado feature_id.
Is it possible to use the chado's feature's uniquename as accession of
tripal?

        This is useful when you try to access a tripal feature page from an
external application without access to chado database.
        I thing is not a good idea to use feature_id as accession because
feature_id is an internal id of chado and it could change in a database
regeneration. Showing this data to users could confuse them if

Maybe I haven't understand tripal, so I someone could clarify me...

Thanks in advance
p.



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Re: tripal feature accession

Scott Cain
In reply to this post by P. Ziarsolo
Hi p,

I'll let Stephen and others address the internals of Tripal, but a
note about using feature.uniquename to uniquely identify something: be
very careful.  The value of feature.uniquename is not guaranteed
unique; the unique constraint is on the combination of uniquename,
type_id and organism_id, so if you wanted to use uniquename, it should
really be a concatenation of those three fields.

Scott


On Fri, Jun 11, 2010 at 5:26 AM, P. Ziarsolo <[hidden email]> wrote:

> Hi!
>        I am new to tripal(awesome project). I have found that the accession
> used in tripal is a sum of a site specific prefix and chado feature_id.
> Is it possible to use the chado's feature's uniquename as accession of
> tripal?
>
>        This is useful when you try to access a tripal feature page from an
> external application without access to chado database.
>        I thing is not a good idea to use feature_id as accession because
> feature_id is an internal id of chado and it could change in a database
> regeneration. Showing this data to users could confuse them if
>
> Maybe I haven't understand tripal, so I someone could clarify me...
>
> Thanks in advance
> p.
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: tripal feature accession

P. Ziarsolo
In reply to this post by Stephen Ficklin
Hi Stephen,

Jatorrizko mezua: or., 2010-06-11 09:31 -0400, egilea: Stephen Ficklin
> Hi P?,

Peio :)

>
> We appreciate your feedback!
>
> Yes, you are correct about the accession number being a combination of a site specific prefix and the feature_id.  We agree that this should be fixed.
>
> In designing Tripal we wanted each feature to have its own site-specific accession.  To accomplish this, rather than use the feature_id, as you point out, we really should have a db table entry for the site and assign site-specific accessions by way of the dbxref table and dbxref_id foreign key in the feature table.  
>
> However, it sounds like you would like to use external accessions and have those be used as links into the site.  I can see that in some cases folks may want unique site-specific accessions but in other cases would prefer to use external accessions.   So, I think what we should do to fix this is the following:
>
> 1. Correct the use of feature_ids as a component of the site-specific accession.
> 2. Make the use of site-specific accessions optional and require users to manually generate accessions for features with a NULL dbxref_id rather than have this occur automatically.
> 3. Use the accession provided by the dbxref_id in the feature table as the true accession that get's linked into the site.
>
> This way, users can have a site-specific accession if they want, or they can have external accessions, or none at all.
>
This seems good to me. It resolves my issues.
Do you have a public code repository to follow the improvements?
Thanks !!!

p.



> I welcome comments from anyone about this idea.  But I'll put it on our task list of things to fix.
>
> Stephen
>
>
> -----Original Message-----
> From: P. Ziarsolo [mailto:[hidden email]]
> Sent: Friday, June 11, 2010 5:27 AM
> To: [hidden email]
> Subject: [Gmod-tripal] tripal feature accession
>
> Hi!
> I am new to tripal(awesome project). I have found that the accession
> used in tripal is a sum of a site specific prefix and chado feature_id.
> Is it possible to use the chado's feature's uniquename as accession of
> tripal?
>
> This is useful when you try to access a tripal feature page from an
> external application without access to chado database.
> I thing is not a good idea to use feature_id as accession because
> feature_id is an internal id of chado and it could change in a database
> regeneration. Showing this data to users could confuse them if
>
> Maybe I haven't understand tripal, so I someone could clarify me...
>
> Thanks in advance
> p.
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal



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_______________________________________________
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