annotation upload via GFF3 into Tripal

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annotation upload via GFF3 into Tripal

Marc Farnum Rendino
Folks -

I'm setting up a new system for community annotation of a (de novo)
eukaryotic genome. And I'm more of a sysadmin than a biologist.

I've got the command-line fu to script the loading of a GFF3 into my
Chado DB; now I'd like to code this up for annotators to
point-and-shoot their way to upload their annotation to Chado, via a
page in Tripal.

(I do have Apollo speaking directly with the Chado DB just fine -
however accepting annotations via GFF3 files is required as well.)

Is a new Content Type the way to go? Or perhaps I should add something
to the Feature page to do it right from there?

I'm envisioning a field for the GFF3 file to be uploaded. (I do
already have uploads enabled and working.) When that file is received
at the server, I do some sanity-checking, feed it to
"gmod_bulk_load_gff3.pl", check for errors, do some indexing/updating
and then notify the user.

BTW: I have added a Download link to the Feature page, to enable
download of the feature (as FASTA, via the URL format used by Tripal
Search) - though I did this by directly editing the Tripal theme's
"node-chado_feature.tpl.php", which I'm sure is the least
elegant/proper way to do it.

What's the preferred way to make these sorts of mods/additions to Tripal?

Thanks!

- Marc

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Re: annotation upload via GFF3 into Tripal

Stephen Ficklin-2
Hi Marc,

Would these be annotations on a per feature basis or would they be more in
bulk for many features?

If a small GFF file just for a feature then I think a field on the feature
edit page would be appropriate, yes.  The CCK Drupal module will let you
easily add a file upload field to the feature node type.

As an aside, I'm in the process of working on a PHP GFF loader. It would
plug into Tripal directly. But I don't know if it will be ready in time for
your needs.  If you have the "PHP fu" to work on it I'd be happy to share
it...

Adding the download link to the node-chado_feature.tpl.php is the correct
way to adjust the feature page for just a local site customization.  If
you'd like this to be a permanent feature you can enter the feature request
on the sourceforge page: https://sourceforge.net/tracker/?group_id=353315
(which is brand new for Tripal).  

If you feel that you want to do some development to make Tripal do what you
want, let us know and we can help direct your efforts in the event that
you'd like to share your code with others.


Thanks,
Stephen

-----Original Message-----
From: Marc Farnum Rendino [mailto:[hidden email]]
Sent: Friday, November 19, 2010 4:07 PM
To: [hidden email]
Subject: [Gmod-tripal] annotation upload via GFF3 into Tripal

Folks -

I'm setting up a new system for community annotation of a (de novo)
eukaryotic genome. And I'm more of a sysadmin than a biologist.

I've got the command-line fu to script the loading of a GFF3 into my
Chado DB; now I'd like to code this up for annotators to
point-and-shoot their way to upload their annotation to Chado, via a
page in Tripal.

(I do have Apollo speaking directly with the Chado DB just fine -
however accepting annotations via GFF3 files is required as well.)

Is a new Content Type the way to go? Or perhaps I should add something
to the Feature page to do it right from there?

I'm envisioning a field for the GFF3 file to be uploaded. (I do
already have uploads enabled and working.) When that file is received
at the server, I do some sanity-checking, feed it to
"gmod_bulk_load_gff3.pl", check for errors, do some indexing/updating
and then notify the user.

BTW: I have added a Download link to the Feature page, to enable
download of the feature (as FASTA, via the URL format used by Tripal
Search) - though I did this by directly editing the Tripal theme's
"node-chado_feature.tpl.php", which I'm sure is the least
elegant/proper way to do it.

What's the preferred way to make these sorts of mods/additions to Tripal?

Thanks!

- Marc

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Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
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Re: annotation upload via GFF3 into Tripal

Marc Farnum Rendino
On Fri, Nov 19, 2010 at 4:38 PM, Stephen Ficklin <[hidden email]> wrote:
> Would these be annotations on a per feature basis

Yes; I'm most concerned with those on a per-feature basis.

> If a small GFF file just for a feature then I think a field on the feature
> edit page would be appropriate, yes.  The CCK Drupal module will let you
> easily add a file upload field to the feature node type.

Ah; great!

> As an aside, I'm in the process of working on a PHP GFF loader. It would
> plug into Tripal directly. But I don't know if it will be ready in time for
> your needs.  If you have the "PHP fu" to work on it I'd be happy to share
> it...

I'm not a PHP master yet, though I do have some code out there in
production; I'd love to take a look at what you've got.

> Adding the download link to the node-chado_feature.tpl.php is the correct
> way to adjust the feature page for just a local site customization.

I figured that was a "hacky" way to do it, but as long as there's no
better way yet, I guess that's OK then. :)

> If
> you'd like this to be a permanent feature you can enter the feature request
> on the sourceforge page: https://sourceforge.net/tracker/?group_id=353315
> (which is brand new for Tripal).

I didn't know about the SourceForge page; thanks!

> If you feel that you want to do some development to make Tripal do what you
> want, let us know and we can help direct your efforts in the event that
> you'd like to share your code with others.

Indeed; I'd love to contribute - sign me up!

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Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
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