Re: [Gmod-schema] [Gmod-tripal] How are additional GFF3 attributes stored and retrieved?

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Hi Stephen,

When the perl bulk loader sees tags that it doesn't recognize, it just
adds that term to the feature_propery cv.

Scott

PS: I wrote this last week but apparently never hit "send".  Sorry
about the delay.

On Wed, Jun 15, 2011 at 9:13 PM, Stephen Ficklin <spf...@gm...> wrote:
> Hi Olen,
>
>
>
> Okay, thanks for pointing me down in the thread.  Hadn’t read that far.
>
>
>
> I’ll work on getting this fixed.
>
>
>
> Thanks,
>
> Stephen
>
>
>
> From: Olen Vance Sluder Jr [mailto:ol...@ac...]
> Sent: Wednesday, June 15, 2011 6:15 PM
> To: GMOD Schema List; gmod-tripal
> Subject: Re: [Gmod-tripal] [Gmod-schema] How are additional GFF3 attributes
> stored and retrieved?
>
>
>
> >From what Scott said in his response of June 1 (below), the attribute's tag
> is the cvterm and if it is not already present it is created.
>
> --
>
> Olen
>
>
>
> On Wed, Jun 15, 2011 at 16:42, Stephen Ficklin <spf...@gm...> wrote:
>
> Hi Olen,
>
>
>
> Currently the GFF Loader with Tripal doesn’t load attributes that aren’t
> part of the GFF3 definition. Although the GFF3 does support attributes in
> the definition.  We can make this fix for you.   But, I’m not familiar with
> the cvterm that are required by GBrowse to find these attributes.  Does
> anyone have a reference they can point me to?
>
>
>
> Thanks,
>
> Stephen
>
>
>
> From: Olen Vance Sluder Jr [mailto:ol...@ac...]
> Sent: Wednesday, June 15, 2011 5:05 PM
> To: GMOD Schema List; gmod-tripal
> Subject: Re: [Gmod-tripal] [Gmod-schema] How are additional GFF3 attributes
> stored and retrieved?
>
>
>
> [Cross-posting to the Tripal mailing list. -- Olen]
>
>
>
> Stephen, I hadn't seen a response on this question, but I realize you've
> likely been busy with the Tripal 0.3b release, etc.
>
> I have loaded a couple of GFF3 files via the Tripal loader, but additional
> attributes are not inserted into featureprop. For example, for gaps I have
> "gap_type" and "gap_bridge":
>
> ##gff-version 3
> chr1 hg18_gap gap 167281 217280 . . .
> ID=chr1_gap1;Name=chr1_gap1;gap_type=clone;gap_bridge=yes
> ...
>
> and for chromosome bands I have "stain":
>
> ##gff-version 3
> chr1 hg18_cytoBand chromosome_band 1 2300000 . . .
> ID=1p36.33;Name=1p36.33;stain=gneg
> ...
>
> In the latter case, the "stain" attribute is required by the GBrowse
> ideogram glyph in order to properly render.
> --
> Olen
>
>
> On Wed, Jun 1, 2011 at 12:31, Olen Vance Sluder Jr <ol...@ac...> wrote:
>> Thanks, Scott.
>>
>> Stephen, is the behavior of the Tripal GFF3 loader the same?
>>
>> --
>> Olen
>>
>>
>> On Wed, Jun 1, 2011 at 12:10, Scott Cain <sc...@sc...> wrote:
>>> Hi Olen,
>>>
>>> For any tag that isn't stored elsewhere (that is, all initial-lower
>>> case tags), they go in featureprop.  The perldoc for
>>> gmod_bulk_load_gff3.pl describes where all of the data in a GFF file
>>> goes, though I realized that the text for custom tags was out of date,
>>> so I rewrote it just now.  Here's what it says now:
>>>
>>> =item Any custom (ie, lowercase-first) tags
>>>
>>> Custom tags are supported.  If the tag doesn't already exist in
>>> the cvterm table, it will be created.  The value will stored with its
>>> associated cvterm in the featureprop table.
>>>
>>> With regard to getting the data out, the Chado GBrowse adaptor
>>> supports Bio::SeqFeatureI methods for retrieving values, like the
>>> attributes method, which is presumably what the ideogram glyph uses.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Jun 1, 2011 at 10:49 AM, Olen Vance Sluder Jr <ol...@ac...>
>>> wrote:
>>>> Clarification: The question about retrieval is in the context of using
>>>> the attributes in GBrowse.
>>>> --
>>>> Olen
>>>>
>>>>
>>>> On Wed, Jun 1, 2011 at 09:42, Olen Vance Sluder Jr <ol...@ac...> wrote:
>>>>> Looking over the Bio::Graphics::Glyph::ideogram docs, I see the
>>>>> attribute "stain" is included in Column 9: "attributes" of the GFF3
>>>>> example. For something like sequence gaps, I could see additional
>>>>> attributes of type and bridge that could then be used for display in
>>>>> GBrowse. How are these additional attributes stored in Chado? Are
>>>>> these attributes retrieved by the Chado adaptor and accessible through
>>>>> feature->attributes in callbacks?
>>>>>
>>>>> Thanks,
>>>>> Olen
>>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> 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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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research