Re: [Gusdev-gusdev] dots.nalocation table

[Sucheta T. <su...@vb...>]

Steve,

You are right, parent_ids are there for some of them, but some others like
transcript does not have one. I feel a parent_id needs to be there for
transcript rather than genefeature. Since a transcript is derived from a
gene.

sucheta

> sucheta-
>
> i *think* the answer to your question may be that features have
> parent_id.  this is used to build feature trees.
>
> steve
>
> Sucheta Tripathy wrote:
>
>> Thank you all for the response. My original question was bit premature
>> and based on more of our convenience than the design of GUS per se.
>>
>> But these are some issues, I think the group may need to consider:
>>
>> By keeping different prediction outputs as different feature_ids and
>> finally merging them through gene and gene_instance seems fine. But we
>> need to distinguish between features within a gene and features of a
>> gene. What I mean by that is a gene may have different features like
>> an UTR feature , a promoter element feature etc, a cpg island feature
>> and so on. which needs to be linked to a particular prediction output.
>>
>> For example I have gene 1 with gene_id 1 which has several
>> gene_instances represented by different prediction algorithms and each
>> having a different na_feature_id say: 1,2,3,4.
>>
>> For prediction algorithm with na_feature_id=1, I have a set of UTR
>> locations and say I have feature_id 5 for UTR_5 and 6 for UTR_3 and a
>> promoter feature with na_feature_id 7. Then how would I link
>> na_feature_ids 1,5,6 and 7.
>>
>> So, for this I was thinking if one na_feature_id could represent a
>> gene and its locations could have a description each with reviewer's
>> status etc. And to save the geneinstances for any kind of splice
>> variants or any other types of instances.
>>
>> Many thanks
>>
>> Sucheta
>>
>> At 09:40 AM 2/14/2005 -0500, you wrote:
>>
>>> This question is a bit more complex than it seems.
>>>
>>> All three of these may be necessary for every level of
>>> analysis.  first, was the overall gene prediction/feature
>>> prediction reviewed and how was it algorithmically arrived at?
>>>  Then you can ask the same question about the locations.
>>> Early locations may be provided by the same algorithm as the
>>> feature, but these may be further defined later and require
>>> their own review annotations.
>>>
>>> One thing that I think needs to be addressed, however, is how
>>> these columns appear throughout the schema like mushrooms.  I
>>> have been told that GUS was hyper-normalized when it was first
>>> written to 4N or 5N form, but that is definitely not the case
>>> now.  Why do you want review_status, reviewer and algorithm in
>>> the feature table?  Since these usually will appear in
>>> clusters (i.e. running an algorithm once gives you 500 cases
>>> of the same entry for all three on the same date), shouldn't
>>> we have a table to collect these into an annotation_status
>>> table and just have an FK to an entry in that table for every
>>> table that uses these?  The same goes for other SRes entries
>>> such as taxon, project, etc.
>>>
>>> -Ed
>>>
>>>
>>>
>>> ---- Original message ----
>>> >Date: Sat, 12 Feb 2005 22:34:03 -0500 (EST)
>>> >From: "Sucheta Tripathy" <su...@vb...>
>>> >Subject: [Gusdev-gusdev] dots.nalocation table
>>> >To: Gus...@li...
>>> >
>>> >
>>> >Hi Group,
>>> >
>>> >From community annotation point of view, I was wondering if
>>> it is a good
>>> >idea to have is_reviewed, algorithm_id and reviewer_id in
>>> dots.nalocation
>>> >table.
>>> >
>>> >Since one na_feature_id( a transcript or a gene) may be
>>> having multiple
>>> >sets of nalocations, so one can easily capture them in
>>> nalocation with
>>> >different algorithms and with a reviewed option.
>>> >
>>> >In our application we need several gene calling programs to
>>> have locations
>>> >as well as related information registered.
>>> >
>>> >Sucheta
>>> >
>>> >
>>> >--
>>> >Sucheta Tripathy
>>> >Virginia Bioinformatics Institute Phase-I
>>> >Washington street.
>>> >Virginia Tech.
>>> >Blacksburg,VA 24061-0447
>>> >phone:(540)231-8138
>>> >Fax:  (540) 231-2606
>>> >
>>> >
>>> >-------------------------------------------------------
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>>> -----------------
>>> Ed Robinson
>>> Center for Tropical and Emerging Global Diseases
>>> University of Georgia, Athens, GA 30602
>>> ero...@ug.../(706)542.1447/254.8883
>>>
>>>
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>>
>>
>>
>>
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>
>
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606