Re: [GUSDEV] loading COG and blast annotation results into GUS

[Chris S. <sto...@pc...>]

See answers in-line. Also, did you look at the documentation in the  
GUS schema browser? The tables (I know many don't) actually have  
table and attribute descriptions. Were they too vague (i.e. do we  
need to improve them?

Chris

> Thanks for replying. I have currently been working on putting my  
> blast results in similarity and similarityspan tables. But, I have  
> two questions about these tables. Maybe you could help me out here.
>
> 1. SImilarity and SImilarityspan have pretty much the same fields  
> except than similarityspan is a child table of Similarity. So, why  
> do I even need the SImilaritySpan table?
These tables have different purposes (and semantics). Think of  
Similarity as global (what's the overall similarity between two  
proteins) and SimilaritySpan as local (what are the individual HSPs).

> 2. I couldnt find any fields in the Similarity table for storing  
> the actual query and subject annotation. Most probably this can be  
> done by referring to some other table with the annotation. But I  
> find that the only two fields refferring to other tables are  
> query_table_id and subject_table_id which just refer to the  
> core.TableInfo. I'm confused about these two fields and exactly how  
> they can be used to refer to the query and subject annotation?

The query and subject sequences are identified (as you may have  
guessed) with the soft links query_table_id and subject_table_id  
although these attributes can point to anything relevant. Our  
semantics are that they point the entities (e.g., nucleic acid  
sequence, amino acid sequence, possibly dbref) and annotation is  
associated with those entities.

> Any help or suggestions would be helpful.
>
> Thanks
> dhivya
>
> Chris Stoeckert <sto...@pc...> wrote:
> Dear Dhivya,
> Sorry for the long delay in replying.
> You guessed correctly about Similarity and SImilaritySpan. These were
> designed to hold BLAST results (as well as results from other  
> analyses).
>
> For ortholog tables you might check the GUS schema browser (http://
> www.gusdb.org/SchemaBrowser/) and scroll down to the categories:
> Paralogs and Family; Sequence Ortholog, Paralog, Family AA Ortholog.
>
> Looking over old notes for OrthoMCL, it looks like
> DoTS.BestSimilarityPair is the table that we store summarized
> ortholog info data for queries.
>
> Hope this helps,
> Chris
>
> On Dec 16, 2006, at 3:38 PM, Dhivya Aras wrote:
>
> > Hi everyone,
> >
> > I would like to store COG annotation and blast results in GUS. I
> > did find two tables named similarity and similarityspan in the dots
> > schema - It looks like this can hold blast results but I need to
> > investigate more.
> >
> > As far as COG is concerned, I couldnt find any table supporting
> > this data. I was told that orthoMcl data is stored in
> > dots.SequenceGroup and dots.SequenceSequenceGroup, but I'm not
> > sure it that would best suit my needs. So, if anyone who has used
> > GUS for these purposes before or just has an idea, pleas let me
> > know. I would really appreciate it.
> >
> > thanks
> > dhivya arasappan
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