Thread: [GUSDEV] schema documentation ( and the plugins), revisited

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[GUSDEV] schema documentation ( and the plugins), revisited

From: Josef J. <ju...@cs...> - 2005-09-21 17:05:05

I have been working with the InsertSequenceFeatures
plugin and it has been invaluable towards understanding
the intended use of the schema.

The provided genbank2gus.xml file is in itself, quite a
useful piece of schema documentation, however it only
documents tables which are views on NAFeatureImp.

Is there such a document for views on AAFeatureImp?
If not, does anyone have similar documentation on
AAFeature tables?

Thank you for your help;


Josef


Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648

Re: [GUSDEV] schema documentation ( and the plugins), revisited

From: Steve F. <sfi...@pc...> - 2005-09-21 17:37:52

there isn't any parallel document for AAFeatureImp as of yet, that i 
know of.

steve

Josef Jurek wrote:

>I have been working with the InsertSequenceFeatures
>plugin and it has been invaluable towards understanding
>the intended use of the schema.
>
>The provided genbank2gus.xml file is in itself, quite a
>useful piece of schema documentation, however it only
>documents tables which are views on NAFeatureImp.
>
>Is there such a document for views on AAFeatureImp?
>If not, does anyone have similar documentation on
>AAFeature tables?
>
>Thank you for your help;
>
>
>Josef
>
>
>Josef Jurek, Ph.D.
>
>Daphne Preuss Laboratory
>Molecular Genetics and Cell Biology
>The University of Chicago
>ju...@cs...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>
>
>
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
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[GUSDEV] schema documentation ( and the plugins), revisited

From: Josef J. <ju...@cs...> - 2005-09-21 18:06:13

Steve Fischer <sfi...@pc...> writes:
>
> there isn't any parallel document for AAFeatureImp as of yet, that i
> know of.

Then let's start one.  First we need a mapping of
genbank features to gus tables.  Here is the list of
aa feature names from the genbank files I am presently
working with:

  Bond
  CDS
  gene            DoTS::AAGene (** see below)
  Het
  mat_peptide
  proprotein
  Protein
  Region
  SecStr          DoTS::SecondaryStructureAAFeature
  sig_peptide     DoTS::SignalPeptideFeature
  Site
  source          (I assume we don't bother to put this one in a featuretable).

The right side is my guess as to what view on AAFeature that
this particular feature uses.  Ok, I did not get very far.

Can someone help me by filling in the rest?

Also, is the following a complete list of views on DoTS.AAFeatureImp?:

    DoTS::AAFeature
    DoTS::AASeqVariation
    DoTS::DomainFeature
    DoTS::EpitopeFeature
    DoTS::LowComplexityAAFeature
    DoTS::MassSpecFeature
    DoTS::PlasmoAPFeature
    DoTS::PostTranslationalModFeature
    DoTS::PredictedAAFeature
    DoTS::RepeatRegionAAFeature
    DoTS::SecondaryStructureAAFeature
    DoTS::SignalPeptideFeature
    DoTS::TertiaryStructureAAFeature
    DoTS::TranslatedAAFeature

Thank you for your help!

Josef

** Why is DoTS.GeneFeature a view on DoTS.NAFeatureImp though
DoTS.AAGene not a view on DoTS.AAFeature?

Thanks again.