Re: [Gusdev-gusdev] Sequence Type controlled vocab

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

Steve,
There are two complementary standards for sequence type. One comes from 
the MGED Ontology.
see 
http://mged.sourceforge.net/ontologies/MGEDontology.php#BioSequenceType
The other is SO  http://song.sourceforge.net/
Chris

On Feb 2, 2005, at 5:14 PM, Steve Fischer wrote:

> folks-
>
> in gus we have a Dots.SequenceType table.
>
> here are the columns:
> nucleotide_type
> sub_type
> strand
> hierarchy    [should be hierarchy_depth]
> parent_sequence_type_id
> name
> description
>
> First question:  does anybody know of an "emerging standard" for this?
>
> If there is one, then we should include it in the Controlled Vocabs 
> that we package with GUS.
>
> Otherwise, we have, I think, two candidate SequenceTypeCVs:
>   - the one provided by Sanger on the wiki:  
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data#ExternalDatabase
>   - the one currently housed in CBIL's GUS instance
>
> As part of the GUS 3.5 install, we are getting serious about making 
> the loading of CVs much easier.   A central part of that is making the 
> CVs available from CBIL's download site (eg, the CBIL anatomy CV).
>
> So, i am thinking that CBIL should chose one (or more) sequence type 
> CVs to provide as downloads.  They could be offered in GUS XML format.
>
> Then, the automated GUS CV installer would find them from CBIL just 
> like it will find GO from the GO Consortium.
>
> Any plugin that uses SequenceTypes should *not* hard code the 
> transform, but, instead, take a SequenceTypeMapping file.  The file 
> specifies the mapping from input sequence type to that stored in gus 
> (by name).  The plugin should pre-scan the input file to detect if 
> there are any illegal sequence types, and warn the user before loading 
> any data
>
> If users find sequence types that the CBIL CV is missing, they can 
> propose them via the mailing list.
>
> The objective is to:
> 1. work with the fact that different input files for a plugin may use 
> different sequence types
> 2. get out of the business of ad hoc changes to the sequence types 
> stored in the db
>
> comments?
>
> steve
>
> as a candidate CV the Sequence the SequenceTypesCV as developed by
>
> If not, then, how about this.   Plugins that depend on sequence type 
> use a standard config file for sequence type.  (this might apply to 
> other loose CVs).  The config file specifies the
>
>
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