[Gusdev-gusdev] Sequence Type controlled vocab

[Steve F. <sfi...@pc...>]

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