Re: [Gusdev-gusdev] Sequence Type controlled vocab

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

folks-

Having looked at SO and MGED, I am not sure they are capturing what I 
have in mind, or, what we have captured in our SequenceType table

Here is the way I am thinking about breaking down "sequence type."   (If 
somebody can show me how these map into either of the ontologies Chris 
has mentioned that would be great).

For NA sequences:

Polymer Type
  - DNA
  - RNA
Molecule
  - chromosome
  - mRNA
  - tRNA
  - rRNA
  - oligo
Strandedness
  - single
  - double
Sequencing process
  - Genomic
  - EST
  - predicted
  - transcribed
  - what else?
Source
  - nucleus
  - mitochondria
  - plastid
  - plasmid
  - episome

Steve

Chris Stoeckert wrote:

> 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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