[Gusdev-gusdev] Re: GUS 3.0 schema changes: ASCII art redux

[Arnaud K. <ax...@sa...>]

Hi Jonathan

Jonathan Crabtree wrote:

>
> Arnaud-
>
>> A quick question regarding evidences, you're mentioning that the 
>> Evidence table will connect Features and Experimental evidences. 
>> Where will the latter be stored ?
>
>
> Hopefully others will chime in if I get this wrong...  I believe that the
> relevant tables are DoTS.Comments (for free text notes/comments 
> entered by
> an annotator) and SRes.BibliographicReference (for published 
> experiments.)
> However, I don't think that we have a generic table to represent 
> unpublished
> laboratory experiments in a structured way.  Perhaps we need some use 
> cases
> here?  We do have your new table for representing RNAi constructs, but I
> don't think that we have a corresponding table to represent the actual
> RNAi experiment.  Do we need/want such a table (either for RNAi 
> experiments
> or in general) and, if so, how detailed does it need to be?

Should be fine for now. In the future the evidence design could be 
extended for assignment of evidence codes, the same way it is done for 
GO annotations.

>
>>> -Modified DoTS.ProteinProperty table to reference ProteinPropertyType
>>> One question I have regarding these tables is how will the units be 
>>> specified?
>>> Should I make the "property_value" column a varchar2 column?  It may 
>>> have had this type originally, and I might have changed it without 
>>> considering the consequences.  One option would be to specify in the 
>>> ProteinPropertyType table
>>> what units are to be used, though this is clumsy if there is more 
>>> than one
>>> choice of units for a given property.
>>>
>> Whatever the unit they're in, they should all be numbers (some would 
>> be integer) so we can go for the "number" data type but float or 
>> varchar could also be fine!
>
>
> Right, but the question is how does somebody querying the table know what
> a mass of "25" means?  Are molecular masses always expressed in the same
> units, no matter what?  My recollection is that you can sometimes have
> some pretty big polypeptides, but I don't know what the convention is.
>
If we want to query "value" attribute it might be better to have it as a 
number. It doesn't matter for charge et isoelectric point pH but you're 
right re. the molecular mass "25" could mean 25 Da but also 25 kDa. Why 
not storing as a convention the molecular mass always in Daltons and 
then the API code would do the conversion in kiloDaltons if needed. This 
way we don't need a "unit" attribute in ProteinPropertyType.

>
>
> Jonathan
>
Arnaud