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

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

Hi Arnaud and Jonathan,
>>>> -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.

This sounds dangerous and unenforceable. We should add a units field. 
This can either be a varchar or a foreign key to units stored are 
Sres:MGEDOntology terms.

Chris