[Go] documentation for the new 'Experimental' evidence code.

[Chris Mungall]

On Apr 14, 2008, at 11:38 AM, Mike Cherry wrote:

>
> On Apr 14, 2008, at 11:28 AM, Chris Mungall wrote:
>>
>> As a possible short term measure: what about allowing >3 letters?
>> We'd need to give a little lead time for people who have hardcoded a
>> <=3 letter assumption in software and database schemas, but this is
>> relatively trivial compared to switch to a full blown ontology. We
>> could then call EXP "EXPT". Or "EXPERIMENT". Or how about
>> "Experiment" even. So it's not a "code". Does that matter? It does
>> have the advantage of being in the same language that the majority of
>> scientists (outside the GO cognoscenti) use.
>>>
>
> I could go either way, however having a full and short name could  
> be useful.  We already have things like FB = FlyBase, and GB =  
> GenBank.  The longer name provides clarity and the short name could  
> be around to provide backward compatibility.  If we do go down the  
> road of allowing the longer "Experiment" then I feel we should do  
> this for all the evidence codes.

We already have this, in the form of ECO. We can use ECO to expand  
any existing code to either name (eg "inferred from electronic  
annotation") or even a definition. We could certainly do more to  
ensure that this information is presented to users via software  
interfaces.

But I think that even with this in place, the sociotechnological   
problems of the 3 letter code remain - many people consume gene  
association files with minimal software insulation. With meaningless  
GO IDs you are forced to a lookup, but with a partially meaningful  
possibly misleading 3 letter code it's too tempting to avoid the  
lookup step and go with builtin assumptions.

>   After all I understood EXP(T) was to be used for a limited set of  
> annotations, particularly Reactome that does not track experiment  
> type.  Thus EXP(T) wouldn't be seen very often on most of our web  
> interfaces.

The code itself may be used frequently (eg as a filter), although as  
this is via software we can always present the more meaningful name  
(but this would also mean presenting all other codes as the  
meaningful names consistently throughout all interface software)

> -Mike
>
>