[MOBY-l] discussion of GO abbs's and Re: [MOBY] Constructing MOBY objects

[Beatrice Schildknecht]

Hi Mark,

Thanks for the explanation, and the updates on the website--- this is 
all really useful. :-)

>I believe you are going ahead with this already, and have already
>registered this namespace with GO... right?
>
Yes. (Thanks Midori) NASC_code is now registered with GO. I will 
register this with BioMOBY shortly.
So does each namespace registered in mobycentral first need to be 
registered with GO? I was not aware of this, if it is indeed the case.

><PhenotypeDescription namespace='StockNumber' id="blahblah">
>	<CrossReference>
>		<Object namespace="EMBL" id="7234676'/>
>		<Object namespace="AGI_Locus" id="AP3"/>
>		<Object namespace="AGI_Author" id="Wilkinson, MD"/>
>		<Object namespace="AGI_Donor" id="98765"/>
>		<Object namespace="AGI_Ecotype" id="Ler"/>
>	</CrossReference>
>	<String namespace='' id='' articleName='Phenotype'>
>		phenotypic description fits in here
>	</String>
></PhenotypeDescription>
>

This object will be a general phenotype description, that could traverse 
all species. Ok, that makes sense--- a re-usable object. Is it possible 
then, to alter/extend an already established object?
Will each Object namespace within the cross reference block have to be 
registered separately? The number of namespaces will grow exponentially 
if this is the case, as each and every piece of data could potentially 
have an id of some kind.
How are relationships between cross reference objects ascertained/Are 
there relationships between cross reference objects? (Maybe this has all 
been discussed elsewhere?? Is there a way to search the archives?)

>Do you think this is
>sufficiently descriptive for your needs?
>

Yes. I think this object structure does describe the Arabidopsis 
mutant.  I had thought of describing it a different way, but you are 
right in saying that there is more integration and connectivity by using 
the cross references.
I am not, however, very clear about how the Invocation Class object 
works, and how it is different from the Object within the CRIB. Looking 
at the hypothetical examples in the API, I do not see differences in the 
response.

>Perhaps we should toss this out to
>the various plant genome db's to see if there are additional fields that
>should be included in an 'ecotype' object?
>
In our database we do not have much additional information except that 
from the actual donors.  Since objects are to be kept lightweight and 
generic,  I have only mentioned the 'relevant' fields. This one may be 
for the plant community.

Thanks again,
Beatrice