[Ontology-editors] Disjointness [was Re: constituent part]

[Chris Mungall]

On Aug 6, 2008, at 1:48 AM, Midori Harris wrote:

>
>
> On Tue, 5 Aug 2008, Chris Mungall wrote:
>
>> For now I'm maintaining the disjoint statements in a separate file  
>> and running the reasoner in batch and generating reports.
>>
>> Added a tracker item for:
>> http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes#Extracellular_and_cell
>>
>> I have not yet added a tracker item for:
>> http://wiki.geneontology.org/index.php/Cellular_component_disjoint_classes#X_part_and_X
>>
>> There is a section in the OE reasoner paper on disjoint_from  
>> (shared on google docs under the geneontology account - let me know  
>> if you want individual access)
>>
>> Do you think the following example is a good one:
>> ---
>> In 2007 we made some high-level changes to the GO and introduced  
>> three high level mutually disjoint classes within the biological  
>> process ontology: cellular process, multi-cellular process and  
>> multi-organism process.
>> The editors used a configurable disjointness check in OboEdit to  
>> help organize the graph such that these mutual exclusivity  
>> constraints held. At first there were multiple violations of the  
>> disjointness constraint. For example "conjugation with cellular  
>> fusion" was an is_a child of both cellular process and multi- 
>> organism process. On closer examination the definition of the class  
>> was found to be problematic, the definition was changed and the  
>> disjointness violation was resolved by removing the is_a link  
>> between 'conjugation with cellular fusion' and 'reproductive  
>> process in single-celled organism'. [Can a GO editor check this?  
>> See email thread Re: fixing non-disjoint violations Feb 5 2007]
>> ---
>
> This is an accurate representation of what we did, but biologically  
> it's not very satisfying -- so much so that Val recently requested  
> that the relationship be added back! We do need to improve the  
> representation of sexual reproduction in single-celled organisms; as  
> a stopgap, I've added a part_of relationship, which at least doesn't  
> violate disjointness, but the area is still a bit ugly. It might not  
> be a bad idea to pick a different example just for that reason.

Any suggestions? Perhaps something that's come up recently in the  
process of editing?

>
> m
>