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

[Midori Harris]

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.

m