[Ontology-editors] Disjoint_from and symmetry

[David Hill]

Hi Jen,

Isn't this more of a display issue? I know that I've heard a lot of 
folks say that they don't like the graphical display as it stands with 
the disjoint relationships. If we don't include the relationship in the 
stanzas of both terms, how will we represent it for the term where the 
relationship is not indicated?  Does anyone use the obo stanzas in 
isolation? For example, does anyone use the obo file to simply ask show 
me what the realtionships of term X are to other terms. If they do, they 
probably harvest this info from the stanza of the term of interest.

David

Jennifer Deegan (nee Clark) wrote:
> Hi,
>
> The OBO-Edit working group would like to propose a small change to the 
> way that disjoint relationships are handled.
>
> Currently when two terms are disjoint_from one another they each have 
> a disjoint_from relationship to the other as follows.
>
> term1
> disjoint_from: term 2
>
> term2
> disjoint_from: term 1
>
> However, since the disjoint_from relationship is symmetrical, it 
> should not really be necessary to have two relationships connecting 
> two disjoint terms, and the two terms should be able to share one 
> disjoint relationship. This is apparently how the situation is handled 
> in OWL and protege.
>
> We would like to propose to start having just one relationship shared 
> between each pair of terms, as it is thought that this will greatly 
> simplify the handling of the relationships in OBO-Edit.
> We would like to hear what people think about this.
>
> In our discussion last night we did not discuss how the OBO stanza 
> will look if there is only one relationship. We would need to discuss 
> that further, and I would be keen to hear ideas in response to this mail.
>
> Thanks for taking the time to think about this. If we do not hear 
> objections by Friday of this week, then we will proceed to the next 
> stage of planning.
>
> Thanks,
>
> Jennifer
>
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-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430