[Ontology-editors] Disjoint_from and symmetry

[Tanya Berardini]

I agree about it being more of a display issue.  What you're proposing is a
change in the ontology itself.  From looking at the meeting transcript, it
sounds like there are options proposed by Chris that would handle the
display issue (another tab or something like that?).

12/09/2008    10:09:25 AM    from Chris Mungall: 1. Editors should
only need to assert symmetric relations in one direction
12/09/2008    10:10:09 AM    from Chris Mungall: 2. The various
components need to be smarter in general about showing symmetric
relations
12/09/2008    10:10:21 AM    from Chris Mungall: 3. a separate tab for
disjoints is a good idea

This sounds like the way to go.

Tanya

On Wed, Dec 10, 2008 at 5:16 AM, David Hill <dph at informatics.jax.org> wrote:

> 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
>
> _______________________________________________
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>



-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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