Re: [Obo-discuss] Taxonomy Data

[John Day-R. <joh...@ay...>]

No, the current OBO-Edit behavior is wrong (even if it's good that no  
one is trying to subclass is_a).

Right now, is_a is a rigid, read-only construct. There's no way to  
define sub-properties of is_a, and no way to indicate that is_a has any  
super-properties.

This causes problems with the relationship ontology, because the  
relationship ontology defines is_a as a sub-property of the generic  
relationship property. When the relationship ontology is loaded into  
OBO-Edit, the file loader tries to tell is_a that it is a sub-property  
of relationship, and is_a quietly ignores that change. We end up with  
an improperly loaded relationship ontology and some slightly buggy  
behavior.

So the behavior is bad, even if the current usage hides the technical  
problems.

	-John

On Mar 14, 2006, at 12:14 PM, chris mungall wrote:

>
> My view is that the current behavior of obo-edit is correct
>
> On Mar 14, 2006, at 10:57 AM, John Day-Richter wrote:
>
>>
>> In theory, you can create sub-relations of is_a in OBO-Edit. The fact  
>> that you can't is due to a bug/rigid implementation decision.
>>
>> It should be possible to create sub-properties of is_a in an upcoming  
>> version of OBO-Edit.
>>
>> 	-John
>>
>>
>> On Mar 13, 2006, at 4:43 PM, chris mungall wrote:
>>
>>>
>>> I don't think you should be able to create sub-relations of is_a in  
>>> oboedit
>>>
>>> capturing rank as subsets seems like an ok solution for now, but  
>>> there will be a better solution with the obo 1.2 format spec,  
>>> details coming soon..
>>>
>>> On Mar 13, 2006, at 7:04 AM, Pankaj Jaiswal wrote:
>>>
>>>> I agree mostly, that's why I used only is_a. However I did try  
>>>> creating the ontology by using the relationship types describing  
>>>> the ranks. e.g.
>>>>
>>>> X is_a_species_of Y
>>>> Y is_a_genus_of Z
>>>> Z is_a_subclass of A
>>>>
>>>> Abut again these are all subtypes of is_a I think. This was a good  
>>>> way to do it since most of the taxon terms had constant rank in the  
>>>> taxonomy. However the "NO RANK" was creating problem, because terms  
>>>> belonging to this class were coming from all sorts of levels in the  
>>>> hierarchy. Therefore I did not add those.
>>>>
>>>> I also agree that Barry must be consulted. Is Barry on the mailing  
>>>> list? I don't have his address.
>>>>
>>>> Pankaj
>>>>
>>>>
>>>> Jane Lomax wrote:
>>>>> I agree with Michael - Linnean taxonomic classification should be  
>>>>> a subsumption tree with only is_a relations...
>>>>> jane
>>>>> On Mon, 13 Mar 2006, Michael Ashburner (Genetics) wrote:
>>>>>> I would very much like to see Barry's input on the question
>>>>>> of relationships in taxonomy. Surely this is a pure subsumption  
>>>>>> tree
>>>>>> with is_a relationships ?
>>>>>>
>>>>>> I not Nicolas' comments about the Phylocode.  The problem is
>>>>>> that very few have accepted it - at least in comparison to the
>>>>>> many who continue to use the Linnean classification, with all of  
>>>>>> its
>>>>>> faults.
>>>>>>
>>>>>> The ToL project is great, but its coverage is _very_ spotty and,  
>>>>>> for
>>>>>> most groups does not go to the level of species.
>>>>>>
>>>>>>
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>>
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>>>>> Dr Jane Lomax
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>>>>> EMBL-EBI
>>>>> Wellcome Trust Genome Campus
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>>>>
>>>> -- 
>>>> Pankaj Jaiswal
>>>> G-15, Bradfield Hall
>>>> Dept. of Plant Breeding and Genetics
>>>> Cornell University
>>>> Ithaca, NY-14853, USA
>>>>
>>>> Ph. +1-607-255-3103 / 4199
>>>> fax: +1-607-255-6683
>>>>
>>>>
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