[Ontology-editors] GO error: cycle at "integument development"

[Chris Mungall]

I thought this was a check. Perhaps the reasoner needs to be on  
(though it shouldn't be for the trivial self-parent case). Amina, can  
you investigate?

On Apr 15, 2009, at 9:27 AM, Karen Christie wrote:

> Hi all,
>
> There is a problem in the current GO file. The term "integument  
> development" (GO:0080060) is listed as an is_a parent of itself. I  
> can fix that later today, but since you added the term originally  
> Donghui, maybe it would be better if you fix it so that you can also  
> check to make sure it has all the parents you intended this term to  
> have.
>
> Also, since it seems like this should never be allowed, for a term  
> to be its own parent, maybe we could also add a verification check  
> to make sure we catch these before committing to CVS.
>
> thanks,
>
> -Karen
>
>
>> On Apr 15, 2009, at 8:33 AM, Shuai Weng wrote:
>>
>>> There is a bad entry in the current obo file (see below). The GOID  
>>> (80060)
>>> itself is listed as it's parent - so things go to an infinity  
>>> loop...
>>> I guess go curators need to fix that. In the mean time, I'll fix  
>>> the go path loading script to check to make sure the parent goid  
>>> not itself
>>> and try to load the data into SDEV first.
>>> Shuai
>>> ======================
>>> [Term]
>>> id: GO:0080060
>>> name: integument development
>>> namespace: biological_process
>>> def: "The process whose specific outcome is the progression of the  
>>> integument over time, from its formation to the mature structure.  
>>> Integument is one of the layers of tissue that usually covers the  
>>> ovule, enveloping the nucellus and forming the micropyle at the  
>>> apex." [PMID:19054366, PO:0020021]
>>> is_a: GO:0009888 ! tissue development
>>> is_a: GO:0080060 ! integument development
>>> relationship: part_of GO:0048481 ! ovule development
>>> =============
>>> On Wed, 15 Apr 2009, Gail Binkley wrote:
>>>> Thanks Shuai!  No objections from me.
>>>> - Gail
>>>>> I'll look into this and may need to rerun the scripts on fasolt
>>>>> first for testing. Any objections?
>>>>> Shuai
>>>>> On Wed, 15 Apr 2009, Shuai Weng wrote:
>>>>>> I think something is wrong in the obo file.
>>>>>> Shuai
>>>>>> On Wed, 15 Apr 2009, Gail Binkley wrote:
>>>>>>> in both SDEV and SGD with enormous log files.  An example
>>>>>>> DBD::Oracle::st execute failed: ORA-12899: value too large for  
>>>>>>> column
>>>>>>> "BUD"."GO_PATH"."ANCESTOR_PATH" (actual: 241, maximum: 240)  
>>>>>>> (DBD ERROR:
>>>>>>> error possibly near <*> indicator at char 213 in '
>>>>>>>     INSERT INTO BUD.go_path(child_go_no, ancestor_go_no,
>>>>>>>                                 generation, ancestor_path,
>>>>>>>                                 relationship_type)
>>>>>>>     VALUES(:p1, :p2, :p3, :<*>p4, :p5)
>>>>>>> ') [for Statement "
>>>>>>>     INSERT INTO BUD.go_path(child_go_no, ancestor_go_no,
>>>>>>>                                 generation, ancestor_path,
>>>>>>>                                 relationship_type)
>>>>>>>     VALUES(?, ?, ?, ?, ?)
>>>>>>> " with ParamValues: :p5='', :p3=35, :p1=28423,
>>>>>>> :p4 
>>>>>>> = 
>>>>>>> '80060 
>>>>>>> :: 
>>>>>>> 80060::80060::80060::80060::80060::80060::80060::80060::80060::
>>>>>>> 80060 
>>>>>>> :: 
>>>>>>> 80060 
>>>>>>> ::80060::80060::80060::80060::80060::80060::80060::80060::80060
>>>>>>> :: 
>>>>>>> 80060 
>>>>>>> :: 
>>>>>>> 80060 
>>>>>>> ::80060::80060::80060::80060::80060::80060::9888::48513::4873
>>>>>>> 1::48856::32502::8150', :p2=4284] at
>>>>>>> /usr1/fasolt/www-data/bin/util/cron/../../projects/go/ 
>>>>>>> updateGoPath line
>>>>>>> 589.
>>>>>>> What is making the ancestor_path so long?
>>>>>>> - Gail
>>
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