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

[Midori Harris]

It is an available check, and I have it set to run on save -- but the 
check didn't find this one (with the reasoner off; I haven't tested with 
any reasoner or).

m

On Wed, 15 Apr 2009, Chris Mungall wrote:

>
> 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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