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

[Karen Christie]

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
>