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

[Donghui Li]

Hi Karen and all,

Thanks for catching this error.  I'll correct it this afternoon.

I've figured out exactly what happened.

integument development
     is_a tissue development
     part_of ovule development

I first created 'integument development' as a child of tissue  
development by right clicking and choose 'create a new child'.  I then  
used the graphic editor to add the part_of link between the newly  
created integument development and the existing term ovule  
development.  This was done by drawing a line between these two terms,  
pointing from integument development to ovule development. The default  
value is always set as 'is_a', I realized this while I was drawing the  
line/link between these two terms; I then stopped before the line  
reached the parent term ovule development.  So what happened here was  
this created a is_a relationship between integument development and  
itself, although I did not complete the line that links the terms.  I  
then created the part_of link and that worked.

I normally use graphic viewer to verify term parentage before saving,  
the graphic viewer does not display this is_a to itself relationship.  
So the lesson I learned is when using graphic editor to add  
relationship between two terms, choose the right relationship type  
before drawing the line/link. I think it's good to add a verification  
check.

Donghui






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
>


--
Donghui Li
TAIR Curator

http://www.arabidopsis.org
http://www.geneontology.org

Carnegie Institution
260 Panama Street
Stanford, CA 94305
U.S.A

Email donghui at stanford.edu
Tel (650) 325 1521 ext 356
Fax (650) 325 6857