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[bioontology-support] Potential bug on bioportal ontology details view

Natasha Noy noy at stanford.edu
Sun Jul 26 13:38:45 PDT 2009


Ah, sorry, I was looking at a different term. So, the problem with  
this term is that it does not have any parents defined. Let us  
investigate a bit and we'll get back to you.

Chris -- please disregard my message on the visualization problems:  
the visualization is correct and the arrows go in the right direction.  
Sorry for the confusion!

Natasha


On Jul 26, 2009, at 1:13 PM, topalis at imbb.forth.gr wrote:

> Actually the visualisation is correct. The terms not appearing are  
> all "children" of CHEBI:39116 and this explains the direction of the  
> arrow (e.g.
> [Term]
> id: CHEBI:34911
> name: permethrin
> synonym: "(3-Phenoxyphenyl)methyl (+-)-cis,trans-3-(2,2- 
> dichloroethenyl)-2,2-dimethylcyclopropanecarboxylate" RELATED  
> [ChemIDplus:]
> synonym: "Permethrin" EXACT [KEGG COMPOUND:]
> synonym: "3-phenoxybenzyl 3-(2,2-dichloroethenyl)-2,2- 
> dimethylcyclopropanecarboxylate" EXACT IUPAC_NAME [IUPAC:]
> synonym: "3-(2,2-Dichloroethenyl)-2,2-dimethylcyclopropane  
> carboxylic acid, (3-phenoxyphenyl) methyl ester" RELATED [ChemIDplus:]
> synonym: "C21H20Cl2O3" RELATED FORMULA [KEGG COMPOUND:]
> synonym: "CC1(C)C(C=C(Cl)Cl)C1C(=O)OCc1cccc(Oc2ccccc2)c1" RELATED  
> SMILES [ChEBI:]
> synonym: "InChI=1/C21H20Cl2O3/ 
> c1 
> -21 
> (2 
> )17 
> (12-18(22)23)19(21)20(24)25-13-14-7-6-10-16(11-14)26-15-8-4-3-5-9-15/ 
> h3-12,17,19H,13H2,1-2H3" RELATED InChI [ChEBI:]
> synonym: "InChIKey=RLLPVAHGXHCWKJ-UHFFFAOYAS" RELATED InChIKey  
> [ChEBI:]
> xref: KEGG COMPOUND:C14388 "KEGG COMPOUND"
> xref: KEGG COMPOUND:52645-53-1 "CAS Registry Number"
> xref: ChemIDplus:52645-53-1 "CAS Registry Number"
> relationship: has_role CHEBI:39116
> relationship: has_role CHEBI:39259
> relationship: has_functional_parent CHEBI:39308
> relationship: has_role CHEBI:33286
> relationship: has_role CHEBI:38956)
>
> In fact this term is not appearing at all in the ontology details  
> view. And this is the case with other terms not only in ChEBI. I  
> recently submitted IDOMAL to bioportal and this exactly what is  
> happening with the terms related with has_role relation to others.
>
> Thanks for your reply
>
>
> Quoting Natasha Noy <noy at stanford.edu>:
>
>> It's a bug in visualization, I think: this concept has only has_role
>> links coming *into* it. The graph shouldn't display them at all  
>> (Chris,
>> these properties start with "[R]"). Below is the definition from the
>> OBO file:
>>
>> [Term]
>> id: CHEBI:39116
>> name: pyrethroid ester insecticide
>> synonym: "pyrethroid ester insecticides" RELATED [ChEBI:]
>> is_a: CHEBI:26413
>>
>> And the service returns a bunch of "[R]" relations:
>> http://rest.bioontology.org/bioportal/concepts/40196/CHEBI%3A39116?email=example@example.org
>>
>> Natasha
>>
>>
>> On Jul 26, 2009, at 10:28 AM, Pantelis Topalis wrote:
>>
>>> Dear bioportal developers,
>>>
>>> I noticed that on ontology details view the only terms they show  
>>> up  are those that are related to their parents with an is_a or  
>>> part_of  relation only.
>>> At the same moment the terms which are "hidden" from the ontology   
>>> details view are appearing correctly to the visualisation tab.
>>> An example of this behaviour it can be found on ChEBI and term   
>>> "pyrethroid ester resistance" (CHEBI:39116) . On the  
>>> visualization  tab several children related with has_role relation  
>>> can be found  but none of them is appearing on the ontology  
>>> details view.
>>>
>>> Best regards,
>>> Pantelis Topalis
>>> VectorBase at IMBB
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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