Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

topalis at imbb.forth.gr topalis at imbb.forth.gr
Sun Jul 26 13:13:33 PDT 2009


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



----------------------------------------------------------------
         This message was sent using IMBB - WebMail.




More information about the bioontology-support mailing list