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[Gofriends] GO tool for semantic similarity

Erick Antezana erant at psb.ugent.be
Sat Oct 11 05:04:22 PDT 2008


Hi Rachael,

  how does he/she defines "semantic similarity of two genes"?  We have 
been working on something we named 'semantic comparative analysis' based 
on the GOA annotations to support hypotheses generation within a 
Semantic Systems Biology approach. With the system we're building, 
BioGateway [1], it is possible to retrieve proteins sharing similar 
"semantic treats" (=annotations) such as the same or compatible 
localizations, processes in which they participate or functions so that 
a hypothesis about any of those features could be proposed. For 
instance, the following query, retrieves the proteins sharing the same 
function (GO_0016505 = apoptotic protease activator activity), process 
(GO_0006915 = apoptosis) and location (GO_0005737= cytoplasm):

BASE   <http://www.semantic-systems-biology.org/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX ssb:<http://www.semantic-systems-biology.org/SSB#>
SELECT ?organism ?protein_name ?uniprot_id
WHERE {
 GRAPH ?organism {
   ?uniprot_id ssb:has_function      ssb:GO_0016505 .
   ?uniprot_id ssb:located_in         ssb:GO_0005737.
   ?uniprot_id ssb:participates_in   ssb:GO_0006915.
   ?uniprot_id rdfs:label                 ?protein_name.
 }
 FILTER (?organism != <GOA> && ?organism != <SSB>) .
}

The result shows 8 proteins with *similar* characteristics...

On the other hand, two proteins can also be compared, for instance, we 
can ask for similar locations, processes and functions (GO IDs) of the 
following two proteins  APAF_MOUSE (O88879) and C8AP2_MOUSE (Q9WUF3):

BASE   <http://www.semantic-systems-biology.org/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX ssb:<http://www.semantic-systems-biology.org/SSB#>
SELECT ?f ?p ?l
WHERE {
 GRAPH <59.M_musculus> {
   <SSB#O88879> ssb:has_function     ?f .
   <SSB#O88879> ssb:located_in       ?l.
   <SSB#O88879> ssb:participates_in  ?p.
 }
 GRAPH <59.M_musculus> {
   <SSB#Q9WUF3> ssb:has_function     ?f .
   <SSB#Q9WUF3> ssb:located_in       ?l.
   <SSB#Q9WUF3> ssb:participates_in  ?p.
 }
}

Anyway, I guess that a "semantic similarity of two genes/proteins"  
would suggest a score indicating how those two genes are "similar" or 
"dissimilar"; however, we avoided such score since the resources (GO, 
GOA) are constantly changing and that number might be biased by the 
current annotations...

cheers,
Erick
[1] http://www.semantic-systems-biology.org/biogateway/querying

huntley at ebi.ac.uk wrote:
> Hi,
>
> I have a user who has asked the following question;
>
> "i want a tool or website which compute semantic similarity of two
> genes based on their go annotation. is there any website which does that?"
>
> Does anyone have any suggestions?
>
> Many thanks,
> Rachael.
>
> GOA group
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
>
> Tel: +44 (0)1223 492 515
> email: huntley at ebi.ac.uk
>
> _______________________________________________
> Gofriends mailing list
> Gofriends at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/gofriends
>   
-- 
==================================================================
Erick Antezana                    http://www.cellcycleontology.org
PhD student                http://www.semantic-systems-biology.org
Tel:+32 (0)9 331 38 24                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology           Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
erant at psb.ugent.be                  http://www.psb.ugent.be/~erant
==================================================================



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