[Gofriends] GO tool for semantic similarity

[Erick Antezana]

Hi Wacek,

Wacek Kusnierczyk wrote:
> Erick Antezana wrote:
>   
>> 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...
>>
>>     
>
> at the moment, it shows 6 protein identifiers.
>   
yes, indeed, there are 6 instead of 8 (typo ;-))
> what's interesting is the filter line: does biogateway consider GOA and
> SSB organisms?
>   
no, SSB and GOA are RDF graphs. I just added that filter (as a trick) to 
also get the "?organism" variable pointing out to the organism. 
Alternatively, you can use the following query:

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  ?protein_name ?uniprot_id
WHERE {
GRAPH <SSB> {
  ?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.
}
}

cheers,
Erick
> vQ
>   
-- 
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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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