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[Gofriends] GO tool for semantic similarity

Wacek Kusnierczyk Waclaw.Marcin.Kusnierczyk at idi.ntnu.no
Sat Oct 11 05:50:48 PDT 2008


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.
what's interesting is the filter line: does biogateway consider GOA and
SSB organisms?

vQ



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