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[Gofriends] GO tool for semantic similarity

Iddo Friedberg idoerg at gmail.com
Sat Oct 11 08:51:01 PDT 2008


There are various measures of semantic similarity using the GO DAG.  The
most commonly used is Lord's:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/10/1275

But there are others. See the citing papers.

Iddo

On Sat, Oct 11, 2008 at 5:04 AM, Erick Antezana <erant at psb.ugent.be> 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...
>
> 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<http://www.psb.ugent.be/%7Eerant>
> ==================================================================
>
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> http://fafner.stanford.edu/mailman/listinfo/gofriends
>



-- 
Iddo Friedberg, Ph.D.
Atkinson Hall, mail code 0446
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0446, USA
T: +1 (858) 534-0570
http://iddo-friedberg.org
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