[BiO BB] Extracting GeneNames from a GO class and their syblings

[Dan Bolser]

On 28/11/2007, Gaj Stan (BIGCAT) <Stan.Gaj at bigcat.unimaas.nl> wrote:
> Dear all,
>
>
>
> My question today concerns GeneOntology annotation extraction. Is it
> possible to extract a list of genes which belong to a specific
> GO-process and it's children?
>
>
>
> Or, to put it in a more clearer context:
>
>
>
> - I'm interested in all genes belonging to the Lipid Metabolic process
> category (GO:0006629 : lipid metabolic process
> <http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_
> constraint=terms&depth=0&query=GO:0006629&session_id=4045b1196258143&sho
> w_associations=list>  ).
>
> - I aim to have a list of ALL genes that belong to this GO category or
> below, up untill the smallest, most specific node (i.e. cellular lipid
> metabolic process
> <http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_
> constraint=terms&depth=0&query=GO:0044255&session_id=4045b1196258143&sho
> w_associations=list>   -> cellular lipid catabolic process
> <http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_
> constraint=terms&depth=0&query=GO:0044242&session_id=4045b1196258143&sho
> w_associations=list>   --> etc)
>
> - This list can afterwards be filtered for duplicate names / IDs using
> Perl or something similar (can do that part myself (-; )
>
> - In the end, I would like to have a list that consists of gene names or
> any other usable ID(i.e. like EnsEMBL, UniProt, EntrezGene, ...) which
> are classfied as having a Lipid Metabolic activity!
>
>
>
> Is there a specific GO-Tool available (or am I unaware that this is even
> possible in GO itself) that can do this? If the solution presents itself
> by using R and specific GO-libraries, then I'm eager to hear about it as
> well (-: (since I know it is possible to extract both parent and
> children nodes, but am unaware on how to do this for gene names/IDs).

Sounds like an interesting (if not uncommon) request.... You should be
able to achieve this using the 'go-database', which you can find under
here;

http://www.geneontology.org/


Seems that you need to traverse the hierarchy, querying a specific
mapping as you go (performing iterative SQL queries via Perl should
allow you to do this). I don't know why the database dump isn't
provided in a convenient tab delimited format.

You can try asking for a more direct solution on either the "GO
Friends" mailing list or the "GO Database" mailing list, here;

http://www.geneontology.org/GO.mailing.lists.shtml


Which reminds me... (more in the next email).


Dan.

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