[BioC] GOLOCUSID

[Marc Carlson]

Hi John,

Because the KEGG pathway IDs have a species specific ID in front of
them, those can still be found in KEGG.db.  Look for the
KEGGPATHID2EXTID and KEGGEXTID2PATHID mappings.

  Marc




John Lande wrote:
> thank you very much,
>
> for the gene ontology worked. I remeber there was something similar
> for Kegg pathways. is there something similar now?
>
> thank you
>
>
>
> On Mon, Mar 16, 2009 at 4:52 PM, Marc Carlson <mcarlson at fhcrc.org
> <mailto:mcarlson at fhcrc.org>> wrote:
>
>     Hi John,
>
>     Saroj is correct in that you should find the mappings you seek in the
>     appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial
>     of the genus and species of the organism you are studying).  You
>     probably want to look at the GO2ALLEGS mapping.
>
>      Marc
>
>
>
>     Saroj K Mohapatra wrote:
>     > Hi John:
>     >
>     > I do not have a general answer. However, the "org." packages do
>     have a mapping from GO to Entrez gene. For example, there is the
>     mouse package org.Mm.eg.db that has org.Mm.egGO which maps between
>     the two identifiers.
>     >
>     >> library("org.Mm.eg.db")
>     >> ?org.Mm.egGO2EG
>     >>
>     >
>     > -----------
>     >      org.Mm.egGO is an R object that provides mappings between
>     entrez
>     >      gene identifiers and the GO identifiers that they are  directly
>     >      associated with. This mapping and its reverse mapping do NOT
>     >      associate the child terms from the GO ontology with the gene.
>     >      Only the directly evidenced terms are represented here.
>     > -----------
>     >
>     > You could use the appropriate org package for your species.
>     >
>     > Hope this helps,
>     >
>     > Saroj
>     >
>     > ----- Original Message -----
>     > From: "John Lande" <john.lande77 at gmail.com
>     <mailto:john.lande77 at gmail.com>>
>     > To: bioconductor at stat.math.ethz.ch
>     <mailto:bioconductor at stat.math.ethz.ch>
>     > Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern
>     > Subject: [BioC] GOLOCUSID
>     >
>     > dear Bioc,
>     >
>     > I have retrieved an old stript to extract genes associated with
>     a specific
>     > GO term from a previous release of BioC.
>     >
>     > it exploited the enviroment GOLOCUSID form the package GO.
>     >
>     > thei enviroment is no longer available in the current release
>     bioc 2.3.
>     > is there an equivalent enviroment in some other package?
>     >
>     > how can I retrieve the genes associated with a specific go term
>     in bioc now.
>     >
>     > thank you
>     >
>     >       [[alternative HTML version deleted]]
>     >
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