[BioC] GO's to gene's

[Vincent Carey]

Perhaps there is a package with such functionality.  However, with the
GO.db package in place, you need to do a little
programming, perhaps along the lines of

querGO = function(str, attr = "definition", ont = "MF") {
  require(GO.db, quietly = TRUE)
  gc = GO_dbconn()
  quer.1 = paste("select go_id, term from go_term where",
  attr, "like('%")
  quer.2 = "%') and ontology = '"
  quer.3 = "'"
  quer = paste(quer.1, str, quer.2, ont, quer.3, collapse = "",
  sep = "")
  dbGetQuery(gc, quer)
}

whereby

> querGO("collagen", "term")
       go_id                                                           term
1 GO:0004656                     procollagen-proline 4-dioxygenase activity
2 GO:0005518                                               collagen binding
3 GO:0008475                      procollagen-lysine 5-dioxygenase activity
4 GO:0019797                     procollagen-proline 3-dioxygenase activity
5 GO:0019798                       procollagen-proline dioxygenase activity
6 GO:0033823                       procollagen glucosyltransferase activity
7 GO:0042329 structural constituent of collagen and cuticulin-based cuticle
8 GO:0050211                     procollagen galactosyltransferase activity
9 GO:0070052                                             collagen V binding
>


On Sun, Feb 28, 2010 at 8:56 PM, Loren Engrav <engrav at u.washington.edu> wrote:
> Is there a BioC package that will find all the GO terms containing some
> word, like perhaps ³collagen²
> And then find all the genes contained within those found terms
>
> I scanned
> GoProfiles
> GOSemSim
> GOstats
> GoTools and
> TopGO
>
> And could not determine that any would do that.
>
> Thank you.
>
>
>
>
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