[BioC] Possible Data Bug in GO

[Marc Carlson]

Ben Woodcroft wrote:
> Hi,
>
> Apologies if I am missing something obvious. I wanted to get all the child
> terms of MF (molecular function, GO acc GO:0003674):
>
>   
>> library(GO)
>> get("GO:0003674", GOMFCHILDREN)
>>     
>          isa          isa          isa          isa          isa
> isa
> "GO:0000332" "GO:0003774" "GO:0003824" "GO:0005198" "GO:0005215"
> "GO:0005488"
>          isa          isa          isa          isa          isa
> isa
> "GO:0015457" "GO:0016209" "GO:0016530" "GO:0030188" "GO:0030234"
> "GO:0030528"
>          isa          isa          isa          isa          isa
> isa
> "GO:0031386" "GO:0042056" "GO:0045182" "GO:0045499" "GO:0045735"
> "GO:0060089"
>
>
> GO:0000332 is not a child (though it is a descendent) of molecular function:
> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0000332&session_id=8078b1205284490
>
> Any idea what I am missing? According to AMIGO, the rest of the terms there
> are correct (and that's the full set).
>
> Thanks in advance,
> ben
>
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>
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>   

First of all thanks for pointing this out. I have looked into why this
was happening and have found the cause to be the source files that come
from ftp.geneontology.org . As you observed, the error appears to only
affect the direct term to term association mapping for this one term. I
have notified them of the error and I anticipate that it will probably
be cleaned up very soon.

Marc