A Grep For Gene Ontology ?

Question

[Pierre Lindenbaum]

Is there a kind of grep for GeneOntology? I would like to filter a tsv file containing a gene/protein identifier having a Go annotation that would be a children of a given GO term. For example:

cat myfile.txt |\
gogrep -f <path-to-my-go-db> \
       -d <column delimiter> \
       -c <column-index-for-identifier> \
       -t <serched GO term  e.g: GO:0003146> \
       -s <identifier-type (uniprot...) > result.txt

Thanks
Pierre

Answer 1

[Ian Simpson]

There is a Perl package called GoPerl to traverse GO architecture which you could pull into a Perl script to do the same as you describe. Might be a bit of a sledge-hammer to crack a walnut though.

Answer 2

[Michael Kuhn]

You could probably query AmiGO, at least if you're doing this on a small scale: http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=UniProtKB/Swiss-Prot:P21728&format=go_assoc

(Though you in particular might prefer the RDF/XML format ;-)

Answer 3

[Khader Shameer]

I have used Onto-perl for something similar - you may give it a try : http://search.cpan.org/~easr/ONTO-PERL-1.10/. There are some sample scripts that will give you parent terms or child terms of a given term.