A Grep For Gene Ontology ?

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

gene go

• 5,305 views • link

updated 2.7 years ago by Ram

• written 16.3 years ago by Pierre Lindenbaum

3 answers

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.

• 27 views • link

updated 7.9 years ago by Ram

• written 16.3 years ago by Ian Simpson

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 ;-)

• 34 views • link

updated 2.7 years ago by Ram

• written 16.3 years ago by Michael Kuhn

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.

• 6 views • link

updated 7.9 years ago by Ram

• written 16.3 years ago by Khader Shameer