A Grep For Gene Ontology ?
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4
Entering edit mode
11.8 years ago

Is there a kind of grep fro 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 filter • 3.7k views
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5
Entering edit mode
11.8 years ago
Ian Simpson ▴ 960

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.

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4
Entering edit mode
11.8 years ago

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 ;-)

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3
Entering edit mode
11.8 years ago

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.

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