Question: A Grep For Gene Ontology ?
4
gravatar for Pierre Lindenbaum
9.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

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

filter gene • 2.9k views
ADD COMMENTlink modified 9 months ago by RamRS21k • written 9.2 years ago by Pierre Lindenbaum120k
5
gravatar for Ian Simpson
9.2 years ago by
Ian Simpson910
Edinburgh
Ian Simpson910 wrote:

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.

ADD COMMENTlink modified 9 months ago by RamRS21k • written 9.2 years ago by Ian Simpson910
4
gravatar for Michael Kuhn
9.2 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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 ;-)

ADD COMMENTlink written 9.2 years ago by Michael Kuhn5.0k
3
gravatar for Khader Shameer
9.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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.

ADD COMMENTlink modified 9 months ago by RamRS21k • written 9.2 years ago by Khader Shameer18k
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