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Fwd: Help

Anand Kumar anand.kumar at ifomis.uni-leipzig.de
Wed Aug 4 00:04:36 PDT 2004


Danny,

Have you looked into example SQLs at
http://www.godatabase.org/dev/index.html

You should also wait till Chris Mungal gets back from Glasgow after ISMB and he might be able to help you with scripts, should the SQLs be not enough.

Anand.

Am Di 03.08.2004 14:40, John Richter <jrichter at bdgp.lbl.gov> schrieb:

> 
> Another option would be to use the DAG-Edit search/filter facility. You would
> create a search that looked something like:
> 
> "Term" has "descendant" with "id" that "equals" [Whatever parent id]
> 
> Note that you would either need to run a new search for each parent id you
> wanted to find, or you would have to create a boolean OR filter to wrap the
> search for each individual id.
> 
>        -John
> 
> > ---------- Forwarded message ----------
> > From: Danny Yoo <danny.yoo at gmail.com>
> > Date: Mon, 2 Aug 2004 18:30:30 +0000
> > Subject: Re: Help
> > To: "Benoist, Christophe" <christophe.benoist at joslin.harvard.edu>
> > 
> > On Mon, 2 Aug 2004 08:01:52 -0400, Benoist, Christophe
> > <christophe.benoist at joslin.harvard.edu> wrote:
> > > Help !
> > > We are trying to obtain lists of all GO numbers that are children or
> grandchildren of a given GO number (list below, if anyone is tempted). Can't
> find any such function on any of the sites. Any suggestions as how to proceed,
> and/or strategy that would do the trick?
> > 
> > 
> > Hi Christophe,
> > 
> > Using the GO API might be a good way to do this.  For example:
> > 
> > ###
> > #!/usr/bin/perl -w
> > 
> > ## Small program to print out the descendents of a particular term.
> > ## Arguments: argv[0]:  acc number
> > 
> > use strict;
> > use warnings;
> > use GO::AppHandle;
> > use GO::Parser;
> > 
> > my $graph = getGraph();
> > my $term = $graph->get_term({acc=>$ARGV[0]});
> > printChildren($graph, $term);
> > 
> > ## Note: to make this faster, use the database instead of the flat
> > ## files as a source.
> > sub getGraph {
> >     my $parser = GO::Parser->new({handler => "obj"});
> >     $parser->parse("component.ontology");
> >     my $graph = $parser->handler->graph;
> >     return $graph;
> > }
> > 
> > ## Prints a list of a term's descendents
> > sub printDescendents {
> >     my ($graph, $term) = @_;
> >     my $iter = $graph->create_iterator($term);
> >     while (my $t = $iter->next_node) {
> >         print $t->{name}, "\t", $t->acc, "\n";
> >     }
> > }
> > ###
> > 
> > This program is written to read off the flat files, but you can easily
> > change it to read from the MySQL database instead.  Here's a sample of
> > what it does:
> > 
> > ###
> > [dyoo at tesuque ontology]$ perl find_children.pl GO:0048196
> > extracellular matrix (sensu Magnoliophyta)      GO:0048196
> > primary cell wall       GO:0009530
> > cellulose microfibril   GO:0009549
> > glycoprotein network    GO:0048222
> > hemicellulose network   GO:0048223
> > pectic matrix   GO:0048217
> > secondary cell wall     GO:0009531
> > Casparian strip GO:0048226
> > cellulose microfibril   GO:0009549
> > hemicellulose network   GO:0048223
> > lignin network  GO:0048224
> > pectic matrix   GO:0048217
> > suberin network GO:0048225
> > ###
> > 
> > See:
> > 
> >     http://www.godatabase.org/dev/
> > 
> > for more details about the perl-api module.  Hope this helps!
> > 
> > --
> > This message is from the GOFriends moderated mailing list.  A list of public
> > announcements and discussion of the Gene Ontology (GO) project.
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> > 
> -- 
> 
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends at geneontology.org
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> 

Anand Kumar MBBS, PhD
IFOMIS
Faculty of Medicine
University of Leipzig
Härtelstraße 16-18
04107 Leipzig
Germany
http://www.uni-leipzig.de/~akumar/







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