View source for GO Graphic Viewer

==Description==

The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the [http://genome-www5.stanford.edu/ Stanford Microarray Database (SMD)]. This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in Web-based user interfaces (goView.pl and goTermFinder.pl). It is a component of the Generic Model Organism Systems Database project.


==Demo & Screenshots==

[http://seq.yeastgenome.org/cgi-bin/GMOD/goTermFinder.pl Demo at Stanford]

==Requirements==

* The Apache web server ([http://www.apache.org http://www.apache.org/])
* Perl 5.005 or higher
* [http://search.cpan.org/search?query=GD GD.pm]
* [http://search.cpan.org/search?query=CGI CGI.pm]
* [http://www.graphviz.org/ GraphViz]
* [http://search.cpan.org/dist/GO-TermFinder/ GO::TermFinder]
* [http://bioperl.org Bioperl]


==Documentation==

From the README:

The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that 
displays the parent and child relationships of a selected GO term. Two 
examples of its use in web-based user interfaces are included, goView.pl and 
goTermFinder.pl.  

The goView.pl program uses the Bio::GMOD::GO::View module to create a 
web-based user interface that can be used to view and browse the Gene Ontology. 
The terms are color coded based on whether they have child terms. A blue box 
indicates that the term has child terms while a gray box indicates that the term 
does not have child terms. Clicking on a blue box will expand that branch of the 
ontology. The blue up arrow indicates that there are additional parent terms
available for the selected GO term.  Clicking on the up arrow will display the 
parents of the selected GO term.

The goTermFinder.pl program combines the Bio::GMOD::GO::View module with the 
GO::TermFinder module to create a user-friendly resource for analyzing and viewing 
GO terms that are shared by a group of genes. The Bio::GMOD::GO::View will display 
the ontology based on the GO terms that are common among a group of genes (as 
determined by the GO::TermFinder module). The boxes will be color-coded to indicate 
how significant a GO term is as a parent for a given group of genes. In addition, 
GO terms from the gene-association files that cannot be found in the ontology files 
will be displayed at the top of the graphic.

This distribution includes the Bio::GMOD::GO::View module, an example of the 
Bio::GMOD::GO::View module used in a web-based interface (goView.pl), and the 
Bio::GMOD::GO::View module as a web-based interface in conjunction with the 
GO::TermFinder (goTermFinder.pl). 


==Contact==

[[Shuai Weng]]


==Downloads==

[http://sourceforge.net/project/showfiles.php?group_id=27707 From SourceForge]


[[Category:GMOD Components]]
Available on platform	web +, linux +, os x + and unix +
Has URL	http://sourceforge.net/projects/gmod/files/GOView/ + and http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl +
Has description	The GO Graphic Viewer module (Bio::GMOD::G … The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in web browser-based user interfaces (goView.pl and goTermFinder.pl).nterfaces (goView.pl and goTermFinder.pl). +
Has development status	inactive +
Has input format	gene or ORF names + and OBO ontology +
Has software maturity status	mature +
Has support status	active +
Has topic	GO Graphic Viewer +
Is open source	Yes +
Link type	source code + and public server +
Release date	2003 +
Tool functionality or classification	Ontology Visualization +
Written in language	Perl +
Has subobjectThis property is a special property in this wiki.	GO Graphic Viewer#http://sourceforge.net/projects/gmod/files/GOView/ + and GO Graphic Viewer#http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl +