Difference between revisions of "GO Graphic Viewer"

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==Description==
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{{Tool data
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|use template=yes
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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.
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|name=GO Graphic Viewer
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|full name=
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|status=mature
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==Demo & Screenshots==
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|dev=inactive
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|support=active
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[http://seq.yeastgenome.org/cgi-bin/GMOD/goTermFinder.pl Demo at Stanford]
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|type=Ontology Visualization
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|platform=web, linux, os x, unix
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|about=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).
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==Requirements==
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|gmod date=2003
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|release date=2003
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* The Apache web server ([http://www.apache.org http://www.apache.org/])
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|open source=Yes
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|licence=
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|language=Perl
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|input=gene or ORF names, OBO ontology
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|output=
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|audience=Public
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|logo=
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|screenshot=
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|dl=
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|contact email=For support, please contact the GO Graphic Viewer developer, [mailto:sweng@stanford.edu Shuai Weng].
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|integration=
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|papers=
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|presentations=
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|tutorials=
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|getting started preamble=
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|req=
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* [http://www.apache.org Apache web server]
 
* Perl 5.005 or higher
 
* Perl 5.005 or higher
 
* {{CPAN|GD}}
 
* {{CPAN|GD}}
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* {{CPAN|GO::TermFinder}}
 
* {{CPAN|GO::TermFinder}}
 
* [http://bioperl.org Bioperl]
 
* [http://bioperl.org Bioperl]
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|install=
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|config=
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==Documentation==
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|doc=Documentation is provided in the README file in the [http://sourceforge.net/projects/gmod/files/GOView/ GO Graphic Viewer download package].
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|dev ppl=Gavin Sherlock, Stanford University
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From the README:
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|dl tracking=
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The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that
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|logo info=
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displays the parent and child relationships of a selected GO term. Two
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|see also=
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examples of its use in web-based user interfaces are included, goView.pl and
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|extra=
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goTermFinder.pl. 
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}}
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{{SemanticLink
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The goView.pl program uses the Bio::GMOD::GO::View module to create a
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|linkurl=http://sourceforge.net/projects/gmod/files/GOView/
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web-based user interface that can be used to view and browse the Gene Ontology.
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|linktype=source code
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The terms are color coded based on whether they have child terms. A blue box
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}}
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indicates that the term has child terms while a gray box indicates that the term
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{{SemanticLink
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does not have child terms. Clicking on a blue box will expand that branch of the
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|linkurl=http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl
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ontology. The blue up arrow indicates that there are additional parent terms
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|linktype=public server
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available for the selected GO term.  Clicking on the up arrow will display the
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}}
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parents of the selected GO term.
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The goTermFinder.pl program combines the Bio::GMOD::GO::View module with the
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GO::TermFinder module to create a user-friendly resource for analyzing and viewing
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GO terms that are shared by a group of genes. The Bio::GMOD::GO::View will display
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the ontology based on the GO terms that are common among a group of genes (as
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determined by the GO::TermFinder module). The boxes will be color-coded to indicate
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how significant a GO term is as a parent for a given group of genes. In addition,
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GO terms from the gene-association files that cannot be found in the ontology files
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will be displayed at the top of the graphic.
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This distribution includes the Bio::GMOD::GO::View module, an example of the
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Bio::GMOD::GO::View module used in a web-based interface (goView.pl), and the
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Bio::GMOD::GO::View module as a web-based interface in conjunction with the
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GO::TermFinder (goTermFinder.pl).
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==Contact==
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[[Shuai Weng]]
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==Downloads==
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[http://sourceforge.net/project/showfiles.php?group_id=27707 From SourceForge]
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[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
 
[[Category:Ontologies]]
 
[[Category:Ontologies]]
 
[[Category:SGD]]
 
[[Category:SGD]]
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[[Category:GMOD Component]]

Latest revision as of 23:44, 3 December 2013

Status
  • Mature release
  • Development: inactive
  • Support: active


{{{PAGENAME}}} is open source
Resources


About GO Graphic Viewer

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).



Downloads

Using GO Graphic Viewer

System Requirements


Documentation

Documentation is provided in the README file in the GO Graphic Viewer download package.



Contacts and Mailing Lists

GO Graphic Viewer Development

Development team

Gavin Sherlock, Stanford University


More on GO Graphic Viewer

Retrieved from "http://gmod.org/mediawiki/index.php?title=GO_Graphic_Viewer&oldid=24899"
Facts about "GO Graphic Viewer"RDF feed
Available on platformweb +, linux +, os x + and unix +
Has URLhttp://sourceforge.net/projects/gmod/files/GOView/ + and http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl +
Has descriptionThe 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 statusinactive +
Has input formatgene or ORF names + and OBO ontology +
Has software maturity statusmature +
Has support statusactive +
Has topicGO Graphic Viewer +
Is open sourceYes +
Link typesource code + and public server +
Release date2003 +
Tool functionality or classificationOntology Visualization +
Written in languagePerl +
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 +