Section contents

• FAQ: Answers to frequently asked Gene Ontology questions
• An Introduction to the Gene Ontology: A description of the aims of the Gene Ontology Consortium and an explanation of how the ontologies work.
  Topics include:
  • What does the Gene Ontology Consortium do?
  • Terms in the Gene Ontology
  • The Ontologies
  • What GO is not
  • Annotation and Tools
  • Downloads
  • Beyond GO
  • Contributing to GO
• Annotation Guide: An introduction to annotation and the rules and SOPs used for annotating gene products to GO terms.
• Evidence Code Guide: Explanation of the codes that are used to indicate the nature of the evidence that supports a particular annotation.
• Component Ontology: Rules governing content and stylistic aspects of GO terms in the cellular component ontology.
  Topics include:
  • The Cell
  • Protein Complexes
  • Membranes and Envelopes
  • Membrane Proteins
• Function Ontology: Rules governing content and stylistic aspects of GO terms, standard definitions and term relationships in the molecular function ontology.
• Process Ontology: Rules governing content and stylistic aspects of GO terms, standard definitions and term relationships in the biological process ontology.
  Topics include:
  • The Cell Cycle
  • The Development Node
  • Interaction Between Organisms
  • Metabolism
  • Regulation
  • Detection of and Response to Stimulus
  • Sensory Perception
  • Signaling Pathways
  • Transport and Localization
• GO Database documentation: information about the GO database, including the database schema, accessing or downloading the database, and tips on usage
• File Format Guide: Syntax of the individual files.
  Topics include:
  • Anatomy of a GO Term
  • Ontology Flat File Formats
  • XML version
  • MySQL version
  • Mappings to Other Classification Systems
• OBO File Format Guide: the ontology file format used and recommended by the GO Consortium
• GO Annotation File Format Guide: the annotation (gene association) file format used by the GO Consortium
• GO Slim Guide: information about GO slims, cut-down versions of the ontologies useful for providing an overview of GO
• Meeting minutes: minutes from all GO meetings

Other Useful Links

• SourceForge links: Useful links for the SourceForge site, including both general and GO-specific pages.
• CVS Help: Help page for those who wish to access the anonymous GO CVS repository
• GO cardiovascular: information on the cardiovascular-related work on both GO annotation and ontology development.
• GO immunology: information on the immunology-related work on both GO annotation and ontology development.
• GO Editor Guides: A set of guides for curators editing the ontologies.
• Editorial Style Guide: Rules governing content and stylistic aspects of GO terms, such as phrasing, spelling, case, and so on.

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