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GO::Parsers::go_ont_parser.3pm

NAME

   GO::Parsers::go_ont_parser     - syntax parsing of GO .ontology flat files
 
 

SYNOPSIS

   do not use this class directly; use GO::Parser
 
 

DESCRIPTION

This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details

Examples of these files can be found at http://www.geneontology.org

A description of the event streams generated follows; Stag or an XML handler can be used to catch these events

GO ONTOLOGY FILES

These files have the .ontology suffix. The stag-schema for the event streams generated look like this:

   (ontology
    (source
      (source_type "s")
      (source_path "s")
      (source_mtime "i"))
    (term+
      (id "s")
      (name "s")
      (is_root? "i")
      (relationship+
        (type "s")
        (to "s"))
      (dbxref*
        (dbname "s")
        (acc "s"))
      (synonym* "s")
      (secondaryid* "s")
      (is_obsolete? "i")))
 
 

AUTHOR