Reference

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

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