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GO::Parsers::go_assoc_parser.3pm

NAME

   GO::Parsers::go_assoc_parser     - syntax parsing of GO gene-association flat files
 
 

SYNOPSIS

DESCRIPTION

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

This generates Stag/XML event streams from GO association files. Examples of these files can be found at http://www.geneontology.org, an example of lines from an association file:

   SGD     S0004660        AAC1            GO:0005743      SGD:12031|PMID:2167309 TAS             C       ADP/ATP translocator    YMR056C gene    taxon:4932 20010118
   SGD     S0004660        AAC1            GO:0006854      SGD:12031|PMID:2167309 IDA             P       ADP/ATP translocator    YMR056C gene    taxon:4932 20010118
 
 

See <http://www.geneontology.org/GO.annotation.shtml#file>

See <http://www.godatabase.org/dev/xml/dtd/go_assoc-parser-events.dtd> For the DTD of the event stream that is generated

The following stag-schema describes the events that are generated in parsing an assoc file:

   (assocs
    (dbset+
      (proddb "s")
      (prod+
        (prodacc "s")
        (prodsymbol "s")
        (prodtype "s")
        (prodtaxa "i")
        (assoc+
          (assocdate "i")
          (source_db "s")
          (termacc "s")
          (is_not "i")
          (aspect "s")
          (evidence+
            (evcode "s")
            (ref "s"))))))