Chris Mungall > go-perl-0.14 > GO::Parsers::go_assoc_parser

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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")))))) 
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