Chris Mungall > go-perl-0.14 > GO::Model::Evidence;

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NAME ^

  GO::Model::Evidence;

SYNOPSIS ^

  my $ev_l = $association->evidence_list;
  foreach my $ev (@$ev_l) {
    print "Evidence for association %s : %s\n",
      $association->gene_product->symbol,
      $ev->code;
  }

DESCRIPTION ^

evidence for an association

see http://www.geneontology.org/GO.evidence.html for a list of evidence codes

code

  Usage   - $ev->code("IEA");
  Returns -
  Args    -

gets/sets the evidence code

see http://www.geneontology.org/GO.evidence.html

seq_acc

  Usage   -
  Returns -
  Args    -

gets/sets the sequence accesion GO::Model::Xref

ALPHA CODE - API may change

used to set the GO::Model::Xref list from a text string. eg

  $ev->seq_acc("SGD:RRP41; SGDID:L0003550");

will actually add two GO::Model::Xref objects

This method doesnt really belong in the GO::Model::* hierarchy as it contains parsing code. Its a minor hack mainly due to the fact that this data is still denormalized in the database.

add_seq_xref

  Usage   -
  Returns -
  Args    -

equivalent to WITH column in gene_association files, and evidence_dbxref tables in db

add_pub_xref

  Usage   -
  Returns -
  Args    -

xref

  Usage   -
  Returns -
  Args    -

gets/sets the literature or sequence reference GO::Model::Xref

NOTE: at some point we may want to deprecate this method and persuade API client code to call

  $ev->literature_xref

instead, to make explicit the fact that this is a literature reference as opposed to a sequence reference

xref_list

  Usage   -
  Returns - GO::Model::Xref listref
  Args    -

returns all (sequence and literature) references

xref

  Usage   -
  Returns -
  Args    -

deprected - sets first pub_xref_list

valid_codes

  Usage   - print join("; ", GO::Model::Evidence->valid_codes);
  Returns - string array
  Args    -

list of valid evidence codes

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