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GO::Model::Evidence.3pm

NAME

   GO::Model::Evidence - evidence for an association
 
 

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