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GO::Model::Evidence

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 doesn’t 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 -

deprecated - 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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