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GO::Model::Evidence(3pm) User Contributed Perl Documentation 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 ", $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 perl v5.14.2 2013-02-07 GO::Model::Evidence(3pm)
