go::model::evidence(3pm) [debian man page]

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)

GO::Model::Relationship(3pm)				User Contributed Perl Documentation			      GO::Model::Relationship(3pm)

NAME

	 GO::Model::Relationship - relationship between two terms

SYNOPSIS

DESCRIPTION

       a relationship between two GO::Model::Terms

       relationships can be thought of as statements or sentences of the form

	 SUBJECT-TERM PREDICATE OBJECT-TERM

       for example,

	 "dog" IS_A "animal"

	 "G-Protein coupled receptor" IS_A "transmembrane receptor"

       Statements have a subject (i.e. the subject of the sentence/statement), a predicate/relationship-type and an object (i.e. the object of the
       sentence/statement)

       Relationships can also be seen as arcs in a directed graph, with the subject being equivalent to the child, and the object equivalent to
       the parent. The arc is labeled with the predicate/relationship-type.

       A Relationship object currently does not contain an actual pointer to a GO::Model::Term object. Instead it stores the ID of that term. This
       is intended to be used in conjunction with the Graph object, or with the database.

   subject_acc
	Title	: subject_acc
	Usage	: $obj->subject_acc($newid)
	Usage	: $currid = $obj->subject_acc()
	Synonyms: subj_acc, acc2, child_acc
	Function: gets or sets the identifier for the child/subject term
	Example :
	Returns : value of subject_acc (string)
	Args	: on set, new value (string)

       All Relationships can be thought of "subject-predicate-object" statements. The statement is *about* the subject, and states something about
       the relationship *to* the object.

       For example, the if we have a Relationship:

	 cell
	   ^
	   |
	   | [part_of]
	   |
	cell nucleus

       This is a statement about cell nuclei in general, so "cell nucleus" is the subject (sometimes called the child node). The Relationship
       tells us that all cell nuclei are part_of some cell, so the object of the relationship (sometimes called the parent node) is "cell"

   object_acc
	Title	: object_acc
	Usage	: $obj->object_acc($newid)
	Usage	: $currid = $obj->object_acc()
	Synonyms: obj_acc, acc1, parent_acc
	Function: gets or sets the identifier for the parent/object term
	Example :
	Returns : value of object_acc (string)
	Args	: on set, new value (string)
	See Also: subj_acc

   type
	Title	: type
	Usage	: $obj->type($newval)
	Usage	: $currval = $obj->type()
	Synonyms:
	Function: gets or sets the relationship type (a string)
	Example :
	Returns : value of type (string)
	Args	: on set, new value (string)

       Currently any string is allowed; in future the type string may be constrained to come from a controlled vocabulary of relationship types

perl v5.14.2							    2013-02-07					      GO::Model::Relationship(3pm)