GO::Model::Relationship - GO::Model::Relationship documentation

go-perl documentation Contained in the go-perl distribution.

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NAME

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  GO::Model::Relationship

SYNOPSIS

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DESCRIPTION

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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

go-perl documentation Contained in the go-perl distribution. 
# $Id: Relationship.pm,v 1.6 2006/10/19 18:38:28 cmungall Exp $
#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
#          - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself

package GO::Model::Relationship;



use Carp;
use Exporter;
use GO::Utils qw(rearrange);
use GO::Model::Root;
use strict;
use vars qw(@ISA);

@ISA = qw(GO::Model::Root Exporter);

sub _valid_params {
    return qw(acc1 acc2 is_inheritance complete type);
}


sub _initialize {
    my $self = shift;
    $self->SUPER::_initialize(@_);
}

sub acc1 {
    my $self = shift;
    $self->{"acc1"} = shift if @_;
    return $self->{"acc1"};
}
*obj_acc = \&acc1;
*object_acc = \&acc1;
*parent_acc = \&acc1;

sub acc2 {
    my $self = shift;
    $self->{"acc2"} = shift if @_;
    return $self->{"acc2"};
}
*subj_acc = \&acc2;
*subject_acc = \&acc2;
*child_acc = \&acc2;



sub type {
    my $self = shift;
    if (@_) {
	my $type = shift;
	if ($type) {
            $self->{type} = $type;
        }
    }
    return $self->{type} || "unknown";
}

sub is_obsolete {
    my $self = shift;
    $self->{is_obsolete} = shift if @_;
    return $self->{is_obsolete} ? 1:0;
}

sub as_str {
    my $self = shift;
    sprintf("%s:%s:%s", $self->type, $self->acc1, $self->acc2);
}

sub to_ptuples {
    my $self = shift;
    warn("deprecated");
    my ($th) =
      rearrange([qw(tuples)], @_);
    (["rel", $self->type, $self->acc1, $self->acc2]);
}



sub is_inheritance {
    my $self = shift;
    warn("deprecated");
    if (@_) {
	my $is = shift;
	$is && $self->type("isa");
	!$is && $self->type("partof");
    }
    return $self->type eq "isa";
}

1;