Provided by: libgo-perl_0.15-1_all 
NAME
GO::Model::Graph - a collection of relationships over terms
SYNOPSIS
# FETCHING GRAPH FROM FILES
use GO::Parser;
my $parser = new GO::Parser({handler=>'obj'});
$parser->parse("gene_ontology.obo"); # ontology
$parser->parse("gene-associations.sgd"); # gene assocs
# get L<GO::Model::Graph> object
my $graph = $parser->handler->graph;
my $terms = $graph->term_query("/transmembrane/"); # matching terms
foreach my $term (@$terms) {
# find gene products associated to this term
my $assocs = $graph->deep_association_list($term->acc);
printf "Term: %s %s\n", $term->acc, $term->name;
print " Associations (direct and via transitive closure_\n";
foreach my $assoc (@$assocs) {
next if $assoc->is_not;
printf " Assoc evidence: %s to: %s %s\n",
join(';', map {$_->code} @{$assoc->evidence_list}),
$assoc->gene_product->xref->as_str,
$assoc->gene_product->symbol;
}
}
# -- alternatively, use this code... --
# FETCHING FROM DATABASE (requires go-db-perl library)
# pretty-printing a subgraph from "nuclear pore"
$apph = GO::AppHandle->connect(-dbname=>"$dbname");
$term = $apph->get_term({name=>"nuclear pore"});
$graph =
$apph->get_graph_by_terms([$term], $depth);
$it = $graph->create_iterator;
# returns a GO::Model::GraphIterator object
while (my $ni = $it->next_node_instance) {
$depth = $ni->depth;
$term = $ni->term;
$reltype = $ni->parent_rel->type;
printf
"%s %8s Term = %s (%s) // number_of_association=%s // depth=%d\n",
"----" x $depth,
$reltype,
$term->name,
$term->public_acc,
$term->n_associations || 0,
$depth;
}
DESCRIPTION
Object containing Nodes (GO::Model::Term objects) and relationships
(:<GO::Model::Relationship> objects)
this may be either the whole ontology tree, or a subgraph, depending on how the object is
instantiated.
ONTOLOGY GRAPH MODEL
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.
perl doesnt handle bidirectional links between objects too well, so rather than having the
relationship object know about the terms or the term know about the realtionships, all the
graph info is in the Graph object
the Relationship object gives you the accessions of the related terms, use the Graph
methods to fetch these actual terms.
The idea is to keep the Term & Relationship objects lightweight, and keep the Graph logic
in the Graph object. The Graph object is responsible for stuff like making sure that a
Term object is not instantiated twice if it can be reached by two different paths.
Currently all graphs are acyclic, cyclic graphs may be allowed in the future when such
relationships are added to GO/OBOA
TRANSITIVE CLOSURES
graph object will calculate transitive closures for you - that is it
will follow the path in the graph to the root or to all leafs
ITERATORS
Using the create_iterator and iterate methods, you can create "visitors" that will
traverse the graph, performing actions along the way. Functional-style programming is
encouraged, as the iterature() method allows for the passing of lexical closures:
$graph->iterate(sub {$term=shift->term;
printf "%s %s\n", $term->acc,$term->name},
{direction=>'up',
acc=>"GO:0008045"})
SEE ALSO
go-perl GO::Model::Term GO::Parser GO::AppHandle
new
Usage - $g = GO::Model::Graph->new;
Returns - GO::Model::Graph;
Args -
Normally you would not create a graph object yourself - this is typically done for you by
either a GO::Parser object or a GO::AppHandle object
create_iterator
Usage - $it = $graph->create_iterator("GO:0003677")
Usage - $it = $graph->create_iterator({acc=>"GO:0008045",
direction=>"up"});
Returns - GO::Model::GraphIterator;
Args - accession no [optional] or GO::Model::Term [optional]
makes a GO::Model::GraphIterator, an object which traverses the graph
iterate
Usage - $graph->iterate(sub {$ni=shift;printf "%s\n", $ni->term->name});
Usage - sub mysub {...}; $graph->iterate(\&mysub);
Returns -
Args - CODE
iterates through the graph executing CODE on every GO::Model::GraphNodeInstance object
term_filter
Alias - node_filter
Usage - $terms =
$graph->term_filter(sub {shift->term->name =~ /transmembrane/});
Usage - sub mysub {...}; $graph->iterate(\&mysub);
Returns - ref to an array of GO::Model::Term objects
Args - CODE
iterates through the graph executing CODE on every GO::Model::GraphNodeInstance object. If
CODE returns true, that node will be returned
term_query
Usage - $terms = $graph->term_query({name=>'/transmembrane/'});
Usage - $terms = $graph->term_query({acc=>'GO:0008045'});
Usage - $terms = $graph->term_query('/transmembrane/');
Returns - ref to an array of GO::Model::Term objects
Args - hashref of constraints
OR name constraint as string
returns a set of terms matching query constraints. If the constraint value is enclosed in
// a regexp match will be performed
constraints are ANDed. For more complex queries, use node_filter()
subgraph
Usage - my $subgraph = $graph->subgraph({acc=>"GO:0008045"});
Returns - GO::Model::Graph
Args - as term_query()
creates a subgraph of the current graph containing the terms returned by a term_query()
call and all paths to the root
subgraph_by_terms
Usage - my $subgraph = $graph->subgraph_by_terms($terms);
Usage - my $subgraph = $graph->subgraph_by_terms($terms,{partial=>1});
Returns - GO::Model::Graph
Args - GO::Model::Term listref
creates a subgraph of the current graph containing the specified terms
The path-to-top will be calculated for all terms and added to the subgraph, UNLESS the
partial option is set; in this case a relationship between
get_all_nodes
Usage - my $node_listref = $graph->get_all_nodes();
Synonyms- get_all_terms
Returns - ref to an array of GO::Model::Term objects
Args - none
The returned array is UNORDERED
If you want the returned list ordered (eg breadth first or depth first) use the
create_iterator() method to get a GO::Model::GraphIterator
See also GO::Model::Term
get_term
Usage - my $term = $graph->get_term($acc);
Synonyms- get_node
Returns - GO::Model::Term
Args - id
returns a GO::Model::Term object for an accession no.
the term must be in the Graph object
See also GO::Model::Term
get_term_by_name
Usage - my $term = $graph->get_term_by_name("blah");
Returns - GO::Model::Term
Args - string
returns a GO::Model::Term object for a name
the term must be in the Graph object
CASE INSENSITIVE
See also GO::Model::Term
get_terms_by_subset
Usage - my $term = $graph->get_terms_by_subset("goslim_plant");
Returns - GO::Model::Term
Args - string
returns a GO::Model::Term object for a subset
the term must be in the Graph object
CASE INSENSITIVE
See also GO::Model::Term
get_top_nodes
Usage - my $node_listref = $graph->get_top_nodes();
Synonyms- get_top_terms
Returns - ref to an array of GO::Model::Term objects
Args - none
usually returns 1 node - the root term
See also GO::Model::Term
get_leaf_nodes
Usage - my $node_listref = $graph->get_top_nodes();
Synonyms- get_leaf_terms
Returns - ref to an array of GO::Model::Term objects
Args - none
See also GO::Model::Term
is_leaf_node
Usage - if ($graph->is_leaf_node($acc)) {...}
Returns - bool
Args - accession str
See also GO::Model::Term
seed_nodes
Usage - $nodes = $graph->seed_nodes;
Returns - GO::Model::Term listref
Args - GO::Model::Term listref [optional]
gets/sets the "seed" nodes/terms - these are the terms the Graph is started from, e.g. for
building a node ancestory graph, the seed term would be the leaf of this graph, but not
term that are expanded or collpased from the ancestory graph.
This is mostly relevant if you are fetching your graphs from a database via go-db-perl
See also GO::Model::Term
focus_nodes
Usage - $nodes = $graph->focus_nodes;
Synonyms- focus_terms
Returns - GO::Model::Term listref
Args - GO::Model::Term listref [optional]
gets/sets the "focus" nodes/terms - these are the terms the Graph is centred around; for
instance, if the graph was built around a query to "endoplasmic*" all the terms matching
this string would be focused
This is mostly relevant if you are fetching your graphs from a database via go-db-perl
See also GO::Model::Term
is_focus_node
Usage - if ($g->is_focus_node($term)) {..}
Returns - bool
Args - GO::Model::Term
add_focus_node
Usage - $g->add_focus_node($term)
Returns -
Args - GO::Model::Term
See also GO::Model::Term
paths_to_top
Usage - my $paths = $graph->paths_to_top("GO:0005045");
Returns - arrayref of GO::Model::Path objects
Args -
See also GO::Model::Path
node_count
Usage - my $count = $g->node_count
Synonyms- term_count
Returns - int
Args -
returns the number of terms/nodes in the graph
See also GO::Model::Term
n_associations
Usage - my $count = $g->n_associations($acc);
Returns - int
Args -
if you parsed an association file into this graph, this will return the number of
instances attached directly to acc
See also GO::Model::Association See also GO::Model::GeneProduct
n_deep_associations
Usage - my $count = $g->n_deep_associations($acc);
Returns - int
Args -
if you parsed an association file into this graph, this will return the number of
instances attached directly to acc OR to a node subsumed by acc
See also GO::Model::Association See also GO::Model::GeneProduct
n_children
Usage - $n = $graph->n_children('GO:0003677');
Synonyms- n_sterms, n_subj_terms, n_subject_terms
Returns - int
Args -
returns the number of DIRECT children/subject/subordinate terms beneath this one
n_parents
Usage - $n = $graph->n_parents(3677);
Synonyms- n_oterms, n_obj_terms, n_object_terms
Returns - int
Args -
returns the number of DIRECT parent/object/superordinate terms above this one
association_list
Usage - $assocs = $g->association_list('GO:0003677')
Returns - listref of GO::Model::Association
Args - acc (string)
returns a list of association objects directly attached to the specified term
See also GO::Model::Association
get_direct_associations
Usage -
Returns -
Args -
See also GO::Model::Association
deep_association_list
Usage - $assocs = $g->association_list('GO:0003677')
Returns - listref of GO::Model::Association
Args - acc (string)
returns a list of association objects directly and indirectly attached to the specified
term. (ie assocs attached to the term or to terms subsumed by the specified term).
See also GO::Model::Association
product_list
Usage - $prods = $g->product_list('GO:0003677')
Returns - listref of GO::Model::GeneProduct
Args - acc (string)
returns a list of distinct gene product objects directly attached to the specified term.
See also GO::Model::GeneProduct
deep_product_list
Usage - $prods = $g->deep_product_list('GO:0003677')
Returns - listref of GO::Model::GeneProduct
Args - acc (string)
returns a list of distinct gene product objects directly and indirectly attached to the
specified term. (ie assocs attached to the term or to terms subsumed by the specified
term).
See also GO::Model::GeneProduct
deep_product_count
Usage - $n_prods = $g->deep_product_count('GO:0003677')
Returns - int
Args - acc (string)
returns a count of distinct gene product objects directly and indirectly attached to the
specified term. performs transitive closure. will not count gene products twice
See also GO::Model::GeneProduct
get_relationships
Usage - my $rel_listref = $graph->get_relationships('GO:0003677');
Returns - ref to an array of GO::Model::Relationship objects
Args - identifier/acc (string)
returns relationships which concern the specified term; the specified term can be the
subject or object term in the relationship (ie child or parent)
See also GO::Model::Relationship
get_parent_relationships
Usage - my $rel_listref = $graph->get_parent_relationships('GO:0003677');
Synonym - get_relationships_by_child
Synonym - get_relationships_by_subj
Synonym - get_relationships_by_subject
Synonym - get_obj_relationships
Synonym - get_object_relationships
Returns - ref to an array of GO::Model::Relationship objects
Args - identifier/acc (string)
See also GO::Model::Relationship
get_child_relationships
Usage - my $rel_listref = $graph->get_child_relationships('GO:0003677');
Synonym - get_relationships_by_parent
Synonym - get_relationships_by_obj
Synonym - get_relationships_by_object
Synonym - get_subj_relationships
Synonym - get_subject_relationships
Returns - ref to an array of GO::Model::Relationship objects
Args - identifier/acc (string)
See also GO::Model::Relationship
get_all_relationships
Usage -
Returns - GO::Model::Relationship list
Args -
returns all the relationships/statements in this graph
See also GO::Model::Relationship
get_parent_terms
Usage - my $term_lref = $graph->get_parent_terms($parent_term->acc);
Synonym - get_obj_terms
Synonym - get_object_terms
Returns - ref to array of GO::Model::Term objs
Args - the accession of the query term
See also GO::Model::Term
get_parent_terms_by_type
Usage -
Synonym - get_obj_terms_by_type
Synonym - get_object_terms_by_type
Returns - ref to array of GO::Model::Term objs
Args - the accession of the query term
- the type by which to constrain relationships
See also GO::Model::Term
get_recursive_parent_terms
Title : get_recursive_parent_terms
Usage :
Synonyms: get_recursive_obj_terms
Synonyms: get_recursive_object_terms
Function:
Example :
Returns :
Args : accession of query term
See also GO::Model::Term
get_recursive_parent_terms_by_type
Title : get_recursive_parent_terms_by_type
Usage :
Synonyms: get_recursive_obj_terms_by_type
Synonyms: get_recursive_object_terms_by_type
Function:
Example :
Returns :
Args :
if type is blank, gets all
See also GO::Model::Term
get_reflexive_parent_terms
Title : get_reflexive_parent_terms
Usage :
Function:
Example :
Returns :
Args : acc
returns parent terms plus the term (for acc) itself
[reflexive transitive closure of relationships in upward direction]
See also GO::Model::Term
get_reflexive_parent_terms_by_type
Title : get_reflexive_parent_terms_by_type
Usage :
Function:
Example :
Returns : listref of terms
Args : acc, type
closure of relationship including the term itself
See also GO::Model::Term
get_child_terms
Usage - my $term_lref = $graph->get_child_terms($parent_term->acc);
Synonym - get_subj_terms
Synonym - get_subject_terms
Returns - ref to array of GO::Model::Term objs
Args -
See also GO::Model::Term
get_child_terms_by_type
Synonym - get_subj_terms_by_type
Synonym - get_subject_terms_by_type
Returns - ref to array of GO::Model::Term objs
Args - the accession of the query term
- the type by which to constrain relationships
See also GO::Model::Term
get_recursive_child_terms
Title : get_recursive_child_terms
Usage :
Synonyms: get_recursive_subj_terms
Synonyms: get_recursive_subject_terms
Function:
Example :
Returns : a reference to an array of L<GO::Model::Term> objects
Args : the accession of the query term
See also GO::Model::Term
get_recursive_child_terms_by_type
Title : get_recursive_child_terms_by_type
Usage :
Synonyms: get_recursive_subj_terms_by_type
Synonyms: get_recursive_subject_terms_by_type
Function:
Example :
Returns : a reference to an array of L<GO::Model::Term> objects
Args : accession, type
if type is blank, gets all
See also GO::Model::Term
_get_recursive_related_terms_by_type
Title : _get_recursive_related_terms_by_type
Usage :
Function: Obtain all relationships of the given kind and type for the
term identified by its accession, and recursively repeat
this with all parents and children as query for parent and
child relationships, respectively.
This is an internal method.
Example :
Returns : A reference to an array of L<GO::Model::Term> objects.
Args : - the kind of relationship, either "child" or "parent"
- the accession of the term with which to query
- the type to which to constrain relationships (optional,
all types if left undef)
- TRUE if reflexive and FALSE otherwise (default FALSE)
See also GO::Model::Term
_get_related_terms_by_type
Usage - my $term_lref = $graph->_get_related_terms_by_type("child",$acc);
Returns - ref to array of GO::Model::Term objs
Args - the kind of relationship, either "child" or "parent"
- the accession of the term for which to obtain rel.ships
- the type by which to constrain relationships (optional,
defaults to all terms if left undef)
This is an internal method.
get_parent_accs_by_type
Usage -
Returns -
Args - acc, type
get_reflexive_parent_accs_by_type
Title : get_reflexive_parent_accs_by_type
Usage :
Function:
Example :
Returns : listref of terms
Args : acc, type
closure of relationship including the term itself
See also GO::Model::Term
get_relationships_between_terms
Title : get_relationships_between_terms
Usage :
Function:
Example :
Returns : [] of relationships
Args : parent id, child id
See also GO::Model::Relationship
get_parent_closure_hash_by_type
Title : get_parent_closure_hash_by_type
Usage :
Function: given a term-acc and relationship type, will give a hash that
can be used to check if a term X is a parent of term Y
Example :
Returns :
Args :
keys will be lower-cased
add_child_relationship
See also GO::Model::Relationship
add_parent_relationship
parent relationships are as valued as child relationships
See also GO::Model::Relationship
close_below
Usage - $graph->close_below(3677);
Returns -
Args - term (as acc or GO::Model::Term object)
gets rid of everything below a node
used by AmiGO for when a user closes a term in the graph
find_roots
Usage - my $terms = $graph->find_roots;
Returns - arrayref of GO::Model::Term objects
Args -
All terms withOUT a parent
See also GO::Model::Term
get_all_products
Usage -
Returns -
Args -
See also GO::Model::GeneProduct
merge
Usage - $g->merge($g2);
Returns -
Args - GO::Model::Graph
merges two graphs
export
Usage - $graph->export({format=>$format});
Returns -
Args - opt hash
writes out the graph in any export format, including obo, go_ont, owl, png (graphviz) etc
to_xml
Usage -
Returns -
Args -
add_term
Usage - $g->add_term($term)
Returns -
Args - GO::Model::Term
add_node
Usage -
Returns -
Args -
synonym for add_term
add_relationship
Usage - $graph->add_relationship({acc1=>from_id, acc2=>to_id});
Usage - $graph->add_relationship($from_id, $to_id, $type});
Usage - $graph->add_relationship($obj, $subj, $type});
Returns -
Args -
only one relationship between id1 and id2 is allowed
See also GO::Model::Relationship
add_buckets
Usage -
Returns -
Args -
adds bucket terms to non-leaf nodes
this is useful for making GO slims
to_text_output
Usage -
Returns -
Args - fmt, assocs [bool]
hacky text output
this method should probably move out of the model code into output adapters