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go-perl-0.08
River stage one • 1 direct dependent • 1 total dependent
/ GO::Model::Graph

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