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"})
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::Relationshipadd_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