Erick Antezana > ONTO-PERL > OBO::Core::Ontology

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id

  Usage    - print $ontology->id() or $ontology->id($id)
  Returns  - the ID space of this ontology (string)
  Args     - the ID space of this ontology (string)
  Function - gets/sets the ID space of this ontology

name

  Usage    - print $ontology->name() or $ontology->name($name)
  Returns  - the name (string) of the ontology
  Args     - the name (string) of the ontology
  Function - gets/sets the name of the ontology

imports

  Usage    - $onto->imports() or $onto->imports($id1, $id2, $id3, ...)
  Returns  - a set (OBO::Util::Set) with the imported id ontologies
  Args     - the ontology id(s) (string) 
  Function - gets/sets the id(s) of the ontologies that are imported by this one

treat_xrefs_as_equivalent

  Usage    - $onto->treat_xrefs_as_equivalent() or $onto->treat_xrefs_as_equivalent($xref1, $xref2, $xref3, ...)
  Returns  - a set (OBO::Util::Set) of ontology id spaces
  Args     - an ontology ID space(s) (string) 
  Function - gets/sets the id spaces(s) of the ontologies that their xrefs are treated as equivalent
  Remark   - Macro. Treats all xrefs coming from a particular ID-Space as being statements of exact equivalence.

treat_xrefs_as_is_a

  Usage    - $onto->treat_xrefs_as_is_a() or $onto->treat_xrefs_as_is_a($xref1, $xref2, $xref3, ...)
  Returns  - a set (OBO::Util::Set) of ontology id spaces
  Args     - an ontology ID space(s) (string) 
  Function - gets/sets the id spaces(s) of the ontologies that their xrefs are treated as equivalent
  Remark   - Treats all xrefs coming from a particular ID-Space as being is_a relationships.

date

  Usage    - print $ontology->date()
  Returns  - the current date (in dd:MM:yyyy HH:mm format) of the ontology
  Args     - the current date (in dd:MM:yyyy HH:mm format) of the ontology
  Function - gets/sets the date of the ontology
  Remark   - for historic reasons, this is NOT a ISO 8601 date, as is the case for the creation-date field

default_relationship_id_prefix

  Usage    - print $ontology->default_relationship_id_prefix() or $ontology->default_relationship_id_prefix("OBO_REL")
  Returns  - the default relationship ID prefix (string) of this ontology
  Args     - the default relationship ID prefix (string) of this ontology
  Function - gets/sets the default relationship ID prefix of this ontology
  Remark   - Any relationship lacking an ID space will be prefixed with the value of this tag.

default_namespace

  Usage    - print $ontology->default_namespace() or $ontology->default_namespace("cellcycle_ontology")
  Returns  - the default namespace (string) of this ontology
  Args     - the default namespace (string) of this ontology
  Function - gets/sets the default namespace of this ontology

idspaces

  Usage    - $ontology->idspaces() or $ontology->idspaces($IDspace)
  Returns  - the id spaces, as a set (OBO::Util::IDspaceSet) of OBO::Core::IDspace's, of this ontology
  Args     - the id spaces, as a set (OBO::Util::IDspaceSet) of OBO::Core::IDspace's, of this ontology
  Function - gets/sets the idspaces of this ontology

data_version

  Usage    - print $ontology->data_version()
  Returns  - the data version (string) of this ontology
  Args     - the data version (string) of this ontology
  Function - gets/sets the data version of this ontology

saved_by

  Usage    - print $ontology->saved_by()
  Returns  - the username of the person (string) to last save this ontology
  Args     - the username of the person (string) to last save this ontology
  Function - gets/sets the username of the person to last save this ontology

remarks

  Usage    - print $ontology->remarks()
  Returns  - the remarks (OBO::Util::Set) of this ontology
  Args     - the remarks (OBO::Util::Set) of this ontology
  Function - gets/sets the remarks of this ontology

subset_def_map

  Usage    - $onto->subset_def_map() or $onto->subset_def_map($subset_def_map)
  Returns  - a map (OBO::Util::SubsetDefMap) with the subset definition(s) used in this ontology. A subset is a view over an ontology
  Args     - a subset definitions map (OBO::Core::SubsetDefMap)
  Function - gets/sets the subset definition(s) of this ontology

synonym_type_def_set

  Usage    - $onto->synonym_type_def_set() or $onto->synonym_type_def_set($st1, $st2, $st3, ...)
  Returns  - a set (OBO::Util::SynonymTypeDefSet) with the synonym type definitions used in this ontology. A synonym type is a description of a user-defined synonym type 
  Args     - the synonym type definition(s) (OBO::Core::SynonymTypeDef) used in this ontology 
  Function - gets/sets the synonym type definitions (s) of this ontology

add_term

  Usage    - $ontology->add_term($term)
  Returns  - the just added term (OBO::Core::Term)
  Args     - the term (OBO::Core::Term) to be added. The ID of the term to be added must have already been defined.
  Function - adds a term to this ontology
  Remark   - adding a term to an ontology does not mean adding its instances

add_instance

  Usage    - $ontology->add_instance($instance)
  Returns  - the just added instance (OBO::Core::Instance)
  Args     - the instance (OBO::Core::Instance) to be added. The ID of the instance to be added must have already been defined.
  Function - adds a instance to this ontology

add_term_as_string

  Usage    - $ontology->add_term_as_string($term_id, $term_name)
  Returns  - the just added term (OBO::Core::Term)
  Args     - the term id (string) and the term name (string) of term to be added
  Function - adds a term to this ontology

add_instance_as_string

  Usage    - $ontology->add_instance_as_string($instance_id, $instance_name)
  Returns  - the just added instance (OBO::Core::Instance)
  Args     - the instance id (string) and the instance name (string) of instance to be added
  Function - adds a instance to this ontology

add_relationship_type

  Usage    - $ontology->add_relationship_type($relationship_type)
  Returns  - the just added relationship type (OBO::Core::RelationshipType)
  Args     - the relationship type to be added (OBO::Core::RelationshipType). The ID of the relationship type to be added must have already been defined.
  Function - adds a relationship type to this ontology

add_relationship_type_as_string

  Usage    - $ontology->add_relationship_type_as_string($relationship_type_id, $relationship_type_name)
  Returns  - the just added relationship type (OBO::Core::RelationshipType)
  Args     - the relationship type id (string) and the relationship type name (string) of the relationship type to be added
  Function - adds a relationship type to this ontology

delete_term

  Usage    - $ontology->delete_term($term)
  Returns  - none
  Args     - the term (OBO::Core::Term) to be deleted
  Function - deletes a term from this ontology
  Remark   - the resulting ontology might be segmented, i.e., the deleted node might create an unconnected sub-ontology
  Remark   - the term (OBO::Core::Term) still exits after removing it from this ontology

delete_instance

  Usage    - $ontology->delete_instance($instance)
  Returns  - none
  Args     - the instance (OBO::Core::Instance) to be deleted
  Function - deletes a instance from this ontology
  Remark   - the instance (OBO::Core::Instance) still exits after removing it from this ontology

delete_relationship

  Usage    - $ontology->delete_relationship($rel)
  Returns  - none
  Args     - the relationship (OBO::Core::Relationship) to be deleted
  Function - deletes a relationship from this ontology
  Remark   - the relationship (OBO::Core::Relationship) still exits after removing it from this ontology

has_term

  Usage    - print $ontology->has_term($term)
  Returns  - true or false
  Args     - the term (OBO::Core::Term) to be tested
  Function - checks if the given term belongs to this ontology

has_instance

  Usage    - print $ontology->has_instance($instance)
  Returns  - true or false
  Args     - the instance (OBO::Core::Instance) to be tested
  Function - checks if the given instance belongs to this ontology

has_term_id

  Usage    - print $ontology->has_term_id($term_id)
  Returns  - true or false
  Args     - the term id (string) to be tested
  Function - checks if the given term id corresponds to a term held by this ontology

has_instance_id

  Usage    - print $ontology->has_instance_id($instance_id)
  Returns  - true or false
  Args     - the instance id (string) to be tested
  Function - checks if the given instance id corresponds to a instance held by this ontology

has_relationship_type

  Usage    - print $ontology->has_relationship_type($relationship_type)
  Returns  - true or false
  Args     - the relationship type (OBO::Core::RelationshipType) to be tested
  Function - checks if the given relationship type belongs to this ontology

has_relationship_type_id

  Usage    - print $ontology->has_relationship_type_id($relationship_type_id)
  Returns  - true or false
  Args     - the relationship type id (string) to be tested
  Function - checks if the given relationship type id corresponds to a relationship type held by this ontology

has_relationship_id

  Usage    - print $ontology->has_relationship_id($rel_id)
  Returns  - true or false
  Args     - the relationship id (string) to be tested
  Function - checks if the given relationship id corresponds to a relationship held by this ontology

equals

  Usage    - print $ontology->equals($another_ontology)
  Returns  - either 1 (true) or 0 (false)
  Args     - the ontology (OBO::Core::Ontology) to compare with
  Function - tells whether this ontology is equal to the parameter

get_terms

  Usage    - $ontology->get_terms() or $ontology->get_terms("APO:I.*") or $ontology->get_terms("GO:012*")
  Returns  - the terms held by this ontology as a reference to an array of OBO::Core::Term's
  Args     - none or the regular expression for filtering the terms by id's
  Function - returns the terms held by this ontology

get_instances

  Usage    - $ontology->get_instances() or $ontology->get_instances("APO:K.*")
  Returns  - the instances held by this ontology as a reference to an array of OBO::Core::Instance's
  Args     - none or the regular expression for filtering the instances by id's
  Function - returns the instances held by this ontology

get_terms_sorted_by_id

  Usage    - $ontology->get_terms_sorted_by_id() or $ontology->get_terms_sorted_by_id("APO:I.*")
  Returns  - the terms held by this ontology as a reference to a sorted (by ID) array of OBO::Core::Term's
  Args     - none or the regular expression for filtering the terms by id's
  Function - returns the terms held by this ontology, the terms are sorted by ID (using the Schwartzian Transform)

get_instances_sorted_by_id

  Usage    - $ontology->get_instances_sorted_by_id() or $ontology->get_instances_sorted_by_id("APO:K.*")
  Returns  - the instances held by this ontology as a reference to a sorted (by ID) array of OBO::Core::Instance's
  Args     - none or the regular expression for filtering the instances by id's
  Function - returns the instances held by this ontology, the instances are sorted by ID (using the Schwartzian Transform)

get_terms_by_subnamespace

  Usage    - $ontology->get_terms_by_subnamespace() or $ontology->get_terms_by_subnamespace("P") or or $ontology->get_terms_by_subnamespace("Pa")
  Returns  - the terms held by this ontology corresponding to the requested subnamespace as a reference to an array of OBO::Core::Term's
  Args     - none or the subnamespace: 'P', 'I', 'Pa', 'Ia' and so on.
  Function - returns the terms held by this ontology corresponding to the requested subnamespace

get_instances_by_subnamespace

  Usage    - $ontology->get_instances_by_subnamespace() or $ontology->get_instances_by_subnamespace("K") or or $ontology->get_instances_by_subnamespace("Ka")
  Returns  - the instances held by this ontology corresponding to the requested subnamespace as a reference to an array of OBO::Core::Instance's
  Args     - none or the subnamespace: 'K', 'L', 'Ka', 'La' and so on.
  Function - returns the instances held by this ontology corresponding to the requested subnamespace

get_terms_by_subset

  Usage    - $ontology->get_terms_by_subset("GO_SLIM")
  Returns  - the terms held by this ontology belonging to the given subset as a reference to an array of OBO::Core::Term's
  Args     - a subset name
  Function - returns the terms held by this ontology belonging to the requested subset

get_instances_by_subset

  Usage    - $ontology->get_instances_by_subset("INSTANCES_SLIM")
  Returns  - the instances held by this ontology belonging to the given subset as a reference to an array of OBO::Core::Instance's
  Args     - a subset name
  Function - returns the instances held by this ontology belonging to the requested subset

get_relationships

  Usage    - $ontology->get_relationships()
  Returns  - the relationships held by this ontology as a reference to an array of OBO::Core::Relationship's
  Args     - none
  Function - returns the relationships held by this ontology

get_relationship_types

  Usage    - $ontology->get_relationship_types()
  Returns  - a reference to an array with the relationship types (OBO::Core::RelationshipType) held by this ontology
  Args     - none
  Function - returns the relationship types held by this ontology

get_relationship_types_sorted_by_id

  Usage    - $ontology->get_relationship_types_sorted_by_id()
  Returns  - the relationship types held by this ontology as a reference to a sorted (by ID) array of OBO::Core::Term's
  Args     - none or the regular expression for filtering the terms by id's
  Function - returns the relationship types held by this ontology, the relationship types are sorted by ID (using the Schwartzian Transform)

get_term_local_neighbourhood

  Usage    - $ontology->get_term_local_neighbourhood($term, $rel_type)
  Returns  - the neighbourhood of a given term as a reference to an array with the relationships (OBO::Core::Relationship)
  Args     - the term (OBO::Core::Term) for which its relationships will be found out; and optionally the relationship type name (e.g. 'participates_in') to select only those types of relationships
  Function - returns the local neighbourhood of the given term as a reference to an array with the relationships (OBO::Core::Relationship)
  Remark   - this subroutine, which is an alias of OBO::Core::get_relationships_by_source_term, might change its interface in the future (a new module, named e.g. TermNeighbourhood, might be implemented)

get_relationships_by_source_term

  Usage    - $ontology->get_relationships_by_source_term($source_term, $rel_type)
  Returns  - a reference to an array with the relationships (OBO::Core::Relationship) connecting the given term to its children
  Args     - the term (OBO::Core::Term) for which its relationships will be found out; and optionally the relationship type name (e.g. 'participates_in') to filter out those types of relationships
  Function - returns the relationships associated to the given source term

get_relationships_by_target_term

  Usage    - $ontology->get_relationships_by_target_term($target_term, $rel_type)
  Returns  - a reference to an array with the relationships (OBO::Core::Relationship) connecting the given term to its parents
  Args     - the term (OBO::Core::Term) for which its relationships will be found out; and optionally the relationship type name (e.g. 'participates_in') to filter out those types of relationships
  Function - returns the relationships associated to the given target term

get_term_by_id

  Usage    - $ontology->get_term_by_id($id)
  Returns  - the term (OBO::Core::Term) associated to the given ID
  Args     - the term's ID (string)
  Function - returns the term associated to the given ID

get_instance_by_id

  Usage    - $ontology->get_instance_by_id($id)
  Returns  - the instance (OBO::Core::Instance) associated to the given ID
  Args     - the instance's ID (string)
  Function - returns the instance associated to the given ID

set_term_id

  Usage    - $ontology->set_term_id($term, $new_term_id)
  Returns  - the term (OBO::Core::Term) with its new ID
  Args     - the term (OBO::Core::Term) and its new term's ID (string)
  Function - sets a new term ID for the given term 

set_instance_id

  Usage    - $ontology->set_instance_id($instance, $new_id)
  Returns  - the instance (OBO::Core::Instance) with its new ID
  Args     - the instance (OBO::Core::Instance) and its new instance's ID (string)
  Function - sets a new instance ID for the given instance 

get_relationship_type_by_id

  Usage    - $ontology->get_relationship_type_by_id($id)
  Returns  - the relationship type (OBO::Core::RelationshipType) associated to the given id
  Args     - the relationship type's id (string)
  Function - returns the relationship type associated to the given id

get_term_by_name

  Usage    - $ontology->get_term_by_name($name)
  Returns  - the term (OBO::Core::Term) associated to the given name
  Args     - the term's name (string)
  Function - returns the term associated to the given name
  Remark   - the argument (string) is case sensitive

get_instance_by_name

  Usage    - $ontology->get_instance_by_name($name)
  Returns  - the instance (OBO::Core::Instance) associated to the given name
  Args     - the instance's name (string)
  Function - returns the instance associated to the given name
  Remark   - the argument (string) is case sensitive

get_term_by_name_or_synonym

  Usage    - $ontology->get_term_by_name_or_synonym($name, $scope)
  Returns  - the term (OBO::Core::Term) associated to the given name or synonym (given its scope, EXACT by default)
  Args     - the term's name or synonym (string) and optionally the scope of the synonym (EXACT by default)
  Function - returns the term associated to the given name or synonym (given its scope, EXACT by default)
  Remark   - this function should be carefully used since among ontologies there may be homonyms at the level of the synonyms (e.g. genes)
  Remark   - the argument (string) is case sensitive

get_instance_by_name_or_synonym

  Usage    - $ontology->get_instance_by_name_or_synonym($name, $scope)
  Returns  - the instance (OBO::Core::Instance) associated to the given name or synonym (given its scope, EXACT by default)
  Args     - the instance's name or synonym (string) and optionally the scope of the synonym (EXACT by default)
  Function - returns the instance associated to the given name or synonym (given its scope, EXACT by default)
  Remark   - this function should be carefully used since among ontologies there may be homonyms at the level of the synonyms (e.g. locations)
  Remark   - the argument (string) is case sensitive

get_terms_by_name

  Usage    - $ontology->get_terms_by_name($name)
  Returns  - the term set (OBO::Util::TermSet) with all the terms (OBO::Core::Term) having $name in their names 
  Args     - the term name (string)
  Function - returns the terms having $name in their names 

get_instances_by_name

  Usage    - $ontology->get_instances_by_name($name)
  Returns  - the instance set (OBO::Util::InstanceSet) with all the instances (OBO::Core::Instance) having $name in their names 
  Args     - the instance name (string)
  Function - returns the instances having $name in their names 

get_relationship_types_by_name

  Usage    - $ontology->get_relationship_types_by_name($name)
  Returns  - the relationship types set (OBO::Util::RelationshipTypeSet) with all the relationship types (OBO::Core::RelationshipType) having $name in their names 
  Args     - the relationship type name (string)
  Function - returns the relationship type having $name in their names 

get_relationship_type_by_name

  Usage    - $ontology->get_relationship_type_by_name($name)
  Returns  - the relationship type (OBO::Core::RelationshipType) associated to the given name
  Args     - the relationship type's name (string)
  Function - returns the relationship type associated to the given name

add_relationship

  Usage    - $ontology->add_relationship($relationship)
  Returns  - none
  Args     - the relationship (OBO::Core::Relationship) to be added between two existing terms or two relationship types
  Function - adds a relationship between either two terms or two relationship types.
  Remark   - If the terms or relationship types bound by this relationship are not yet in the ontology, they will be added
  Remark   - if you are adding relationships to an ontology, sometimes it might be better to add their type first (usually if you are building a new ontology from an extant one)  

get_relationship_by_id

  Usage    - print $ontology->get_relationship_by_id()
  Returns  - the relationship (OBO::Core::Relationship) associated to the given id
  Args     - the relationship id (string)
  Function - returns the relationship associated to the given relationship id

create_rel

  Usage    - $ontology->create_rel->($tail, $type, $head)
  Returns  - the OBO::Core::Ontology object
  Args     - an OBO::Core::(Term|Relationship) object, a relationship type string (e.g. 'is_a'), and an OBO::Core::(Term|Relationship) object, 
  Function - creates and adds a new relationship to this ontology

get_child_terms

  Usage    - $ontology->get_child_terms($term)
  Returns  - a reference to an array with the child terms (OBO::Core::Term) of the given term
  Args     - the term (OBO::Core::Term) for which the children will be found
  Function - returns the child terms of the given term

get_parent_terms

  Usage    - $ontology->get_parent_terms($term)
  Returns  - a reference to an array with the parent terms (OBO::Core::Term) of the given term
  Args     - the term (OBO::Core::Term) for which the parents will be found
  Function - returns the parent terms of the given term

get_head_by_relationship_type

  Usage    - $ontology->get_head_by_relationship_type($term, $relationship_type) or $ontology->get_head_by_relationship_type($rel_type, $relationship_type)
  Returns  - a reference to an array of terms (OBO::Core::Term) or relationship types (OBO::Core::RelationshipType) pointed out by the relationship of the given type; otherwise undef
  Args     - the term (OBO::Core::Term) or relationship type (OBO::Core::RelationshipType) and the pointing relationship type (OBO::Core::RelationshipType)
  Function - returns the terms or relationship types pointed out by the relationship of the given type

get_tail_by_relationship_type

  Usage    - $ontology->get_tail_by_relationship_type($term, $relationship_type) or $ontology->get_tail_by_relationship_type($rel_type, $relationship_type)
  Returns  - a reference to an array of terms (OBO::Core::Term) or relationship types (OBO::Core::RelationshipType) pointing out the given term by means of the given relationship type; otherwise undef
  Args     - the term (OBO::Core::Term) or relationship type (OBO::Core::RelationshipType) and the relationship type (OBO::Core::RelationshipType)
  Function - returns the terms or relationship types pointing out the given term by means of the given relationship type

get_root_terms

  Usage    - $ontology->get_root_terms()
  Returns  - the root term(s) held by this ontology (as a reference to an array of OBO::Core::Term's)
  Args     - none
  Function - returns the root term(s) held by this ontology

get_number_of_terms

  Usage    - $ontology->get_number_of_terms()
  Returns  - the number of terms held by this ontology
  Args     - none
  Function - returns the number of terms held by this ontology

get_number_of_instances

  Usage    - $ontology->get_number_of_instances()
  Returns  - the number of instances held by this ontology
  Args     - none
  Function - returns the number of instances held by this ontology

get_number_of_relationships

  Usage    - $ontology->get_number_of_relationships()
  Returns  - the number of relationships held by this ontology
  Args     - none
  Function - returns the number of relationships held by this ontology

get_number_of_relationship_types

  Usage    - $ontology->get_number_of_relationship_types()
  Returns  - the number of relationship types held by this ontology
  Args     - none
  Function - returns the number of relationship types held by this ontology

export2obo

  See - OBO::Core::Ontology::export()

export2rdf

  See - OBO::Core::Ontology::export()

export2owl

  See - OBO::Core::Ontology::export()

export2xml

  See - OBO::Core::Ontology::export()

export2dot

  See - OBO::Core::Ontology::export()

export2gml

  See - OBO::Core::Ontology::export()

export

  Usage    - $ontology->export($export_format, $output_file_handle, $error_file_handle)
  Returns  - exports this ontology
  Args     - the format: obo, xml, owl, dot, gml, xgmml, sbml
           - the output file handle (e.g. STDOUT), and
           - the error file handle (STDERR by default; if not writable, STDOUT is used)
  Function - exports this ontology
  Remark   - warning and errors are printed to the STDERR (by default)
  Remark   - you may use this method to check your OBO file syntax and/or to clean it up
  Remark   - Standard arguments:
           -   1. Format, one of 'obo', 'rdf', 'xml', 'owl', 'dot', 'gml', 'xgmml', 'sbml'
           -   2. Otput filehandle \*OUT
           -   3. Error filehandle \*ERR ( default \*STDERR, but for RDF or OWL )
           - Extra arguments:
           -   'rdf':
           -     1. base URI (e.g. 'http://www.semantic-systems-biology.org/')
           -     2. name space (e.g. 'SSB')
           -     3. Flag, 1=construct closures, 0=no closures (default)
           -     4. Flag, 1=skip exporting Typedefs, 0=export Typedefs (default)
           -   'owl':
           -     1. URI for content
           -     2. URI for OboInOwl (optional)

subontology_by_terms

  Usage    - $ontology->subontology_by_terms($term_set)
  Returns  - a subontology with the given terms from this ontology 
  Args     - the terms (OBO::Util::TermSet) that will be included in the subontology
  Function - creates a subontology based on the given terms from this ontology
  Remark   - instances of terms (classes) are added to the resulting ontology

get_subontology_from

  Usage    - $ontology->get_subontology_from($new_root_term)
  Returns  - a subontology from the given term of this ontology 
  Args     - the term (OBO::Core::Term) that is the root of the subontology, and optionally, a reference to relationship type ids
  Function - creates a subontology having as root the given term

get_terms_idspace

  Usage    - $ontology->get_terms_idspace()
  Returns  - the idspace (e.g. GO) of the terms held by this ontology (or 'NN' is there is no idspace)
  Args     - none
  Function - look for the idspace of the terms held by this ontology
  Remark   - it is assumed that most of the terms share the same idspace (e.g. GO)

get_instances_idspace

  Usage    - $ontology->get_instances_idspace()
  Returns  - the idspace (e.g. GO) of the instances held by this ontology (or 'NN' is there is no idspace)
  Args     - none
  Function - look for the idspace of the instances held by this ontology
  Remark   - it is assumed that most of the instances share the same idspace (e.g. GO)

get_descendent_terms

  Usage    - $ontology->get_descendent_terms($term) or $ontology->get_descendent_terms($term_id)
  Returns  - a set with the descendent terms (OBO::Core::Term) of the given term
  Args     - the term, as an object (OBO::Core::Term) or string (e.g. GO:0003677), for which all the descendents will be found
  Function - returns recursively all the child terms of the given term

get_ancestor_terms

  Usage    - $ontology->get_ancestor_terms($term)
  Returns  - a set with the ancestor terms (OBO::Core::Term) of the given term
  Args     - the term (OBO::Core::Term) for which all the ancestors will be found
  Function - returns recursively all the parent terms of the given term

get_descendent_terms_by_subnamespace

  Usage    - $ontology->get_descendent_terms_by_subnamespace($term, subnamespace)
  Returns  - a set with the descendent terms (OBO::Core::Term) of the given subnamespace 
  Args     - the term (OBO::Core::Term), the subnamespace (string, e.g. 'P', 'R', 'Ia' etc)
  Function - returns recursively the given term's children of the given subnamespace

get_ancestor_terms_by_subnamespace

  Usage    - $ontology->get_ancestor_terms_by_subnamespace($term, subnamespace)
  Returns  - a set with the ancestor terms (OBO::Core::Term) of the given subnamespace 
  Args     - the term (OBO::Core::Term), the subnamespace (string, e.g. 'P', 'R', 'Ia' etc)
  Function - returns recursively the given term's parents of the given subnamespace

get_descendent_terms_by_relationship_type

  Usage    - $ontology->get_descendent_terms_by_relationship_type($term, $rel_type)
  Returns  - a set with the descendent terms (OBO::Core::Term) of the given term linked by the given relationship type
  Args     - OBO::Core::Term object, OBO::Core::RelationshipType object
  Function - returns recursively all the child terms of the given term linked by the given relationship type

get_ancestor_terms_by_relationship_type

  Usage    - $ontology->get_ancestor_terms_by_relationship_type($term, $rel_type)
  Returns  - a set with the ancestor terms (OBO::Core::Term) of the given term linked by the given relationship type
  Args     - OBO::Core::Term object, OBO::Core::RelationshipType object
  Function - returns recursively the parent terms of the given term linked by the given relationship type

get_term_by_xref

  Usage    - $ontology->get_term_by_xref($db, $acc)
  Returns  - the term (OBO::Core::Term) associated with the given external database ID. 'undef' is returned if there is no term for the given arguments.        
  Args     - the name of the external database and the ID (strings)
  Function - returns the term associated with the given external database ID

get_instance_by_xref

  Usage    - $ontology->get_instance_by_xref($db, $acc)
  Returns  - the instance (OBO::Core::Instance) associated with the given external database ID. 'undef' is returned if there is no instance for the given arguments.    
  Args     - the name of the external database and the ID (strings)
  Function - returns the instance associated with the given external database ID

get_paths_term1_term2

  Usage    - $ontology->get_paths_term1_term2($term1_id, $term2_id)
  Returns  - an array of references to the paths between term1 and term2
  Args     - the IDs of the terms for which a path (or paths) will be found
  Function - returns the path(s) linking term1 and term2, where term1 is more specific than term2

get_paths_term_terms

  Usage    - $ontology->get_paths_term_terms($term, $set_of_terms)
  Returns  - an array of references to the paths between a given term ID and a given set of terms IDs 
  Args     - the ID of the term (string) for which a path (or paths) will be found and a set of terms (OBO::Util::Set)
  Function - returns the path(s) linking the given term and the given set of terms

get_paths_term_terms_same_rel

  Usage    - $ontology->get_paths_term_terms_same_rel($term_id, $set_of_terms, $type_of_relationship)
  Returns  - an array of references to the paths between a given term ID and a given set of terms IDs 
  Args     - the ID of the term (string) for which a path (or paths) will be found, a set of terms (OBO::Util::Set) and the ID of the relationship type 
  Function - returns the path(s) linking the given term (term ID) and the given set of terms along the same relationship (e.g. is_a)

obo_id2owl_id

  Usage    - $ontology->obo_id2owl_id($term)
  Returns  - the ID for OWL representation.
  Args     - the OBO-type ID.
  Function - Transform an OBO-type ID into an OWL-type one. E.g. APO:I1234567 -> APO_I1234567

owl_id2obo_id

  Usage    - $ontology->owl_id2obo_id($term)
  Returns  - the ID for OBO representation.
  Args     - the OWL-type ID.
  Function - Transform an OWL-type ID into an OBO-type one. E.g. APO_I1234567 -> APO:I1234567

__char_hex_http

  Usage    - $ontology->__char_hex_http($seq)
  Returns  - the sequence with the numeric HTML representation for the given special character
  Args     - the sequence of characters
  Function - Transforms a character into its equivalent HTML number, e.g. : -> :

NAME ^

OBO::Core::Ontology - An ontology holding terms, instances and relationships.

SYNOPSIS ^

use OBO::Core::Ontology;

use OBO::Core::Term;

use OBO::Core::Relationship;

use OBO::Core::RelationshipType;

use strict;

# three new terms

my $n1 = OBO::Core::Term->new();

my $n2 = OBO::Core::Term->new();

my $n3 = OBO::Core::Term->new();

# new ontology

my $onto = OBO::Core::Ontology->new;

$n1->id("APO:P0000001");

$n2->id("APO:P0000002");

$n3->id("APO:P0000003");

$n1->name("One");

$n2->name("Two");

$n3->name("Three");

my $def1 = OBO::Core::Def->new();

$def1->text("Definition of One");

my $def2 = OBO::Core::Def->new();

$def2->text("Definition of Two");

my $def3 = OBO::Core::Def->new();

$def3->text("Definition of Three");

$n1->def($def1);

$n2->def($def2);

$n3->def($def3);

$onto->add_term($n1);

$onto->add_term($n2);

$onto->add_term($n3);

$onto->delete_term($n1);

$onto->add_term($n1);

# new term

my $n4 = OBO::Core::Term->new();

$n4->id("APO:P0000004");

$n4->name("Four");

my $def4 = OBO::Core::Def->new();

$def4->text("Definition of Four");

$n4->def($def4);

$onto->delete_term($n4);

$onto->add_term($n4);

# add term as string

my $new_term = $onto->add_term_as_string("APO:P0000005", "Five");

$new_term->def_as_string("This is a dummy definition", '[APO:vm, APO:ls, APO:ea "Erick Antezana"]');

my $n5 = $new_term;

# five new relationships

my $r12 = OBO::Core::Relationship->new();

my $r23 = OBO::Core::Relationship->new();

my $r13 = OBO::Core::Relationship->new();

my $r14 = OBO::Core::Relationship->new();

my $r35 = OBO::Core::Relationship->new();

$r12->id("APO:P0000001_is_a_APO:P0000002");

$r23->id("APO:P0000002_part_of_APO:P0000003");

$r13->id("APO:P0000001_participates_in_APO:P0000003");

$r14->id("APO:P0000001_participates_in_APO:P0000004");

$r35->id("APO:P0000003_part_of_APO:P0000005");

$r12->type('is_a');

$r23->type('part_of');

$r13->type("participates_in");

$r14->type("participates_in");

$r35->type('part_of');

$r12->link($n1, $n2);

$r23->link($n2, $n3);

$r13->link($n1, $n3);

$r14->link($n1, $n4);

$r35->link($n3, $n5);

# get all terms

my $c = 0;

my %h;

foreach my $t (@{$onto->get_terms()}) {

        $h{$t->id()} = $t;
        
        $c++;

}

# get terms with argument

my @processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("APO:P.*")};

my @odd_processes = sort {$a->id() cmp $b->id()} @{$onto->get_terms("APO:P000000[35]")};

$onto->idspace_as_string("APO", "http://www.cellcycle.org/ontology/APO");

my @same_processes = @{$onto->get_terms_by_subnamespace("P")};

my @no_processes = @{$onto->get_terms_by_subnamespace("p")};

# add relationships

$onto->add_relationship($r12);

$onto->add_relationship($r23);

$onto->add_relationship($r13);

$onto->add_relationship($r14);

$onto->add_relationship($r35);

# add relationships and terms linked by this relationship

my $n11 = OBO::Core::Term->new();

my $n21 = OBO::Core::Term->new();

$n11->id("APO:P0000011"); $n11->name("One one"); $n11->def_as_string("Definition One one", "");

$n21->id("APO:P0000021"); $n21->name("Two one"); $n21->def_as_string("Definition Two one", "");

my $r11_21 = OBO::Core::Relationship->new();

$r11_21->id("APO:R0001121"); $r11_21->type("r11-21");

$r11_21->link($n11, $n21);

$onto->add_relationship($r11_21); # adds to the ontology the terms linked by this relationship

# get all relationships

my %hr;

foreach my $r (@{$onto->get_relationships()}) {

        $hr{$r->id()} = $r;

}

# get children

my @children = @{$onto->get_child_terms($n1)};

@children = @{$onto->get_child_terms($n3)};

my %ct;

foreach my $child (@children) {

        $ct{$child->id()} = $child;

}

@children = @{$onto->get_child_terms($n2)};

# get parents

my @parents = @{$onto->get_parent_terms($n3)};

@parents = @{$onto->get_parent_terms($n1)};

@parents = @{$onto->get_parent_terms($n2)};

# get all descendents

my @descendents1 = @{$onto->get_descendent_terms($n1)};

my @descendents2 = @{$onto->get_descendent_terms($n2)};

my @descendents3 = @{$onto->get_descendent_terms($n3)};

my @descendents5 = @{$onto->get_descendent_terms($n5)};

# get all ancestors

my @ancestors1 = @{$onto->get_ancestor_terms($n1)};

my @ancestors2 = @{$onto->get_ancestor_terms($n2)};

my @ancestors3 = @{$onto->get_ancestor_terms($n3)};

# get descendents by term subnamespace

my @descendents4 = @{$onto->get_descendent_terms_by_subnamespace($n1, 'P')};

my @descendents5 = @{$onto->get_descendent_terms_by_subnamespace($n2, 'P')};

my @descendents6 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'P')};

my @descendents6 = @{$onto->get_descendent_terms_by_subnamespace($n3, 'R')};

# get ancestors by term subnamespace

my @ancestors4 = @{$onto->get_ancestor_terms_by_subnamespace($n1, 'P')};

my @ancestors5 = @{$onto->get_ancestor_terms_by_subnamespace($n2, 'P')};

my @ancestors6 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'P')};

my @ancestors6 = @{$onto->get_ancestor_terms_by_subnamespace($n3, 'R')};

# three new relationships types

my $r1 = OBO::Core::RelationshipType->new();

my $r2 = OBO::Core::RelationshipType->new();

my $r3 = OBO::Core::RelationshipType->new();

$r1->id("APO:R0000001");

$r2->id("APO:R0000002");

$r3->id("APO:R0000003");

$r1->name('is_a');

$r2->name('part_of');

$r3->name("participates_in");

# add relationship types

$onto->add_relationship_type($r1);

$onto->add_relationship_type($r2);

$onto->add_relationship_type($r3);

# get descendents or ancestors linked by a particular relationship type

my $rel_type1 = $onto->get_relationship_type_by_name('is_a');

my $rel_type2 = $onto->get_relationship_type_by_name('part_of');

my $rel_type3 = $onto->get_relationship_type_by_name("participates_in");

my @descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n5, $rel_type1)};

@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n5, $rel_type2)};

@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n2, $rel_type1)};

@descendents7 = @{$onto->get_descendent_terms_by_relationship_type($n3, $rel_type3)};

my @ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type1)};

@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type2)};

@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n1, $rel_type3)};

@ancestors7 = @{$onto->get_ancestor_terms_by_relationship_type($n2, $rel_type2)};

# add relationship type as string

my $relationship_type = $onto->add_relationship_type_as_string("APO:R0000004", "has_participant");

# get relationship types

my @rt = @{$onto->get_relationship_types()};

my %rrt;

foreach my $relt (@rt) {

        $rrt{$relt->name()} = $relt;

}

my @rtbt = @{$onto->get_relationship_types_by_term($n1)};

my %rtbth;

foreach my $relt (@rtbt) {

        $rtbth{$relt} = $relt;

}

# get_head_by_relationship_type

my @heads_n1 = @{$onto->get_head_by_relationship_type($n1, $onto->get_relationship_type_by_name("participates_in"))};

my %hbrt;

foreach my $head (@heads_n1) {

        $hbrt{$head->id()} = $head;

}

DESCRIPTION ^

This module supports the manipulation of OBO-formatted ontologies, such as the Gene Ontology (http://www.geneontology.org/) or the Cell Cycle Ontology (http://www.cellcycleontology.org). Basically, it represents a directed acyclic graph (DAG) holding terms (OBO::Core::Term) which in turn are linked by relationships (OBO::Core::Relationship). Those relationships have an associated relationship type (OBO::Core::RelationshipType).

AUTHOR ^

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE ^

Copyright (c) 2006-2013 by Erick Antezana

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

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