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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
SYNOPSIS
my $goa =
$registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
my $term = $goa->fetch_by_accession('GO:0010885');
my @children = @{ $goa->fetch_all_by_parent_term($term) };
my @descendants = @{ $goa->fetch_all_by_ancestor_term($term) };
my @parents = @{ $goa->fetch_all_by_child_term($term) };
my @ancestors = @{ $goa->fetch_all_by_descendant_term($term) };
my %ancestor_chart = %{ $goa->_fetch_ancestor_chart($term) };DESCRIPTION
An abstract adaptor class for fetching ontology terms, creates Bio::EnsEMBL::OntologyTerm objects.
METHODS
fetch_all_by_name
Arg [1] : String, name of term, or SQL pattern
Arg [2] : (optional) String, name of ontology
Arg [3] : (optional) Boolean, search through obsolete terms as well
Description : Fetches ontology term(s) given a name, a synonym, or a
SQL pattern like "%splice_site%"
Example :
my ($term) =
@{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };
# Will find terms in both SO and GO:
my @terms = @{ $ot_adaptor->fetch_by_name('%splice_site%') };
Return type : listref of Bio::EnsEMBL::OntologyTermfetch_by_accession
Arg [1] : String
Arg [2] : (optional) Boolean, search through obsolete terms as well
Description : Fetches an ontology term given an accession.
Example :
my $term = $ot_adaptor->fetch_by_accession('GO:0030326');
Return type : Bio::EnsEMBL::OntologyTermfetch_by_alt_id
Arg [1] : String
Description : Fetches an ontology term given an alt_id.
Example :
my $term = $ot_adaptor->fetch_by_alt_id('GO:0019952');
Return type : Bio::EnsEMBL::OntologyTermfetch_all_by_parent_term
Arg [1] : Bio::EnsEMBL::OntologyTerm
The term whose children terms should be fetched.
Description : Given a parent ontology term, returns a list of
its immediate children terms.
Example :
my @children =
@{ $ot_adaptor->fetch_all_by_parent_term($term) };
Return type : listref of Bio::EnsEMBL::OntologyTermfetch_all_by_ancestor_term
Arg [1] : Bio::EnsEMBL::OntologyTerm
The term whose descendant terms should be fetched.
Description : Given a parent ontology term, returns a list of
all its descendant terms, down to and including
any leaf terms. Relations of the type 'is_a' and
'part_of' are followed.
Example :
my @descendants =
@{ $ot_adaptor->fetch_all_by_ancestor_term($term) };
Return type : listref of Bio::EnsEMBL::OntologyTermfetch_all_by_child_term
Arg [1] : Bio::EnsEMBL::OntologyTerm
The term whose parent terms should be fetched.
Description : Given a child ontology term, returns a list of
its immediate parent terms.
Example :
my @parents = @{ $ot_adaptor->fetch_all_by_child_term($term) };
Return type : listref of Bio::EnsEMBL::OntologyTermfetch_all_by_descendant_term
Arg [1] : Bio::EnsEMBL::OntologyTerm
The term whose ancestor terms should be fetched.
Arg [2] : (optional) String
The subset within the ontolgy to which the query
should be restricted. The subset may be specified as
a SQL pattern, e.g., "%goslim%" (but "goslim%" might
not do what you expect), or as a specific subset name,
e.g., "goslim_generic".
Arg [3] : (optional) Boolean
If true (non-zero), only return the closest
term(s). If this argument is true, and the
previous argument is left undefined, this method
will return the parent(s) of the given term.
Arg [4] : (optional) Boolean
If true we will allow the retrieval of terms whose distance
to the current term is 0. If false then we will only return
those which are above the current term in the ontology
Description : Given a child ontology term, returns a list of
all its ancestor terms, up to and including any
root term. Relations of the type 'is_a' and
'part_of' are followed. Optionally, only terms in
a given subset of the ontology may be returned,
and additionally one may ask to only get the
closest term(s) to the given child term.
Example :
my @ancestors =
@{ $ot_adaptor->fetch_all_by_descendant_term($term) };
Return type : listref of Bio::EnsEMBL::OntologyTerm_fetch_ancestor_chart
Arg [1] : Bio::EnsEMBL::OntologyTerm
The term whose ancestor terms should be fetched.
Description : Given a child ontology term, returns a hash
structure containing its ancestor terms, up to and
including any root term. Relations of the type
'is_a' and 'part_of' are included.
Example :
my %chart = %{ $ot_adaptor->_fetch_ancestor_chart($term) };
Return type : A reference to a hash structure like this:
{
'GO:XXXXXXX' => {
'term' => # ref to Bio::EnsEMBL::OntologyTerm object
'is_a' => [...], # listref of Bio::EnsEMBL::OntologyTerm
'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
},
'GO:YYYYYYY' => {
# Similarly for all ancestors,
# and including the query term itself.
}
}fetch_all_alt_ids
Arg [1] : String
Description : Fetches all alt_ids for a given ontology term
Example :
my ($accessions) =
@{ $ot_adaptor->fetch_all_alt_ids( 'GO:0000003' ) };
Return type : listref of accessionsfetch_all_roots
Arg [1] : (optional) String, name of ontology
Description : Fetches all roots for all ontologies
Optionally, can be restricted to a given ontology
Example :
my ($terms) =
@{ $ot_adaptor->fetch_all_roots( 'SO' ) };
# Will find terms in EFO, SO and GO:
my @terms = @{ $ot_adaptor->fetch_all_roots() };
Return type : listref of Bio::EnsEMBL::OntologyTerm