| Bio::Ontology::TermI(3pm) | User Contributed Perl Documentation | Bio::Ontology::TermI(3pm) |
Bio::Ontology::TermI - interface for ontology terms
#get Bio::Ontology::TermI somehow.
print $term->identifier(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->comment(), "\n";
foreach my $synonym ( $term->get_synonyms() ) {
print $synonym, "\n";
}
This is "dumb" interface for ontology terms providing basic methods (it provides no functionality related to graphs).
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121
The rest of the documentation details each of the object methods.
Title : identifier
Usage : $term->identifier( "0003947" );
or
print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional).
Title : name
Usage : $term->name( "N-acetylgalactosaminyltransferase" );
or
print $term->name();
Function: Set/get for the name of this Term.
Returns : The name [scalar].
Args : The name [scalar] (optional).
Title : definition
Usage : $term->definition( "Catalysis of ..." );
or
print $term->definition();
Function: Set/get for the definition of this Term.
Returns : The definition [scalar].
Args : The definition [scalar] (optional).
Title : ontology
Usage : $ont = $term->ontology();
or
$term->ontology( $ont );
Function: Get the ontology this term is in.
An implementation may not permit the value of this
attribute to be changed once it is set, since that may have
serious consequences (note that with the ontology in hand
you can query for all related terms etc).
Note for implementors: you will almost certainly have to
take special precaution in order not to create cyclical
references in memory.
Returns : The ontology of this Term as a Bio::Ontology::OntologyI
implementing object.
Args : On set, the ontology of this Term as a Bio::Ontology::OntologyI
implementing object or a string representing its name.
See Bio::Ontology::OntologyI.
Title : version
Usage : $term->version( "1.00" );
or
print $term->version();
Function: Set/get for version information.
Returns : The version [scalar].
Args : The version [scalar] (optional).
Title : is_obsolete
Usage : $term->is_obsolete( 1 );
or
if ( $term->is_obsolete() )
Function: Set/get for the obsoleteness of this Term.
Returns : the obsoleteness [0 or 1].
Args : the obsoleteness [0 or 1] (optional).
Title : comment
Usage : $term->comment( "Consider the term ..." );
or
print $term->comment();
Function: Set/get for an arbitrary comment about this Term.
Returns : A comment.
Args : A comment (optional).
Title : get_synonyms
Usage : @aliases = $term->get_synonyms();
Function: Returns a list of aliases of this Term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_synonym() and remove_synonyms(), with obvious
functionality.
Returns : A list of aliases [array of [scalar]].
Args :
Title : get_dblinks()
Usage : @ds = $term->get_dblinks();
Function: Returns a list of each dblink of this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dblink() and remove_dblinks(), with obvious
functionality.
Returns : A list of dblinks [array of [scalars]].
Args :
Note : This has been deprecated in favor of get_dbxrefs()
Title : get_dbxrefs()
Usage : @ds = $term->get_dbxrefs();
Function: Returns a list of each link for this term.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_dbxref() and remove_dbxrefs(), with obvious
functionality.
Returns : A list of dblinks. This can return a mixed 'bag' of scalars and
L<Bio::Annotation::DBLink> instances, or specific subgroups
can be returned based on passed arguments
Args : implementation-specific
Title : get_secondary_ids
Usage : @ids = $term->get_secondary_ids();
Function: Returns a list of secondary identifiers of this Term.
Secondary identifiers mostly originate from merging terms,
or possibly also from splitting terms.
If an implementor of this interface permits modification of
this array property, the class should define at least
methods add_secondary_id() and remove_secondary_ids(), with
obvious functionality.
Returns : A list of secondary identifiers [array of [scalar]]
Args :
Used for looking up the methods that supersedes them.
Title : category
Usage :
Function: This method is deprecated. Use ontology() instead. We provide
an implementation here that preserves backwards compatibility,
but if you do not have legacy code using it you should not be
calling this method.
Example :
Returns :
Args :
| 2018-10-27 | perl v5.26.2 |