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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Ontology::Term

NAME

Bio::Ontology::Term - implementation of the interface for ontology terms

SYNOPSIS

#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->each_synonym() ) {
    print $synonym, "\n";
}

DESCRIPTION

This is a simple implementation for ontology terms providing basic methods (it provides no functionality related to graphs). It implements the Bio::Ontology::TermI interface.

This class also implements Bio::IdentifiableI and Bio::DescribableI.

FEEDBACK

Mailing Lists

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

Support

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.

Reporting Bugs

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://redmine.open-bio.org/projects/bioperl/

AUTHOR

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

APPENDIX

The rest of the documentation details each of the object methods.

new

Title   : new
Usage   : $term = Bio::Ontology::Term->new(
               -identifier  => "16847",
               -name        => "1-aminocyclopropane-1-carboxylate synthase",
               -definition  => "Catalysis of ...",
               -is_obsolete => 0,
               -comment     => "" );
Function: Creates a new Bio::Ontology::Term.
Returns : A new Bio::Ontology::Term object.
Args    : -identifier            => the identifier of this term [scalar]
          -name                  => the name of this term [scalar]
          -definition            => the definition of this term [scalar]
          -ontology              => the ontology this term lives in
                                    (a Bio::Ontology::OntologyI object)
          -version               => version information [scalar]
          -is_obsolete           => the obsoleteness of this term [0 or 1]
          -comment               => a comment [scalar]
          -dblinks               => Bio::Annotation::DBLink objects
                                    [reference to array]
          -references            => Bio::Annotation::Reference objects
                                    [reference to array]

See Bio::Ontology::OntologyI, Bio::Annotation::Reference, Bio::Annotation::DBLink.

identifier

Title   : identifier
Usage   : $term->identifier( "GO:0003947" );
          or
          print $term->identifier();
Function: Set/get for the identifier of this Term.
Returns : The identifier [scalar].
Args    : The identifier [scalar] (optional).

name

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).

definition

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).

ontology

Title   : ontology
Usage   : $ont = $term->ontology();
          or
          $term->ontology( $ont );
Function: Get the ontology this term is in.

          Note that with the ontology in hand you can query for all
          related terms etc.

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.

version

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).

is_obsolete

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).

comment

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).

get_synonyms

Title   : get_synonyms
Usage   : @aliases = $term->get_synonyms;
Function: Returns a list of aliases of this Term.
Returns : A list of aliases [array of [scalar]].
Args    :

add_synonym

Title   : add_synonym
Usage   : $term->add_synonym( @asynonyms );
          or
          $term->add_synonym( $synonym );
Function: Pushes one or more synonyms into the list of synonyms.
Returns :
Args    : One synonym [scalar] or a list of synonyms [array of [scalar]].

remove_synonyms

Title   : remove_synonyms()
Usage   : $term->remove_synonyms();
Function: Deletes (and returns) the synonyms of this Term.
Returns : A list of synonyms [array of [scalar]].
Args    :
Title   : get_dblinks()
Usage   : @ds = $term->get_dblinks();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args    : A scalar indicating the context (optional).
          If omitted, all dblinks will be returned.
Note    : deprecated method due to past use of mixed data types; use
          get_dbxrefs() instead, which handles both strings and DBLink
          instances

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 L<Bio::Annotation::DBLink> instances
Args    : [optional] string which specifies context (default : returns all dbxrefs)
Title   : get_dblink_context
Usage   : @context = $term->get_dblink_context;
Function: Return all context existing in Term
Returns : a list of scalar
Args    : [none]
Note    : deprecated method due to past use of mixed data types; use
          get_dbxref_context() instead

get_dbxref_context

Title   : get_dbxref_context
Usage   : @context = $term->get_dbxref_context;
Function: Return all context strings existing in Term
Returns : a list of scalars
Args    : [none]
Title   : add_dblink
Usage   : $term->add_dblink( @dbls );
          or
          $term->add_dblink( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args    : One or more L<Bio::Annotation::DBLink> instances
Note    : deprecated method due to past use of mixed data types; use
          add_dbxref() instead, which handles both strings and
          DBLink instances

add_dbxref

Title   : add_dbxref
Usage   : $term->add_dbxref( @dbls );
          or
          $term->add_dbxref( $dbl );
Function: Pushes one or more dblinks onto the list of dblinks.
Returns :
Args    : -dbxrefs : array ref of Bio::Annotation::DBLink instances
          -context : string designating the context for the DBLink
                      (default : '_default' - contextless)
Title   : has_dblink
Usage   : $term->has_dblink($dblink);
Function: Checks if a DBXref is already existing in the OBOterm object
Return  : TRUE/FALSE
Args    : [arg1] A DBxref identifier
Note    : deprecated method due to past use of mixed data types; use
          has_dbxref() instead, which handles both strings and
          DBLink instances

has_dbxref

Title   : has_dbxref
Usage   : $term->has_dbxref($dbxref);
Function: Checks if a dbxref string is already existing in the OBOterm object
Return  : TRUE/FALSE
Args    : [arg1] A DBxref identifier (string).
          Bio::Annotation::DBLink::display_text() is used for comparison
          against the string.
Title   : add_dblink_context
Usage   : $term->add_dblink_context($db, $context);
Function: add a dblink with its context
Return  : [none]
Args    : [arg1] a Bio::Annotation::DBLink instance
          [arg2] a string for context; if omitted, the
                 default/context-less one will be used.
Note    : deprecated method due to past use of mixed data types; use
          add_dbxref() instead
Title   : remove_dblinks()
Usage   : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args    : Context. If omitted or equal to 'all', all dblinks
          will be removed.
Note    : deprecated method due to past use of mixed data types; use
          remove_dblinks() instead, which handles both strings and
          DBLink instances

remove_dbxrefs

Title   : remove_dbxrefs()
Usage   : $term->remove_dbxrefs();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args    : Context. If omitted or equal to 'all', all dblinks
          will be removed.

get_references

Title   : get_references
Usage   : @references = $self->get_references
Fuctnion: Returns a list of references
Return  : A list of objects
Args    : [none]

add_reference

Title   : add_reference
Usage   : $self->add_reference($reference);
          $self->add_reference($reference1, $reference2);
Fuctnion: Add one or more references
Returns : [none]

remove_references

Title   : remove_references
Usage   : $self->remove_references;
Function: Deletes (and returns) all references
Returns : A list of references
Args    : [none]

get_secondary_ids

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.

Returns : A list of secondary identifiers [array of [scalar]]
Args    :

add_secondary_id

Title   : add_secondary_id
Usage   : $term->add_secondary_id( @ids );
          or
          $term->add_secondary_id( $id );
Function: Adds one or more secondary identifiers to this term.
Returns :
Args    : One or more secondary identifiers [scalars]

remove_secondary_ids

Title   : remove_secondary_ids
Usage   : $term->remove_secondary_ids();
Function: Deletes (and returns) the secondary identifiers of this Term.
Returns : The previous list of secondary identifiers [array of [scalars]]
Args    :

Methods implementing Bio::IdentifiableI and Bio::DescribableI

object_id

Title   : object_id
Usage   : $string    = $obj->object_id()
Function: a string which represents the stable primary identifier
          in this namespace of this object.

          This is a synonym for identifier().

Returns : A scalar

authority

Title   : authority
Usage   : $authority    = $obj->authority()
Function: a string which represents the organisation which
          granted the namespace, written as the DNS name for
          organisation (eg, wormbase.org)

          This forwards to ontology()->authority(). Note that you
          cannot set the authority before having set the ontology or
          the namespace (which will set the ontology).

Returns : A scalar
Args    : on set, the new value (a scalar)

namespace

Title   : namespace
Usage   : $string    = $obj->namespace()
Function: A string representing the name space this identifier
          is valid in, often the database name or the name
          describing the collection.

          This forwards to ontology() (set mode) and
          ontology()->name() (get mode). I.e., setting the namespace
          will set the ontology to one matching that name in the
          ontology store, or to one newly created.

Returns : A scalar
Args    : on set, the new value (a scalar)

display_name

Title   : display_name
Usage   : $string    = $obj->display_name()
Function: A string which is what should be displayed to the user.

          The definition in Bio::DescribableI states that the
          string should not contain spaces. As this is not very
          sensible for ontology terms, we relax this here. The
          implementation just forwards to name().

Returns : A scalar
Args    : on set, the new value (a scalar)

description

Title   : description
Usage   : $string    = $obj->description()
Function: A text string suitable for displaying to the user a
          description. This string is likely to have spaces, but
          should not have any newlines or formatting - just plain
          text.

          This forwards to definition(). The caveat is that the text
          will often be longer for ontology term definitions than the
          255 characters stated in the definition in
          Bio::DescribableI.

Returns : A scalar
Args    : on set, the new value (a scalar)

Deprecated methods

Used for looking up the methods that supercedes them.