Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Ontology::Term.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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    :
 
 

get_dblinks

  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)
 
 

get_dblink_context

   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]
 
 

add_dblink

  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)
 
 

has_dblink

   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.
 
 

add_dblink_context

   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
 
 

remove_dblinks

  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.