Bio::AnnotationCollectionI

NAME

Bio::AnnotationCollectionI - Interface for annotation collections

SYNOPSIS

   # get an AnnotationCollectionI somehow, eg
   $ac = $seq->annotation();
   foreach $key ( $ac->get_all_annotation_keys() ) {
       @values = $ac->get_Annotations($key);
       foreach $value ( @values ) {
          # value is an Bio::AnnotationI, and defines a "as_text" method
          print "Annotation ",$key," stringified value ",$value->as_text,"\n";
          # also defined hash_tree method, which allows data orientated
          # access into this object
          $hash = $value->hash_tree();
       }
   }

DESCRIPTION

Annotation Collections are a way of storing a series of "interesting facts" about something. We call an "interesting fact" in Bioperl an Annotation (this differs from a Sequence Feature, which is called a Sequence Feature and may or may not have an Annotation Collection). A benefit of this approach is that all sorts of simple, interesting observations can be collected, the possibility is endless. The Bioperl approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees two methods

   $obj->as_text(); # string formatted to display to users

and

   $obj->hash_tree(); # hash with defined rules for data-orientated discovery

The hash_tree method is designed to play well with XML output and other "nested-tag-of-data-values", think BoulderIO and/or Ace stuff. For more information see Bio::AnnotationI. Annotations are stored in AnnotationCollections, each Annotation under a different "tag". The tags allow simple discovery of the available annotations, and in some cases (like the tag "gene_name") indicate how to interpret the data underneath the tag. The tag is only one tag deep and each tag can have an array of values. In addition, AnnotationCollections are guaranteed to maintain consistent types of objects under each tag - at least that each object complies to one interface. The "standard" AnnotationCollection insists the following rules are set up:

  Tag            Object
  ---            ------
  comment        Bio::Annotation::Comment
  dblink         Bio::Annotation::DBLink
  description    Bio::Annotation::SimpleValue
  gene_name      Bio::Annotation::SimpleValue
  ontology_term  Bio::Annotation::OntologyTerm
  reference      Bio::Annotation::Reference

These tags are the implict tags that the SeqIO system needs to round-trip GenBank/EMBL/Swissprot. However, you as a user and us collectively as a community can grow the "standard" tag mapping over time and specifically for a particular area.

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.

  [email protected]

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

ACCESSOR METHODS

Use these for Bio::AnnotationI object access.

get_all_annotation_keys()

 Usage   : $ac->get_all_annotation_keys()
 Function: gives back a list of annotation keys, which are simple text strings
 Returns : list of strings
 Args    : none

get_Annotations()

 Usage   : my @annotations = $collection->get_Annotations('key')
 Function: Retrieves all the Bio::AnnotationI objects for a specific key
 Returns : list of Bio::AnnotationI - empty if no objects stored for a key
 Args    : string which is key for annotations

add_Annotation()

 Usage   : $self->add_Annotation('reference',$object);
           $self->add_Annotation($object,'Bio::MyInterface::DiseaseI');
           $self->add_Annotation($object);
           $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
 Function: Adds an annotation for a specific key.
           If the key is omitted, the object to be added must provide a value
           via its tagname().
           If the archetype is provided, this and future objects added under
           that tag have to comply with the archetype and will be rejected
           otherwise.
 Returns : none
 Args    : annotation key ('disease', 'dblink', ...)
           object to store (must be Bio::AnnotationI compliant)
           [optional] object archetype to map future storage of object
           of these types to

remove_Annotations()

 Usage   :
 Function: Remove the annotations for the specified key from this collection.
 Returns : an list of Bio::AnnotationI compliant objects which were stored
           under the given key(s)
 Args    : the key(s) (tag name(s), one or more strings) for which to
           remove annotations (optional; if none given, flushes all
           annotations)

get_num_of_annotations()

 Usage   : my $count = $collection->get_num_of_annotations()
 Function: Returns the count of all annotations stored in this collection
 Returns : integer
 Args    : none