Ewan Birney

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).

The trouble about this is we are not that sure what "interesting facts" someone might want to store: the possibility is endless.

Bioperl's approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarentees two methods

   $obj->as_text(); # string formated 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 info read Bio::AnnotationI docs

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, AnnotationCollectionI's are guarentee to maintain a consistent set object values under each tag - at least that each object complies to one interface. The "standard" AnnotationCollection insists the following rules are set up

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

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.

  bioperl-l@bio.perl.org

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

Describe contact details here

APPENDIX

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

get_all_annotation_keys

 Title   : 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

 Title   : 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

get_num_of_annotations

 Title   : 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