Bio::AnnotationCollectionI 1.4 review

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow,

License: Perl Artistic License File size: 4788K Developer: Ewan Birney

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Bio::AnnotationCollectionI is a Perl 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();
}
}

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
--- ------
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.

What's New in This Release:
Perl