Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy $factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names. $factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument. $factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument. juguang@tll.org.sg Additional contributors' names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

fetch
Title: fetch Usage: my $taxonomy = $factory->fetch(-taxon_id => 9605); my $taxonomy = $factory->fetch(-common_name => 'mammals'); Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name. Returns: an instance of Bio::Taxonomy Args: -taxon_id => NCBI taxonomy ID -common_name => comon name, such as 'human', 'mammals' -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'

fuzzy_fetch
Title: fuzzy_fetch Usage: my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse'); Function: Fuzzy fetch by name, or any text information found in DB Returns: an array reference of Bio::Taxonomy objects Args: -name => any name, such as common name, variant, scientific name -description, or -desc => any text information

fetch_parent
Title: fetch_parent Usage: my $parent_taxonomy = $factory->fetch_parent($taxonomy); Function: Fetch the parent that is one-rank higher than the argument. Returns: an instance of Bio::Taxonomy, or undef if the arg is the top one. Args: a Bio::Taxonomy object.

fetch_children
Title: fetch_children Usage: my @children_taxonomy = $factory->fetch_children($taxonomy); Function: Fetch all children those are one-rank lower than the argument. Returns: an array reference of Bio::Taxonomy objects Args: a Bio::Taxonomy object.