NAME
FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database
SYNOPSIS
# see load_interpro.pl in bioperl-db/scripts/biosql/DESCRIPTION
This module is for parsing an InterPro XML file and persist the resulting terms to a Biosql database as soon as the term is complete as signaled by the appropriate xml tag. This parser takes advantage of SAX, a stream-based XML parser technology, to keep the used memory as small as possible. The alternative parser for InterPro, module InterProHandler, builds up the entire ontology in memory, which given the size of the latest InterPro releases requires a huge amount of memory.
This module takes the following non-standard arguments upon instantiation.
-db the adaptor factory as returned by a call to
FAST::Bio::DB::BioDB->new()
-version the InterPro version (not available as property!)
-term_factory the object factory to use for creating termsNote that there are two alternatives for how to persist the terms and relationships to the database. The default is using the adaptor factory passed as -db or set as a property to create persistent objects and store them in the database. The alternative is to specify a term persistence and a relationship persistence handler; if one or both have been set, the respective handler will be called with each term and relationship that is to be stored. See properties persist_term_handler and persist_relationship_handler.
AUTHOR
Juguang Xiao, juguang@tll.org.sg
Contributors
Hilmar Lapp, hlapp at gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Interal methods are usually preceded with a _
term_factory
Title : term_factory
Usage : $obj->term_factory($newval)
Function: Get/set the ontology term factory to use.
As a user of this module it is not necessary to call this
method as there will be default. In order to change the
default, the easiest way is to instantiate
L<FAST::Bio::Ontology::TermFactory> with the proper -type
argument. Most if not all parsers will actually use this
very implementation, so even easier than the aforementioned
way is to simply call
$ontio->term_factory->type("FAST::Bio::Ontology::MyTerm").
Example :
Returns : value of term_factory (a FAST::Bio::Factory::ObjectFactoryI object)
Args : on set, new value (a FAST::Bio::Factory::ObjectFactoryI object, optional)db
Title : db
Usage : $obj->db($newval)
Function: Sets or retrieves the database adaptor factory.
The adaptor factory is a FAST::Bio::DB::DBAdaptorI compliant
object and will be used to obtain the persistence adaptors
necessary to serialize terms and relationships to the
database.
Usually, you will obtain such an object from a call to
FAST::Bio::DB::BioDB. You *must* set this property before
starting the parse.
Note that this property is immutable once set, except that
you may set it to undef. Therefore, be careful not to set
to undef before setting the desired real value.
Example :
Returns : value of db (a FAST::Bio::DB::DBAdaptorI compliant object)
Args : on set, new value (a FAST::Bio::DB::DBAdaptorI compliant object
or undef, optional)persist_term_handler
Title : persist_term_handler
Usage : $obj->persist_term_handler($handler,@args)
Function: Sets or retrieves the persistence handler for terms along
with the constant set of arguments to be passed to the
handler.
If set, the first argument will be treated as a closure and
be called for each term to persist to the database. The
term will be passed as a named parameter (-term), followed
by the other arguments passed to this setter. Note that
this allows one to pass an arbitrary configuration to the
handler.
If not set, terms will be persisted along with their
relationships using the respective persistence adaptor
returned by the adaptor factory (see property db).
Example :
Returns : an array reference with the values passed on set, or an empty
array if never set
Args : On set, an array of values. The first value is the handler
as a closure; all other values will be passed to the handler
as constant argument.persist_relationship_handler
Title : persist_relationship_handler
Usage : $obj->persist_relationship_handler($handler,@args)
Function: Sets or retrieves the persistence handler for relationships
along with the constant set of arguments to be passed to
the handler.
If set, the first argument will be treated as a closure and
be called for each relationship to persist to the database. The
relationship will be passed as a named parameter (-rel), followed
by the other arguments passed to this setter. Note that
this allows one to pass an arbitrary configuration to the
handler.
If not set, relationships will be persisted along with their
relationships using the respective persistence adaptor
returned by the adaptor factory (see property db).
Example :
Returns : an array reference with the values passed on set, or an empty
array if never set
Args : On set, an array of values. The first value is the handler
as a closure; all other values will be passed to the handler
as constant argument._persist_term
Title : _persist_term
Usage :
Function: Persists a term to the database, using either a previously
set persistence handler, or the adaptor factory directly.
Example :
Returns :
Args : the ontology term to persist_persist_relationship
Title : _persist_relationship
Usage :
Function: Persists a relationship to the database, using either a
previously set persistence handler, or the adaptor factory
directly.
Example :
Returns :
Args : the term relationship to persist_persist_ontology
Title : _persist_ontology
Usage :
Function: Perists the ontology itself to the database, by either
inserting or updating it.
Note that this will only create or update the ontology as
an entity, not any of its terms, relationships, or
relationship types.
Example :
Returns : the ontology as a peristent object with primary key
Args : the ontology to persist as a FAST::Bio::Ontology::OntologyI
compliant object