NAME

MOBY::OntologyServer - A way for MOBY Central to query the object, service, namespace, and relationship ontologies

SYNOPSIS

 use MOBY::OntologyServer;
 my $OS = MOBY::OntologyServer->new(ontology => "object");

 my ($success, $message, $existingURI) = $OS->objectExists(term => "Object");

 if ($success){
     print "object exists and it has the LSID $existingURI\n";
 } else {
    print "object does not exist; additional message from server: $message\n";
 }

DESCRIPTION

Swappable interface to ontologies. It should deal with LSID's 100% of the time, and also deal with MOBY-specific common names for objects, services, namespaces, and relationship types.

AUTHORS

Mark Wilkinson (markw@illuminae.com)

BioMOBY Project: http://www.biomoby.org

METHODS

new

 Title     :    new
 Usage     :    my $OS = MOBY::OntologyServer->new(%args)
 Function  :    
 Returns   :    MOBY::OntologyServer object
 Args      :    ontology => [object || service || namespace || relationship]
                database => mysql databasename that holds the ontologies
                host =>  mysql hostname
                username => mysql username
                password => mysql password
                port => mysql port
                dbh => pre-existing database handle to a mysql database

objectExists

 moby:newterm will return (0, $message, $MOBYLSID)
 newterm will return (0, $message, $MOBYLSID
 oldterm will return (1, $message, undef)
 newLSID will return (0, $desc, $lsid)

objectInfo

serviceInfo

createObject

retrieveObject

deprecateObject

deleteObject

relationshipExists

addObjectRelationship

addServiceRelationship

serviceExists

createServiceType

deleteServiceType

namespaceExists

createNamespace

deleteNamespace

retrieveAllServiceTypes

retrieveAllNamespaceTypes

retrieveAllObjectClasses

getObjectCommonName

getNamespaceCommonName

getServiceCommonName

getServiceURI

getObjectURI

getNamespaceURI

getRelationshipURI

consumes ontology (object/service) consumes relationship term as term or LSID

getRelationshipTypes

RelationshipsDEPRECATED

Relationships

setURI

traverseDAG

cpanm MOBY

perl -MCPAN -e shell
install MOBY