Search results for "dist:BioPerl Bio::Ontology::RelationshipI"
Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms
This is the minimal interface for a relationship between two terms in an ontology. Ontology engines will use this. The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in additi...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::PathI - Interface for a path between ontology terms
This is the minimal interface for a path between two terms in an ontology. Ontology engines may use this. Essentially this is a very thin extension of the Bio::Ontology::RelationshipI interface. It basically adds an attribute distance(). For a Relati...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::Ontology - standard implementation of an Ontology
This is a no-frills implementation of Bio::Ontology::OntologyI. The query functions are implemented by delegation to an OntologyEngineI implementation....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::OntologyI - Interface for an ontology implementation
This describes the minimal interface an ontology implementation must provide. In essence, it represents a namespace with description on top of the query interface OntologyEngineI. This interface inherits from Bio::Ontology::OntologyEngineI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
Needs Graph.pm from CPAN. This module replaces SimpleGOEngine.pm, which is deprecated....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
This object will build Bio::Ontology::RelationshipI objects generically....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::Relationship - a relationship for an ontology
This is a basic implementation of Bio::Ontology::RelationshipI. The terminology we use here is the one commonly used for ontologies, namely the triple of (subject, predicate, object), which in addition is scoped in a namespace (ontology). It is calle...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy
This describes the minimal interface an ontology query engine should provide. It intentionally does not make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a vocabulary. Rather, it tries to generically expre...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface
This is a "simple" implementation of Bio::Ontology::OntologyEngineI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC