A package for ontology-oriented programming in Python: load OWL 2.0 ontologies as Python objects, modify them, save them, and perform reasoning via HermiT. Includes an optimized RDF quadstore.
Owlready2 is a module for ontology-oriented programming in Python 3, including an optimized RDF quadstore.
- Import OWL 2.0 ontologies in NTriples, RDF/XML or OWL/XML format.
- Export OWL 2.0 ontologies to NTriples or RDF/XML.
- Manipulates ontology classes, instances and properties transparently, as if they were normal Python objects.
- Add Python methods to ontology classes.
- Perform automatic classification of classes and instances, using the HermiT reasoner.
- Tested up to 200 millions of RDF triples (but can potentially support more).
- In addition, the quadstore is compatible with the RDFlib Python module, which can be used to perform SPARQL queries.
- Finally, Owlready2 can also be used as an ORM (Object-Relational mapper) or an object database.
Owlready has been created by Jean-Baptiste Lamy at the LIMICS reseach lab. It is available under the GNU LGPL licence v3. If you use Owlready in scientific works, please cite the following article:
Lamy JB. Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies. Artificial Intelligence In Medicine 2017;80:11-28
In case of troubles, questions or comments, please use this Forum/Mailing list: http://owlready.8326.n8.nabble.com
What can I do with Owlready2?
Load an ontology from a local repository, or from Internet:
>>> from owlready2 import * >>> onto_path.append("/path/to/your/local/ontology/repository") >>> onto = get_ontology("http://www.lesfleursdunormal.fr/static/_downloads/pizza_onto.owl") >>> onto.load()
Create new classes in the ontology, possibly mixing OWL constructs and Python methods:
>>> class NonVegetarianPizza(onto.Pizza): ... equivalent_to = [ ... onto.Pizza ... & ( onto.has_topping.some(onto.MeatTopping) ... | onto.has_topping.some(onto.FishTopping) ... ) ] ... def eat(self): print("Beurk! I'm vegetarian!")
Access ontology class, and create new instances / individuals:
>>> onto.Pizza pizza_onto.Pizza >>> test_pizza = onto.Pizza("test_pizza_owl_identifier") >>> test_pizza.has_topping = [ onto.CheeseTopping(), ... onto.TomatoTopping(), ... onto.MeatTopping () ]
Export to RDF/XML file:
Perform reasoning, and classify instances and classes:
>>> test_pizza.__class__ onto.Pizza >>> # Execute HermiT and reparent instances and classes >>> sync_reasoner() >>> test_pizza.__class__ onto.NonVegetarianPizza >>> test_pizza.eat() Beurk! I'm vegetarian !
For more documentation, look at the doc/ directories in the source.
version 1 - 0.2
- Fix sync_reasonner and Hermit call under windows (thanks Clare Grasso)
version 1 - 0.3
- Add warnings
- Accepts ontologies files that do not ends with ‘.owl’
- Fix a bug when loading ontologies including concept without a ‘#’ in their IRI
version 2 - 0.1
- Full rewrite, including an optimized quadstore
version 2 - 0.2
- Implement RDFXML parser and generator in Python (no longer use rapper or rdflib)
- Property chain support
- Add ntriples_diff.py utility
- Bugfixes: - Fix breaklines in literal when exporting to NTriples
version 2 - 0.3
- Add destroy_entity() global function
- Greatly improve performance for individual creation
- When searching, allow to use “*” as a jocker for any object
- Bugfixes: - Fix nested intersections and unions - Fix boolean - Fix bug when removing parent properties - Fix parsing of rdf:ID - Fix multiple loading of the same ontology whose IRI is modified by OWL file, using an ontology alias table - Fix ClassConstruct.subclasses() - Check for properties with multiple incompatible classes (e.g. ObjectProperty and Annotation Property)
version 2 - 0.4
- Add methods for querying the properties defined for a given individuals, the inverse properties and the relation instances (.get_properties(), .get_inverse_properties() and .get_relations())
- Add .indirect() method to obtain indirect relations (considering subproperties, transivitity, symmetry and reflexibity)
- search() now takes into account inheritance and inverse properties
- search() now accepts ‘None’ for searching for entities without a given relation
- Optimize ontology loading by recreating SQL index from scratch
- Optimize SQL query for transitive quadstore queries, using RECURSIVE Sqlite3 statements
- Optimize SQL query for obtaining the number of RDF triples (ie len(default_world.graph))
- Add Artificial Intelligence In Medicine scientific article in doc and Readme
- Bugfixes: - Fix properties loading when reusing an ontology from a disk-stored quadstore - Fix _inherited_property_value_restrictions() when complement (Not) is involved - Fix restrictions with cardinality - Fix doc on AllDisjoint / AllDifferent
version 2 - 0.5
- Add individual/instance editor (require EditObj3, still largely untested)
- Add support for hasSelf restriction
- Optimize XML parsers
- Check for cyclic subclass of/subproperty of, and show warning
- PyPy 3 support (devel version of PyPy 3)
- Bugfixes: - Fix search() for ‘*’ value on properties with inverse - Fix individual.annotation = “…” and property.annotation = “…” - Fix PlainLiteral annotation with no language specified - Fix doc for Creating classes dynamically - Fix loading ontologies with python_name annotations - Fix _inherited_property_value_restrictions when multiple is-a / equivalent-to are present - Align Python floats with xsd:double rather than xsd:decimal - Rename module ‘property’ as ‘prop’, to avoid name clash with Python’s ‘property()’ type
version 2 - 0.6
- Add set_datatype_iri() global function for associating a Python datatype to an IRI
- Add nquads ontology format (useful for debugging)
- Add support for dir() on individuals
- Add support for ontology using https: protocol (thanks Samourkasidis Argyrios)
- Add observe module (for registering callback when the ontology is modified)
- Improve docs
- Bugfixes: - Align Python floats with xsd:decimal rather than xsd:double, finally, because decimal accepts int too - Fix Class.instances() so as it returns instances of subclasses (as indicated in the doc) - Fix direct assignation to Ontology.imported_ontologies - Fix a bug in reasoning, when adding deduced facts between one loaded and one non-loaded entity
version 2 - 0.7
- Bugfixes: - Restore HermiT compiled with older Java compilator (higher compatibility)
version 2 - 0.8
- Bugfixes: - REALLY restore HermiT compiled with older Java compilator (higher compatibility) - Fix search(prop = “value”) when value is a string and the ontology uses localized string
version 2 - 0.9
- PostgresQL backend (in addition to SQLite3)
- Add ‘exclusive = False’ option for SQLite3 backend (slower, but allows multiple uses)
- Use unique index in sqlite3 quadstore on resources table
- Optimize sqlite3 quadstore by caching IRI dict (5% faster)
- Add == support for class construct
- Add get_namespace() support on World
- Add ‘existential restrictions as class properties’ feature
- Bugfixes: - Fix imported ontologies - Fix saving ontologies in onto_path - Fix clear() on CallbackList - Fix bug in Class IRI in ontologies whose base IRI ends with a / - Fix imported ontologies in ontologies whose base IRI ends with a /
version 2 - 0.10
- Add Ontology.metadata for adding/querying ontology metadata
- Allows multiple individual creations with the same name/IRI, now returning the same individuals
- Add OwlReadyInconsistentOntologyError and Word.inconsistent_classes()
- Implement RDF/XML and OWL/XML parsing in Cython (25% speed boost for parsing)
- Small optimization
- Extend individual.prop.indirect() to include relations asserted at the class level
- Add .query_owlready() method to RDF graph
- Bugfixes: - Fix reasoning when obtaining classes equivalent to nothing - Fix World creation with backend parameters - Fix error when adding property at the class definition level - Fix loading of ontology files with no extension from onto_path - Fix properties defined with type ‘RDF Property’ and subproperty of ‘OWL Data/Object/Annotation Property’ - Support old SQLite3 versions that do not accept WITHOUT ROWID - Fix reference to undeclared entities (they were replaced by None, now by their IRI) - Fix loading and saving ontologies whose base IRI ends with / - Fix RDF query using string
version 2 - 0.11
- Optimized Full-Text Search
- Support Pellet reasoner in addition to HermiT
- Support loading of huge OWL files (incremental load)
- Use Class.property.indirect() for indirect Class property (instead of Class.property)
- Add reload and reload_if_newer parameters to Ontology.load()
- search() is now much faster on properties that have inverse
- Add shortcut for SOME ConstrainedDatatype: e.g. age >= 65
- Bugfixes: - Fix creation of an individual that already exists in the quadstore - Fix missing import of EntityClass in class_construct.py - Fix World.save() with RDF/XML format - Fix Thing.subclasses() and Thing.descendants() - Fix ontology’s update time for ontologies created de novo in Python with Owlready - Fix reasoning when asserting new parents with equivalent classes
version 2 - 0.12
- New quadstore
- Numerical search (NumS, e.g. all patients with age > 65)
- Nested searches
- Synchronization for multithreading support
- Add Class.inverse_restrictions() and Class.direct_instances()
- Drop PostgresQL support (little interest: more complex and slower than Sqlite3)
- Bugfixes: - Fix call to _get_by_storid2 - Fix rdfs_subclassof in doc - Fix FTS triggers - Fix boolean in RDFlib / SPARQL - Fix bug when destroying an AnnotationProperty