Owlready2 is a module for ontology-oriented programming in Python 3. It can manage ontologies and knwoledge graphs, and includes an optimized RDF/OWL quadstore.
Owlready2 can:
- 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 or Pellet reasoner (included)
- Load DBpedia or UMLS (for medical terminology, using the integrated PyMedTermino2 submodule)
- Native support for optimized SPARQL queries
- Tested up to 1 billion of RDF triples! (but can potentially support more)
- In addition, the quadstore is compatible with the RDFlib Python module
- Finally, Owlready2 can also be used as an ORM (Object-Relational mapper) -- as a graph/object database, it beats Neo4J, MongoDB, SQLObject and SQLAlchemy in terms of performances
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.306.s1.nabble.com
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:
>>> with onto:
... 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:
>>> test_onto.save()
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 !
Perform SPARQL queries:
>>> list(default_world.sparql("""SELECT * { ?x a owl:Class . FILTER(ISIRI(?x)) }"""))
[[pizza_onto.CheeseTopping], [pizza_onto.FishTopping], [pizza_onto.MeatTopping], [pizza_onto.Pizza], [pizza_onto.TomatoTopping], [pizza_onto.Topping], [pizza_onto.NonVegetarianPizza]]
Access to medical terminologies from UMLS:
>>> from owlready2 import *
>>> from owlready2.pymedtermino2.umls import *
>>> default_world.set_backend(filename = "pym.sqlite3")
>>> import_umls("umls-2018AB-full.zip", terminologies = ["ICD10", "SNOMEDCT_US", "CUI"])
>>> default_world.save()
>>> PYM = get_ontology("http://PYM/").load()
>>> ICD10 = PYM["ICD10"]
>>> SNOMEDCT_US = PYM["SNOMEDCT_US"]
>>> SNOMEDCT_US[186675001]
SNOMEDCT_US["186675001"] # Viral pharyngoconjunctivitis
>>> SNOMEDCT_US[186675001] >> ICD10 # Map to ICD10
Concepts([
ICD10["B30.9"] # Viral conjunctivitis, unspecified
])
For more documentation, look at the doc/ directories in the source.
- Fix sync_reasonner and Hermit call under windows (thanks Clare Grasso)
- Add warnings
- Accepts ontologies files that do not ends with '.owl'
- Fix a bug when loading ontologies including concept without a '#' in their IRI
- Full rewrite, including an optimized quadstore
- 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
- 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)
- 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
- 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
- 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
- Bugfixes: - Restore HermiT compiled with older Java compilator (higher compatibility)
- 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
- 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 /
- 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
- 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
- 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
- Bugfixes: - Fix performance regression due to suboptimal index in the quadstore - Fix messing up with IRI ending with a / - Fix error in World cloning - Fix the addition of Thing in class's parent when redefining a class with Thing as the only parent - Fix inverse_resctriction() - Add error message when creating an existent quadstore
- UMLS support (owlready2.pymedtermino2 package)
- Can infer object property values when reasoning (thanks W Zimmer)
- New implementation of property values; use INDIRECT_prop to get indirect values
- Support several class property types : some, only, some + only, and direct relation
- Automatically create defined classes via class properties
- Support anonymous individuals, e.g. Thing(0)
- Optimize search() when only the number of returned elements is used
- Optimize FTS search() when using also non-FTS statements
- Can restrict reasoning to a list of ontologies
- Union searches (i.e. default_world.search(...) | default_world.search(...))
- Bugfixes: - Fix functional class properties with inheritance - Fix dupplicated instance list restrictions when calling close_world(ontology) - Fix use of '*' in search - Fix synchronization, using contextvars for global variables
- Can infer data property values when reasoning with Pellet
- Optimize searches with 'type =', 'subclass_of =', or 'is_a =' parameters
- Add Property.range_iri
- Add _case_sensitive parameter to search()
- Add inverse property support in RDFlib support
- Show Java error message when reasoners crash
- Bugfixes: - Consider inverse property in get_properties() - Fix parsing bug in reasoning with HermiT and infer_property_values = True - Namespace prefix support in RDFlib binding - Fix dupplicates values when a relation involving a property with inverse is asserted in both directions - Better workaround in case of metaclass conflict - Fix 'sqlite3.OperationalError: too many SQL variables' in searches with 'type =', 'subclass_of =', or 'is_a =' parameters
- Optimize nested searches
- search(sublclass_of = xxx) now returns xxx itself in the results
- Support "with long_ontology_name as onto" syntax
- In UMLS import, add optional parameters for preventing extraction of attributes, relations, etc
- Support SPARQL INSERT queries
- Optimize Pymedtermino mapping
- Doc for PyMedTermino2
- Bugfixes: - Fix 'Cannot release un-acquired lock' error when reasoning on inconsistent ontologies inside a 'with' statement - Fix bug when loading a property that refers to another property from a quadstore stored on disk - Fix RDF triple suppression with RDFlib when object is a datatype
- SWRL rule support
- Allows importing UMLS suppressed terms
- Uncache entities when relaoding an ontology
- Bugfixes: - Fix PyMedTermino2 installation - Fix data property value inferrence with debug = 1 - Fix sort() in LazyList (thanks fiveop!) - Fix World.get() and add World.get_if_loaded() - Add appropriate error message when importing UMLS with Python 3.6 - Fix individuals belonging to multiple, equivalent, classes after reasoning
- Add UNIQUE constraints for preventing dupplicated RDF triples in the quadstore
- Add Individual.INDIRECT_is_a / Individual.INDIRECT_is_instance_of
- Add isinstance_python() (faster than isinstance(), but do not consider equivalent_to relations)
- Bugfixes: - Force UTF-8 encoding when importing UMLS - Be more tolerant when loading OWL file
- Consider symmetric properties as their own inverse properties
- Update Python objects after basic SPARQL update/delete queries (works on user-defined properties, hierarchical properties (type/subclassof) and equivalence properties)
- Add individual.INVERSE_property
- Add Class.INDIRECT_is_a
- INDIRECT_is_a / INDIRECT_is_instance_of now include class contructs. ancestors() has a 'include_constructs' parameter, which defaults to False.
- Add more aliases for XMLSchema datatypes
- Add is_a property to class constructs
- Add bottomObjectProperty and bottomDataProperty
- Support ReflexiveProperties in individual.INDIRECT_property
- Optimize Thing.subclasses()
- Optimize search() with multiple criteria, including those done by PyMedTermino
- Add support for destroy_entity(SWRL_rule)
- Add support for UMLS "metathesaurus" format in addition to "full" format
- Bugfixes: - After reasoning, keep all equivalent classes as parents of individuals (as they may have methods) - Fix IndividualPropertyAtom when creating SWRL rule - Fix SWRL parser - Fix RDF serialization for nested RDF lists - Fix removing inverse property (i.e. Prop.inverse = None) - Fix datetime parsing for date with time zone or milliseconds
- Add support for undoable destroy_entity()
- Small database optimizations
- No longer treat properties associated with exactly-1 or max-1 restriction as functional properties, returning single values instead of a list (you can restore the previous behaviour as follows: import owlready2.prop; owlready2.prop.RESTRICTIONS_AS_FUNCTIONAL_PROPERTIES = True)
- Bugfixes: - Fix performance bug on UMLS mapping in PyMedTermino
- Use Pellet 2.3.1 (same version as Protégé) instead of 2.4 (which has a bug in SWRL for many builtin predicates including equals and matches)
- Much faster mangement of annotations on relations
- Bugfixes: - Fix bug on blank node in RDFlib/SPARQL support - Fix bug on blank node deletion in RDFlib/SPARQL support - Fix data loss in Restriction modification - Fix 'no query solution' error in search() - Fix literal support in RDF lists, causing "TypeError: '<' not supported between instances of 'NoneType' and 'int'" when saving ontologies - Fix DifferentFrom SWRL builtin - Fix string parsing in SWRL rules - Fix string and boolean literal representation (str/repr) in SWRL rules - Fix the inverse of subproperties having a symmetric superproperty
- Add support for disjoint unions (Class.disjoint_unions)
- Add deepcopy support on class constructs, and automatically deep-copy constructs when needed (i.e. no more OwlReadySharedBlankNodeError)
- Support the creation of blank nodes with RDFlib
- Add get_parents_of(), get_instances_of(), get_children_of() methods to ontology, for querying the hierarchical relations defined in a given ontology
- Use Thing as default value for restrictions with number, instead of None
- Add 'filter' parameter to save(), for filtering the entities saved (contributed by Javier de la Rosa)
- Bugfixes: - Fix value restriction with the false value - Fix blank node loading from different ontologies - Fix constructs reused by several classes - Fix 'Class.is_a = []' was not turning the list into an Owlready list - Fix destroy_entity() - was not destroying the IRI of the entity - Improve setup.py: ignore Cython if Cython installation fails
- Support intersection of searches (e.g. World.search(...) & World.search(...))
- Add owlready2.reasoning.JAVA_MEMORY
- Move development repository to Git
- Bugfixes: - Fix parsing of NTriples files that do not end with a new line - Fix KeyError with Prop.python_name when several properties share the same name - Fix get_ontology() calls in Python module imported by ontologies in a World that is not default_world - Fix use of PyMedTermino2 in a World that is not default_world - Fix World.as_rdflib_graph().get_context(onto) for ontology added after the creation of the RDFLIB graph - Fix destroying SWRL rules - Fix disjoint with non-atomic classes
- Allow the declaration of custom datatypes with declare_datatype()
- Support the annotation of annotations (e.g. a comment on a comment)
- search() now support the "subproperty_of" argument
- search() now support the "bm25" argument (for full-text searches)
- Bugfixes: - Fix Concept.descendant_concepts() in PymedTermino2 - Update already loaded properties when new ontologies are loaded - Now accept %xx quoted characters in file:// URL - Improve error message on punned entities - Property.get_relations() now considers inverse properties - Fix "AttributeError: 'mappingproxy' object has no attribute 'pop'" error - Fix Thing.instances()
- Module owlready2.dl_render allows rendering entities to Description Logics (contributed by Simon Bin)
- Bugfixes: - Adjustment in the comparison of strings from SameAs and DiferrentFrom, allowing equal comparison regardless of the case-sensitive (contributed by Thiago Feijó) - Fix transitive equivalent_to relations between classes and OWL constructs - Fix AnnotationProperty[entity] where entity is a predefined OWL entity (e.g. comment or Thing) - Fix entity.AnnotationProperty where entity is a predefined OWL entity (e.g. comment or Thing) - Fix HermiT when reasoning on several ontologies with imports statement - Ignore "A type A", with a warning
- When Pellet is called with debug >= 2 on an inconsistent ontology, Pellet explain output is displayed (contributed by Carsten Knoll)
- Update doc theme (contributed by Carsten Knoll)
- Adapt setup.py to allow 'python setup.py develop' and 'pip install -e .' (contributed by Carsten Knoll)
- Add 'url' argument to Ontology.load() method
- Add 'read_only' argument to World.set_backend() method
- Bugfixes: - Fix XML/RDF file parsing/writing for entity having ':' in their name - Fix destroy_entity(), was leaking some RDF triples when class contructs or equivalent_to were involved - Fix 'Class1(entityname); Class2(entityname)' (was changing the individual namespace) - Fix annotation request on RDF annotation properties, e.g. label.label
- Bugfixes: - Fix installation under Windows (contributed by CVK) - Under Windows, run the reasoners without opening a DOS windows
- Bugfixes: - Fix installation as a requirement of another Python module
- New native SPARQL engine that translates SPARQL queries to SQL
- Direct support for Dublin Core via the integration of an OWL translation
- Bugfixes: - Fix RecursionError when saving very deep ontologies to RDF/XML - Fix IRI of the form 'urn:uuid:...' - Fix loading ontologies that modify an imported property
- Can open SPARQL endpoints (see module owlready2.sparql.endpoint and doc)
- Support ClaML file format in PyMedTermino2 for French ICD10
- Bugfixes: - Fix prefix in SPARQL that does not correspond to an existing ontology - Fix ! in SPARQL FILTER - Fix Thing.subclasses() so as it now returns classes that have parent constructs but no parent named classes - Fix metaclass of FusionClass when creating individuals belonging to several classes, including one from PyMedTermino - Fix Prop[individual] for functional properties with no relation for the given individual
- Add scripts to import OMOP-CDM as an ontology (see directory pymedtermino2/omop_cdm/)
- SPARQL engine optimization
- Bugfixes: - Fix name clash when creating individuals from classes whose names end with a number, e.g. "c1" + "1" vs "c" + "11" - Fix block with only a FILTER in SPARQL
- Bugfixes: - Fix 'sqlite3.OperationalError: no such table: sqlite_schema' with SQLite3 < 0.33
- NEW FORUM ADDRESS: http://owlready.306.s1.nabble.com
- Support SPARQL property path expressions with parentheses without sequences, repeats or negative property set nested inside repeats
- Add define_datatype_in_ontology() global function for defining a new user-defined datatype in an ontology
- Class.instances() now takes into account equivalent classes (like other class methods such as .descendants())
- Add the LOADED(iri) SPARQL function
- Support Thing.is_a.append(...)
- Faster loading of very large quadstores
- list(onto.metadata) now lists the annotations present on the ontology
- Add OntologyClass and NamespaceClass argument to get_ontology() and get_namespace(), allowing the use of custom classes
- Bugfixes: - Accept UTF8 and latin encoding from reasoners (thanks Francesco Compagno) - Fix SPARQL query with a UNION without variables - Fix semantic type support in UMLS
- SPARQL optimizations
- Support for VALUES in SPARQL
- Add STATIC optimization keyword extension to SPARQL
- Accept GROUP BY, HAVING, LIMIT in INSERT and DELETE SPARQL query
- Add the STORID(iri), DATE(), TIME() and DATETIME() SPARQL function
- UMLS CUI are now hierarchized by Semnatic Types (TUI)
- Improved parallelism
- Bugfixes: - Fix 'sqlite3.OperationalError: circular reference: prelim1_objs' in .instances(), caused by a bug in old versions of SQLite3 - Fix SPARQL INSERT query with data parameters in the INSERT clause - Fix RDF list parsing when the list includes the integer number 5 - Fix nb_parameter in SPARQL query when numbered parameters are used - Fix ObjectProperty.subclasses(), ObjectProperty.descendants(), Property.subclasses(), DataProperty.descendants(), AnnotationProperty.subclasses(), AnnotationProperty.descendants() - Fix declare_datatype() for datatype already used in Owlready, such as AnyURI - Fix Pellet on properties having annotations that are not declared in the loaded ontologies
- Faster ontology operation (e.g. ontology deletion) on big quadstores
- Automatically add .owl, .rdf or .xml to ontology IRI if the IRI itself does not yield an OWL file
- Bugfixes: - Fix FusionClasses (= individuals belonging to several classes, i.e. multiple instanciation) when using several worlds - Fix OPTIONAL SPARQL clause when guessing variable types - Fix typo in undo entity destruction (thanks Lukas Westhofen) - Fix IRI from OWL namespace in SWRL rules - Fix Pellet explanation on inconsistent ontology - Fix MEDDRA parent-child relation of LLT in PyMedTermino2
Owlready2 on BitBucket (Git development repository): https://bitbucket.org/jibalamy/owlready2
Owlready2 on PyPI (Python Package Index, stable release): https://pypi.python.org/pypi/Owlready2
Documentation: http://owlready2.readthedocs.io/
Forum/Mailing list: http://owlready.306.s1.nabble.com
Contact "Jiba" Jean-Baptiste Lamy:
<jean-baptiste.lamy *@* univ-paris13 *.* fr> LIMICS Université Sorbonne Paris Nord, Sorbonne Université, INSERM Bureau 149 74 rue Marcel Cachin 93017 BOBIGNY FRANCE