owlready2 0.29

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.

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)

• Tested up to 1 billion 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) – 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.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:

::

>>> 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 !

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.

Changelog

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

version 2 - 0.13

• 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

version 2 - 0.14

• 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

version 2 - 0.15

• 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

version 2 - 0.16

• 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

version 2 - 0.17

• 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

version 2 - 0.18

• 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

version 2 - 0.19

• 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

version 2 - 0.20

• 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

version 2 - 0.21

• 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

version 2 - 0.22

• 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

version 2 - 0.23

• 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

version 2 - 0.24

• 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

version 2 - 0.25

• 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()

version 2 - 0.26

• 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

version 2 - 0.27

• 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

version 2 - 0.28

• Fix installation under Windows (contributed by CVK)

• Under Windows, run the reasoners without opening a DOS windows

Links

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.8326.n8.nabble.com

Contact “Jiba” Jean-Baptiste Lamy:

<jean-baptiste.lamy *@* univ-paris13 *.* fr>
LIMICS
University Paris 13, Sorbonne Paris Cite
Bureau 149
74 rue Marcel Cachin
93017 BOBIGNY
FRANCE