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Owlready2

.. image:: https://readthedocs.org/projects/owlready2/badge/?version=latest :target: http://owlready2.readthedocs.io/en/latest/ :alt: documentation

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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. <http://www.lesfleursdunormal.fr/_downloads/article_owlready_aim_2017.pdf>_ 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)

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

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