Owlready2

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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