owlready2 0.50
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.
Requires Python: >=3.6

Owlready2
=========

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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)

 - Perfom 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. <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.306.s1.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 !

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.

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
****************

* Bugfixes:
  - Fix installation under Windows (contributed by CVK)
  - Under Windows, run the reasoners without opening a DOS windows

version 2 - 0.29
****************

* Bugfixes:
  - Fix installation as a requirement of another Python module

version 2 - 0.30
****************

* 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

version 2 - 0.31
****************

* 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

version 2 - 0.32
****************

* 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

version 2 - 0.33
****************

* Bugfixes:
  - Fix 'sqlite3.OperationalError: no such table: sqlite_schema' with SQLite3 < 0.33

version 2 - 0.34
****************

* 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

version 2 - 0.35
****************

* 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

version 2 - 0.36
****************

* Support xsd:duration, including DATETIME_DIFF(), DATETIME_ADD(), DATETIME_SUB() SPARQL non-standard functions
* 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
  - Make sure the filename is a file before returning (Thanks Nicolas Rouquette)
    
version 2 - 0.37
****************

* Add World.forget_reference(entity)
* Add NamedIndividual (for SPARQL results on rdf:type)
* Add 'update_relation' optional args to Ontology.destroy()
* Add Ontology.set_base_iri() and Ontology.base_iri = "new_base_iri"
* Bugfixes:
  - Fix SPARQL queries having a UNION but using no variable from the UNION
  - Fix SPARQL queries on read only quadstores
  - Fix SPARQL queries mixing OPTIONAL and VALUES / STATIC 
  - Fix property defined as a subproperty of TransitiveProperty (and the like), but not of type ObjectProperty
  - Fix importlib.reload(owlready2)
  - Fix RDF/XML serialization of individuals whose class name start by a digit
  - Fix RDF/XML serialization when ontology base IRI ends with /
  - Fix Or.Classes = ... and And.Classes = ...
  - Fix ONLY class properties with more than two values

version 2 - 0.38
****************

* Accepts localized language codes, such as fr_FR or fr_BE, and wildcard fr_any
* Add 'update_is_a' optional args to Ontology.destroy()
* Bugfixes:
  - Fix individual.INVERSE_prop update when prop is functional
  - Fix performance regression on complex SPARQL queries with OPTIONAL
  - Fix declare_datatype after a World has been closed
  - Fix Pellet reasoning on blank nodes (ignoring them)
  - Fix Pellet reasoning on strings data property that include comma ","
  - Fix boolean constant 'true' and 'false' in SPARQL engine
  - Fix INSERT SPARQL queries with UNION that insert RDF triples without variables
  - Fix SPARQL queries with only a FILTER NOT EXISTS in the WHERE part
  - Accept empty lines at the beginning of NTriple files
  - Support non-ASCII characters when parsing SWRL rules

version 2 - 0.39
****************

* Make RDF triple deletion non-ontology-specific
* Faster creation of individual with property value (e.g. MyClass(prop = [value]))
* Bugfixes:
  - Fix entity.prop.remove(x) and entity.prop = x when existing values are defined in another ontology than the entity
  - Fix inverse property update when referenced entity is destroyed (thanks Franzlst)
  - Prevent reasoners from reparenting OWL base entities such as Thing
  - Fix the reloading of an ontology that has been destroyed, when a local filename is provided as the ontology base IRI
  - Fix destroying object property involved in a property chain
  - Fix reloading of ontologies when the IRI of the ontology was a local filename
  - Fix SELECT * in SPARQL coumpound queries
  - Fix Class.get_class_properties() when some properties are defined as restriction on an Inverse property
  - Fix for RDFlib 0.6.2 (supports bind() override optional argument)
    
version 2 - 0.40
****************

* General class axiom support
* Update Log4J in Pellet for security purpose
* Add get_lang_first() for annotations.
* Bugfixes:
  - Add trailing / to ontology URL if missing
  - Fix Individual.is_a when loading ontologies with individuals belonging to two classes, one being the descendant of the other
  - Fix datetime to make them XSD-compatible (thanks Lukas Müller)
  - Ensure that Things are properly initialized so that the __init__ method can be safely overwritten (thanks Lukas Müller)
  - Fix destroy_entity()

version 2 - 0.41
****************

* Parallelized huge OWL file parsing (about 25% faster on GO)
* Parallelized SPARQL queries (see owlready2.sparql.execute_many() and execute(spawn = True))
* Bugfixes:
  - Fix Class.INDIRECT_get_class_properties() with restriction on Inverse(Prop)
  - Fix Restriction of type HasSelf
  - Fix delattr in destroy_entity()
  - Fix blank nodes importation from RDFlib
  - Fix ', + and - in FTS search

version 2 - 0.42
****************

* INCOMPATIBLE CHANGE: Consider literal with different language as different (e.g. locstr("Test", "en") != locstr("Test", "fr"))
* Support GRAPH clauses in SPARQL SELECT queries
* World now supports custom lock (e.g. World(lock = ...))
* Bugfixes:
  - Fix World(enable_thread_parallelism = True) (was named enable_gevent)
  - Fix blank nodes in rdflib_store
  - Fix FILTER in SPARQL when the filter was just after a recursive query
  - Fix recursive query in SPARQL involving variables in their right part
  - Fix SPARQL query with annotations containing entities
  - Fix property creation when using a Union in the '>>' syntax (e.g. class Prop((MyClass | MyOtherClass) >> str): pass)
  - Fix UMLS extraction in PyMedTermino2
  - Fix Class IRI with brackets (or other special characters) when writing RDF/XML file
    
version 2 - 0.43
****************

* Bugfixes:
  - Fix != operator on locstr

version 2 - 0.44
****************

* New syntax for annotations on relation, e.g. AnnotatedRelation(s,p,o).comment = "abc" (the old syntax remains supported)
* Optimize annotations on relations
* Support GRAPH clauses in SPARQL INSERT queries
* Observation framework (see owlready2.observe and doc on the observation framework)
* Bugfixes:
  - Fix the update of equivalent_to after destroying a class
  - Fix the update of annotations on class when modified with SPARQL queries
  - Fix SPARQL GRAPH clause in SELECT queries when querying the graph as a variable and all triples are not inside the GRAPH clause
  - Fix LANGMATCHES SPARQL function
  - Prevent multiprocessing loading of large ontologies when fork is not available (i.e. on Mac)
  - Fix subproperties parent classes when destroying a property
  - Fix loading of TransitiveProperty, SymmetricProperty, AsymmetricProperty, ReflexiveProperty, IrreflexiveProperty
    
version 2 - 0.45
****************

* The PREDEFINED_ONTOLOGIES global dictionary can now be used to map ontology IRI to arbitrary local pathes or URL.
* The new FTSSqlite3Phrase() string type can be used to perform FTS search using Sqlite3 special syntax, e.g. default_world.search(label = FTSSqlite3Phrase("Electrocardiographic OR ECG"))
* Add support for RDF plain literals, via the plainliteral Python datatype.
* Bugfixes:
  * Fix set_name() on property when python_name is the same as name
  * Fix some special characters (e.g. :) and keyword (e.g. OR) in FTS search
  * Fix literal with no datatype (should be considered as string, see https://www.w3.org/TR/rdf11-concepts/#section-Graph-Literal
  * Fix wrong inheritance of TransitiveProperty, ReflexiveProperty and SymmetricProperty
  * Fix 'DeprecationWarning: invalid escape sequence' in regexp
  * Raise an error when creating a new ontology inside a with ontology:... block
  * Use rdf:langString for locstr (was rdf:plainLiteral)
    
version 2 - 0.46
****************

* Remove warning when Cython module is not available
* Update import OMOP CDM for their new CSV format
* Basic support for enumerated datatypes (= defined with an equivalent_to and a OneOf)
* Improved synchronization and multiprocessor support
* Bugfixes:
  * Fix IRI() return type in SPARQL
  * Fix SPARQL queries with two UNIONs when there is no shared variables between the unions members
  * Fix parsing ontology with IRI ending by '?'
  * Avoid reusing ID of destroyed entity (storid; reuse is problematic when sharing the quadstore with other processes)

version 2 - 0.47
****************

* Support binary data: Python bytes are now mapped to XML base64Binary.
* Bugfixes:
  * Fix OPTIONAL blocks in SPARQL queries that share variable outside the OPTIONAL block
  * Fix prop1[prop2 in OPTIONAL blocks in SPARQL queries
  * Fix individuals belonging to several classes when one of these classes has a OneOf construct including that individual
  * Fix descendants when using subclasses of ThingClass (as PyMedTermino2 does)
  * Fix and update pymedtermino2
  * Fix SPARQL queries with BIND and UNION

version 2 - 0.48
****************

* Faster ontology loading (espescially when having a lot of small ontologies)
* Add support for Full Text Search (FTS) in SPARQL (see FTS() SPARQL function)
* Accept list as parameter in SPARQL queries when using the IN operator
* Make prepared SPARQL queries picklable
* Support DELETE SPARQL queries with free variables in the DELETE part
* Improve DELETE SPARQL queries in order to delete IRI/storid of entirely deleted entities
* Add support for SNOMED CT French translation in PyMedTermino2
* Add function owlready2.pymedtermino2.umls.prune() to prune terminologies to the descendants of the given concepts
* Add add_terminology() and add_term() methods in owlready2.pymedtermino2
* Add owlready2.pymedtermino2.model.TerminologySearcher for fast search in terminologies
* Bugfixes:
  * Fix RDF parsing of axiom with restriction in the optimized C-compiled module.
  * Properly close database when a World is destroyed
  * Use requests module for importing French ICD10 (urllib does not work)
  * Fix SPARQL query with fixed parameters
    
version 2 - 0.49
****************

* Support custom Python-defined SPARQL functions (thanks Ehe)
* Optimize STATIC SPARQL extention when used in simple union
* Optimize SPARQL simple UNION on literals and paramaters
* Support SPARQL queries using GROUP BY, HAVING, ORDER BY, LIMIT and/or OFFSET in subqueries
* Support ORDER BY in SPARQL GROUP_CONCAT() aggregate function
* Permits to customize XMLNS abbreviation for ontologies
* Bugfixes:
  * Fix usage of OWL classes as individual's attribute value (e.g. individual.attribute = Class)
  * Fix BOUND() SPARQL function
  * Fix SPARQL queries with 2 recursive parts that refer to each other
  * Fix SPARQL queries with FILTER referring to variables inside a recursive part
  * Fix FILTER NOT EXISTS in SPARQL when using new variables
  * Fix string escape in dataproperty when using the Pellet reasoner (thanks Max Cutlyp)
  
version 2 - 0.50
****************

* Improve French ICD10 import to support the RDF format from ATIH (now the default)
* Improve French ICD10 import with management of sub-codes defined by modifers (CLAML format)
* Fix vulnerability CVE-2021-39239 in Jena (used by Pellet)
  This vulnerability concerns XML parsing but Owlready2 does not use XML for communicating with Pellet (it uses NTriple)
  For more security, XMLRDF loading has been disabled in Jena
* Fix for Python 3.14 (tests, Cython-optimized module)
* Bugfixes:
  * Fix ontology loading from file object inside a Zip file
  * Fix test test_parallel_4
    
   
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.306.s1.nabble.com


Contact "Jiba" Jean-Baptiste Lamy:

::

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