I have published a new journal paper:

[j70] Ritchie JB, Frey L, Lamy JB, Bellcross C, Morrison H, Schiffman JD, Welch BM. Automated clinical practice guideline recommendations for hereditary cancer risk using chatbots and ontologies: System description. JMIR Cancer 2022;8(1):e29289

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

This version can open SPARQL endpoints, with the new SPARQL engine, and fixes several bogues, in particular in the SPARQL engine.

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

This version brings two new features:

• a SPARQL engine which translates the queries into SQL. This engine is much faster than RDFlib (around 60x), it has no dependencies and a shorter loading time. It currently supports a subset of SPARQL: SELECT, INSERT and DELETE queries, sub-queries, UNION, OPTIONAL, FILTER, BIND, FILTER EXISTS, FILTER NOT EXISTS, all functions of SPARQL, blank node notation with square brackets, e.g. ‘[a XXX]’, and property path expressions except those with parentheses.

  This new SPARQL engine can be used as follows (see documentation):

  list(default_world.sparql("""<query>"""))

• Dublin Core support via integrated OWL translation. It is possible to load Dublin Core directly as follows:

  dc = get_ontology("http://purl.org/dc/elements/1.1").load()

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

I have published a new journal paper:

[j66] Lamy JB. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. Artificial Intelligence in Medicine 2021;115:102074

I have published a new preprint:

[p2] Ritchie JB, Frey L, Lamy JB, Bellcross C, Morrison H, Schiffman JD, Welch BM. Enabling patients to receive clinical practice guideline recommendations for hereditary cancer risk using chatbots, family history, application programming interfaces (API), ontologies, and Owlready2: System description. Preprint 2021

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

This version fix an installation problem under Windows, and also improve the execution of reasoners under Windows (no more DOS windows).

Here are the changes:

• Fix installation under Windows (contributed by CVK)

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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

Owlready is a Python module for ontology-oriented programming. It can load OWL 2.0 ontologies and manipulate them transparently in Python.

Here are the changes:

• 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

The new version be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

I presented my work on data science and drug safety: visual mining of adverse drug events observed in clinical trials of pain treatments.

Slides are available here (in French), the preprint that describes the study here (in English), the online platform here (in English and French) and the video of the seminar here (in French)!