Ontologies with Python, Jean-Baptiste Lamy, Apress Éditions, 350 pages Python et les ontologies, Jean-Baptiste Lamy, ENI Éditions, 310 pages Sombre comme l'Aurore, Jean-Baptiste Lamy, Éditions 38, 466 pages

The blog and personal site of Jean-Baptiste Lamy (Jiba).

My French novel "Sombre comme l'Aurore - La légende de Tienn Halidenn" has been published by Éditions du 38!

My book on Python and ontologies is available in English (Ontologies with Python) and French (Python et les ontologies).

Good reading!

Owlready2 0.32 has been released!

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

Owlready2 0.32 has been released!

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

Owlready2 0.31 has been released!

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

Owlready2 0.30 has been released!

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

New journal paper "A data science approach to drug safety"

I have published a new journal paper:

journalif [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

Owlready2 0.29 has been released!

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

Owlready2 0.28 has been released!

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

Owlready2 0.27 has been released!

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

Seminar at LIMICS

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)!

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Happy new year 2021!

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English book "Ontologies with Python"

Ontologies with Python, Jean-Baptiste Lamy, Apress Éditions, 350 pages

My book "Ontologies with Python" has just been published by Apress editions.

This 350-pages book describes how to use OWL 2.0 ontologies in Python 3.x, with the Owlready2 Python module for ontology-oriented programming.

Use ontologies in Python, with the Owlready2 module developed for ontology-oriented programming. You will start with an introduction and refresher on Python and OWL ontologies. Then, you will dive straight into how to access, create, and modify ontologies in Python. Next, you will move on to an overview of semantic constructs and class properties followed by how to perform automatic reasoning. You will also learn about annotations, multilingual texts, and how to add Python methods to OWL classes and ontologies. Using medical terminologies as well as direct access to RDF triples is also covered.

Python is one of the most used programming languages, especially in the biomedical field, and formal ontologies are also widely used. However, there are limited resources for the use of ontologies in Python. Owlready2, downloaded more than 60,000 times, is a response to this problem, and this book is the first one on the topic of using ontologies with Python.

What You Will Learn:

  • Use Owlready2 to access and modify OWL ontologies in Python

  • Publish ontologies on dynamic websites

  • Perform automatic reasoning in Python

  • Use well-known ontologies, including DBpedia and Gene Ontology, and terminological resources, such as UMLS (Unified Medical Language System)

  • Integrate Python methods in OWL ontologies

Who Is This Book For: Beginner to experienced readers from biomedical sciences and artificial intelligence fields would find the book useful.

The book is an updated translation of the French book "Python et les ontologies" published at ENI éditions last year.

More informations on the editor website:

https://www.apress.com/fr/book/9781484265512

Owlready2 0.26 has been released!

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

This new release includes a new module for displaying entities in Description Logics (DL), and bugfixes.

Here are the changes:

  • 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

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

Owlready2 0.25 has been released!

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

This new release includes a few new features, and bugfixes.

Here are the changes:

  • 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()

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

New journal paper "Identifying the mitochondrial DNA mutations that cause cancer"

I have published a new journal paper:

journal [j64] Mbaye F, Lamy JB, Sembene M. Identifying the mitochondrial DNA mutations that cause cancer. Research Outbreak 2020;117:50-53