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 French book "Python et les ontologies" is still available at ENI editions.

Good reading!

New preprint "A data science approach to drug safety"

I have published a new preprint:

preprint [p1] Lamy JB. A data science approach to drug safety: Semantic and visual mining of adverse drug events from clinical trials of pain treatments. Arxiv preprint arxiv:2006.16910 2020

Owlready2 0.24 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 several small changes and bugfixes. It now uses the Git versionning system, instead of Mercurial.

Here are the changes:

  • 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

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

New journal paper "Explainable decision support through the learning and visualization of preferences from a formal ontology of antibiotic treatments"

I have published a new journal paper:

journalif [j54] Lamy JB, Sedki K, Tsopra R. Explainable decision support through the learning and visualization of preferences from a formal ontology of antibiotic treatments. Journal of Biomedical Informatics 2020;104C:103407

New journal paper "Somatic mitochondrial mutations in oral cavity cancers among senegalese patients"

I have published a new journal paper:

journal [j51] Toure S, Mbaye F, Gueye MD, Fall M, Dem A, Lamy JB, Sembene M. Somatic mitochondrial mutations in oral cavity cancers among senegalese patients. Asian Pacific journal of cancer prevention (APJCP) 2019;20(7):2203-2208

Owlready2 0.23 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 several small changes and bugfixes.

Here are the changes:

  • 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

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

New journal paper "AntibioGame®"

I have published a new journal paper:

journalif [j52] Tsopra R, Courtine M, Sedki K, Eap D, Cabal M, Cohen S, Bouchaud O, Mechaï F, Lamy JB. AntibioGame®: A serious game for teaching medical students about antibiotic use. International Journal of Medical Informatics 2020;136:104074

New journal paper "AntibioGame®"

I have published a new journal paper:

journalif [j53] Tsopra R, Courtine M, Sedki K, Eap D, Cabal M, Cohen S, Bouchaud O, Mechaï F, Lamy JB. AntibioGame®: A serious game for teaching medical students about antibiotic use. International Journal of Medical Informatics 2020;136:104074

Happy new year 2020!

_images/voeux_2020.png

Owlready2 0.22 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 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

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

A presentation at ICABME 2019!

I presented my works on visual decision support for breast cancer therapy, at the ICABME 2019 congress in Tripoli.

My paper was entitled "Hierarchical visual case-based reasoning for supporting breast cancer therapy". It is available here and the presentation there.

Owlready2 0.21 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 realease fixes several bugs and now includes Pellet 2.3.1 (same version as in Protégé) instead of version 2.4 (which seems to have problems with some SWRL builtins).

Here are the changes:

  • 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

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

New journal paper "Une plateforme multimodale d’aide à la décision"

I have published a new journal paper:

journal [j50] Séroussi B, Lamy JB, Prebet C, Ngo C, Teixeira L, Ugarriza A, Sekar B, Larburu N, Muro N, Guézennec G, Bouaud J. Une plateforme multimodale d’aide à la décision : Application à la prise en charge du cancer du sein dans le cadre du projet DESIREE. Technique et Science Informatiques (TSI) 2019;accepté

A presentation and an award at MEDINFO 2019!

I presented my works on the use of icons for browsing medical terminologies, in particular in pharmacovigilance, at MEDINFO 2019.

My paper was entitled "An iconic approach to the browsing of medical terminologies". It is available here and the presentation there.

And I obtained the Best paper award (first place)!

French book "Python et les ontologies"

Python et les ontologies, Jean-Baptiste Lamy, ENI Éditions, 310 pages

My French book "Python et les ontologies" has been published by ENI editions.

This 310-pages book describes how to use OWL 2.0 ontologies in Python 3.x, with the Owlready2 Python module for ontology-oriented programming.

More informations (in French) on the editor website:

https://www.editions-eni.fr/livre/python-et-les-ontologies-9782409020223

I plan to translate the book in English in the coming year.