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!

New preprint "Enabling patients to receive clinical practice guideline recommendations for hereditary cancer risk using chatbots, family history, application programming interfaces (API), ontologies, and Owlready2"

I have published a new preprint:

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

New journal paper "Enabling patients to receive clinical practice guideline recommendations for hereditary cancer risk using chatbots, family history, application programming interfaces (API), ontologies, and Owlready2"

I have published a new journal paper:

journal [j70] 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

New journal paper "Early prediction of all-cause clinical deterioration in general ward patients"

I have published a new journal paper:

journalif [j73] Saab A, Abi Khalil C, Jammal M, Saikali M, Lamy JB. Early prediction of all-cause clinical deterioration in general ward patients: development and validation of a biomarker-based machine learning model derived from Rapid Response Team activations. Journal of Patient Safety 2022;18(6)

New journal paper "Early prediction of all-cause clinical deterioration in general ward patients"

I have published a new journal paper:

journalif [j74] Saab A, Abi Khalil C, Jammal M, Saikali M, Lamy JB. Early prediction of all-cause clinical deterioration in general ward patients: development and validation of a biomarker-based machine learning model derived from Rapid Response Team activations. Journal of Patient Safety 2022;accepted

Admitted to the INSERM competitive examination

I passed the CRCN competition at INSERM!

After 13 years of good and loyal service at the university, I am therefore going to become a full-time researcher.

Owlready2 0.38 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:

  • 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

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

New journal paper "Decision-support systems for managing polypharmacy in the elderly"

I have published a new journal paper:

journalif [j73] Mouazer A, Tsopra R, Sedki K, Letord C, Lamy JB. Decision-support systems for managing polypharmacy in the elderly: A scoping review. Journal of Biomedical Informatics 2022;130:104074

New journal paper "Decision-support systems for managing polypharmacy in the elderly"

I have published a new journal paper:

journalif [j72] Mouazer A, Tsopra R, Sedki K, Letord C, Lamy JB. Decision-support systems for managing polypharmacy in the elderly: A scoping review. Journal of Biomedical Informatics 2022;130:104074

Owlready2 0.37 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 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

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

Happy new year 2022!

_images/voeux_2022.png

Owlready2 0.36 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:

  • 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)

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

New journal paper "Automated clinical practice guideline recommendations for hereditary cancer risk using chatbots and ontologies"

I have published a new journal paper:

journal [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

New journal paper "Automated clinical practice guideline recommendations for hereditary cancer risk using chatbots and ontologies"

I have published a new journal paper:

journal [j71] 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

Owlready2 0.35 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:

  • 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