New journal paper "Formalization of the semantics of iconic languages"

I have published a new journal paper:

journalif [j37] Lamy JB, Soualmia LF. Formalization of the semantics of iconic languages: An ontology-based method and four semantic-powered applications. Knowledge-Based Systems 2017;135:159-179

New journal paper "Rainbow boxes"

I have published a new journal paper:

journalif [j36] Lamy JB, Berthelot H, Capron C, Favre M. Rainbow boxes: a new technique for overlapping set visualization and two applications in the biomedical domain. Journal of Visual Language and Computing 2017;43:71-82

New journal paper "Owlready"

I have published a new journal paper:

journalif [j35] Lamy JB. Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies. Artificial Intelligence in Medicine 2017;80:11-28

Owlready2 0.3 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.

The 2 - 0.3 version of Owlready is mostly a bugfix release. It also add the ability to destroy entities from ontologies.

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

Owlready2 0.2 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.

The 2 - 0.2 version of Owlready now includes a RDF/XML written in Python. This parser can load big files rapidly.

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

Owlready2 0.1 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.

The 2 - 0.1 version of Owlready is a full rewrite that integrates an optimized RDF quadstore. It can now load big ontologies (several millions of RDF triples).

It can be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/Owlready2

New journal paper "Using visual analytics for presenting comparative information on new drugs"

I have published a new journal paper:

journalif [j34] Lamy JB, Berthelot H, Favre M, Ugon A, Duclos C, Venot A. Using visual analytics for presenting comparative information on new drugs. Journal of biomedical informatics 2017;71:58-69

Towards Owlready 2...!

Owlready is a Python module for ontology-oriented programming. The version 2 currently under development keep the functionalities of the first version, but now relies on an optimized RDF quadstore in SQL. This version is now able to load big ontologies (several millions of RDF triples) with good performances.

The development version of Owlready2 is available here: https://bitbucket.org/jibalamy/owlready2

Happy new year 2017!

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New journal paper "Formalisation de la sémantique des langages iconiques"

I have published a new journal paper:

journal [j31] Lamy JB, Soualmia LF, Duclos C, Venot A. Formalisation de la sémantique des langages iconiques : méthode à base d'ontologie et applications. Revue d’intelligence artificielle (RIA) 2016;30(5):579-606

ORMithorynque 0.1.1 has been released!

ORMithorynque is an ORM Python module (object database).

ORMithorynque 0.1.1 has been released and can be downloaded from PyPI (Python Package Index): https://pypi.python.org/pypi/ORMithorynque

Using Webex on ArchLinux

Webex is a videoconference system from Cisco. It works under Linux but it is only available in 32 bits... This tuto explains how to use it under ArchLinux 64 bits.

1- Install Firefox (32 bits), Java (32 bits) and Webex 32 bits dependencies

Install the 32 bits version of Firefox, Java, and the 32 bits libraries needed by Webex. For ArchLinux, you need to install AUR package bin32-firefox, bin32-jre, webex-meta.

2- Test Java in Firefox

Launch Firefox 32 bits and test the java installation from this page: https://java.com/en/download/installed8.jsp

If the Java plugin is not found by Firefox, verify the plugin presence (file /usr/lib32/mozilla/plugins/libnpjp2-jre8.so) and start Firefox after specifying the plugin directory, as following :

MOZ_PLUGIN_PATH=/usr/lib32/mozilla/plugins/ /usr/lib32/bin32-firefox/firefox32

3- Test Webex

Test Webex from this page : https://www.webex.com/test-meeting.html

Attention, seeing the interface is not enough to garantee that everything is OK. You need to wait until you see the following screen :

(View comments...)

OwlReady at the STC 2016 conference

OwlReady and ontology-oriented programming were presented at the STC 2016 conference (Special Topic Conference). The article is available online and the presentation too. Please cite it if you use OwlReady!

Ontology-Oriented Programming for Biomedical Informatics
JB Lamy.
Studies in Health Technology and Informatics 2016 ; 221:64-68

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

Happy new year 2016!

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