Jean-Baptiste LAMY ("Jiba")

Contact: email: (see on the left)

Current activities


I am currently lecturer at University Paris 13 (Bobigny, France), in the LIMICS lab. LIMICS is the fusion of two labs: LIM&BIO (University Paris 13) and ICS (University Paris 6 and INSERM).

My field of research includes:

  • Information and knowledge visualisation

  • Knowledge representation

  • Decision support

with a medical application domain, in particular drugs.

Iconic language in medicine

One of my first research work was the conception of VCM, an iconic language for medical concept. In fact, medical knowledge is more and more voluminous, and during consultations, health professionals lack of time for reading texts. This is why we propose to improve the knowledge access with icons. These icons represent the main medical concepts (diseases, patient characteristics, drugs, tests,...). The objective is not to replace all texts by icons, but to combine both using appropriate graphical interfaces. Using icons, one can quickly find and select the right text paragraph he want to read.

During my PhD, I designed the VCM language using solid medical and cognitive bases, as well as the associated graphical interfaces. These tools have been applied to drug knowledge, in particular to the Summaries of Product Characteristics (SPCs), and then evaluated under controlled conditions. My thesis was entitled "Design and evaluation of visualisation methods for medical knowledge: design of a graphical language and application to drug knowledge", and was realized under the direction of Alain Venot.

Further work on VCM have lead to the implementation of VCM in several clinically-used products:

Main publications on this topic : (see all my publications)

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

journal Lamy JB, Duclos C, Bar-Hen A, Ouvrard P, Venot A. An iconic language for the graphical representation of medical concepts. BMC Medical Informatics and Decision Making 2008;8:16

journal Lamy JB, Venot A, Bar-Hen A, Ouvrard P, Duclos C. Design of a graphical and interactive interface for facilitating access to drug contraindications, cautions for use, interactions and adverse effects. BMC Medical Informatics and Decision Making 2008;8:21

journal Pereira S, Hassler S, Hamek S, Boog C, Leroy N, Beuscart-Zéphir MC, Favre M, Venot A, Duclos C, Lamy JB. Improving access to clinical practice guidelines with an interactive graphical interface using an iconic language. BMC medical informatics and decision making 2014;14(1):77

journal Griffon N, Kerdelhué G, Hamek S, Hassler S, Boog C, Lamy JB, Duclos C, Venot A, Darmoni SJ. Design and usability study of an iconic user interface to ease information retrieval of medical guidelines. J Am Med Inform Assoc 2014;21(e2):e270-7

Rainbow boxes

Rainbow boxes are a new information visualization technique for visualizing overlapping sets. It consists in representing several elements and several sets made of these elements; a typical example is the presentation of the amino acids properties (see image below). In this example, elements are the amino-acids and sets are the various properties (small size, positive charge, aromatic group, etc).


I invented this visualization technique during the VIIIP projet (Integrated and Interactive Visualization of Pharmaceutical Innovation), funded by ANSM (French drug agency) in 2013, and coordinated by myself. Rainbow boxes were first applied to the comparison of drug properties: it consisted in comparing contraindications, adverse effects, etc, of a new drug with 1 to 9 already existent similar drugs, in order to help a physician to forge his own opinion about the new drug.

Then, rainbow boxes were applied to the visualization of extracts of Gene Onotology. They were also extended for allowing the visual translation of the reasoning of a perceptron, with an application in antibiotherapy.

Main publications on this topic : (see all my publications)

journal 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

journal Lamy JB, Berthelot H, Favre M, Ugon A, Duclos C, Venot A. Using visual analytics for presenting comparative information on new drugs. J Biomed Inform 2017;71:58-69

conf Lamy JB, Berthelot H, Favre M. Rainbow boxes: a technique for visualizing overlapping sets and an application to the comparison of drugs properties. International Conference Information Visualisation (iV) 2016;253-260

conf Lamy JB, Tsopra R. Translating visually the reasoning of a perceptron: the weighted rainbow boxes technique and an application in antibiotherapy. International Conference Information Visualisation (iV) 2017;256-261, Best paper

ontology programming interface

In order to solve the difficulties I encountered when using formal ontologies (in OWL) in an object-programming langage (such as Python), I developed the Owlready module. This module allows ontology-oriented programming in Python: OWL classes and individuals can be used as if they were Python classes and instances.

Main publications on this topic : (see all my publications)

journal Lamy JB. Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies. Artif Intell Med 2017;80:11-28

conf Lamy JB. Ontology-Oriented Programming for Biomedical Informatics. Stud Health Technol Inform 2016;221:64-68


Recently, I'm also interested in meta-heuristics and nature-inspired algorithms. My works lead to an algorithm inspired from the behavior of pigeons.

Main publication on this topic : (see all my publications)

conf Lamy JB. Les oiseaux picorant artificiels : une nouvelle méta-heuristique inspirée du comportement des pigeons. Actes des Journées d'Intelligence Artificielle Fondamentale (JIAF) 2017

Medical decision support

I worked in medical decision support for chronic diseases, in particular during the ASTI 2 and ASTI 3 research projects.

These works continue now in the PEPS project, focused on prevention for cardiovascular disorders, and the DESIREE european project, focused on breast cancer.

Main publications on this topic : (see all my publications)

journal Lamy JB, Ebrahiminia V, Riou C, Séroussi B, Bouaud J, Simon C, Dubois S, Butti A, Simon G, Favre M, Falcoff H, Venot A. How to translate therapeutic recommendations in clinical practice guidelines into rules for critiquing physician prescriptions? Methods and application to five guidelines. BMC Medical Informatics and Decision Making 2010;10:31

conf Lamy JB, Ugon A, Berthelot H, Favre M. A visual decision support system for helping physicians to make a decision on new drugs. Decision Support Systems VII. Data, information and knowledge visualization in decision support systems, Lecture Notes in Business Information Processing 2017;282, Springer

Free Software

I am a fervent user and code of free softwares. In addition to videogames (see below), I coded Songwrite 3, a tablature and music notation editor, BibReview, a bibliographic database manager for the IMIA Yearbook, PyMedTermino, a Python module for accessing medical terminologies,...

Medieval lyre and harp, historic reenactment

After playing guitar for years, and never mastering it, I finally build my own instrument by myself: a medieval lyre! This nice instrument can play sweet melody like a harp, but also rhythmics like a guitar. It is also a great instrument for songwriting.

Then, I made a medival harp during a session with Sylvestre Charbin. I'm still learning this instrument !

I play sometimes in medieval event with the Fief et Chevalerie association. I also play at the Lavomatic tour! More information about the medieval lyre is available in the French part of this site.

Bird watching

I like also watching birds!

Past activities

2000-2009: Free software videogames

I have made several Free Software games (in chronological order: Arkanae, Slune, Balazar and Balazar Brothers), a 3D engine (Soya). These software are still freely available here. As I love simple and object oriented programming language, I was one of the first to develop games and 3D applications in these languages (Java and then Python).

I was very active in the Nekeme Prod. association, which aims to develop and support Libre video games.

I was also often present at Free Software conferences in France (such as LSM, Libre Software Meeting).

2008-2010: the Zaurus years

I was a proud Zaurus user!

2001-2003: research on health smart home

During my pharmacy and master training period, I worked on the concept of "health smart home" at the AFIRM team of the TIMC-IMAG laboratory, at Grenoble (France), with Vincent Rialle.

My researches were focuses on the recognition and 3D visualization of scenarii. These scenarii were every-day-life situations or pathological behaviours. The scenarii were written during a period at Sherbrooke, Quebec, with Hélène Pigot.

Main publication on this topic : (see all my publications)

journal Rialle V, Lamy JB, Noury N, Bajolle L. Telemonitoring of patients at home: A Software Agent approach. Comput Methods Programs Biomed 2003;72(3):257-268


  • Habilitation (HDR, Rouen-Normandie)

  • PhD in medical informatics (Paris 6)

  • Pharmaceutical doctor

Publications and communications

The list of my publications can be found here: Publications.