Research engineer position: Web architect – JEE, Ruby/RoR – Semantic web technologies


Employer:           University of Montpellier (ex UM2)

Context:              SIFR project (Semantic Indexing of French Biomedical Data Resources) - ANR

When:                 January 2015 – for 12 months minimum eventually extensible of one year.

Where:                LIRMM (collaboration with UMR TETIS (Cirad) and the NCBO (Stanford Univ.))


Web development, (biomedical)ontologies & terminologies, semantic web, biomedical data integration, semantic interoperability, linked data, scientific data workflows, annotation, text mining.


Web development, Java/JEE, Ruby/Rails, MySQL, RESTful web services, XML/JSON, Web client technologies (HTML5, JavaScript, CSS, Ajax), Semantic Web technologies (OWL, RDF, SPARQL, 4store, Linked data), NCBO technologies (BioPortal).


The SIFR project (http://www.lirmm.fr/sifr/) investigates the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data. The project is mainly funded by the French ANR, the University of Montpellier, the CNRS and the Montpellier Institute for Computational Biology (IBC).

We are seeking an experienced Web developer to take hands on the different prototypes developed within the project and to setup and support the project’s platform of services. One main aspect will be the maintenance and integration of new services inside our local instance of BioPortal.

Detailed description:

The volume of data in biomedicine is constantly increasing. Despite a large adoption of English in science, a significant quantity of these data uses the French language. The community has turned toward terminologies and ontologies to design semantic indexes of data that leverage the medical knowledge for better information mining and retrieval. However, besides the existence of various English tools, there are considerably less ontologies available in French and there is a strong lack of related tools and services to exploit them. This lack does not match the huge amount of biomedical data produced in French, especially in the clinical world (e.g., electronic health records).

Within the SIFR project we build an ontology-based indexing workflow similar to what exists for English resources (e.g., NCBO Annotator) but dedicated and specialized for French and make it available as a service for the community. We will use this workflow for semantic indexing of French biomedical data. We also develop such a workflow for bioontologies (English) related to plants within the WP5 of the IBC project.

We investigate issues related to multilingual knowledge representation (alignments between multilingual ontologies) and maintenance/evolution of created annotations and mappings over time. Especially, the use of the multilingual (French-English) mappings will enable us to index French resources using English ontologies and to search English resources, already indexed with English ontologies. We envision potential interesting result in semantic search and automatic translation. We will also investigate the process of lifting the annotated data in the web of linked data.

We are reusing the technologies developed by the National Center for Biomedical Ontologies: (https://github.com/ncbo): the BioPortal Web application (http://bioportal.bioontology.org) and the BioPortal service architecture (http://data.bioontology.org/documentation).

The developer will have:

- to manage, administrate and modify a local instance of BioPortal (as described http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance) both for the SIFR and IBC projects.

- to modify the data workflows in the platform to customize it for our project needs.

- to integrate new prototypes such as BioTex (http://tubo.lirmm.fr/biotex) within the platform.

- to implement new data workflows within the platform such as mapping extraction, plant linked data, semantic distances

Expected profile:

- Web developer with good knowledge of JEE technologies (such as Spring) and Ruby/Ruby On rails.

- Experience with semantic Web technologies.

- Computer science engineer or master degree. PhD applicants are welcome and preferable if they can demonstrate a strong development experience and commitment.

- Between 2 and 5 years of experience. Including experience in private companies.

- Excellent technical skills to push prototypes into production environment.

- Interested by the Semantic Web field and cutting edge Web technologies.

- Perfect English oral and writing skills.

- Experience or few knowledge with French with objective to learn the language during the contract.

- Excellent writing skills as reports, documentations, and technical notes will always be necessary.

- International trips accepted (collaboration with Stanford) and possibility to get a visa for the USA.

- Autonomy and initiative, take on technical decisions within the project and justify choices.

- Friendly person to join a small research team in Montpellier and to listen to their needs.

- Eventually interested in research valorization of the outcomes (everything will be published).

- Open source developer.


For more information about this position, please contact Clement Jonquet (jonquet@lirmm.fr). To apply, please send an email including links to (NO ATTACHED DOCUMENTS) the following:

- a motivation letter describing an explanation of YOUR interest for the position;

- a curriculum vitae describing your experience and the matches with the expected profile;

- copies of diplomas and other relevant certificates;

- names and contact details of referees.