Web Development

Ontologies & Terminologies

Semantic Web

Ontology repository

Knowledge Engineering

Semantic Interoperability, Annotation

Natural Language Processing

Text and Data Mining

Web development, Java/JEE, Ruby/Rails, RESTful web services, XML/JSON, Web technologies (HTML5, Bootstrap, JavaScript), Semantic web technologies (OWL, RDF, SPARQL, triplestore, Linked data), NCBO technology (BioPortal), OpenMinTeD technology.

 To apply, please send an email  to <[email protected]> (Clement Jonquet ) 

including links to (NO ATTACHED DOCUMENTS) the following:

• a Curriculum Vitae describing your training and experience;
• a motivation letter describing Your Interest for the position and the matches with the expected profile;
• reference to already developed web application or project (URL, GitHub, technical documentation) clarifying your role;
• copies of diplomas and possibly other relevant certificates;
• names and contact details of referees.

A key aspect in addressing SEMANTIC INTEROPERABILITY is the use of TERMINOLOGIES, VOCABULARIES and ONTOLOGIES as a common denominator to structure data and make them interoperable.

In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories:

(i) SIFR BioPortal which targets the French biomedical community and offers an ontology-based annotation workflow to semantically index text biomedical and clinical data;

(ii) AgroPortal - a reference repository for semantic resources in agronomy, agriculture, food, plant sciences and biodiversity.

These platforms allow us to tackle scientific problems in natural language processing, semantic annotation, ontology engineering, while being driven by concrete use cases with impacts in biomedicine and agronomy.

In the context of the ANR PractiKPharma and VisaTM projects, we are seeking a motivated, curious and interested research engineer and web developer to take hands on the platforms and prototypes developed.

Your role will be both to support the current platforms and investigate technical decisions to enable the development of new features in relation to text and data mining.

• Within PractiKPharma, your role will consist in enhancing the SIFR Annotator to facilitate its use to annotate clinical data (in collaboration with HEGP and LORIA).
• Within the VisaTM project, your role will be to enable interoperation of both AgroProtal and BioPortal with the text and data mining infrastructure developed in the OpenMinTeD project (in collaboration with INRA and INIST). You will work with a small team (4 persons) at LIRMM in both a national and international context. Further extension of the proposed 12-month-contract are possible.

We are seeking a motivated, curious and interested research engineer candidate with a computer science or bioinformatics training (master/engineer or PhD).

Besides an important motivation for the technical challenges and excellent software development expertise, we are also looking for someone with some interest for the research topics presented.

The candidate will demonstrate aptitudes or matches with some of the following aspects:

- Web developer with good knowledge of JEE technologies, Ruby/Ruby On rails, Bootsrap.

- Experience with semantic web technologies, especially JSON/RDF/SPARQL.

- Experience with text and data mining software (knowledge extraction, use of ontologies, etc.)

- Between 1 and 5 years of experience. Including experience in private companies.

- Excellent technical skills to push prototypes into production environment.

- Excellent remote working capabilities (emails, trackers, collaborative tools, etc.)

- Perfect English oral and writing skills.

- Few knowledge with French language with objective to learn the language during the contract.

- Excellent writing skills as reports, documentation, 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 valorisation of the outcomes (everything will be published).

 - Open source developer.

For more information about this position, please contact Clement Jonquet <[email protected]>.