Research engineer/developer position
Montpellier, France


Research engineer/developer position: Web architect – Semantic web technologies – Ontology-based services


Employer:        University of Montpellier

Context:                ANR D2KAB ( project

When:                ASAP – for 24 months (other extensions might be possible)

Where:                LIRMM, Montpellier, France

Net salary:         Between 25K€ and 35K€ brut per year. More flexibility for experienced

                researcher engineer, depending on qualifications. Includes benefits.


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/AgroPortal)


Standards vocabularies and ontologies are key elements to achieve data interoperability. In partnership with Stanford University, LIRMM designs, develops and maintains two vocabulary and ontology repositories: (i) the 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.

The D2KAB project ( develops and supports AgroPortal ( an advanced ontology repository prototype for agronomy, food and plant sciences offering ontology-based services and hosting 106 ontologies or vocabularies including some reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc.

Extended description

The semantic Web relies on the construction of standard vocabularies and ontologies to formally capture the knowledge of a domain into semantic resources computers use to index, search or reason on the data. In recent years, we have seen an explosion in the number of knowledge resources (thesaurus, terminologies, vocabularies and ontologies) being developed in life sciences, agronomy and biodiversity. However, those resources are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for common reference platforms to receive and host them, align them, and enabling their use in external applications. More generally, ontologies and vocabularies are a key element to make data FAIR (Findable, Accessible, Interoperable and Reusable). For example, ontologies and terminologies are highly valuable in text and data mining workflows.

We are reusing the technology developed by the National Center for Biomedical Ontologies at Stanford University: the BioPortal web application ( made available via its virtual appliance ( Please refer to our GitHub repository for more detail:

The research engineer/developer will have:

Expected profile

We are seeking a motivated, curious and interested research engineer and/or web developer with experience in developing web applications to take hands on the platforms developed. The candidate will hold a engineer or master degree in computer science or informatics.

Your role will be both to support the current platforms and investigate technical decisions to develop new features for ontology management and ontology-based services. You will work with a small team (4-5 persons) at LIRMM in both a national and international context. Further extension of the proposed 24-month-contract are possible. The candidate will demonstrate aptitudes or matches with most of the following aspects:

Web developer with excellent development experience with knowledge of REST/JSON web services, JEE technologies, Ruby/Ruby On rails, Bootstrap.


Application for this position will EXCLUSIVELY BY ACCEPTED via the following platform:   

Documents required are (include everything in one single PDF file):

No application by email will be accepted, but for more information about this position, please contact Clement Jonquet ( Please avoid attached documents and include links if you would like to send a document.  Remote and face to face interviews will be organized.


Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzale Yeumo, et al.. AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, Elsevier, 2018, 144, pp.126-143. 〈10.1016/j.compag.2017.10.012〉. 〈lirmm-01679502〉

Clement Jonquet, Anne Toulet, Biswanath Dutta, Vincent Emonet. Harnessing the power of unified metadata in an ontology repository: the case of AgroPortal. Journal on Data Semantics, Springer, 2018, pp.1-31. 〈10.1007/s13740-018-0091-5〉. 〈lirmm-01852080v2〉

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet. SIFR Annotator: Ontology-Based Semantic Annotation of French Biomedical Text and Clinical Notes. BMC Bioinformatics, BioMed Central, 2018, 19 (1), pp.405-431. 〈10.1186/s12859-018-2429-2〉. 〈lirmm-01934127〉

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Soumia Melzi, Jitendra Jonnagaddala, et al.. Enhanced Functionalities for Annotating and Indexing Clinical Text with the NCBO Annotator+. Bioinformatics, Oxford University Press (OUP), 2018, 34 (11), pp.1962-1965. 〈10.1093/bioinformatics/bty009〉. 〈lirmm-01680514〉