Employer: University of Montpellier
Context: ANR D2KAB (www.d2kab.org) and ANR PractiKPharma (http://practikpharma.loria.fr) projects
When: April 2019 – for 24 months (other extensions might be possible)
Where: LIRMM, Montpellier, France
Collaboration: NCBO(Stanford, USA), LORIA & INSIT (Nancy, France), HEGP (Paris, France), INRA
(France), EMA (Alès, France)
Support: ANR D2KAB, ANR PractikPharma
Net salary: Between 25K€ and 35K€ brut per year. More flexibility for experienced
researcher engineer, depending on qualifications. Includes benefits.
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 (www.d2kab.org) develops and supports AgroPortal (http://agroportal.lirmm.fr) 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.
The ANR PractiKPharma project (http://practikpharma.loria.fr) and previously ANR SIFR project (www.lirmm.fr/sifr) developed the SIFR Annotator, a web service allowing scientists to utilize available biomedical ontologies and terminologies for annotating their French biomedical or clinical text automatically. The SIFR Annotator service processes raw textual descriptions, tags them with relevant biomedical ontology concepts and returns the annotations to the users.
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 (http://bioportal.bioontology.org) made available via its virtual appliance (http://www.bioontology.org/wiki/index.php/Category: NCBO_Virtual_Appliance). Please refer to our GitHub repository for more detail:
The research engineer/developer will have:
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 an 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.
- Between 1 and 5 years of experience. Including experience in private companies.
- Experience with semantic web technologies, especially JSON-LD/RDF/OWL/SKOS/SPARQL
- High motivation for exploratory work in relation with scientists
- Data science and management expertise (implementing data processing workflows)
- Background knowledge and/or experience in the biological / agronomical context is preferred
- Excellent remote working capabilities (emails, trackers, collaborative tools, etc.)
- Excellent aptitude to work with others and engage external users
- Perfect English oral and writing skills
- Basic knowledge of French with objective to learn the language during the contract
- International trips accepted (collaboration with Stanford)
- Autonomy and initiative, take on technical decisions within the project and justification of choices
- Eventually interested in research valorization of the outcomes (everything will be published)
- Open source developer
- Friendly person to join a small research team in Montpellier
Documents required are (include everything in one single PDF file):
- a curriculum vitae describing your education and experience;
- a motivation letter describing your interest in 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 highest diploma and other relevant certificates;
- names and contact details of referees.
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〉
Job Types: Full-time, Contract
Salary: 25,000.00€ to 35,000.00€ /year