Research engineer position: Web architect – JEE,
Ruby/RoR – Semantic web technologies
Employer: University of Montpellier
Context: SIFR project (Semantic Indexing of French
Biomedical Data Resources) - ANR
2016 – for 12 months minimum eventually extensible
Where: LIRMM, Montpellier (collaboration with the NCBO (Stanford University, USA.))
(biomedical)ontologies & terminologies, semantic web, knowledge
engineering, biomedical data integration, semantic interoperability, linked
data, scientific data workflows, annotation, text mining.
Web development, Java/JEE, Ruby/Rails, MySQL, RESTful web services,
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
applications are in biomedicine and agronomy.
We are seeking a motivated, curious and interested Web developer to
take hands on the different platforms and prototypes developed within the
project. You will work closely with another research engineer and a small team
of researchers. One main aspect will be the development, and support as well as
the integration of new features inside our local instances of BioPortal: http://bioportal.lirmm.fr and http://agroportal.lirmm.fr
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.
The project develops
and support two semantic web ontology repositories both for the French
biomedical domain and for the international agronomic domain. The ontology
portal features hosting, search, versioning, visualization, comment, etc. All
of these within a fully semantic web compliant infrastructure. The main
objective of this project is to enable straightforward use of ontologies,
avoiding data managers and researchers the burden to deal with complex
knowledge engineering issues.
We are reusing the technologies developed by the National Center for
Biomedical Ontologies at Stanford University: the BioPortal Web application (http://bioportal.bioontology.org)
and the BioPortal service architecture (http://data.bioontology.org/documentation).
Please refer to our GitHub repository for more detail: https://github.com/sifrproject
The developer will have:
- to manage, administrate and modify two local instances of
BioPortal (as described http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance)
both for the SIFR and AgroPortal projects.
- to modify the data workflows in the platform to customize it for
our project needs.
- to integrate new prototypes such as
within the platform.
- to implement new data workflows
within the platform such as mapping extraction, plant linked data, semantic
- to work remotely on an day-to-day
basis (supervisor will be at Stanford)
- Web developer with good knowledge of JEE technologies and Ruby/Ruby
- Experience with semantic Web technologies, especially RDF/SPARQL
- Computer science engineer or master
degree. PhD applicants are welcome and preferable if they can demonstrate a
strong development experience and commitment.
- 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.)
- Interested by the Semantic Web field
and cutting edge Web technologies.
- Interested by open and linked data.
- Perfect English oral and writing
- Few knowledge with French language 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 (firstname.lastname@example.org). To apply, please send an
email including links to (NO ATTACHED DOCUMENTS) the following:
motivation letter describing an explanation of YOUR interest for the position;
curriculum vitae describing your experience and the matches with the expected
of diplomas and other relevant certificates;
names and contact details of referees.
engineer will be hired under the “Ingénieur d’étude” status (social security,
will be included between 1400 and 1600€ net per month depending on experience.
contract will be for 1 year with possible extensions.