position: Web architect – JEE, Ruby/RoR – Semantic
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.))
(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
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.
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
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
- 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 (firstname.lastname@example.org).
To apply, please send an email including links to (NO ATTACHED DOCUMENTS) the
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;
and contact details of referees.