Postdoc position: Ontology
alignment and engineering in agriculture and biodiversity
Employer: University of Montpellier
Context: AgroPortal project
by NUMEV labex
When: Sept. 2017 – for 12 months (extensions might be
Where: LIRMM (collaboration
with IRD, INRA, CNRS (CEFE), as well as with the NCBO (Stanford University)). Possible
short missions at SupAgro (INRA) and/or Stanford.
Net salary: Between 2100 and 2500€ per month depending on
qualifications. Includes benefits.
(agronomical) ontologies & vocabularies,
semantic web, ontology management, ontology alignment, semantic
interoperability, linked data, semantic annotation, application to agronomy
Web development, Ruby/Rails, Java/JEE,
RESTful web services, XML/JSON, Semantic Web technologies (OWL, RDF, SPARQL,
4store, Linked data), NCBO technology (AgroPortal/BioPortal).
Standards vocabularies and
ontologies are key elements to achieve data interoperability. The AgroPortal
develops and supports a
reference ontology repository for agronomy, plant sciences, biodiversity and
nutrition. We have already designed and implemented an advanced prototype offering
ontology-based services that hosts 64 ontologies or vocabularies including some
reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. One
of the challenges when dealing with multiple ontologies is to determine their overlap
and align them.
We are offering a postdoc position to
develop ontology mapping capabilities to align AgroPortal ontologies and
participate into the international Global Agricultural Concept Scheme (GACS)
project. With the experience and technology developed with the YAM++
application (LIRMM’s ontology alignment matcher), we will make AgroPortal a
state-of-the-art platform for mapping extraction, generation, validation,
evaluation, storage and retrieval by adopting a complete semantic web and
linked open data approach and engaging the community for curation. We will
first focus on the ontologies of the Montpellier community (agronomy, food,
biodiversity) and then join the GACS project (integration of Agrovoc,
NALt & CABt) in partnership with RDA AgriSemantics working group.
A key aspect in addressing semantic
interoperability in agronomy, plant sciences, nutrition and biodiversity is
the use of ontologies as a common denominator to describe data, make them
interoperable and turn them into structured and formalized knowledge.
Biomedicine has always been a leading domain for semantic interoperability
pioneering the development of reference ontologies such as the Gene Ontology.
This has served as model for the agronomic, environmental and plant sciences
e.g., Plant Ontology ,
Crop Ontology , opening the space to various types
of semantic applications , to data integration or decision
support. Semantic interoperability has been identified as a key issue for
agronomy and biodiversity sciences, and the use of ontologies a way to address
it , . The more ontologies and
vocabularies are being produced in the domain, the more the need to create,
store and retrieve alignments between those ontologies becomes important.
By reusing the NCBO BioPortal technology,
we have designed AgroPortal, an ontology repository for the agronomy domain (http://agroportal.lirmm.fr) . The main objective of the
AgroPortal project is to develop and support a reference ontology repository
for agronomy, plant sciences, nutrition, and biodiversity. It offers a robust
and reliable service to the community that features ontology hosting, search,
versioning, visualization, comment, services for semantically annotating data
with the ontologies, as well as storing and exploiting ontology alignments, all
of these in a semantic web compliant infrastructure. Ontologies in the portal
are being developed within multiple agronomic use cases, including the Agronomic
Linked Data (http://agrold.org), INRA Linked Open Vocabularies (http://lovinra.inra.fr)
which is an effort to publish vocabularies produced or co-produced by INRA.
YAM++ is a state-of-the-art ontology
alignment system being developed at LIRMM . YAM++ uses machine-learning
techniques to combine different similarity measures, exploiting the intrinsic
textual features of ontologies to provide similarity scores based on
information retrieval techniques. YAM++ obtained excellent results during the
OAEI 2013 campaign. Since 2016, YAM++ exists also in the form of a
multifunctional web service application (http://yamplusplus.lirmm.fr)
allowing manual mapping validation and enrichment.
The postdoc mission will be to:
with partners on the design (with use of semantic web standards) of
their ontologies/vocabularies and the integration (when not done yet) within
ontologies within AgroPortal to one another and to the GACS vocabulary (cf. below),
focusing on ontologies developed by the Montpellier partners first. Release
mappings as linked open data.
YAM++/AgroPortal the reference platform to extract, generate, validate,
evaluate, store and retrieve ontology alignments by designing and developing a
state-of-the-art ontology alignment framework. Work with partners on generating
and curating mappings thanks to the framework developed.
to the GACS project with the AgroPortal alignment framework and become
the preferred platform for hosting and browsing the GACS vocabulary.
each partner (mainly INRA & CEFE) the outcomes of the use of ontologies,
mappings and annotations.
The project will have four uses
AgroLD uses the OWL versions of multiple AgroPortal ontologies and rely on the
AgroPortal Annotator web service to annotate more than 50 datasets. We will
build a resource that bridges the gap between these references ontologies and
formalize their alignments to AgroLD data.
LovInra ontologies are not always interconnected one another (when relevant)
therefore, we will especially focus on producing alignments between LovInra
ontologies. Ontologies will be mapped to GACS to implement a larger
agricultural interoperability strategy (cf. GACS here after).
In partnership with CEFE, we will work on integrating the Thesaurus Of Plant
characteristics (TOP) , within AgroPortal and work on the
alignments (existing and to be created) to other ontologies.
collaboration with RDA Agrisemantics working group (http://agrisemantics.org) we will work on the development of
Global Agricultural Concept Scheme (GACS) which is an important international
initiative to integrate the Agrovoc, CAB Thesaurus, and NAL Thesaurus (www.agrisemantics.org/gacs). Because of this size and
endorsements by major organizations, the GACS will certainly become the future
pivot vocabulary in the lingua franca for agriculture (and related domains) and
AgroPortal has been proposed to the Agrisemantics WG as the platform for
accessing each of the three original thesaurus as well as the GACS itself. We
will produce alignments to build GACS and to interconnect it to other ontologies
with a recent PhD in Informatics / Computer science.
abroad (PhD or previous postdoc done outside of France), strongly recommended.
- Good Web
developer experience with knowledge of JEE technologies and Ruby/Ruby On rails.
Experience with semantic Web technologies.
Background knowledge and/or experience in the biological / agronomical context is
- Excellent research skills to gather both the
local and international community on AgroPortal.
- Perfect English oral and writing skills.
- Basic knowledge of French with objective to
learn the language during the contract.
- Excellent writing skills and publication
- 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 justification of choices.
- Friendly person to join a small research team
For more information about this position,
please contact Clement Jonquet (firstname.lastname@example.org)
and Konstantin Todorov (email@example.com).
To apply, please send an email including links to (PLEASE, 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;
and contact details of referees.
 L. Cooper et al., “The Plant Ontology
as a Tool for Comparative Plant Anatomy and Genomic Analyses,” Plant Cell
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 R. Shrestha et al., “Multifunctional
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plq008, Jan. 2010.
 X. Meng, “Special Issue – Agriculture Ontology,”
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 R. L. Walls et al., “Semantics in
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 T. Baker, C. Caracciolo, and O. Suominen,
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Conference on Biomedical Ontologies, ICBO’16, Demo Session, 2016, no. D203, p. 3. EXTENDED VERSION UNDER REVIEW COMPAG
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 D. Ngo and Z. Bellahsene, “YAM++ results for
OAEI 2013,” in 8th Int. Work.
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