Postdoc position: Ontology
alignment and engineering in agriculture and biodiversity
Context: Lingua
project, in the context of AgroPortal project (http://agroportal.lirmm.fr), supported
by
NUMEV, AGRO
and CEMEB Labex. Collaboration between IRD, INRA,
CNRS (CEFE), as well
as
with the NCBO (Stanford University).
When: January 2018 – June 2019 (18 months) - extensions
might be possible on other supports.
Application
will be accepted until November 28th
Where: Montpellier. LIRMM
mainly, with assignments at INRA and/or CEFE. Missions at 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
& biodiversity.
Web development, Ruby/Rails, Java/JEE,
RESTful web services, XML/JSON, Semantic Web technologies (OWL, RDF, SPARQL, triplestore (4store), Linked data), NCBO technology (AgroPortal/BioPortal).
Standards vocabularies and
ontologies are key elements to achieve data interoperability. The AgroPortal
project (http://agroportal.lirmm.fr)
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
investigate and develop ontology mapping capabilities for 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 - http://yamplusplus.lirmm.fr), 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, NAL Thesaurus & CAB Thesaurus) of the RDA AgriSemantics working
group (http://agrisemantics.org).
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 [1],
Crop Ontology [2], opening the space to various types
of semantic applications [3], 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 [4], [5]. 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) [7]. 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 [8]. 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’s mission will be to:
·
Work
with partners on the design (with use of semantic web standards) of
their ontologies/vocabularies and the integration (when not done yet) within
AgroPortal.
·
Align the
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.
·
Design and develop a state-of-the-art ontology alignment framework based on
YAM++/AgroPortal to extract, generate, validate, evaluate, store and retrieve ontology
alignments. Work with partners on generating and curating mappings
thanks to the framework developed.
·
Contribute
to the GACS project with the AgroPortal alignment framework and customize
AgroPortal to use GACS as a pivot vocabulary.
·
Demonstrate to/with
each partner (mainly INRA & CEFE) the outcomes of the use of ontologies,
mappings and annotations.
The project will have four uses
cases:
·
AgroLD:
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: 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).
·
Biodiversity:
In partnership with CEFE, we will work on integrating the Thesaurus Of Plant
characteristics (TOP) [10], within AgroPortal and work on the
alignments (existing and to be created) to other ontologies.
·
GACS: In
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)[6]. 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 in AgroPortal.
- Researcher
with a recent (less than 5 years) PhD in Informatics / Computer science.
- Experience
abroad (PhD or previous postdoc done outside of France), strongly recommended.
- Good Web
developer experience with knowledge of Web, JEE technologies and Ruby/Ruby On
rails.
-
Experience with semantic Web technologies.
-
Background knowledge and/or experience in the biological / agronomical context is
preferred.
- 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
motivation.
- 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
in Montpellier.
For more information about this
position, please contact Clement Jonquet (jonquet@lirmm.fr)
and Konstantin Todorov (konstantin.todorov@lirmm.fr).
To apply, please send an email including links to (PLEASE, NO ATTACHED
DOCUMENTS) the following:
- a
motivation letter describing an explanation of your interest for the position;
- a
curriculum vitae describing your experience and the matches with the expected
profile;
- copies
of diplomas and other relevant certificates;
- names
and contact details of referees.
[1] L. Cooper et al., “The Plant Ontology
as a Tool for Comparative Plant Anatomy and Genomic Analyses,” Plant Cell
Physiol., 54, 2, 2012.
[2] R. Shrestha et al., “Multifunctional
crop trait ontology for breeders’ data: field book, annotation, data discovery
and semantic enrichment of the literature.,” AoB Plants, vol. 2010, p.
plq008, Jan. 2010.
[3] X. Meng, “Special Issue – Agriculture
Ontology,” Journal of Integrative Agriculture, vol. 11, no. 5. Elsevier, p. i, 2012.
[4] J. S. Madin, S. Bowers, et al. “Advancing
ecological research with ontologies.,” Trends Ecol. Evol., 23,
no. 3, pp. 159–68, Mar. 2008.
[5] R. L. Walls et al., “Semantics in
Support of Biodiversity Knowledge Discovery: An Introduction to the Biological
Collections Ontology and Related Ontologies,” PLoS One, vol. 9, no. 3,
p. e89606, Mar. 2014.
[6] T. Baker, C. Caracciolo, and O. Suominen,
“GACS Core: Creation of a Global Agricultural Concept Scheme,” 2016, pp.
311–316.
[7] C. Jonquet et al., “Reusing the NCBO
BioPortal technology for agronomy to build AgroPortal,” in 7th International
Conference on Biomedical Ontologies, ICBO’16, Demo Session, 2016, no. D203, p. 3. EXTENDED VERSION UNDER REVIEW COMPAG
JOURNAL
[8] D. Ngo and Z. Bellahsene, “YAM++ : A
Multi-strategy Based Approach for Ontology Matching Task,” in 18th
International Conference on Knowledge Engineering and Knowledge
Management,EKAW’12, 2012, vol. 7603, pp. 421–425.
[9] D. Ngo and Z. Bellahsene, “YAM++ results for
OAEI 2013,” in 8th Int. Work.
on Ontology Matching, 2013, vol.
1111, pp. 211–218.
[10] E. Garnier et al., “Towards a thesaurus
of plant characteristics: an ecological contribution,” Ecology, 105, 2,
pp. 298-309, Mar. 2016.