Semantic Web postdoc/researcher position: Ontology management and alignment in agronomy & biodiversity
Employer: University of Montpellier
Context: ANR Project D2KAB (www.d2kab.org) and AgroPortal project (http://agroportal.lirmm.fr)
When: April 2019 – for 24 months (other extensions might be possible)
Where: LIRMM, Montpellier, France
Collaboration: INRA, IRD, CEFE and Stanford University
Support: Labex NUMEV and Agro, ANR D2KAB
Net salary: Between 32K€ and 35K€ brut per year for postdoc. More flexibility for experienced researcher, depending on qualifications. Includes benefits.
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, SKOS, SPARQL, Linked data), NCBO technology (AgroPortal/BioPortal).
Standards vocabularies and ontologies are key elements to achieve data interoperability. The D2KAB project (www.d2kab.org) develops and supports AgroPortal (http://agroportal.lirmm.fr) a reference ontology repository for agronomy, food and plant sciences. We collaborate with the Stanford NCBO BioPortal group to synchronize our efforts and mutualize technology development. We have already designed and implemented an advanced prototype offering ontology-based services that hosts 106 ontologies or vocabularies including some reference resources in the domain: Agrovoc, NAL thesaurus, Crop Ontology, etc. With such a number of ontologies, new problems have raised such as describing, selecting, evaluating, trusting and interconnecting ontologies as well as using them for semantic annotation of data.
We are offering a postdoc or researcher position to develop new ontology management and alignment capabilities inside AgroPortal, including: to capture and synchronize metadata descriptions, to facilitate the cohabitation, interoperation and appropriate use of different types of semantic resources (e.g., from SKOS vocabularies to formal OWL ontologies), to improve ontology selection and recommendation, and to enable ontology interoperation. Also relying on the experience and technology developed with the YAM++ (http://yamplusplus.lirmm.fr) application –LIRMM’s ontology alignment matcher– we will develop a state-of-the-art framework 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.
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 host them, described them appropriately and manage the 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, food, plant sciences, and biodiversity. It offers a robust and reliable advanced prototype 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/researcher mission will be to:
The project will have be driven by the use cases of the D2KAB ANR project (e.g., food packaging, agro-agri linked data, wheat phenotype, ecosystems & plant biogeography). 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). Because of this size and endorsements by major organizations, the GACS will certainly a major element 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.
We are looking for a motivated postdoc or experienced researcher. The candidate must hold a PhD in Informatics / Computer science and must have experience in the semantic web area and using ontologies. The candidate will demonstrate aptitudes or matches with most of the following aspects:
- High motivation for scientific research
- Experience with semantic web technologies, especially JSON-LD/RDF/OWL/SKOS/SPARQL
- Data science and management expertise (implementing data processing workflows)
- Excellent technical skills to conduct experiments. Good Web developer experience with knowledge of REST/JSON web services, JEE technologies and Ruby/Ruby On rails
- Knowledge of ontology alignment issues and tools
- 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
- Excellent writing skills and publication motivation
- 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
- 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;
- link to relevant related publications;
- copies of PhD diploma and other relevant certificates;
- names and contact details of referees.
 L. Cooper et al., “The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses,” Plant Cell Physiol., 54, 2, 2012.
 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.
 X. Meng, “Special Issue – Agriculture Ontology,” Journal of Integrative Agriculture, vol. 11, no. 5. Elsevier, p. i, 2012.
 J. S. Madin, S. Bowers, et al. “Advancing ecological research with ontologies.,” Trends Ecol. Evol., 23, no. 3, pp. 159–68, Mar. 2008.
 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.
 T. Baker, C. Caracciolo, and O. Suominen, “GACS Core: Creation of a Global Agricultural Concept Scheme,” 2016, pp. 311–316.
 Jonquet, C., Toulet, A., Arnaud, E., Aubin, S., Yeumo, E. D., Emonet, V., ... & Larmande, P. (2018). AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, 144, 126-143
 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.
 D. Ngo and Z. Bellahsene, “YAM++ results for OAEI 2013,” in 8th Int. Work. on Ontology Matching,2013, vol. 1111, pp. 211–218.
 Martínez-Romero, M., Jonquet, C., O’connor, M. J., Graybeal, J., Pazos, A., & Musen, M. A. (2017). “NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.” Journal of biomedical semantics, 8(1), 21.
 Jonquet, C., Toulet, A., Dutta, B., & Emonet, V. (2018). “Harnessing the power of unified metadata in an ontology repository: the case of AgroPortal.” Journal on Data Semantics, 7(4), 191-221.
Job Types: Full-time, Temporary
Salary: 32,000.00€ to 40,000.00€ /year