Semantic Web Applications and Tools for Healthcare and Life Sciences
11th International SWAT4HCLS Conference, Antwerp 2018

Spotlight on Agrisemantics


SWAT4HCLS Agriculture sponsor

This year SWAT4HCLS includes a spotlight on the fast emerging arena of Agrisemantics. The program will include a tutorial, a keynote talk and apanel session each highlighting the opportunities, challenges and successes in this important new application area.

Schedule (tentative)

December 3rd

Presented by: Marie-Angélique Laporte (Bioversity-France)

December 4th

Half day program on Agri Semantic Web Applications and Tools

13.15-14.00 Keynote by Medha Devare Spinning a Semantic Web for Agriculture
14.00-15.00 Selected talks (agro and nutrition)
15.00-15.30 Lightning poster presentations
15.30-16.30 Poster/demo session
16.30-17.30 Selected talks (agro and nutrition)
17.30-18.30 Panel discussion (Agrisemantics) A spotlight on Semantic Technologies for the reuse of Agri-Open Data
19.00 – 22:00                     Social dinner


Agricultural semantics: challenges, opportunities and the AgroFIMS fieldbook

Presented by: Marie-Angélique Laporte (Bioversity-France)

Unlike in the biomedical domain, the agricultural domain lags in adopting semantic technologies. However, the tremendous amount of data produced by a wide variety of actors, from farmers to researchers to private companies will benefit from the gains in interoperability and semantic richness conferred by these technologies. Indeed, unifying access to and linking this data with other domains can unlock powerful analytical capabilities and help to accelerate innovations to address global food security challenges. Several semantic standards and tools currently exist in the agricultural domain but the overlap in their content makes them difficult to reuse.

This tutorial is designed for anyone keen to learn about new use cases in the agrisemantics domain, to enhance skills that could be applied towards meaningful outcomes in leveraging the agricultural data ecosystem more effectively.

The tutorial will be organized in 4 parts. First, we will introduce the agricultural domain and its challenges in terms of the data landscape and the inherent sensitive nature of some data. A basic introduction to ontologies and semantic web technologies will be also part of this first session. Then, an in-depth overview of the existing semantic standards and tools used in the agri-community will be presented. Finally, we will take an example of how CGIAR is using semantic technologies to harmonize agronomic data from data collection to publishing. We will present the AgroFIMS fieldbook builder which relies on the Agronomy Ontology. Then, we will present how the data produced are semantically annotated from the start, and can therefore be easily published as Linked Open Data. We will also show how these data may be queried using SPARQL and presented in a user-friendly interface. This tutorial will also support an interactive discussion on how the SWAT4HCLS community can become engaged in the Agrisemantics domain.


Spinning a Semantic Web for Agriculture

CGIAR is a global research partnership of 15 Centers primarily located in developing countries, working in the agricultural research for development sector. The CGIAR system is charged with tackling challenges at a variety of scales from the local to the global, which generally means being able to query and/or aggregate a variety of data types and streams. CGIAR aspires to FAIRness in its research outputs, and while progress is being made, the I of FAIR is the frog that doesn’t readily turn into a prince for the FAIR ringmistress in this tale. Yet, interoperability – particularly semantic interoperability— is critical to providing meaning and context to CGIAR’s varied information resources and enabling integration between linked or related data (e.g. an agronomic data set and related socioeconomic data). CGIAR’s approach to interoperability and data harmonization focuses on the use of standard vocabularies, and strong reliance on ontologies developed across CGIAR (efforts such as the Crop Ontology, the Agronomy Ontology – AgrO, the in-development socioeconomic ontology – SociO), and other entities (ENVO, UO, PO etc.) Spinning these into a semantic web for agriculture is a primary focus of the CGIAR’s Big Data Platform for Agriculture, and its Global Agricultural Research Data Innovation and Acceleration Network (GARDIAN). GARDIAN is intended to provide seamless, semantically-linked access to CGIAR publications and data, to demonstrate the full value of CGIAR research, enable new analyses and discovery, and enhance impact. In this talk, I will discuss CGIAR’s path to a FAIRy tale ending, complete with the sticky considerations entailed in web-spinning.

Medha Devare

Medha DevareMedha Devare Ph.D. is Senior Research Fellow with the International Food Policy Research Institute (IFPRI). She led the CGIAR System‘s Open Access/Open Data Initiative, and currently leads efforts to organize data and enable semantic interoperability across CGIAR’s 15 agriculture for development-focused Centers through its Big Data Platform. Medha is a Cropping Systems Agronomist with significant experience leading projects addressing food security and sustainable resource management in South Asia. She also has expertise in data management and semantic web tools; while at Cornell University, she was instrumental in the development of VIVO, a semantic web application for representing academic scholarship.



Semantic Technologies for the reuse of Agri-Open Data

Christopher Brewster

Senior Scientist, Data Science Dept., TNO | Soesterberg, Netherlands
Professor, Application of Emerging Technologies,
Institute of Data Science, Maastrich University.

Brewster_Work_photo_20170726_croppedDr. Christopher Brewster is a Senior Scientist at TNO, and Professor in the Application of Emerging Technologies at the Institute of Data Science, Mastricht University. He specializes in semantics and interoperability architectures with an interest in emerging technologies such as blockchains. He was scientific co-ordinator for the Dutch public-private funded Techruption Blockchain project , and co-led the Blockchain in agrifood project funded by Dutch Ministry of Economic Affairs. His research focus is Semantic Technologies, Open and Linked Data, interoperability architectures and Data Governance, with a special interest in the roles of Blockchain technology in solving real world problems, the ethical implications of blockchain technology, and the interaction of semantics with smart contacts. He has focussed on the agrifood domain as an application domain focussing on the use of Semantic Technologies to the food supply chain and logistics. He has published over 60 papers in conferences and journals, and organised many workshops.
Further details

Thomas Baker

Independent FAO consultant

tombakerTom Baker has worked on Semantic Web standards and vocabularies since the late 1990s, when he helped organize the Dublin Core Metadata Initiative (DCMI), which he now co-directs. Tom co-chaired the W3C working group that published Simple Knowledge Organization System (SKOS) in 2009 and currently contributes to the community developing the Shape Expressions language (ShEx) for RDF validation. In the area of agriculture he has worked on projects about AGROVOC and the FAO Geopolitical Ontology and helped FAO, NAL, and CABI develop the Global Agricultural Concept Scheme (GACS). He studied at the Ecole Normale Supérieure, Paris, and has an MLS from Rutgers and PhD in anthropology from Stanford University. Since working as a research sociologist in Italy, he has worked as Semantic Web researcher at the German National Research Center for Informatics (GMD), Fraunhofer, and the Goettingen State Library and has taught at the Asian Institute of Technology in Bangkok and Sungkyunkwan University in Seoul. Fluent in several languages, he promotes pragmatically simple metadata solutions that are useful across multiple languages and disciplinary perspectives.
Further details

Graham Mullier

IT Lead Business Sustainability, Open Publishing
CP R&D IT, Syngenta
Open Data Champion and Digital Advocate  

Graham-Cereals2018crop3Graham Mullier was originally trained as a natural scientist and computational chemist. He has over three decades of experience of R&D, most recently from within R&D IT. He has run teams specialising in software architecture, research informatics, data visualisation and for 4 years ran a data science group. He now works with Crop Protection R&D and Business Sustainability within Syngenta, championing the use of data, digital approaches in general, and open data publishing to engage with a wider range of partners and collaborators. He is particularly interested in leveraging Syngenta’s Good Growth Plan to catalyse a data ecosystem supporting sustainability for the whole agriculture sector.

Twitter handle: @GrahamMullier

Matthew Lange

Food and Health Informatician
Food Science Department
University of California, Davis, USALange Headshot2

Dr. Matthew Lange is a Food and Health Informatician in the Food Science Department at UC Davis  with over 20 years experience building data, information, and knowledge systems for academia, industry, and government operations. He is the Principal Investigator and Director of IC-FOODS, the International Center for Food Ontology, Operability, Data, and Semantics ( IC-FOODS is dedicated to building global computable infrastructure for the Internet of Food and the Semantic Web of Food. Synergistic with IC-FOODS, Dr. Lange co-leads the GODAN Working Group for Alignment of Authoritative Vocabularies of Food, and is designing ontological infrastructure for a new FoodCentral Repository for USDA food composition databases. The Semantic Web of Food (SWoF) and Internet of Food (IoF) hold promise to fundamentally alter the way we produce, process, deliver and consume food: giving rise to ecosystems of next-generation knowledge tools that lower technical innovation barriers for creation of novel, traceable, ecologically-friendly foods, products, medicines, and lifestyle regimens: precisely personalized for health and delight, and aggregatable for population and market analyses. The IoF holds potential to provide infrastructure enabling companies to compete to deliver healthier, more sustainable, and more trustworthy foods.