Interest Group on Agricultural Data (IGAD) Pre-plenary meeting, 28 - 29 February, University of Tokyo

Session

Registration

Introduction by hosting organizations

Presentation about the Pre-Meeting Agenda by the IGAD Co-Chairs

Advocacy agenda on Global Open Data for Agriculture and Nutrition

Andre Lapierre (GODAN, United Kingdom)

Open access to research, and open publication of data, are vital resources for food security and nutrition, driven by farmers, farmer organizations, researchers, extension experts, policy makers, governments, and other private sector and civil society stakeholders participating in “innovation systems” and along value chains. Lack of institutional, national, and international policies and openness of data limit the effectiveness of agricultural and nutritional data from research and innovation. Making open data work for agriculture and nutrition requires a shared agenda to increase the supply, quality, and interoperability of data, alongside action to build capacity for the use of data by all stakeholders.

Key research priorities for GODAN partners

Ben Schaap (GODAN, The Netherlands)

GODAN encourages the agreement on and release of a common set of agricultural and nutrition data on a global scale in support of: Innovation and Economic Growth, Improved Service Delivery and Effective Governance, and Improved Environmental and Social Outcomes. Within the initiative our partners collaborate on interoperability of data and on determining and filling the most important data gaps that exist to achieve impact with open data. An important question for research is: "What data release will have the most impact on better food security, sustainable agriculture and healthy nutrition"? While the release of data and data interoperability is important, GODAN also acknowledges the balance of openness with legitimate concerns in relation to privacy, security, community rights and commercial interests.

Challenges, Issues and Solutions in Synergizing National Agricultural Research Systems with Rice Research Data Alliance (Piloting with Rice Knowledge Management Portal of India)

Dr. Shaik N.Meera (Indian Institute of Rice Research, India)

Rice Knowledge Management Portal (www.rkmp.co.in) is considered to be one of the largest repositories of knowledge and data on rice crop across the globe. It hosts a range of data platforms developed especially of multi-location rice research and extension data. The research data repository has more than 27000 datasets of multi-location testing done for last 50 years in India. The real time data flows are enabled (using AICRIP Intranet) from 106 research centres from across India. This makes a case that is worth deliberated upon.

Data, databases, and database interoperability at the International Rice Research Institute: Practices, Perspectives, and Outlook

Kenneth L. McNally, Ramil P. Mauleon, Locedie Mansueto, Kevin Christian Palis, Venice Juanillas, Jeffrey Detras, Marko Karkkainen, Mylah Anacleto, Tobias Kretschmar, Michael Dingkuhn, W. Paul Quick, Steve Klassen,  Nickolai Alexandrov,  Ruaraidh Sackville Hamilton, George Kotch and Hei Leung (IRRI, Philippines)

The International Rice Research Institute has a long history of rice breeding , conservation of germplasm diversity, and more recently gene discovery and genome re-sequencing researches. Through the years, IRRI has developed databases for internal  and  public use entailing the use of standards for phenotypic and other observations. Advances in research technologies (e.g. genomics, high throughput and automated phenotyping) have moved the throughput of data generation at IRRI into the realm of big data. In keeping with IRRI's mandate of making research data available as public goods, the need to build data exchange standards and enhance database interoperability has become a priority development area. This talk, divided into two parts, provides an overview of current data management solutions in place at IRRI, the challenges posed by the big data realm, and the initial steps taken to address these challenges. Cases to be highlighted are the systems (data content, ontologies/controlled vocabularies,  software technologies including APIs) for germplasm/diversity management (GRIMS, IRIS), breeding workflow (Breeding4Rice), and rice high throughput genotyping/genomics (Genotyping4Rice, IRIC).

Harmonizing semantics for phenotyping and agronomy data – the Crop and Agronomy ontologies

Elizabeth Arnaud (Bioversity International, France) 

The Crop Ontology (CO), as service of the Integrated Breeding Platform (www.integratedbreeding.net)  and provider of controlled trait description for the Breeding Management System, is expending  to new crops and will be completed by an Agronomy Ontology (AgrO). The Crop Ontology  (www.cropontology.org) provides harmonized and validated breeders’ trait names, measurement methods, scales and variables for currently 20 crops namely : cassava, banana, barley, chickpea, common bean, cowpea, groundnut, lentil, maize, oat, pearl millet, pigeon pea, potato, rice, sorghum, soybean, sweet potato, vitis,  wheat and yam. The NextGeneration Breeding Databases developed by Boyce Thompson Institute for banana,  cassava, potato, sweet potato also embed the Crop Ontology traits. Combining results of field management practices with crop traits is important to fully understand the dynamic of varying factors within any cropping system. Therefore, an Agronomy Ontology (AgrO) is under development and currently compiles 350 variables selected out of the set of the variables produced by the  International Consortium for Agricultural Systems Applications (ICASA). All variables were documented with a method and a scale to follow the Crop Ontology model.

A new Trait Dictionary Template was released in 2015 that now includes the ‘standard variable’ composed by a property, a method and a scale and needed to accurately annotate the measurements stored in the databases and asupport the creation of standard electronic fieldbooks. This template is currently tested by INRA to describe the Wheat traits of Ephesis database, by  The Crop Ontology project is a partner of the NSF-awarded project Planteome to contribute improving the reference ontologies for plants by mapping the crop traits of CO to reference ontologies (http://www.planteome.org/) which is also a DivSeek project (http://www.divseek.org/ ). Additionally, the Crop Ontology is a partner of the pilot project Agroportal (http://agroportal.lirmm.fr/ ) developed by LIRRM, IRD and Bioversity.

Coffee Break

Ontology Design for Efficient Rice Production Management

Asanee Kawtrakul (Kasetsart University, Thailand)

The proposed ontology has been developed in the RICE WATCH project, to support rice farmers and farmer cooperatives to make the right decisions regarding important aspects of rice production management aiming at optimizing cost. The ontology is used as a conceptual framework underpinning the planning of activities during rice growing, namely from rice planting to rice harvesting. These activities comprise (a) classifications of the preparation stage, which needs rice variety knowledge management, (b) activities during growing, such as fertilizing, pest management, and harvesting which needs harvesting machine management. The main uses of the ontology are 1) enabling consistent implementation of activities management based on shared resources, 2) playing the role of a domain ontology that encompasses the core concepts of rice production such as rice varieties, pest, pesticides or herbicides and that can be updated easily 3) to support information organization in a system implementation without loss of information.

The importance of a harmonized soil information model for the Global Soil Information System

Rainer Baritz (FAO of the United Nations, Italy)

The Global Soil Partnership (GSP) is a global open network supporting the development and sharing of knowledge about sustainable soil management, protection of soils against degradation, awareness raising, promoting soil research, and to make soil information broadly accessible. In that context the network intends to build a global soil information system (GSIS) with improved soil information being exchanged through web services. Each data holder shares data according to own data policies and technical frame conditions. In order to facilitate a coordinated effort providing comparable soil data, specifications need to be elaborated so that the shared information becomes interoperable, but also harmonized as much as possible. These specifications will be based on a globally agreed soil information model. Various models exist within soil information institutions, but also internationally, e.g. INSPIRE for Europe, ISO 25258 globally. Until today, it is still unclear whether data services using existing standards are technically. A test bed for interoperability of soil data has recently been started through OGC. This presentation will provide an overview about the objectives, challenges and current processes striving to develop a global web-based soil information exchange.

TBA

Bruce Simons (CSIRO, Australia), Peter Wilson (CSIRO)

Roadmap of knowledge management and sharing system in China

Xuefu Zhang (CAAS, China)

It introduces a roadmap for CAAS and China to develop an Agricultural Knowledge Management and Sharing System in China to contribute to fulfilling the national vision of agricultural and socialist countryside development. The focus of the Roadmap is to improve information and knowledge management in the Chinese Academy of Agricultural Sciences, the leading national institution for implement China’s vision for agricultural development, which in turn will influence and impact upon the overall agricultural information and knowledge system in China. This roadmap strategizes improvement in the way all partners engaged in China’s agricultural research and innovation systems work together for wider and closer information/knowledge sharing and exchange.

CELL5M: A geospatial data and analytics platform of harmonized multi-disciplinary data layers for agricultural research and development

Jawoo Koo (IFPRI, United States)

Spatially-explicit data is increasingly becoming available across disciplines, yet they are often limited to a specific domain. In order to use such datasets in a coherent analysis, such as to decide where to target specific types of agricultural investment, there should be an effort to make such datasets harmonized and interoperable. For sub-Saharan Africa, the HarvestChoice CELL5M Database was developed in this spirit of moving multidisciplinary data into one harmonized, geospatial database. The database includes over 750 biophysical and socio-economic indicators, many of which can be easily expanded to global scale. The CELL5M database provides a platform for cross-cutting spatial analyses and fine-grain visualization of the mix of farming systems and populations across SSA. It was created as the central core to support a decision-making platform that would enable development practitioners and researchers to explore multi-faceted spatial relationships at the nexus of poverty, health and nutrition, farming systems, innovation, and environment. The database is a matrix populated by over 350,000 grid cells covering SSA at five arc-minute spatial resolution. Users of the database, including those conduct researches on agricultural policy, research, and development issues, can also easily overlay their own indicators. Numerical aggregation of the gridded data by specific geographical domains, either at subnational level or across country borders for more regional analysis, is also readily possible without needing to use any specific GIS software. The database also provides standard-compliant data API that currently powers several web-based data visualization and analytics tools.

Lunch Break

An approach to smart agriculture with integrated information systems for agriculture in Japan

Tomokazu Yoshida (NARO, Japan)

In an effort to streamline agricultural data processing in farm work, including crop growth and environmental conditions affecting crop production, we developed the FIX-pms data format for expressing data related to informational management of production processes in Japanese agriculture. Referring to one of the preceding standards in EU: agroXML format, FIX-pms was designed to express the primary data managed by PMS, that was a farm management information system using field maps developed in Japan. FIX-pms also incorporates GML to express the geographic information of field maps, BIX-pp to express environmental measurement data and GPXX to express mobile measurement data with GPS sensor. Furthermore, with several APIs and existing protocols such as MetXML, SOS, WMS and so on, we are discussing how to integrate existing information systems for agriculture in Japan by adding functionalities for interoperability and data portability.

Toward the goal of integration of agricultural information systems in Japan, a strategy and concept of ‘Open Cloud Application Platform (CLOP)’ in agriculture was advocated. As one of standardized data formats, FIX-pms was discussed to be one of data containers and expressions that APIs on CLOP should handle.

In the new research project from 2014 to 2018: SIP(Cross-ministerial Strategic Innovation Promotion Program) conducted by cabinet office of Japanese government, its goal is the presentation of a typical design and implementation of integrated farm management information system by API mashup manner leading to the commercial ones. It also plans to discuss the terminology in Japanese agriculture used as contents in data expression and APIs for the solution of API matching.

Interoperable field sensor network and multi-layered web services for agricultural applications

Kiyoshi HONDA (Chubu University, Japan), Rassarin Chinnachodteeranun (Chubu University, Japan) , Nguyen Dui Hung (Thammsat University, Thailand), Apichon Witayangkurn (University of Tokyo, Japan), Eunjin Han (Columbia University, USA), Amor Ines  (Michigan State University, USA)

Field sensor network is becoming an important data source for data-driven agriculture. Low-cost sensors and sensor platforms with internet connectivity made it possible to deploy large number of sensors and platforms in agriculture fields that provide us with useful information for researches and farm managements.

Sensor Observation Service (SOS) is a standard web service or standard API defined by OGC (Open Geospatial Consortium). It defines several standard queries and responses encoded as XML so that applications can request sensor metadata and data without knowing physical setup of sensor platforms and their database schemas. We have been constructing SOS-based sensor service as an infrastructure, and agricultural applications on SOS.

In order to further enhance the interoperability of SOS, we are proposing a naming rule in observable property name in agricultural domain. The names are constructed by a combination of aggregation time window, aggregation type, target, physical property, e.g. monthly_maximum_air_temperature. Applications can more accurately find the property of the data, thus they can find the most suitable data source and identify algorithms to process the data further, compared to just naming it as e.g. “temperature” or “air temperature”. Additional properties such as observation time interval are also proposed. The rule is expected to be announced as a guideline by the ministry of internal affairs and communications, Japan soon.

Agriculture Early Warning based on collective intelligence

Asanee Kawtrakul (KU, Thailand), Teerawat Issariyakul (TOT, Thailand), Opas Trithaveesak (NECTEC, Thailand), Frederic Andres (NII, Japan), Alexandre Guitton (LIMOS, France), Jarbas Lopes Cardoso (CTI, Brazil), Silvio Ernesto Barbin (USP, Brazil), Oscar Salviano Silva Filho (CTI, Brazil)

The goal of our joint Asian Pacific Telecommunity (APT) and CyberBrain Mass Agriculture Alarm Acquisition and Analysis  (CBMA4) project is to develop a collective intelligence-based platform that accommodates a decision making process related to agriculture early warning among communities of farmers.  The idea is to translate tacit knowledge from local farmers as well as fundamental knowledge from universities, research institutes, and government agencies into a computerized system. The system alerts and suggests solution for farmers based on two sources of input: Weather data observed automatically from weather stations and contextual data collected by farmers. We also propose an observation object named warncon (Warning Content) and an algebraic model to reduce the semantic gap in agriculture early warning management. The results are collected  from a real experimental farm in Thailand where the local farmers are currently use our system to reduce risk in plant disease.  

Wheat Data Interoperability Working Group

Cyril Pommier (INRA, France)

The Wheat Data Interoperability Working Group aims to provide a common framework for describing, representing linking and publishing Wheat data with respect to open standards. It has been constructed from the inputs of multiple international references like CIMMYT, Crop Ontology, Planteome (Plant Ontology), CSIRO, INRA or IRD and is being coordinated by the WheatIS, a group of the Wheat Initiative a global initiative that aims to reinforce synergies between bread and durum wheat national and international research programmes.

The recommended standards include ontologies, resources or scientific object identification system, tools and file formats for several fields of expertise including genomic and sequence variation, plant material, phenotypes or gene expression. The recommendations available on the WheatIS website ( http://wheatis.org/DataStandards.php ) help data manager to easily identify the best practices, increase data access and reusability.

Most of those recommended standards are proving their usefulness in systems like GnpIS, used for Phenome-FPPN or the Integrated Breeding Platform. The dissemination of the ontologies is ensured by recognized repositories like www.cropontology.org and promising new one, like the agroportal. Data access can be used through datadiscovery systems available on transplantdb.eu or wheatis.org, and semantic and linked data approaches of data sharing are provided by tools like AgroLD.

Coffee Break

Overview of the current RDA Working Groups

Imma Subirats (FAO of the United Nations, Italy) & Devika Madalli (ISI, India)

AgGateway and geopolitical-context-enabled interoperability in precision agriculture field operations and business processes

Andres Ferreyra (Ag Connections LLC, US)

AgGateway is a nonprofit consortium of 240+ businesses working to promote, enable and expand eAgriculture. It provides a non-competitive collaborative environment, transparent funding and governance models,  and anti-trust and intellectual property policies that guide and protect members’ contributions and implementations. AgGateway primarily focuses on implementing existing standards and collaborating with other organizations to extend those standards when necessary.

In 2011 AgGateway identified interoperability in field operations (e.g., planting, harvest) as a major challenge: the multitude of proprietary, incompatible data formats among different machine and implement control systems (MICS) and farm management information systems (FMIS) leads to great frustration among users.

The SPADE project was AgGateway’s first field operations effort. SPADE has generally followed an Agile Methodology for each field operation: collect expert-mediated user stories; formalize them into business process models and use cases; identify data requirements; perform gap analyses of existing standards, and propose extensions thereto. A key SPADE outcome was the identification of a set of flexibly-defined common "documents" that support farm business processes: Crop plan, Observations and measurements (OMs), Recommendation, Work order, and Work record.

SPADE also proposed a system of Reference Data, datasets to distribute across the whole industry so different stakeholders can interpret shared documents the same way. This includes names and identifiers of seed varieties, crop protection products, active ingredients, and so forth. SPADE implemented proof-of-concept (PoC) application programming interfaces (APIs) for machinery and product reference data, and also implemented a PoC index API providing one-stop access to a distributed system of standardized reference data sources hosted by manufacturers and third-party data providers. Other SPADE contributions include defining concepts such as “OK to Spray”, contributing terms to AgGlossary.org, and working with the Agricultural Electronics Manufacturers’ Foundation (AEF) to expand the widely-respected ISO11783-10 MICS-FMIS communication standard’s ability to associate globally-unique identifiers to its own locally-scoped identifiers.

A vocabulary based on agriculture activity ontology to facilitate incompatibility among agriculture IT system

Hideaki Takeda, Sungmin Joo (National Institute of Informatics, NII), Daisuke Horyu, Akane Takezaki (National Agriculture and Food Research Organization,

NARO)

Now it is getting common for farmers to use IT systems to manage their activities. To realize incomparability among IT systems, we are building the vocabulary based on the agricultural activity ontology. The words in the vocabulary have logical definitions because the ontology is formalized based on description logic. As a result, the vocabulary has expendability to add new words and flexibility to generate custom vocabularies such like those for specific crops and regions.

Enabling agricultural data management through semantic web technologies

Erick Antezana (Bayer CropScience SA-NV, Belgium)

Semantic Web technologies have unlocked a new approach to manage life science research data in not only a scalable and flexible manner but mainly in a natural way (e.g. using graphs, modelling with networks better reflecting biological processes) in contrast to classic relational systems. The community using, producing and managing agricultural data (e.g. field trials) has been proactively adopting those technologies to not only integrate data and standardise it through ontologies and controlled vocabularies in general but mainly to get new insights from experimental data though for instance perform better data modelling, enable data consistency checks and ensure a scalable data integration. Here, we present our experience in making use of semantic web technologies within the agricultural domain while managing multiple experimental sources, diversity of organisms and different users demands to exploit Big Data.

AgroPortal : a proposition for ontology-based services in the agronomic domain

Elizabeth Arnaud (Bioversity International, France)  & Cyril Pommier (INRA, France)

Our project is to develop and support a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we have already designed and implemented a prototype ontology repository for plants and a few crops. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic and environment sciences. We will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. All of these within a fully semantic web compliant infrastructure. The main objective of this project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with complex knowledge engineering issues to annotate the research data. The AgroPortal project will specifically pay attention to respect the requirements of the agronomic community and the specificities of the crop domain. We will first focus on the outputs of a few existing driving agronomic use cases related to rice and wheat, with the goal of generalizing to other Crop Ontology related use cases. AgroPortal will offer a robust and stable platform that we anticipate will be highly valued by the community.

GACS Project

Johannes Keizer (FAO of the United Nations, Italy)

The GACS project was started in 2014 by three organizations dealing with agricultural data: FAO (the Food and Agriculture Organization of the UN), NAL (the National Agricultural Library of the USA), and CABI International (a not-for profit international organization, UK based). At the beginning, GACS it was meant to be an exploratory project, to assess the feasibility of a Global Agricultural Concept Scheme (hence the acronym), a global repository of terminological and conceptual information in agriculture. The work started off by taking the thesauri maintained by the three organizations and looking at the concepts in common. Now, two years later, we have a “core” of some 15,000 concepts resulting from a merge of those common concepts, and serious intentions about turning this core into something usable. Something that will eventually supersede the thesauri originally involved in the project.

Current activities of the GACS working group aim at making the core public in the next few months. These activities focus on consolidating the GACS core from the content point of view (arranging the hierarchy, removing duplicated and overlapping labels, standardizing all other pieces of information); on defining editorial guidelines (to track the decisions applied to the GACS content and enable consistent editorial maintenance in the future); on deploying an infrastructure to maintain and disseminate the GACS core. Next, the goal of the GACS partners is to place the GACS core in the larger context of data interoperability. The vision is to define an ecosystem of “connected” vocabularies and metadata standards for data related to agriculture. The “core” will be connected to domain-specific “extensions”, for example on soil, species, chemicals, and to data-specific “extension”, such as thesauri for textual documents, ontologies for data annotation, code lists for statistics, etc. The ultimate goal is thus provide users with appropriate metadata to enhance interoperability of agricultural data. The current intuition about this ecosystem goes under the name of AgriSemantics, the details of which will be defined jointly by current GACS partners together with other key players in the production and consumption of agricultural data, such as CGIAR and INRA.

The Land Portal and Open Development Mekong: Developing a localization framework for creating a sustainable information ecosystem on land

Laura Meggiolaro (Land Portal, Italy)

Countries in the Mekong Delta share features and a historical land governance context, such as efforts to formalize land titles and a transition from an authoritarian or command economy to post-socialist economies. In an effort to address these complex challenges, the East-West Management Institute’s Open Development Initiative (EWMI-ODI) established the Open Development Mekong (OD Mekong) platform  to capture and facilitate moderated crowd-sourced data-on a wide range of development sectors, including land, transcending national borders.

As part of it localization strategy, the Land Portal is taking a collaborative approach to partner with existing networks and transform their land-related information into Linked Open Data in the Greater Mekong, the Land Portal is working with a range of partners who are committed to the common goal of making information accessible, open, and usable by everyone.

One of these partnerships is with Open development Mekong (ODM). As part of its strategy, the Land Portal aims to assist existing information service providers willing to become fully open data compliant to better structure and expose their data by offering capacity building and technical support. Following this pattern, ODM will soon develop its innovative technical infrastructure and will become the first web platform in the region to promote standards, tools and good practices around (Linked) Open Data.

Wrap up and Closure of the day

Details about the 2nd Pre-Meeting Day

Informal get together

Session

Introducing the 2nd Pre-Meeting Day

Discussion Groups

1.     Agricultural Data Interoperability (policies, tools, taxonomies, ontology, standards)

2.     Increase data access and availability (formats, users)

3.     Advocacy for research data.

4.     Adoption of RDA outputs by the agricultural community  (e.g. present existing RDA deliverables relevant to the Agricultural Research Community, discuss how to facilitate their uptake)

5.     Rice & other crop Research Data Interoperability

6.     Soil Research Data Interoperability

Coffee Break

Discussion Groups (continuing)

1.     Agricultural Data Interoperability (policies, tools, taxonomies, ontology, standards)

2.     Increase data access and availability (formats, users)

3.     Advocacy for research data.

4.     Adoption of RDA outputs by the agricultural community  (e.g. present existing RDA deliverables relevant to the Agricultural Research Community, discuss how to facilitate their uptake)

5.     Rice & other crop Research Data Interoperability

6.     Soil Research Data Interoperability

Plenary session

Reports  by the Discussion Group Chairs

Lunch