Patterns (Oct 2020)
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems
- Elizabeth Arnaud,
- Marie-Angélique Laporte,
- Soonho Kim,
- Céline Aubert,
- Sabina Leonelli,
- Berta Miro,
- Laurel Cooper,
- Pankaj Jaiswal,
- Gideon Kruseman,
- Rosemary Shrestha,
- Pier Luigi Buttigieg,
- Christopher J. Mungall,
- Julian Pietragalla,
- Afolabi Agbona,
- Jacqueline Muliro,
- Jeffrey Detras,
- Vilma Hualla,
- Abhishek Rathore,
- Roma Rani Das,
- Ibnou Dieng,
- Guillaume Bauchet,
- Naama Menda,
- Cyril Pommier,
- Felix Shaw,
- David Lyon,
- Leroy Mwanzia,
- Henry Juarez,
- Enrico Bonaiuti,
- Brian Chiputwa,
- Olatunbosun Obileye,
- Sandrine Auzoux,
- Esther Dzalé Yeumo,
- Lukas A. Mueller,
- Kevin Silverstein,
- Alexandra Lafargue,
- Erick Antezana,
- Medha Devare,
- Brian King
Affiliations
- Elizabeth Arnaud
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France; Corresponding author
- Marie-Angélique Laporte
- Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France
- Soonho Kim
- Markets, Trade and Institutions Division (MTID), International Food Policy Research Institute (IFPRI), Washington, DC, USA
- Céline Aubert
- Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA
- Sabina Leonelli
- Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Exeter, UK
- Berta Miro
- Agrifood Policy Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Gideon Kruseman
- Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, Mexico
- Rosemary Shrestha
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, México
- Pier Luigi Buttigieg
- Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christopher J. Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Julian Pietragalla
- Integrated Breeding Platform, Texcoco, State of México, Mexico
- Afolabi Agbona
- Cassava Breeding Program, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Jacqueline Muliro
- Aquaculture and Fisheries Sciences, Worldfish, Penang, Malaysia
- Jeffrey Detras
- Bioinformatics Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
- Vilma Hualla
- Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru
- Abhishek Rathore
- Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
- Roma Rani Das
- Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
- Ibnou Dieng
- Biometrics Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Guillaume Bauchet
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
- Naama Menda
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
- Cyril Pommier
- BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France
- Felix Shaw
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
- David Lyon
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
- Leroy Mwanzia
- Performance, Innovation and Strategic Analysis, International Center for Tropical Agriculture (CIAT), Regional Office for Africa, Nairobi, Kenya
- Henry Juarez
- Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru
- Enrico Bonaiuti
- Monitoring, Evaluation and Learning Team, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
- Brian Chiputwa
- Research Methods Group (RMG), World Agroforestry (ICRAF), Nairobi, Kenya
- Olatunbosun Obileye
- Data Management Section, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Sandrine Auzoux
- UPR AIDA, The French Agricultural Research Centre for International Development (CIRAD), Sainte-Clotilde, Réunion, France; Université de Montpellier, Montpellier, France
- Esther Dzalé Yeumo
- Unité Délégation à l’Information Scientifique et Technique - DIST, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France
- Lukas A. Mueller
- Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
- Kevin Silverstein
- GEMS Informatics Initiative, University of Minnesota, St. Paul, USA
- Alexandra Lafargue
- CP RDIT, Syngenta, St Sauveur, France
- Erick Antezana
- Bayer Crop Science SA-NV, Diegem, Belgium; Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Medha Devare
- Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA
- Brian King
- CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Journal volume & issue
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Vol. 1,
no. 7
p. 100105
Abstract
Summary: Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams. The Bigger Picture: Digital technology use in agriculture and agrifood systems research accelerates the production of multidisciplinary data, which spans genetics, environment, agroecology, biology, and socio-economics. Quality labeling of data secures its online findability, reusability, interoperability, and reliable interpretation, through controlled vocabularies organized into meaningful and computer-readable knowledge domains called ontologies. There is currently no full set of recommended ontologies for agricultural research, so data scientists, data managers, and database developers struggle to find validated terminology. The Ontologies Community of Practice of the CGIAR Platform for Big Data in Agriculture harnesses international expertise in knowledge representation and ontology development to produce missing ontologies, identifies best practices, and guides data labeling by teams managing multidisciplinary information platforms to release the FAIR data underpinning the evidence of research impact.
