The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Elizabeth Arnaud¹, Marie-Angélique Laporte¹, Soonho Kim², Céline Aubert³, Sabina Leonelli⁴, Berta Miro⁵, Laurel Cooper⁶, Pankaj Jaiswal⁶, Gideon Kruseman⁷, Rosemary Shrestha⁸, Pier Luigi Buttigieg⁹, Christopher J Mungall¹⁰, Julian Pietragalla¹¹, Afolabi Agbona¹², Jacqueline Muliro¹³, Jeffrey Detras¹⁴, Vilma Hualla¹⁵, Abhishek Rathore¹⁶, Roma Rani Das¹⁶, Ibnou Dieng¹⁷, Guillaume Bauchet¹⁸, Naama Menda¹⁸, Cyril Pommier¹⁹, Felix Shaw²⁰, David Lyon¹⁸, Leroy Mwanzia²¹, Henry Juarez¹⁵, Enrico Bonaiuti²², Brian Chiputwa²³, Olatunbosun Obileye²⁴, Sandrine Auzoux^{25

26}, Esther Dzalé Yeumo²⁷, Lukas A Mueller¹⁸, Kevin Silverstein²⁸, Alexandra Lafargue²⁹, Erick Antezana^{30

31}, Medha Devare³, Brian King³²

Affiliations

¹ Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France.
² Markets, Trade and Institutions Division (MTID), International Food Policy Research Institute (IFPRI), Washington, DC, USA.
³ Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA.
⁴ Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Exeter, UK.
⁵ Agrifood Policy Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
⁶ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
⁷ Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, Mexico.
⁸ Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, México.
⁹ Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
¹⁰ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹¹ Integrated Breeding Platform, Texcoco, State of México, Mexico.
¹² Cassava Breeding Program, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
¹³ Aquaculture and Fisheries Sciences, Worldfish, Penang, Malaysia.
¹⁴ Bioinformatics Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
¹⁵ Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru.
¹⁶ Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
¹⁷ Biometrics Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria.
¹⁸ Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
¹⁹ BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Versailles, France.
²⁰ Digital Biology, Earlham Institute, Norwich, Norfolk, UK.
²¹ Performance, Innovation and Strategic Analysis, International Center for Tropical Agriculture (CIAT), Regional Office for Africa, Nairobi, Kenya.
²² Monitoring, Evaluation and Learning Team, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon.
²³ Research Methods Group (RMG), World Agroforestry (ICRAF), Nairobi, Kenya.
²⁴ Data Management Section, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria.
²⁵ UPR AIDA, The French Agricultural Research Centre for International Development (CIRAD), Sainte-Clotilde, Réunion, France.
²⁶ Université de Montpellier, Montpellier, France.
²⁷ 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.
²⁸ GEMS Informatics Initiative, University of Minnesota, St. Paul, USA.
²⁹ CP RDIT, Syngenta, St Sauveur, France.
³⁰ Bayer Crop Science SA-NV, Diegem, Belgium.
³¹ Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
³² CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia.

PMID: 33205138
PMCID: PMC7660444
DOI: 10.1016/j.patter.2020.100105

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Elizabeth Arnaud et al. Patterns (N Y). 2020.

. 2020 Sep 25;1(7):100105.

doi: 10.1016/j.patter.2020.100105. eCollection 2020 Oct 9.

Authors

Affiliations

¹ Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France.
² Markets, Trade and Institutions Division (MTID), International Food Policy Research Institute (IFPRI), Washington, DC, USA.
³ Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA.
⁴ Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Exeter, UK.
⁵ Agrifood Policy Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
⁶ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
⁷ Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, Mexico.
⁸ Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of México, México.
⁹ Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
¹⁰ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹¹ Integrated Breeding Platform, Texcoco, State of México, Mexico.
¹² Cassava Breeding Program, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria.
¹³ Aquaculture and Fisheries Sciences, Worldfish, Penang, Malaysia.
¹⁴ Bioinformatics Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
¹⁵ Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru.
¹⁶ Statistics, Bioinformatics & Data Management (SBDM) Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
¹⁷ Biometrics Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria.
¹⁸ Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
¹⁹ BioinfOmics, Plant Bioinformatics Facility, Université Paris-Saclay, Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Versailles, France.
²⁰ Digital Biology, Earlham Institute, Norwich, Norfolk, UK.
²¹ Performance, Innovation and Strategic Analysis, International Center for Tropical Agriculture (CIAT), Regional Office for Africa, Nairobi, Kenya.
²² Monitoring, Evaluation and Learning Team, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon.
²³ Research Methods Group (RMG), World Agroforestry (ICRAF), Nairobi, Kenya.
²⁴ Data Management Section, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria.
²⁵ UPR AIDA, The French Agricultural Research Centre for International Development (CIRAD), Sainte-Clotilde, Réunion, France.
²⁶ Université de Montpellier, Montpellier, France.
²⁷ 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.
²⁸ GEMS Informatics Initiative, University of Minnesota, St. Paul, USA.
²⁹ CP RDIT, Syngenta, St Sauveur, France.
³⁰ Bayer Crop Science SA-NV, Diegem, Belgium.
³¹ Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
³² CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia.

PMID: 33205138
PMCID: PMC7660444
DOI: 10.1016/j.patter.2020.100105

Abstract

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.

Keywords: Big Data; Community of Practice; FAIR data; agriculture; agrifood systems; data annotation; data labeling; knowledge representation; ontologies; semantics for agriculture.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Figure 1**
Use of the CoP's Products and Tools for Data Annotation

See this image and copyright information in PMC

References

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The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Affiliations

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Grants and funding

LinkOut - more resources

Full Text Sources

Research Materials