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

Arnaud E 1 , Laporte MA 1 , Kim S 2 , Aubert C 3 , Leonelli S 4 , Miro B 5 Show all authors , Cooper L 6 , Jaiswal P 6 , Kruseman G 7 , Shrestha R 8 , Buttigieg PL 9 , Mungall CJ 10 , Pietragalla J 11 , Agbona A 12 , Muliro J 13 , Detras J 14 , Hualla V 15 , Rathore A 16 , Das RR 16 , Dieng I 17 , Bauchet G 18 , Menda N 18 , Pommier C 19 , Shaw F 20 , Lyon D 18 , Mwanzia L 21 , Juarez H 15 , Bonaiuti E 22 , Chiputwa B 23 , Obileye O 24 , Auzoux S 25 , Yeumo ED 26 , Mueller LA 18 , Silverstein K 27 , Lafargue A 28 , Antezana E 29 , Devare M 3 , King B 30

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 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
  • 27 GEMS Informatics Initiative, University of Minnesota, St. Paul, USA
  • 28 CP RDIT, Syngenta, St Sauveur, France
  • 29 Bayer Crop Science SA-NV, Diegem, Belgium
  • 30 CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia
Patterns (N Y), 2020 Oct 09;1(7):100105.
PMID: 33205138 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.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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