"11741","12","archive","3170",,,"disk0/00/01/17/41","2021-03-14 10:36:11","2021-03-14 10:36:11","2021-03-14 10:36:11","article",,,"show",,,,"","","","","","","","","","",,,,"Arnaud","E","","","","","","","Rathore","A","","","","",,,,,"","",,,,,"","","Digital Solutions Team, Digital Inclusion Lever, Bioversity International, Montpellier Office, Montpellier, France","France","The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems","pub","S7","S15","","public",,,"Big data",,"The Ontologies CoP and Socio-Economic Data CoP are financially supported
by the CGIAR Platform for Big Data in Agriculture that is mainly supported by
the CGIAR Trust Fund, (https://www.cgiar.org/funders/) and UKAID. The Crop
Ontology is currently supported by the CGIAR Platform for Big Data in Agriculture
and the CGIAR Research Programs on Roots, Tubers, and Bananas;
Wheat, Maize, and Rice Programs; Grain Legumes and Dryland Cereals
(CRP-GLDC); and by each CGIAR Center for its mandate crops. The rice
example is based on data generated by the International Rice Research Institute
(IRRI) for the RICE Research program. The Planteome Project, led by P.J.
(Oregon State University), is funded by the National Science Foundation, USA
(IOS:1340112 award). The coordinator of the Environment Ontology and SDG
Interface Ontology is funded by the Frontiers in Arctic Marine Monitoring
(FRAM) program of the Alfred Wegener Institute Helmholtz Centre for Polar
and Marine Research, Helmholtz Centre for Polar and Marine Research
(AWI). COPO was initially funded by a BBSRC Biological and Bioinformatics
Resources (BBR) grant (BB/L024055/1, BB/L024101/1, and BB/L024071/1)
and is now funded by the BBSRC Core Strategic Program grant awarded to
the Earlham Institute (BBS/E/T/000PR9817). COPO is hosted within the Cy-
Verse UK academic cloud, funded by BBSRC (BB/M018431/1 and BB/
R000662/1). S.L. is funded by the Alan Turing Institute under the EPSRC grant
EP/N510129/1. The Elixir and Emphasis contribution to the Crop Ontology and
its adoption have been supported by the Infrastructure Biologie Sante´ ‘‘Phenome-
FPPN0 ’’ supported by the French National Research Agency (ANR-11- INBS-0012), the TransPLANT project (EU 7th Framework Program, contract
no. 283496), the H2020 ELIXIR-EXCELERATE project (funded by the European
Commission within the Research Infrastructures program of Horizon 2020,
grant agreement no. 676559), and the ‘‘Investments for the Future program’’
(PIA) (ANR-11-INBS-0012) as well as by INRAe. Developments of wheat, protein
crops, rapeseed, and miscanthus ontologies have been supported by the
Breedwheat (ANR-10-BTBR-03), BFF (11-BTBR-0006), Rapsodyn (11-BTBR-
0004), and Peamust (11-BTBR-0002) PIA projects.
We acknowledge the contribution of Kate Dreher, data steward at CIMMYT
for actively supporting discussions on semantics within the Data Management
Working Group of the CGIAR Excellence in Breeding Platform. Aman Sidhu,
consultant, for formatting and facilitating the CoP webinars. Olga Spellman,
The Alliance Bioversity International-CIAT, for paper technical review and English
editing.","The increasing application to agrifood research data of the FAIR
(findable, accessible, interoperable, and reusable) principles1
has led to the research community’s growing interest in using ontologies.
FAIR principles indeed recommend that data must be
described with commonly used, controlled vocabularies structured
in thesauri and semantically rich ontologies. An ontology
is a representation of a domain of knowledge where key concepts,
as well as the relationships between those concepts, are
defined.2 By providing standardized definitions for the terms
used by scientists along with defined logical relationships among
these terms, ontologies compile information about the content of
a dataset that can be explicitly used by computers.3 Each
concept has a Uniform Resource Identifier (URI) that uniquely
identifies it as a web resource accessible by anyone for data labeling,
to efficiently support consistent use of ontology terms
within and across disciplines and domains. Therefore, annotating
data with quality and widely used ontologies increases the findability,
interoperability, and reusability of data.","2020-10","published",,"Patterns","1","7","World Scientific Publishers",,"100105",,,,,,"doi:10.1016/j.patter.2020.100105",,,,,"TRUE",,"2666-3899",,,,,,"","https://doi.org/10.1016/j.patter.2020.100105","https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=10.1016%2Fj.patter.2020.100105&btnG=","pub",,"CGIAR Trust Fund","",,,,,,"",,,,,,,"",,,,,"",,,,,"","",,,,,"","",,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Laporte","M A","","",,,,,"Das","R R","","",,,,,,,,,,,,,,,"Markets, Trade and Institutions Division (MTID), International Food Policy Research Institute (IFPRI), Washington, DC, USA","UK",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Kim","S","","",,,,,,,,,,,,,,,,,,,,,,,"Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Exeter","USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Aubert","C","","",,,,,,,,,,,,,,,,,,,,,,,"Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA","Mexico",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Leonelli","S","","",,,,,,,,,,,,,,,,,,,,,,,"Socio-Economics Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of Me´ xico, Mexico","Germany",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Miro","B","","",,,,,,,,,,,,,,,,,,,,,,,"Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany","Nigeria",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Cooper","L","","",,,,,,,,,,,,,,,,,,,,,,,"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA","Malaysia",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Jaiswal","P","","",,,,,,,,,,,,,,,,,,,,,,,"Integrated Breeding Platform, Texcoco, State of Me´ xico, Mexico","Philippines",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Kruseman","G","","",,,,,,,,,,,,,,,,,,,,,,,"Cassava Breeding Program, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria","Peru",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Shrestha","R","","",,,,,,,,,,,,,,,,,,,,,,,"Aquaculture and Fisheries Sciences, Worldfish, Penang, Malaysia","India",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Buttigieg","P L","","",,,,,,,,,,,,,,,,,,,,,,,"Agrifood Policy Platform, International Rice Research Institute (IRRI), Los Ban˜ os, Laguna, Philippines","Kenya",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Mungall","C J","","",,,,,,,,,,,,,,,,,,,,,,,"Research Informatics Unit (RIU), International Potato Center (CIP), Lima, Peru","Belgium",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Pietragalla","J","","",,,,,,,,,,,,,,,,,,,,,,,"ICRISAT (Patancheru)","Norway",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Agbona","A","","",,,,,,,,,,,,,,,,,,,,,,,"Biometrics Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria","Columbia",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Muliro","J","","",,,,,,,,,,,,,,,,,,,,,,,"Mueller Bioinformatics Laboratory, Boyce Thompson Institute for Plant Research, Ithaca, NY, USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Detras","J","","",,,,,,,,,,,,,,,,,,,,,,,"Unite´ De´ le´ gation a` l’Information Scientifique et Technique - DIST, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Hualla","V","","",,,,,,,,,,,,,,,,,,,,,,,"Digital Biology, Earlham Institute, Norwich, Norfolk, UK",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Rathore","A","","",,,,,,,,,,,,,,,,,,,,,,,"Monitoring, Evaluation and Learning Team, International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Das","R R","","",,,,,,,,,,,,,,,,,,,,,,,"Research Methods Group (RMG), World Agroforestry (ICRAF), Nairobi, Kenya",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Dieng","I","","",,,,,,,,,,,,,,,,,,,,,,,"UPR AIDA, The French Agricultural Research Centre for International Development (CIRAD), Sainte-Clotilde, Re´ union, France",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Bauchet","G","","",,,,,,,,,,,,,,,,,,,,,,,"GEMS Informatics Initiative, University of Minnesota, St. Paul, USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Menda","N","","",,,,,,,,,,,,,,,,,,,,,,,"CP RDIT, Syngenta, St Sauveur, France",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Pommier","C","","",,,,,,,,,,,,,,,,,,,,,,,"Bayer Crop Science SA-NV, Diegem, Belgium",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Shaw","F","","",,,,,,,,,,,,,,,,,,,,,,,"Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Lyon","D","","",,,,,,,,,,,,,,,,,,,,,,,"CGIAR Platform for Big Data in Agriculture, International Center for Tropical Agriculture (CIAT), Cali, Colombia",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Mwanzia","L","","",,,,,,,,,,,,,,,,,,,,,,,"BioinfOmics, Plant Bioinformatics Facility, Universite´ Paris-Saclay, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Versailles, France",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Juarez","H","","",,,,,,,,,,,,,,,,,,,,,,,"Performance, Innovation and Strategic Analysis, International Center for Tropical Agriculture (CIAT), Regional Office for Africa, Nairobi, Kenya",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Bonaiuti","E","","",,,,,,,,,,,,,,,,,,,,,,,"Bioinformatics Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Ban˜ os, Laguna, Philippines",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Chiputwa","B","","",,,,,,,,,,,,,,,,,,,,,,,"Data Management Section, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Obileye","O","","",,,,,,,,,,,,,,,,,,,,,,,"Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, State of Me´ xico, Me´ xico",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Auzoux","S","","",,,,,,,,,,,,,,,,,,,,,,,"Environment and Production Technology Division (EPTD), International Food Policy Research Institute (IFPRI), Washington, DC, USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Yeumo","E D","","",,,,,,,,,,,,,,,,,,,,,,,"Universite´ de Montpellier, Montpellier, France",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Mueller","L A","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Silverstein","K","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Lafargue","A","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Antezana","E","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Devare","M","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"11741",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"King","B","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,