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

    Arnaud, E and Laporte, M A and Kim, S and Aubert, C and Leonelli, S and Miro, B and Cooper, L and Jaiswal, P and Kruseman, G and Shrestha, R and Buttigieg, P L and Mungall, C J and Pietragalla, J and Agbona, A and Muliro, J and Detras, J and Hualla, V and Rathore, A and Das, R R and Dieng, I and Bauchet, G and Menda, N and Pommier, C and Shaw, F and Lyon, D and Mwanzia, L and Juarez, H and Bonaiuti, E and Chiputwa, B and Obileye, O and Auzoux, S and Yeumo, E D and Mueller, L A and Silverstein, K and Lafargue, A and Antezana, E and Devare, M and King, B (2020) The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns, 1 (7). p. 100105. ISSN 2666-3899

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    Abstract

    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.

    Item Type: Article
    Divisions: Statistics, Bio-Informatics & Data Management
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Big data
    Subjects: Others > Data & Analytics
    Depositing User: Mr Arun S
    Date Deposited: 14 Mar 2021 10:36
    Last Modified: 14 Mar 2021 10:36
    URI: http://oar.icrisat.org/id/eprint/11741
    Official URL: https://doi.org/10.1016/j.patter.2020.100105
    Projects: UNSPECIFIED
    Funders: CGIAR Trust Fund
    Acknowledgement: 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.
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