The Ontologies Community of Practice: An Initiative by the CGIAR Platform for Big Data in Agriculture

Arnaud, Elizabeth; Laporte, Marie‐Angélique; Kim, Soonho; Aubert, Céline; Leonelli, Sabina; Cooper, Laurel; Jaiswal, Pankaj; Kruseman, Gideon; Shrestha, Rosemary; Buttigieg, Pier Luigi; Mungall, Christopher J.; Pietragalla, Julian; Agbona, Afolabi; Muliro, J.; Detras, Jeffrey; Hualla, Vilma; Rathore, Abhishek; Das, Roma Rani; Dieng, Ibnou; Bauchet, Guillaume; Menda, Naama; Pommier, Cyril; Shaw, Felix; Lyon, David; Mwanzia, Leroy; Juárez, Henry; Bonaiuti, Enrico; Chiputwa, Brian; Obileye, Olatunbosun; Auzoux, Sandrine; Yeumo, Esther Dzalé; Mueller, Lukas A.; Silverstein, Kevin A.T.; Lafargue, Alexandra; Antezana, Erick; Devare, Medha; King, B. R.

doi:10.2139/ssrn.3565982

Cited by 7 publications

(2 citation statements)

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“…Being cognizant of such a broad range of options, our examination considers categories of data which may fit into a functional definition of DSI, namely: DNA, RNA, protein, genetic markers (with or without sequences), non-coding features and other data categories (Houssen et al, 2020;Brink et al, 2021) and specifically suggests ways to link these data to other ontologized knowledge to accommodate expansive views of DSI. As best practice, existing ontology may be used where each concept bears a unique and resolvable identifier, called a Uniform Resource Identifier, for which the definition, context of use and semantic relationships are validated by a large community (Arnaud et al, 2020). For example, the Sequence Ontology, the Protein Ontology, and the Gene Ontology, which include concepts and definitions of Genomic Objects along with other relevant ontologies, such as the NCBI taxonomy for species, and metadata standards, such as the Biosample record, may provide a useful point of departure.…”

Section: Global Policy On Access and Benefit-sharing And The Nexus Wi...mentioning

confidence: 99%

Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability

Manzella

Marsella

Jaiswal

et al. 2022

Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development

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Plant genetic resources are source genetic material for conducting research and breeding. The use of this material is subject to international and national regulations on access and benefit-sharing (ABS). With modern genetic technologies generating desired trait and gene function improvement by replicating genetic signatures, ABS must adapt to the new technological reality. As the constituencies of international ABS conventions discuss if and how to extend the application of the conventions to digital sequence information (DSI) derived from source material, the genomics science community resists any incumbrance to continued free and unrestricted access to such information. Based on current ABS discussions and the likely future co-existence of diverse policy regimes, this paper proposes interoperability among data systems as an essential tool to implement legal solutions for benefit-sharing as well as advance science and innovation objectives. Two information technology tools are suggested for associating DSI to plant genetic resources and reciprocal citations with data exchange, namely digital object identifiers and digital genetic objects. This paper concludes that interoperability should be experimented with in both its technical and social dimensions, in order to support long-term alliances between policy and science through data archives, knowledge bases and live specimen collection resources.

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Section: Global Policy On Access and Benefit-sharing And The Nexus Wi...mentioning

confidence: 99%

Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability

Manzella

Marsella

Jaiswal

et al. 2022

Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development

View full text Add to dashboard Cite

show abstract

“…For example, in order to make given plant traits amenable to large-scale computational analysis, it is necessary to have suitable labels for the data clusters relevant to investigating such traits. This requires the development of reliable and standardised trait descriptors, which in turn involves consultations across breeders, farmers, researchers and consumers concerning which traits are most significant for investigation and which labels are most appropriate in defining thema fraught set of questions to ask within a cross-cultural, multilingual environment plagued by power differentials and inequity between the parties involved (Arnaud et al, 2020;Leonelli, 2022;Curry & Leonelli, 2022). Additionally, analysing data on phenomena ranging from ecological stressors to hostpathogen interactions requires having sufficient metadata about the conditions of origin and the legitimate range of possible uses of such data (Shaw et al, 2020); and linking data from many different sources (whether genomic and experimental data from public or corporate research, knowledge of plant strains and environments held by farmers and breeders, or data related to stored germplasm collections) requires sharing, access and reuse agreements among stakeholders as well as venues in which such agreements can be forged.…”

Section: Dimensions Of Responsible Plant Data Governancementioning

confidence: 99%

Introduction: Towards Responsible Plant Data Linkage

Leonelli

Williamson

2022

Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development

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This chapter provides a framing for this volume by reviewing the significance and the organisational, technical and social opportunities and challenges related to plant data linkage. We review what “responsible practice” means in relation to the plant environments being documented, the infrastructures used to circulate data, the institutions involved in data governance and the communities involved in plant data work. We show how, across these domains, responsible plant data linkage involves consideration of technical, legal, ethical and conceptual dimensions, thereby: (1) creating and maintaining digital infrastructures, technical standards and discussion venues focused on critical data reuse; (2) developing adequate legal and institutional frameworks that work transnationally; (3) identifying and implementing guidelines for what constitutes acceptable data use, together with systems to monitor and allocate responsibility for breaches and mistakes; and (4) considering the variety of views on what constitutes agricultural development in the first place and how plant research can sustainably, reliably and responsibly contribute to achieving food security. The production of sustainable, responsible and reliable agricultural solutions in the face of climatic and political change depends on the flourishing of transnational, interdisciplinary collaborations such as those represented in this volume.

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Innovative Digital Technologies to Monitor and Control Pest and Disease Threats in Root, Tuber, and Banana (RT&B) Cropping Systems: Progress and Prospects

Kreuze

Adewopo²,

Selvaraj

et al. 2022

Root, Tuber and Banana Food System Innovations

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This chapter provides the first comprehensive review of digital tools and technologies available for the identification, monitoring, and control of pests and diseases, with an emphasis on root, tuber, and banana (RT&B) crops. These tools include systems based on identification keys, human and artificial intelligence-based identification based on smart applications, web interfaces, short messages services (SMS), or combinations thereof. We also present ideas on the use of image recognition from smartphones or unmanned aerial vehicles (UAVs) for pest and disease monitoring and data processing for modeling, predictions, and forecasting regarding climate change. These topics will be presented in the context of their current development and future potential but also the challenges, limitations, and innovative approaches taken to reach end users, particularly smallholder farmers, and achieve impacts at scale. Finally, the scope and limitation of private sector involvement demonstrates the need of publicly funded initiatives to maximize sharing of data and resources to ensure sustainability of unbiased advice to farmers through information and communication technology (ICT) systems.

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The Ontologies Community of Practice: An Initiative by the CGIAR Platform for Big Data in Agriculture

Cited by 7 publications

References 0 publications

Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability

Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability

Introduction: Towards Responsible Plant Data Linkage

Innovative Digital Technologies to Monitor and Control Pest and Disease Threats in Root, Tuber, and Banana (RT&B) Cropping Systems: Progress and Prospects

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