Elizabeth Arnaud

Elizabeth Arnaud
Consultative Group on International Agricultural Research | CGIAR

MSc Biology & Sci. Info. Mangt

About

111
Publications
23,517
Reads
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1,390
Citations
Additional affiliations
January 2012 - present
Bioversity International

Publications

Publications (111)
Article
Full-text available
Modern breeding methods integrate next-generation sequencing (NGS) and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations i...
Technical Report
The Crop Ontology Guidelines version 2.1 provide detailed information and numerous examples for the use of the Trait Dictionary Template v.5.2 to develop a high quality Trait Dictionary with trait and variables used for the annotation of crop phenotypic data. The guidelines were developed in collaboration with the Integrated Breeding Platform and C...
Technical Report
Full-text available
A governance & stewardship framework for the Crop Ontology Project is required as this is a collaborative tool developed by a Community of Practice. Over the last 12 years of its existence, it has increased significantly in scope and use. Collecting and storing plant trait data and annotating the data with ontology terms is widely accepted by the c...
Article
Full-text available
The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from more than thirty experts in the private and public sector o...
Book
Full-text available
Tricot (triadic comparisons of technologies) is a citizen science approach for testing technology options in their use environments, which is being applied to on-farm testing of crop varieties. Over the last years, important progress has been made on the tricot methodology of which an overview is given. Trial dimensions depend on several factors bu...
Article
Full-text available
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 an...
Article
Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but th...
Article
Full-text available
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardizing data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release which enhances the existing MIAPPE standar...
Preprint
Full-text available
Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but th...
Article
Full-text available
Today, global food production is the largest driver of environmental degradation and biodiversity loss (Willett et al. 2019). Rising global food demand and limited arable land are pushing us to expand agricultural frontiers and production. This often happens without regard to the environment, causing biodiversity loss, land and water degradation (B...
Article
Full-text available
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data...
Article
Full-text available
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are pr...
Article
Full-text available
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wh...
Article
Full-text available
Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informa...
Article
Full-text available
The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Onto...
Article
Full-text available
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wh...
Article
Full-text available
Background: Opportunities to use data and information to address challenges in international agricultural research and development are expanding rapidly. The use of agricultural trial and evaluation data has enormous potential to improve crops and management practices. However, for a number of reasons, this potential has yet to be realized. This pa...
Article
Plant research produces data in a profusion of types and scales, and in ever-increasing volume. What are the challenges and opportunities presented by data management in contemporary plant science? And how can researchers make efficient and fruitful use of data management tools and strategies?
Article
Full-text available
CGIAR is a global research partnership of 15 geographically and scientifically diverse Centers dedicated to reducing poverty, enhancing food and nutrition security, and improving natural resource management. The Centers are charged with accelerating innovation to tackle challenges at a variety of scales from the local to the global. This requires d...
Article
Full-text available
Background: Opportunities to use data and information to address challenges in international agricultural research and development are expanding rapidly. The use of agricultural trial and evaluation data has enormous potential to improve crops and management practices. However, for a number of reasons, this potential has yet to be realized. This pa...
Technical Report
Full-text available
Human wellbeing and food security in a changing climate depend on productive and sustainable agriculture. For this, policies based on analyses and research results are vital to establish conservation priorities of natural resources that underpin the enhancement of sustainable food production. Therefore, data from agrobiodiversity and wider biodiv...
Article
Full-text available
Background Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing...
Conference Paper
Full-text available
Many vocabularies and ontologies are produced to represent and annotate agronomic data. By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the...
Poster
Crop specific ontologies for phenotype annotations in breeding have proliferated over the last 10 years. Across-crop data interoperability involves linking those ontologies together. For this purpose, the NSF-awarded Planteome project is mapping the Crop Ontology traits (www.cropontology.org) to the reference ontology for plant traits. Trait Ontolo...
Poster
Thesauri are used to tag semi-structured documents, texts, while more complex semantic structures are used to describe (annotate) scientific data. We are creating a Global Agricultural Concept Scheme (GACS) by mapping AGROVOC, CABT and NALT – three major thesauri in the area of food and agriculture, with a beta release in May 2016. We see GACS as a...
Article
Full-text available
Similarly to what happens in biomedicine, communities engaged in agronomic research need to access specific sets of ontologies for data annotation and integration. For instance, it has been established that the scientific challenges in plant breeding have switched from genetics to phenotyping and that standard traits/phenotypes vocabularies are nec...
Research
Full-text available
This report presents a methodological approach for the identification of geographical areas of special interest, or ‘agrobiodiversity hotspots’, at the intersection between SEP and Bioversity priority research areas. This work provides an overview of on-going projects on crop wild relatives (CWR) and negleted and underutilized plant species (NUS) t...
Conference Paper
Full-text available
The objective of plant phenotyping is to advance plant science for breeding and crop management. Phenotyping platforms automate the measurements of traits from the cell to the whole plant by using novel sensors and methods in both controlled environment and in the field. Big data are produced in the form of alphanumeric matrices, images, statistica...
Article
Full-text available
Our project is to develop and support a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we have already designed and implemented a prototype ontology repository for plants and a few crops. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the...
Conference Paper
Full-text available
Participatory Variety Selection (PVS) refers to the evaluation of varieties by farmers through trials that aim to capture the preferences of farmers, women and men for selected traits. This type of selection process has been adopted by several plant breeders involved in crop ontology. During the crop ontology workshop held in April 2014 (http://tin...
Conference Paper
Full-text available
The Crop Ontology web site facilitates the publishing of crop breeding controlled vocabulary and the use by third party web sites and databases. The GCP ontology curators can upload online their standard lists of concepts using either the Trait Dictionary Excel Template or the Open Biomedical Ontologies (OBO) format. Routines were developed this ye...
Conference Paper
Full-text available
El proyecto de Ontología de Cultivos ha sido identificado como una iniciativa del "Generation Challenge Program" (GCP), liderado por "Bioversity International", como una herramienta fundamental para la gestión y análisis de la información relacionada con los cultivos. En los últimos años en la agricultura se ha notado un incremento en las terminolo...
Poster
Full-text available
A review of questions, tools, concepts and methodologies in preparation of Programme Sud Expert Plantes Développement Durable (SEPDD) What are Plant NUS? • Also called ’Orphan Crops’, species and varieties of importance for the rural communities but to which little or no attention is paid by agricultural researchers, plant breeders and policymakers...
Conference Paper
Full-text available
The Crop Ontology (CO) (www.cropontology.org) is a service of the Integrated Breeding Platform (IBP), Generation Challenge Programme (GCP). CO currently includes reference lists of breeders'traits with measurement methods and scales for currently 14 crops – with work ongoing to add barley, lentil and sweet potato – as well as environmental and expe...
Conference Paper
Full-text available
Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvement may be combined with next-generation methods such a...
Article
Full-text available
PREFACE The growth in the capacity of the research community to collect and distribute data presents huge opportunities. It is already transforming old methods of scientific research and permitting the creation of new ones. However, the exploitation of these opportunities depends upon more than computing power, storage, and network connectivity. Am...
Book
Full-text available
Much progress has been made in the past ten years to fulfil the potential of biodiversity informatics. However, it is dwarfed by the scale of what is still required. The Global Biodiversity Informatics Outlook (GBIO) offers a framework for reaching a much deeper understanding of the world’s biodiversity, and through that understanding the means to...
Conference Paper
Full-text available
A recurrent issue for data integration is the lack of a com-mon and structured vocabulary used by different parties to describe their data sets. The Crop Ontology (www.cropontology.org) project aims to provide a central place where the crop community can gather to gener-ate such standardized vocabularies and structure them into ontologies. Having s...
Article
Full-text available
Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Af...
Data
Scree plot of the factorial analysis. Proportion of variance for each component, sorted in decreasing order of variance. (PDF)