BrAPI-an application programming interface for plant breeding applications

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases

Measures for interoperability of phenotypic data: minimum information requirements and formatting

BackgroundPlant 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 datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse.ResultsIn this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented.ConclusionsAcceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data

Trajectories of changes of pig farms in Vietnam – comparison between a northern and a southern district

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Diversity of pig farm types and their sustainability in the northern mountain of Vietnam

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Towards a practical approach to responsible innovation in finance: New Product Committees revisited

International audiencePurpose – The purpose of this paper is to highlight the potentials offered by New Product Committees for the development of responsible innovation in the financial services industry; and to provide grounds for policy recommendations. Design/methodology/approach – The paper takes the form of collective, interdisciplinary reflection and experience within the industry. Findings – New Product Committees can serve a practical approach to responsible innovation in finance. Originality/value – The paper fills a gap in the empirical consideration of New Product Committees in the financial services industry and proposes original directions for policy orientations within organizations and at a regulatory level

RepetDB: a unified resource for transposable element references

Background: Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data. However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. Results: We present here the RepetDB database developed in the framework of GnpIS, a genetic and genomic information system. RepetDB is designed to store and retrieve detected, classified and annotated TEs in a standardized manner. RepetDB is an implementation with extensions of InterMine, an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine can display diverse information for each sequence and allows simple to very complex queries. Finally, TE data are displayed via a worldwide data discovery portal. RepetDB is accessible at urgi.versailles.inra.fr/repetdb. Conclusions: RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes

Developing grapevine FAIR Data

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Data standards for plant phenotyping: MIAPPE and its implementations

International audiencePlant Phenotyping data management following the FAIR (Findable, Accessible, Interoperable, Resusable) is highly challenging because of its heterogenity. Thus, simply integrating and consolidating data within a single dataset like a phenotyping network is already a complicated task which is even more complex when trying to link different datasets together. To adress this problem, the Minimal Information About Plant Phenotyping Experiment standard construction has been initiated four years ago, with the help of experts from European infrastructures and institutes like Elixir, Emphasis, INRA, WUR, iBet, IPK, EBI and IPG PAS. It adresses the need of data publication and reuse through a checklist that formalize and document the minimal metadata necessary to ensure long term FAIRness of field or greenhouse datasets, including high througputs phenotyping ones. This list has been implemented in several databases like GnpIS or eDale, in a file format, ISA Tab, in a web service, the Breeding API and an RDF implementation is under construction. We will review those implementations, show its current adoption state and detail the plans for the future evolutions of the standard