Publications
URGI members are underlined in authors list. In the talks sections, names in bold are the speakers.
There are different types of publications, Papers with reading comittee (ACL), Papers in books (ACT), Invited talks (INV), Talks (COM), Posters (COM), Specialised Media and Press (SMP) and Thesis.
Other
COM (communication)
06 Dec 2024 [hal-04822902] AGENT Guidelines for dataflow
The AGENT project aims at integrating data from different sources (genebanks, research institutes, international archives) and types (passport, phenotypic, genomic data). These guidelines have been developed to explain the data flow within the AGENT project and should be useful for other projects.
In ProdINRA
06 Dec 2024 [hal-04822902] AGENT Guidelines for dataflow
COM (communication)
25 Oct 2024 [hal-04739711] Atelier « L'IA en pratique: de la perception à l'application »
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In ProdINRA
25 Oct 2024 [hal-04739711] Atelier « L'IA en pratique: de la perception à l'application »
COM (communication)
23 Oct 2024 [hal-04750756] Eclairages sur l'infrastructure de recherche RARe
Cet article présente l'Infrastructure de Recherche Nationale RARe (https://www.agrobrc-rare.org) en s'appuyant sur les communications parues dans la Lettre des Unités Expérimentales d'INRAE (LUE). Après une introduction générale de l'organisation de cette Infrastructure en cinq piliers de Centres de Ressources Biologiques, les communications apportent des éclairages sur la complémentarité entre RARe et les unités expérimentales, sur l'organisation du pilier 'plante' et sur quelques exemples de ses activités, avant de terminer sur le modèle économique de l'ensemble.
In ProdINRA
23 Oct 2024 [hal-04750756] Eclairages sur l'infrastructure de recherche RARe
COM (communication)
12 Oct 2024 [hal-04733449] A Benchmark for Transposable Element annotation tools
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In ProdINRA
12 Oct 2024 [hal-04733449] A Benchmark for Transposable Element annotation tools
COM (communication)
12 Oct 2024 [hal-04733446] The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species
Abstract The role of transposable elements (TEs) in host adaptation can be explored with a pangenomic approach. Individuals of the same species undergo independent TE insertions, causing genetic variability upon which natural selection acts. This can lead to improved adaptation of individuals to their environment. The advent of third-generation sequencing has enabled use of multiple whole-genome de novo assemblies for a given species, avoiding bias introduced by a single reference genome. We developed a new pipeline, panREPET, for such data. It compares TE copies between each pair of individuals then identifies copies shared by a group of individuals. This gives the exact sequence and genomic context of each TE copy. We describe here TE insertions shared among 54 Brachypodium distachyo n genomes. We were able to date two major TE bursts corresponding to major climate events: 22 kya during the Last Glacial Maximum and 10 kya during the Holocene.
In ProdINRA
12 Oct 2024 [hal-04733446] The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species
COM (communication)
01 Oct 2024 [hal-04717147] Mapping bread wheat trait ontologies for semantic interoperability
The Wheat Crop ontology was created to annotate phenotypic experimental data (i.e. field and greenhouse measurements standardized and integrated in databases). The Wheat Trait and Phenotype ontology was created to annotate information on wheat traits from the literature (i.e. text found in the abstract, results and discussion of scholarly articles). To enable seamless data retrieval on wheat traits from these complementary sources, the classes in the two ontologies have been aligned. All pairs of ontology classes were examined and categorized in nine groups based on the nature of their relationships (e.g. equivalence, subsumption). General principles emerged from this process which were formalized into rules. The Simple Standard for Sharing Ontological Mappings (SSSOM) representation was chosen to represent the mappings in RDF (Resource Description Framework), including their metadata such as creators, reviewers, and justification (including rules).The mapping dataset is publicly available. It covers 77% of the ontology classes. Most labels of the aligned classes differed significantly and required domain expertise for decisions, especially for traits related to biotic stress. Consequently, most mappings are close mappings rather than exact equivalents. We present the end-to-end manual process used to select and represent mappings in SSSOM within the specific domain of wheat traits. We derive general lessons from the complex alignment process that extend beyond the specific case of these two ontologies and more generally apply to alignments of specialized ontologies for information retrieval purposes. This work demonstrates the relevance of SSSOM for representing these mappings.
In ProdINRA
01 Oct 2024 [hal-04717147] Mapping bread wheat trait ontologies for semantic interoperability