cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/apbgkk
title: Ontology of Experimental Events

description: The Ontology of Experimental Events (OEEv), characterises events that occur during an experiment, e.g. dates of sowing, application of a given treatment, harvesting, measurements or sampling for -omic measurements, or any category of technical problem.
DOI: 10.15454/cvkv1z
title: Le_Cozler_2019_biorxiv760082

description: Data used in: Le Cozler Y., Jurquet J. and Bedere N. Effects of feeding treatment on growth rate and performance of primiparous Holstein dairy heifers. bioRxiv 760082, ver. 3 peer-reviewed and recommended by PCI Animal Science (2019). /!\ French language in the data
DOI: 10.15454/1w4cep
title: RPG complété 2019 département 61

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 61. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/4dkvvv
title: Microsatellite datasets of wild P. brigantina (Alpine plum) accessions and diploid Prunus spp. (P. cerasifera included) originating from Europe, Caucasia and Central Asia

description: This dataset corresponds to the SSR (microsatellite) genotypes of a large set of Prunus brigantina and Prunus cerasifera accessions, those accessions were genotyped with a set of 24 common SSR markers, previously used in Armeniaca species (Liu et al, 2019. https://doi.org/10.15454/560LSH). The dataset was used to infer the relationship of P. brigantina (Briançon plum or Briançon apricot) with Armeniaca (apricot) and Prunus (plums) species, based on microsatellite markers and approximate Bayesian computation.
DOI: 10.15454/4maai0
title: Dataset of a two-year field experiment on the dynamics of Zymoseptoria tritici populations in wheat cultivar mixtures

description: The data and the R scripts that support the findings of this study
DOI: 10.15454/4teo6h
title: Package Fordead

description: Fordead is dedicated to the detection of anomalies in seasonality of vegetation properties derived from SENTINEL-2 time series. It was initially developed as a monitoring tool for bark-beetle induced tree mortality on spruce trees in northeastern part of France, with particularly intense outbreaks in 2018, 2019 and 2020. Fordead includes a full processing chain and a collection of tools to give access to SENTINEL-2 time series analysis easier for non-experts in remote sensing and image processing. It is possibly applicable in other contexts, and experimentations are currently on-going to identify the domain of validity of the method: which species, which sanitary problems? The method developed in fordead takes advantage of full SENTINEL-2 time series, starting from 2015. However, the density of acquisitions reached full capacity in 2017 with the launch of Sentinel-2B. The seasonality analysis is performed at pixel level and allows continuous near real-time monitoring.
DOI: 10.15454/amndto
title: Impact of hybrid and consanguinity depression on reproduction and early growth of second generation hybrid larch

description: This dataset is issued from a study of the impact on reproduction and early growth of hybrid and consanguinity depression in second-generation hybrid larch. Twenty-one first-generation hybrid clones were combined through control crossing to obtain 4 groups of full-sib families from unrelated parents, half-sibs, full-sibs and backcrosses. They were compared to related first-generation hybrid families.
DOI: 10.15454/cphted
title: Agricultural Experiments Ontology

description: AEO is an ontology aimed to represent objects related to agricultural practices.
DOI: 10.15454/34llgn
title: Replication data for : Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

description: Information data on the diversity of bacterial communities present on 12 samples of cold smoked salmon, 18 samples of stainless steal coupons placed in a food processing environment and 115 samples of stainless steal and tri-polyurethane coupons placed in a food processing environment. The aim of this study was to evaluate DNA extraction and sampling methods biases on 16S metabarcoding studies. Sequencing data were generated by using Illumina MiSeq.
DOI: 10.15454/4xibs9
title: Assessment of a Food Consumption DataBase enrichment method using Ciqual, USDA and FoodOn

description: This dataset contains data used to assess a method designed to implement Food Consumption DataBase (FCDB) enrichment task and associated results for a given use case. This use case consists in finding in USDA values associated with nutrients vitamin C, vitamin B12 and iron when they are not known in Ciqual for a given food. This data set contains three files: (1) Automatic alignments of Ciqual foods on FoodOn foods, (2) Automatic alignments of USDA foods on FoodOn foods, (3) the list of 99 Ciqual food products for which at least one of the values associated with the 3 nutrients is not known in Ciqual and at least one similar term can be found in USDA, (4) the subset of 75 alignments Ciqual-&gt;USDA found using FoodOn as pivot ontology.
DOI: 10.15454/6ceyu3
title: Semantic description of Ciqual food terms using Langual thesaurus

description: This dataset contains a OWL representation of Ciqual food terms using Langual thesaurus. Ciqual is the nutritional database managed by ANSES in France. Explanations about the OWL modeling is available in the related publication.
DOI: 10.15454/85e5ql
title: RPG complété 2019 département 02

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 02. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/9bffkg
title: Meloidogyne incognita Interproscan annotation

description: Interproscan annotation on the 43,718 predicted proteins in the genome of the root-knot nematode Meloidogyne incognita (Blanc-Mathieu et al. 2017, PLoS Genetics). vesrion used: interproscan-5.29-68.0 options used: -dp Disables use of the precalculated match lookup service = all match calculations are run locally. -iprlookup lookup of corresponding InterPro annotation -goterms lookup of corresponding Gene Ontology annotation -pa lookup of corresponding Pathway annotation -f TSV format the results in tab-separated values
DOI: 10.15454/9eijwu
title: Process-based emulator to explain the differences in simulated potential yield between Global Gridded Crop Models

description: Scripts at the basis of a study submitted to Geoscientific Model Development called "Potential yield simulated by Global Gridded Crop Models: a process-based emulator to explain their differences". The tgz file encompass three python scripts and shell scripts + directories to use these python scripts.
DOI: 10.15454/9qb9u0
title: Résultats expérimentation ORE Capsules

description: Petit fleuve côtier de 39 km de long, la Nivelle est une rivière à migrateurs (saumons, aloses et truites). Bien présente sur la rivière, la truite sous ses deux écotypes (mer et rivière) est une espèce endémique et emblématique qui est un bon indicateur de la qualité des cours d’eau et qui fait l’objet de nombreux programmes de recherche pour évaluer sa capacité à s’adapter au changement climatique. Dans ce cadre l’UMR Ecobiop a mis en place un suivi à long terme sur trois affluents de la Nivelle dans lequel le protocole propose l’insertion, dans des petites capsules grillagées, d’œufs de truites de la rivière provenant de pontes artificielles obtenues en laboratoire. Des dispositifs expérimentaux placés dans des frayères artificielles creusées dans les ruisseaux accueillent ces capsules avec les œufs. Une fois l’incubation des œufs terminée, les capsules sont retirées des dispositifs et les œufs ou alevins vivants ou morts sont comptabilisés. Cette expérimentation mis en place sur le long terme à partir de 2011, a pour objectif de faire ressortir quel pourraient être les effets du changement climatique sur le long terme au travers d’indicateurs comme les températures, les débits, la modification des substrats. Mais elle est aussi un moyen de vérifier chaque année que les incubations se passent de manière satisfaisante et de pouvoir éventuellement alerter sur des évènements particuliers et uniques comme des pollutions, l’apparition de nouvelles nuisances susceptibles de porter préjudice aux incubations sous gravier. Pour décrire cette expérimentation, le Dataset réunit 4 documents qui synthétisent les opérations récurrentes entreprises chaque année : 1- les résultats des survies des œufs dans les capsules d’incubation, 2- les données températures pour le suivi de l’incubation, 3- les résultats des analyses des échantillons granulométriques prélevés lors de l’expérimentation, 4- un PDF du mode opératoire de l’expérimentation et du matériel utilisé. Pas d'expérimentation pour la saison 2024-2025.
DOI: 10.15454/adicmr
title: Relevés de températures de l'eau en continu sur la station "étangs" de l'U3E depuis 2008

description: Relevés de températures de l'eau en continu sur la station "étangs" de l'U3E depuis 2008. L'enregistreur de type TidBit à été remplacé le 5/3/2024 à 16h00 par un autre type de sonde est situé dans un étang toujours rempli en eau sur la station. Il est situé à un mètre de la berge et à 15 cm de profondeur. Il y a des données manquantes sur le fichier.
DOI: 10.15454/aot7ul
title: Test dataset for assessment FROGS ITS methodology

description: Our objective was to create datasets allowing, among other things, to test methods and tools to process data from Fungi metabarcoding sequencing. Consequently, we have computer-generated reads of 250 nucleotides in length from artificial PCRs produced with the Grinder software on ITS1 or ITS2 from Fungi (UNITES v7.1), as diverse as possible. These data can be used for software benchmarking.
DOI: 10.15454/4zupcp
title: Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators

description: A F2 population consisting of 337 individuals was derived from the inter-specific cross of V. vinifera cv. Cabernet-Sauvignon (CS) x V. riparia cv. Riparia Gloire de Montpellier (RGM). This population, named CS x RGM_F2, resulted from the self-fertilization of the F1_148 individual of the F1 CS X RGM1995-1 described by Marguerit et al. (2009). Simple sequence repeat (SSR) markers were mainly chosen from the markers used to construct the map of the F1 CS X RGM1995-1 population (Marguerit et al., 2009, https://doi.org/10.1007/s00122-009-0979-4). In addition, 46 new SSR markers were designed using the grape genome 12X sequence (http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/). Primers were designed with PRIMER 0.5 software (Whitehead Institute for Biomedical Research). The map was constructed using the software CarthaGene (de Givry et al., 2005, https://doi.org/ 10.1093/bioinformatics/bti222) at a logarithm of the odds (LOD) value of 5.0 and at a maximal distance threshold of 35 cM. Validation of the map obtained was done using the software JoinMap® 3.0 (Stam, 1993) using a Kosambi’s mapping function. The marker order obtained was checked according to the consensus map of the F1 population CS x RGM1995-1 and to the 12X genome sequence. About 1.5 µg of DNA from both BACs VVCS1H018A11 and VVCS1H006A20 were pooled and sequenced using the standard Pacific Biosciences library preparation protocol for 10 kb libraries. Assembly of the PacBio reads was performed following the HGAP workflow (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP). The SMRT® Analysis (v2.3.0) software suite was used for HGAP implementation (https://github.com/PacificBiosciences/SMRT-Analysis). Reads were first aligned by BLASR (https://github.com/PacificBiosciences/blasr) against “Escherichia coli strain K12 substrain DH10B complete genome”. The Quiver algorithm (https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst) was used to enrich the quality scores embedded in Pacific Biosciences bas.h5 files. The “polished assemblies” were identified by matching their BAC end sequences with BLAST. Read coverage was obtained by aligning the raw reads on the assembled sequences with BLASR.
DOI: 10.15454/5i2ro1
title: InterATOME protein-protein interactions, Public

description: This dataset provides the results of many systematic large-scale yeast two-hybrid mappings of the Arabidopsis thaliana protein interactome
DOI: 10.15454/6rzlp9
title: Carte des distributions spatiales des éléments As, Cd, Co, Cr, Cu, Hg, Ni, Mo, Pb, Tl, Zn dans les sols de France à partir des observations issues du RMQS

description: Nous présentons ici les figures du rapport sur les contaminants dans les sols, disponible en ligne ici: https://traitementinfosol.pages.mia.inra.fr/rapport-etm2020. Les figures sont organisées selon quatre catégories : - Teneurs, pour la représentation des teneurs en ETM sur les deux couches d'analyses du RMQS (surface : 0-30 cm, subsurface : 30-50 cm) par le modèle QRF et par la méthode KED. - StockSurf, pour la représentation des stocks de surface (0-30 cm) en ETM par le modèle Quantile Regression Forest (QRF) et par la méthode par KED. - StockTot, pour la représentation des stocks totaux le long des profils de sol du RMQS par le modèle QRF et KED. - FPGa, ou fond pédogéochimique anthropisé, estimé selon deux méthodes: "data-driven" par calcul de statistique par fenêtre flissante et "model-based" basé sur la variance de krigeage d'un modèle de krigegage avec dérive externe (KED). cette dernière a été agrégée par canton afin d'obtenir une visualisation plus opérationnelle. Ces cartes sous forme de figures sont organisées en fonction du de l'extraction de l'élément traces, à savoir extraction total HF ou partielle EDTA.
DOI: 10.15454/6tl2n4
title: DROPS maize GWAS analysis dataset

description: This dataset corresponds to the most significant SNP (-log(p-value)&gt;5) identified by genome-wide association studies between the three traits (Flowering Time, Plant Height, Grain Yield) measured in 22 environments on a panel of 247 maize inbred lines. These analysis were conducted in the DROPS DROught-yielding PlantS european project (F. Tardieu Coord.) and ANR-PIA Amaizing (A. Charcosset, Coord.). These results were published in Negro S., et al (2019) in BMC Plant Biology: Genotyping-by-sequencing and SNP arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies" .
DOI: 10.15454/7zdnd6
title: Carte de la profondeur du sol issue de la Base de Données Géographique des Sols de France

description: Cette carte donne la classe de profondeur du sol dominante par Unité Cartographique de Sol de la Base de Données Géographique des Sols de France à 1/1 000 000. Les valeurs des classes sont données par l'attribut pr-cl et sont : 30 : profondeur &lt;= 30 cm 50 : 30 cm &lt; profondeur &lt;= 50 cm 100 : 50 cm &lt; profondeur &lt;= 100 cm 200 : profondeur &gt;= 100 cm -1, -2, -4 : non sols (villes, lacs, etc.)
DOI: 10.15454/93lpp7
title: Distribution of ticks, tick-borne pathogens and the associated local environmental factors, including small mammals and livestock, in two French agricultural sites: the OSCAR database

description: The data investigated the distribution of ticks and their potential pathogens in two agricultural zones in north-western and south-western France, as well as the distributions of the principal domestic and wild hosts (small mammals), along a gradient of wooded habitats from forest core to more or less isolated hedges bordering pastures. The samples and information on the landscape were collected in spring and autumn of 2012 and 2013 and in spring 2014 corresponding to the main periods of tick activity. All the questing ticks and ticks from small mammals were identified, and ticks and small mammals were analysed to detect Borrelia spp., Babesia spp. and Anaplasma spp.
DOI: 10.15454/ah8crs
title: MINTIA paper Biological samples

description: Reads corresponding to the biological samples initially analysed in "Investigating Host Microbiota Relationships Through Functional Metagenomics" of Laville et al and used to validate MINTIA pipeline on biological samples. The assembled and annotated fosmids of Laville et al are available in the repository of the DDBJ/EMBL/GenBank Nucleotide Sequence Database under accession numbers LR131274-LR131286. Correspondance Fosmid Name - Accession number is as follow : 9D11 - LR131275 14N11 - LR131278 20L12 - LR131279 39E18 - LR131281 47G11 - LR131286 3I21 - LR131274 40B3 - LR131283 41E6 - LR131284 39O22 - LR131282 12O6 - LR131276 47C24 - LR131285 13P9 - LR131277 33D18 - LR131280
DOI: 10.15468/dl.phfp8e
title: Occurrence Download

description: A dataset containing 5026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasCoordinate is TRUE",
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON ((-149.4702536553872 61.428820156872945, -149.79165799905272 61.32178992067055, -150.0708792952471 61.15870143073427, -149.804243886072 61.05573419052165, -149.4702536553872 61.428820156872945))"
 ]
}

 The dataset includes 5026 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035110-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15454/3z1ogu
title: Metabarcoding data analysis of fungal communities associated with 203 full-sib oak trees (Quercus robur) located in Bourran (France).

description: In this study, we consider the diversity and composition of the fungal communities collected on 203 full-sib Quercus robur individuals. Adult trees are located in the Bourran INRAe experimental site (44.34225 N ; 0.38672 W) in Lot-et-Garonne, France. Following fungal ITS1 amplification with ITS1F-ITS2 primers, 11 runs of single-end 454 sequencing were performed (Roche GS junior).The metabarcoding data we obtained have been analyzed using Bioinformatics scripts. Raw and filtered ASV Tables are available here. This work complements Boris Jakuschkin’s PhD available here https://www.theses.fr/2015BORD0170 (see Chapter 3).
DOI: 10.15454/5icggd
title: Willingness-To-Pay for Reshuffling Geographical Indications

description: Data from an economic experiment about consumer perceptions of different reshuffling scenarios for the vineyards of Marsannay, Burgundy, France
DOI: 10.15454/73gaav
title: Full length transcriptome highlights the coordination of plastid transcript processing: supplementary tables

description: This dataset includes the supplementary tables of the article "Full length transcriptome highlights the coordination of plastid transcript processing".
DOI: 10.15454/8cvwrr
title: DNA metabarcoding of a mock community of 189 fungal strains associated to plants and soils.

description: This sequence dataset (FASTQ format) was obtained by metabarcoding an artificial (mock) fungal community. The ribosomal internal transcribed spacer region 1 (ITS1) was amplified with the ITS1F / ITS2 primer pair and sequenced on an Illumina MiSeq platform (v3 chemistry, 2x250 bp). The mock community was composed of an equimolar mixture of the DNA of 189 pure fungal strains isolated from soils, sporocarps or plant tissues. All the strains belonged to the subkingdom Dikarya: 87 Ascomycota strains, 99 Basidiomycota strains and 3 Mucoromycota strains. The mock community was replicated three times (replicates DikA, DikB, DikC) and the three replicates were sequenced independently. The six files correspond to the forward (R1) and reverse (R2) sequences of each replicate. The sequencing was funded by the INRA MEM metaprogramme (Meta-Omics of Microbial Ecosystems, MetaBAR project). This sequence dataset was used to compare several bioinformatic approaches (Pauvert et al. Bioinformatics matters: the accuracy of plant and soil community data is highly dependent on the metabarcoding pipeline. Submitted).
DOI: 10.15454/8nzaba
title: Gene Ontology enrichment in PPN-specific and horizontally acquired proteins

description: We used a hypergeometric test within the FUNC program (Prüfer et al., 2007) to determine whether certain GO terms assigned via InterproScan annotation were significantly enriched in M. incognita : - PPN-specific proteins - PPN-specific putative secreted proteins (PSP) - PPN-specific Candidate effectors - Possible horizontal gene transfers (Alien Index &gt;0) - Candidate horizontal gene transfers (Alien index &gt;14) compared to the rest of the proteins in this species. We used a false discovery rate (FDR) threshold value of 0.05 to consider a term as significantly enriched.
DOI: 10.15454/9jiuxj
title: RPG complété 2019 département 53

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 53. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/9rdhin
title: French soil samples near infrared spectroscopy measurements and associated physico-chemical reference analysis.

description: This dataset presents near infrared spectra of soil samples from the experimental INRAE stations of the CAREX network including Auzeville, Epoisses, Crouel, Theix, Lusignan, Lusignan_Oasys and Ploudaniel sites (n=1040). Spectra data were acquired using a near infrared spectrometer BUCHI at Laboratoire d'Analyses des sols (LAS), Arras. The granulometric fractions and chemical properties measurements are available with their uncertainties. The tables of NIR spectra and chemical analysis and granulometry of soils from Isère (n=28) and from Plaine_de_Versailles (n=99) locations were added. The details of the transformed NIR spectra table of Plaine_de_Versailles are available at https://doi.org/10.15454/LXKFAS.
DOI: 10.15454/9zqkk1
title: Inter-laboratory evaluation of the standard ISO 20130:2018 “Soil quality - Measurement of enzyme activity patterns in soil samples using colorimetric substrates in micro-well plates” – Supporting information

description: This document presents the supporting information (i.e. the global tables of results) obtained during the Inter-laboratory evaluation of the standard ISO 20130:2018 “Soil quality - Measurement of enzyme activity patterns in soil samples using colorimetric substrates in micro-well plates”, managed by the platform Biochem-Env.
DOI: 10.15454/cueho6
title: A stochastic process modelling of phyllochron : script and experimental data from the ITEMAIZE project

description: R script and data to implement the phyllochron model in Plancade et al (2021). See details in Readme.txt.
DOI: 10.15454/58syjv
title: INRAE's Walnut Genetic Resources Observation (Historical data 1965-2016)

description: Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. In this work, historical data have been collected thanks to the team of the late Eric Germain, former head of breeding program at INRAE of Bordeaux from 1977 to 2007 and current data have been collected in the two French walnut experimental stations of Creysse and SENuRA. These data have been processed in order to assess the phenotypic variation among 150 accessions of the 259 accessions of the INRAE's Walnut Genetic Resources. Phenotypical data have been collected for a period from 1965 to 2016, with a majority of data between 1989 and 2016. All accessions are grafted trees mostly located in the arboriculture experimental unit in Toulenne (latitude 44°34’37.442’’N – longitude 0°16’51.48’’O), near Bordeaux (France). For some accessions, several data have been also available from the two French walnut experimental stations of Creysse (latitude 44°53’16.529’’N – longitude 1°36’23.838’’E) and SENuRA (latitude 45°8’38.565’’N – longitude 5°17’34.323’’E). The dataset consists in the raw phenotypic datafile and the three climate datafiles of the three sites of Toulenne, Creysse and SENuRA, all in "tab" format.