cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/fhpjh5
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Dataset overview This dataset provides: a non-redundant high-quality catalog of 13.6 million genes 30,031 Metagenome-Assembled Genomes (MAGs) 2,420 Metagenomic Species Pangenomes (MSPs) This dataset can be used to analyze shotgun sequencing data of the chicken caecal microbiota. How to use this dataset To perform taxonomic, functionnal and strain level profiling with this dataset, we suggest using Meteor. Methods Data sources This dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174). Sequencing data QC and metagenomic assembly First, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed. MAGs recovery MAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness &lt; 70% or contamination &gt; 5% or N50 &lt; 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%). Non-redundant gene catalog Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives. MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer. MAGs and MSPs taxonomic annotation Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs. Construction of the phylogenetic tree 39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
DOI: 10.15454/fqyam8
title: Données carbone sol du projet Life PTD

description: Ce dataset publie les données nécessaires au calcul du stock de carbone du sol de 35 parcelles situées dans des exploitations agricoles gérées en pâturage tournant dynamique dans la région de la Gâtine (département des Deux-Sèvres). Les prélèvements de sol de chaque parcelle ont été effectués à deux dates: 2015 (ou 2016) et 2019 (ou 2018). Les données permettent de calculer les stocks de carbone du sol et la vitesse de stockage entre les deux dates (FAO, 2019: « Measuring and modelling soil carbon stocks and stock changes in livestock production systems ». Guidelines for assessment (version 1)). Sur chaque parcelle, les prélèvements ont été effectués en 3 zones jugées représentatives (A, B, C), géoréférencées. Les prélèvements de sol ont été effectués sur trois horizons: 0-25 cm, 25-50 cm et 50-75 cm (lorsqu'il était possible d'atteindre cette profondeur). Sur chaque zone A, B, C, quatre prélèvements à la tarière et un prélèvement à la bêche (0-25cm) ont été effectués. Les 4 prélèvements à la tarière de chaque zone et chaque profondeur ont été rassemblés, séchés, broyés, tamisés et leurs teneurs en C et N total ont été analysées par méthode Dumas. Les prélèvements bêche (0-25cm) et tarière pour les horizons en dessous (25-75cm) ont permis la détermination de la densité apparente totale, de la densité apparente de la terre fine et des graviers et cailloux (résidu broyage &gt;2mm), ainsi que la proportion de gravier et cailloux du prélèvement de sol. Le protocole de prélèvement et de traitement des échantillons est décrit plus en détail dans la publication Lemoine et al., 2021 (Fourrages 248, pp1-10) et dans le document de synthèse du projet Life PTD (https://drive.google.com/file/d/1TXlzQOPlhsuPn9o0kx-Yuf_SxjnjAGcp/view).
DOI: 10.15454/g2rx0l
title: Cicada sampling in Corsica to assess Xylella fastidiosa prevalence

description: This dataset contains raw cartographic data of cicada sampling in Corsica for the assessment of Xylella fastidiosa prevalence.
DOI: 10.15454/glauqa
title: Ajout d'un jeu de données ou Dataset

description: Documentation en français pour accompagner les chercheurs dans le dépôt de jeu(x) de données
DOI: 10.15454/hhafzf
title: Firmness data

description: Raw data and preparation R scripts of the firmness analysis on apple sticks (raw and cooked) studied in the Pomcuite project (INRAE TRANSFORM internal funding ANS). This dataset contains : - the R Markdown file giving details on the raw dataset and the analysis scripts - the PDF processed from the R Markdown - the data set in CSV format
DOI: 10.15454/kef0yw
title: Typologie des espaces ruraux et des espaces à enjeux spécifiques (littoral, montagne et DOM)

description: Base de données communales ou cantonales de la typologie des campagnes françaises produite en 2011 par les auteurs pour la DATAR. La base inclut les données statistiques utilisées pour le traitement ainsi que les résultats.
DOI: 10.15454/f6vspy
title: Individual records of ultrasound examination for 850 salmon parrs captured in the river Oir

description: Individual records of date and hour of capture, body size, age, maturation status as defined by phenotypic observation and ultrasound examination for 850 salmon parrs captured in the river Oir
DOI: 10.15454/fugvmt
title: Annotation data about Multi Criteria Assessment Methods used in Microbiology and the Food Chain : the French National Institute for Agricultural Research (INRA-MICA) experience

description: This data article contains annotation data characterizing Multi Criteria Assessment Methods proposed in the scientific literature by INRA researchers belonging to the Social Science, Agriculture and Food, Rural Development and Environment department. Those fundamental and applied microbiological researchs aim to understand the functioning of micro-organisms and microbial ecosystems so that they can be better exploited, mastered or controlled.
DOI: 10.15454/gjg5w5
title: RPG complété 2019 département 22

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 22. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/gkfoeh
title: Model and data related to the publication "A model to analyze the post-prandial nutrient concentration in the plasma of pigs"

description: Statistical model (in R) and example data related to the publication "A model to analyze the post-prandial nutrient concentration in the plasma of pigs" to be published in the journal animal - open space.
DOI: 10.15454/h5rltp
title: Tree NSC, RAP and climate data

description: Data used for the systematic review performed in the paper by Zhang et al., (2022), American Journal of Botany
DOI: 10.15454/gerb6u
title: RPG complété 2018 département 40

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 40. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/gr5efs
title: Labeled Entities from Social Media Data Related to Avian Influenza Disease

description: This dataset is composed of spatial (ie. location) and thematic entities (ie. disease, symptoms, virus) concerning avian influenza in social media textual data, in English. It was created from three corpora: - The first one is composed of 10 transcriptions of YouTube videos and 70 tweets annotated manually by an annotator. - The second corpus is composed of the same textual data as corpus 1 but annotated automatically with Named Entity Recognition (NER) tools. These two corpora are create to do an evaluation of the NER tools and apply them to a larger corpus. - The third corpus is composed of 100 transcriptions of YouTube videos automatically annoted with NER tools. The aim of the annotation task was to recognize spatial information, as the name of cities and epidemiological information, as the name of diseases. An annotation guideline was created in order to have an unified annotation and help the annotators. This dataset can be used to train or evaluate natural language processing approaches such as specialized entity recognition.
DOI: 10.15454/i46kx3
title: RPG complété 2019 département 94

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 94. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/io9xf2
title: MPM16A.MA2025.WorkingSet.Aggressivity

description: Bien-être du cheval de sport : recherche d'une signature transcriptomique du niveau d'agressivité L'étude concerne 18 chevaux de sport, 9 chevaux non agressifs et 9 chevaux agressifs. Chaque cheval est caractérisé par un score d'agressivité. L'ARN a été extrait à partir du sang total afin de réaliser une analyse transcriptomique. Le but du projet est d'identifier les gènes marqueurs de l'agressivité chez le cheval ainsi que les voies métaboliques dans lesquelles ils sont impliqués.
DOI: 10.15454/gmrgpo
title: Quantifying anthropogenic effect on S. cerevisiae vineyard metapopulation diversity

description: This dataset contains all genotypes files used in the manuscript for various genetic analyses.
DOI: 10.15454/hlqkdj
title: Echelle de notation du débourrement d'espèces forestières

description: Cet outil excel associe une échelle de notation phénologique du débourrement des résineux (11 pins + 7 autres résineux) et 14 feuillus. Il s'inspire de l'échelle de notation BBCH et contient une description de chaque stade associé à une photo.
DOI: 10.15454/j9rn5s
title: PlantSyntenyViewer Legumes submission file

description: Submission file of Legumes botanic family (16 proto-chromosomes) in PlantSyntenyViewer
DOI: 10.15454/g1ci6d
title: An appraisal of the role of compositional and ripening parameters on CO2 diffusivity in semi-hard cheese - CO2 diffusivity in semi-hard cheese in relation to age

description: value unavailable
DOI: 10.15454/gfbdl6
title: A shiny application to visualize the evolution of thermal comfort of dairy cows

description: A shiny interface has been developped to assist in the visualization and comparison of maps of the annual number of days that dairy cows are in qualified no-stress, mild stress, moderate stress, severe stress and emergengy conditions. A first tab informs about the climatic data and the calculations made. A second tab allows the user to navigate through the data by choosing a simulation exercise, a THI calculation, a thermal comfort class and one of the following displays : 1) the comparison of three RCP with the same time horizon or 2) the comparison of four time horizons with the same RCP.
DOI: 10.15454/gwl0gp
title: Genomes assemblies and annotations of some Elopomorpha and Osteglossomorpha fish species

description: This dataset contains the whole genome assemblies and their annotations for seven Elopomorpha (eel, tarpon, bonefish, moray eel, Atlantic conger, ...) and one Osteglossomorpha (goldeye) species that were used to resolve the phylogenetic relationships of the early-branching teleost clades. These whole-genome analyses converged into a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (bony-tongues) as sister groups with largest lineage (clupeomorpha) as outgroup.
DOI: 10.15454/hcfrwq
title: Data associated to the paper "Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density data" (Boushaba et al, 2018)

description: This data file consists of genotypes of 732 animals for 41183 markers. The animals belong to 23 populations. The file is a "csv" file where the field separator is ";". First line is a header. First column is the population identification the animal belongs to; following colums is the genotype of the animal for the corresponding markers. "0" or "2" code for homozygosity; "0.5" codes for heterozygosity; "NA" codes for missing values
DOI: 10.15454/hgonzv
title: Carbon and Nitrogen leaf traits on 'Golden Delicious' apple trees

description: This dataset was built on ‘Golden Delicious’ apple trees with either high or low crop loads. For these trees, we concomitantly assessed the impacts of intercepted light and crop load on within-tree spatial variability in carbon- and nitrogen-related traits. Furthermore, we analyzed fruiting and nonfruiting shoots to clarify the scale (shoot or tree) at which the source:sink relationships regulate leaf trait acclimation to a light gradient. This dataset was published first in the Journal of Experimental Botany (volume and issue to be updated). See the ReadMe.txt file accompanying this dataset for details on variable units and brief description of the methods.
DOI: 10.15454/hipdpz
title: SICLIMA : Système d’information de données climatiques maillées

description: SICLIMA (Système d’information de données climatiques maillées) est une application web à destination des agents INRAE qui comporte deux parties : - extraction de données pour choisir un jeu de données et préparer des fichiers climatiques de données maillées, - calcul d’indicateurs pour calculer des indicateurs agro-climatiques et éco-climatiques à partir de données maillées choisies dans la partie « extraction de données ». Cette application est portée par l’unité de service AgroClim.
DOI: 10.15454/htbbdx
title: RPG complété 2018 département 59

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 59. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020
DOI: 10.15454/iwetbg
title: RPG complété 2018 département 67

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 67. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/j1qdpm
title: Species-level root trait data (ECOPICS)

description: Species-level root trait data
DOI: 10.15454/gcon7e
title: Longitudinal analysis of the microbiota composition and enterotypes of pigs from post-weaning to finishing

description: Longitudinal analysis of the microbiota composition and enterotypes of pigs from post-weaning to finishing. The raw sequences of 16S rRNA genes are stored on ncbi. SubmissionID: SUB6518439 BioProject ID: PRJNA588139
DOI: 10.15454/gmwb8q
title: Consumer perception data about food packaging functionalities for fresh strawberries - Plastic with plastic film consumers’ arguments
DOI: 10.15454/hiibkw
title: A collection of 3D images of Arabidopsis thaliana embryos

description: This dataset contains ~100 3D confocal images of Arabidopsis thaliana embryos. Following mPS-PI staining of cellular walls, images were acquired with a Zeiss LSM 710 confocal microscope using a 40x objective and digitized as 8-bit 3D image stacks with a near-to-optimal sampling of 0.17 x 0.17 x 0.35 µm^3. More details on sample preparation and image acquisition are available in the associated manuscript (see Related Publication). Embryonic stages vary between 1C and early heart stage (~256C). Images are stored either in LSM or in TIF file formats.
DOI: 10.15454/ihelym
title: Detailed soil chemical properties - Laboratory experiment

description: Detailed soil chemical properties measured in the laboratory inoculation experiment. In this experiment, we extracted soil columns from an arable and secondary woodland and used a third unstructured loamy soil as a control. We sterilized these three soils to remove microbial communities and then inoculated the tops of sterilized soil columns with soil from the secondary woodland or the arable field sites. Control columns of all soil types were not inoculated. In a fully-crossed design, we planted two species possessing distinct root system morphologies: Brachypodium sylvaticum (fibrous system with many thin and fine roots) and Urtica dioica (taproot system with few fine roots). After four months, microbial communities (in bulk and rhizospheric soil) and aggregate stability were measured, along with root traits. In both the field and laboratory experiments, bacterial (16S) and fungal (ITS) diversity was determined using high throughput sequencing.
DOI: 10.15454/ja42uu
title: Analyses phylogénétiques et clonales de châtaigniers _ Thèse C. Bouffartigue

description: Analyses microsatellites de châtaigniers cultivés réalisés dans le cadre de la thèse de C. Bouffartigue : analyses clonales et phylogénétiques.
DOI: 10.15454/jgwc5a
title: Dataset of a two-year field experiment on the dynamics of Zymoseptoria tritici populations in wheat cultivar mixtures : interseason period.

description: The data that support the findings of this study (2022-04-20)
DOI: 10.15454/kc3wao
title: Electrochemical analysis of a microbial electrochemical snorkel in laboratory and constructed wetlands - biom file

description: biom file
DOI: 10.15454/gwkrky
title: SNP4OrphanSpecies: A bio-informatic pipeline to isolate robust molecular markers for phylogeny, phylogeographical and population genetic studies in non-model species.

description: This pipeline performs a de-novo genome assembly, identifies single copy genes in the genome, and designs several pools of pair of primers for amplifying regions of these genes in multiplex. The pipeline is implemented in a SnakeMake workflow and uses Illumina data for the de-novo genome assembly. It was tested for Diplodia sapinea, a fungal pathogen causing severe infections in numerous conifers.
DOI: 10.15454/ih2eri
title: Dataset on the Life Cycle Assessment of 80 pizzas representatives of the French retail market

description: Life-cycle assessments (LCA) were conducted for 80 different pizzas representative of the French retail market to study the possible differences in environmental impact between various items belonging to the same food product category. The LCAs were conducted using the "EF 3.0 Method (adapted) V1.00 / EF 3.0 normalization and weighting set" on SimaPro software. Most of the data used were taken from the AGRIBALYSE 3.0 and EcoInvent 3.6 databases. The dataset contains details on products, life-cycle inventories (LCI) and LCIA results.
DOI: 10.15454/h5c9zs
title: VFA functionalization through the addition of hydroxylic group by a bioelectrochemical approach

description: VFA functionalization by the addition of hydroxylic group in the acidic chain would allow consecutive production of alternative biopolyesters else than microbial PHAs. In particular, the addition of the -OH function in the terminal C (omega-position) was explored by testing the activity on octanoic acid of two alkane/fatty acids degrading bacteria in a bioelectrochemical system. Two different bacterial strains were used for bioconversion tests: Pseudomonas oleovorans ATCC® 29347 and Bacillus megaterium ATCC® 14581. Dedicated bioelectrochemical reactors (BES) were designed and set up: they consisted of two gastight borosilicate glass bottles (total volume of 420 mL each) separated by a 3 cm2 cross-sectional area through a Nafion® 117 proton exchange membrane (PEM). Two different types of monooxygenases capable to hydroxylate alkanes and fatty acids were used. While in open circuit conditions (i.e., controls with no potential applied) both strains produce only traces of difunctional intermediates of octanoic acid degradation, a significant increase of the octanoic acid bioconversion into difunctional intermediates could be obtained with the application of a cathodic potential of -0.4 V vs. SHE, in particular with P. oleovorans and under resting cells conditions (macronutrients limitation). However, no exploitable results were obtained so far, since the application of bioelectrochemical systems to provide reducing power for the hydroxylation of VFA chain was not effective enough and no significant hydroxylated acid production was observed.
DOI: 10.15454/jjz3qq
title: Duck Liver RNA Sequencing

description: Liver RNA-seqencing of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed
DOI: 10.15454/m8sayh
title: Data for: "Integration of genomic selection into bread wheat breeding schemes: a simulation pipeline including economic constraints." Sarah Ben-Sadoun, Aline Fugeray-Scarbel, Jérôme Auzanneau, Gilles Charmet, Stéphane Lemarié, Sophie Bouchet

description: This dataset supports the study of Ben-Sadoun et al. about intagration of genomic selection into simulated wheat breeding schemes. It includes genotypes of the winter wheat lines.
DOI: 10.15454/hr9kux
title: The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming

description: this dataset provides the results of the de novo assembly and annotation of RNA-seq data from the mycoheterotrophic orchids Neottia nidus-avis and Epipogium aphyllum. For each species, a gff file, an annotation file and an expression count table is provided. The raw sequencing data is available from the NCBI Bioproject PRJNA633477.
DOI: 10.15454/irdmyu
title: Article Data - Environmental impacts and their association with performance and excretion traits in growing pigs – in Frontier in Veterinary Science, 2021

description: This dataset provides the data used in the article by A.N.T.R. Monteiro, L. Brossard, H. Gilbert, J.Y. Dourmad, in Frontiers of Veterinary Sciences (2021), entitled "Environmental impacts and their association with performance and excretion traits in growing pigs ". These data were obtained by simulation according to the procedure described in : A.N.T.R. Monteiro, F. Garcia-Launay, L. Brossard, A. Wilfart and J.Y. Dourmad. (2016). Effect of feeding strategy on environmental impacts of pig fattening in different contexts of production: evaluation through life cycle assessment. J Anim Sci 94, 4832–4847.
DOI: 10.15454/ixfdki
title: Background data for the identification of an ideal biorefinery technology for a given region

description: This data set is supplementary information to a study aiming to identify the ideal biorefinery technology for a given region. Biotechnologies are assessed by a combination of techno-economic assessment (TEA) and territorial metabolism life cycle assessment (TM-LCA). Three technology variations for anaerobic digestion (AD) were assessed at two different scales (200 kW and 1 MW) and for two different regions.
DOI: 10.15454/j1vqdo
title: Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes

description: These files includes normalized values for RNAseq data, Fold change Ratio and Gene set enrichment analysis as well as ecophysiological measurement and correlation analysis described in the publication entiled "Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes".
DOI: 10.15454/jqni7g
title: Ajout d'un dataverse

description: Logigramme et document expliquant la marche à suivre pour ajouter un dataverse dans les entrepôts institutionnels (IRD, INRAE et CIRAD)