cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/k9dqpa
title: Descriptive variables of 11,004 roots from 69 Pinus pinaster root systems excavated and digitized in 3D

description: This data set include 11004 roots from 69 coarse root systems of Pinus pinaster trees. These trees belong from the same local provenance of P. pinaster trees germinated in the field and grown in the same area (forest range of the “Landes de Gascogne” in Southwest France).These trees were aged 3, 4, 6, 13 and 50 years. The description of excavation procedure of coarse root system can be found in Danjon et al. 2005 and the measurement procedure is described in Danjon and Reubens (2008) and Saint Cast et al. (2019). The four root traits selected as classifiers, and computed for each root axis (Id Axis), included three geometrics and one vigour traits, as follows: - CSAco : Basal cross-sectional area (CSA) measured 2 cm from the base of the axis, divided by the tree cross-sectional area at the collar (co) to consider the axis size. - Tropism intensity is computed as the ratio of the depth difference between the two ends of each excavated root over the length of the root axis. Roots with tropism close to 0 show a high plagiotropism (trend to bend horizontally), those with tropism close to 1 have a positive gravitropism (trend to bend downwards), and those with tropism close to -1 have a negative gravitropism (trend to bend upwards). - Parent root tropism intensity is the tropism intensity of the parent root of the axis. - Branching angle is estimated using a vector method. It was defined for all roots from two 10-cm long vectors to describe both the parent root direction before the branching point and the daughter root direction after the branching point (see Fig. 1 in Saint Cast et al. 2019). The branching order is also given by root axis. Two calculated attributes can be found in this data set: the root type classification obtained by clustering and the final root type classification (Saint Cast et al., submitted) as: Order1: taproot OverSize: Oversize roots were mainly horizontal roots branching from the stump or secondary sinkers in the oldest root systems. Hh: Horizontal roots branching from horizontal roots Hv: Horizontal roots branching from vertical roots Vh: Vertical roots branching from horizontal roots Vv: Vertical roots branching from vertical roots Danjon F, Fourcaud T, Bert D (2005) Root architecture and wind-firmness of mature Pinus pinaster. New Phytologist 168:387–400. https://doi.org/10.1111/j.1469-8137.2005.01497.x Danjon F, Reubens B (2008) Assessing and analyzing 3D architecture of woody root systems, a review of methods and applications in tree and soil stability, resource acquisition and allocation. Plant and Soil 303:1–34. https://doi.org/10.1007/s11104-007-9470-7 Saint Cast C, Meredieu C, Défossez P, et al (2019) Modelling root system development for anchorage of forest trees up to the mature stage, including acclimation to soil constraints: the case of Pinus pinaster. Plant Soil 439:405–430. https://doi.org/10.1007/s11104-019-04039-4
DOI: 10.15454/mhdzxm
title: R function to run Clapas algorithm

description: Le script R nommé clapas.R permet d'utiliser l'algorithme de Clapas tel que conçu par Jean-Marc Robbez Masson dans sa thèse de 1994 : "Reconnaissance et délimitation de motifs d'organisation spatiale, application à la cartographie des pédopaysages". Il s'agit d'une suite de fonctions qui rassemblent tous les éléments de l'algorithme de Clapas. Cette suite est livrée avec un tutoriel et un jeu de données test, disponible sur demande, pour s'approprier son utilisation.
DOI: 10.15454/nf1glg
title: Morphological and physiological traits of sugar beet seeds from a wide genetic diversity

description: Dataset obtained by high throughput phenotyping of seed morphology, germination and seedling heterotrophic growth traits on sugar beet genotypes (2020-09-14)
DOI: 10.15454/o07sxq
title: Japanese plum small RNA sequencing

description: Deep sequencing of non-transgenic and eIFiso4G-silenced transgenic Japanese plum (Prunus salicina) small RNA libraries. Cultivar Angeleno. Files are in fastq format, compressed in gz
DOI: 10.15454/pcopyw
title: Physico-chemical dataset from an in situ mesocosm experiment simulating extreme climate events in Lake Geneva (MESOLAC)

description: This dataset corresponds to the physico-chemical parameters data series produced during the MESOLAC experimental project. The presented dataset is composed of: 1. In situ profiles (0-3m) of temperature, conductivitivy, pH, oxygen (concentration et saturation). 2. In situ measures of light spectral UV/VIS/IR irradiance (300-950 nm wavelength range) taken at 0, 0.25, 0.5, 1, 1.5, 2 and 2.5m. 3. Laboratory chemical analysis of samples collected at 0 and 2 m (conductivity, pH, total alkalinity, NH4, NO2, NO3, Ntot, Npart, PO4, Ptot, Ppart, Ctot, Cpart-org, Cpart-tot, Cl, SO4, SiO2). 4. Laboratory analysis of pigments extracted from samples collected at 0 and 2 m (Chla, Chlc, carotenoids, phaeopigments). The experiment consisted of nine pelagic mesocosms (about 3000 L, 3m depth) deployed in July 2019 in Lake Geneva near the shore of Thonon les Bains, France, to simulate predicted climate scenarios (i.e. extreme events) and assess the response of pelagic communities, ecosystem functioning and resilience. The experiment lasted 4 weeks (July 4 – 30, 2019) and the design included three treatments each replicated 3 times: a control treatment (no treatment applied – named C) and two different treatments simulating extreme weather events of different intensities. The high intensity treatment (named H) aimed at reproducing short and intense weather events such as violent storms. It consisted of a short-term intense stress applied during the first week, with high pulse of dissolved organic carbon (DOC 5x increased concentration compared to the control), light reduction up the 95% and water column manual mixing daily for 15 mins. The medium intensity treatment (named M), simulated less intense and more prolonged exposures such as during flood events. It was maintained during the 4 weeks and consisted of 1.5x increased concentration of DOC compared to the control, light reduction up to 70 % and water column manual mixing daily for 5 mins. During the experiment, physical parameters were measured twice a week and samples were collected at the same date at the depth of 0 and 2m for subsequent chemical laboratory analyses. These data are presented in the dataset file, ordered by sampling event (numbered from S1 to S8), treatment (Control-C, High-H and Medium-M) and replicates (1 to 3). For each time point the measured parameters are listed in columns, missing data are marked as NA.
DOI: 10.15454/q0xvvd
title: CIRCASA DELIVERABLE D2.3: “Synthesis report on knowledge demands and needs of stakeholders”

description: In this report, we examine knowledge gaps identified by stakeholders. In this way, the find-ings support the creation of an international strategic research agenda for SOC, a central envisioned outcome of the CIRCASA project.
DOI: 10.15454/nkrweo
title: Data on winged insects in melon crops in southeastern France

description: Insect count data obtained in eleven field trials conducted between 2010 and 2021 in southeastern France. Winged insect abundances were monitored daily within melon crops during 8 to 11 weeks in May-July using a suction trap or a yellow pan trap. Aphids were identified under a stereomicroscope.
DOI: 10.15454/ntfycc
title: Shad spawning and energy expenditure

description: This dataset is from an experiment in which nine female Allis shad (Alosa alosa) were tagged with loggers (WACU, Atesys-Montoux) which recorded tri-axial acceleration (8g, 50Hz), temperature (1Hz) and pressure (1Hz) during the 2017 spawning season in the Nivelle river. A characteristic acceleration pattern was used to detect spawning acts. Acceleration on the lateral axis was used to compute tail beat frequency, which coupled with temperature, was fed in a bioenergetic model to compute energy expenditure and mass loss. Pressure was coupled with pressure recorded near the river to compute depth. The static component of acceleration was used to compute the angle of the dorsally attached logger with the vertical. The dataset is composed of four files containing: 1) The exact timing of each spawning act of each shad. 2) The number of spawning acts performed by each shad on each night of the season, with water temperature during the night. 3) For each shad and each 8h period of the spawning season, the angle between the logger and the vertical (°), the angle shift to the next period (°), the mean temperature (°C), the mean pressure (hPa), the mean depth (cm), the mean tail beat frequency (beat/s), the cumulated energy expenditure (kJ) according to the bioenergetic model, the mass (kg) according to the bioenergetic model, an indicator variable whether the fish had been tagged for less (1) or more (0) than three days. 4) For each shad, biometric measures (length, mass at initial capture and at death, ovary mass at death), timing of capture and death, as well as variables computed from acceleration data (number of spawning acts, number of nights with at least one spawning act, total energy spent, predicted mass at death, angle of the logger at initial capture and at death). The dataset is accompanied by a Rmd script of the analyses performed on the dataset for the article found here: https://doi.org/10.1101/436295
DOI: 10.15454/oedaus
title: R-Syst: a network providing curated molecular databases and data analysis tools for taxonomy and systematics (Prokaryotes and Eucaryotes)

description: R-Syst network deals about systematic and (meta) barcoding and provide curated molecular databases for species identification and provide tools for diagnosis and inventories. The stakes are at the same time a precise diagnosis of organisms of interest (for example pathogens detection), and to produce an inventory as complete as possible of various communities like microalgae, fungal communities, trees of French Guyana, bacteria, nematods and viruses (see http://www.rsyst.inra.fr/).
DOI: 10.15454/oqdgdl
title: RPG complété 2019 département 47

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 47. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/omdlod
title: Genoscapist

description: Genoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations.
DOI: 10.15454/pimphz
title: Bread wheat (T. aestivum) variability: Phenotypic and genotypic data from 75 varieties

description: The dataset provides various types of information on traits related to bread wheat grain quality. The dataset describes 75 T. aestivum accessions grown in two replicates at two locations in France, Estrées-Mons (EM) and Clermont-Ferrand (CF). Accessions are classified into three categories depending on the year of their release for modern or old varieties or as landraces. Their geographical origin is specified as well. In total, 300 samples are characterized. Row data are organised into eigth files. The first file describes the field trials and some plant and grain traits. Protein composition of wholemeal flours expressed as dry weight is available in the second file. The fourth file gives technological data of gluten and dough made from flour derived from each accession sample. The fifth file details the 34,746 markers genotyped with Axiom TaBW35K. A characterisation of starch is available in the sixth file. All variables are summarised and explained in the Variables.tab file. The list of accessions is available in the Material.tab file. The two last files consist in two protocols for the determination of wheat grain protein composition.
DOI: 10.15454/qyukwm
title: Durum Wheat

description: The durum wheat ontology (DURUM_WHEAT) is dedicated to the sustainability analysis of the durum wheat chain.Current data available on this ontology concern durum wheat quality criteria criteria used in different countries (Moisture content rate, chemical content, etc.). (OWL)
DOI: 10.15454/shzqbm
title: Dopamine pathway in the pea aphid

description: Raw data accompanying analyses of dopamine pathway in the pea aphid, in a preprint posted un BioRXiv.
DOI: 10.15454/qedx2v
title: Genotypic data and genetic map for Syrah x Grenache bi-parental grapevine population

description: This dataset, intended for QTL detection and genomic prediction, includes : 1) the SNP genotyping data, in vcf format, obtained by GBS in a grapevine bi-parental population, and the script for formatting the data before building the genetic map; 2) the script and custom R functions used for building the map; 3) the script for checking map quality; 4) the consensus genetic map generated from these data, both in R/qtl format and recoded into additive gene-dose. The population is a pseudo-F1 progeny of 188 offsprings of Vitis vinifera L. from a reciprocal cross between cultivars Syrah and Grenache, made at Vassal (French National Grapevine Germplasm Collection, Domaine de Vassal, 34340 Marseillan-Plage, France) in 1995. More details about this Syrah x Grenache (SxG) progeny can be found in Adam-Blondon et al. (2004) and Fournier-Level et al. (2009). SNP genotyping data are in the form of the vcf file obtained after SNP calling and filtering (see details below). All scripts are given as Rmd files including R and bash commands. Genetic maps were built with Carthagene and Lep-MAP3, and checked with custom R scripts and R/qtl.
DOI: 10.15454/qjjjzu
title: Software architecture for environnemental research observatories information systems: central component

description: Information systems have been developed to meet data management needs of environmental research observatories in order to make data available for scientific communities. Software architecture of these IS is structured around (i) a central component dedicated to generic functions shared by all IS and (ii) modular components specific to the environmental themes studied by the observatories. The creation of the IS is done by inheriting the core component and using the appropriate modular components. SI are developed with the Java language (version 8). The components are Java projects that follow the structuring of a "multi-module" Maven project. The web interfaces are developed by using the framework JSF with Primefaces user interface component library. Spring and Hibernate frameworks complete the development tools. PostgreSQL is the relational database management system used. Information system are developed by Eco-Informatics ORE INRA Team, AnaEE-France
DOI: 10.15454/sujjsq
title: Distribution of 4654 cows milk proteins among different milk fractions

description: The “milk fractions” dataset informs on protein location in a specific or several milk fractions.
DOI: 10.15454/nouqy2
title: Scripts and data of the genetic analysis of Syrah x Grenache progeny

description: R-scripts and data associated with the publication "Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine". Article abstract: Viticulture has to cope with climate change and decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a key lever to meet this challenge, and genomic prediction is a promising tool to accelerate breeding programs. Multivariate methods are potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and allowing the identification of positional candidate genes. To study both genomic prediction and QTL detection for drought-related traits in grapevine, we applied several methods, interval mapping as well as univariate and multivariate penalized regression, in a bi-parental progeny. We used a new denser genetic map, simulated two traits under four QTL configurations, and re-analyzed 14 traits measured in semi-controlled conditions under different watering conditions. According to our simulations, we recommend the penalized regression method Elastic Net (EN) for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than interval mapping for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using experimental data, penalized regression methods proved as very efficient for intra-population prediction whatever the genetic architecture of the trait, with accuracies reaching 0.68. These methods applied on the denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. Overall, these findings provide a strong evidence base for implementing genomic prediction in grapevine breeding. Scripts and data associated with the SNP genetic map of Syrah x Grenache progeny are available at: https://doi.org/10.15454/QEDX2V. Raw phenotypic data of Syrah x Grenache progeny in the phenotypic platform PhenoArch are available at: https://doi.org/10.15454/YTRKV6.
DOI: 10.15454/pa6duz
title: Frimouss Clementine

description: Fruit features : Fruit growth has been measured from anthesis to harvest on plants with regular crop load. The anthesis date have been observed in order to describe the data collected according to days and degree-days from anthesis. Fruit growth has been monitored using non-destructive measurements that measure fruit dimensions (diameters, length) and using destructive sampling to estimate the fruit fresh and dry mass accumulation. Metabolites : Biomass compounds and accumulated metabolites that constitute the major carbon sinks have been quantified and their contents expressed on fresh- and dry weight bases. Total proteins, nucleic acids and starch have been quantified via spectrophotometric or fluorimetric measurements after specific extraction, preparation and calibration. Culture location : INRA UE 1398 CITRUS (INRA San Giuliano, Corse)
DOI: 10.15454/pijxcr
title: Life Cycle Assessment of pig production for eco-friendly feed formulation and on-farm feed production

description: This dataset provides inputs, Python code and outputs for the environmental evaluation of pig production performed in the article by de Quelen el al. in Frontiers of Veterinary Sciences, entitled "Eco-friendly feed formulation and on-farm feed production as ways to reduce the environmental impacts of pig production without consequences on animal performance". The Python code is built in order to be run in any PC computer with Windows 10, equiped with either Pyzo or PyCharm environments.
DOI: 10.15454/py9kdc
title: Data for replication : Natural variation of Arabidopsis thaliana responses to Cauliflower mosaic virus infection upon water deficit

description: Data for replication of Figures.
DOI: 10.15454/qblsxp
title: A ready-to-use database for DADA2: Diat.barcode_rbcL_263bp_DADA2 based on Diat.barcode v9

description: This database is an adaptation for DADA2 of Diat.barcode v9. Length of sequences is 263 bp ------------------------- Rimet, Frederic; Chonova, Teofana; Gassiole, Gilles; Gusev, Evgenuy; Kahlert, Maria; Keck, François; Kelly, Martyn; Kulikovskiy, Maxim; Maltsev, Yevhen; Mann, David; Pfannkuchen, Martin; Trobajo, Rosa; Vasselon, Valentin; Wetzel, Carlos; Zimmermann, Jonas; Bouchez, Agnès, 2018, "Diat.barcode, an open-access barcode library for diatoms", https://doi.org/10.15454/TOMBYZ
DOI: 10.15454/s0drr1
title: Données surfaciques du Référentiel Régional Pédologique de la carte des pédopaysages du département des Landes en format DoneSol.

description: Richer-de-Forges A.C. (2013) Base de données du Référentiel Régional Pédologique du département des Landes à 1/250 000, en format DoneSol3.4. INRA InfoSol.
DOI: 10.15454/mbmoqc
title: Orthofinder rooted species tree

description: Rooted phylogenomics species tree performed by Orthofinder on the 63 species, in Newick format. An annotated version of the tree in PDF format, produced with iTOL is also available.
DOI: 10.15454/myhbsi
title: Synaqua - Datatable giving for each sample the number of reads per ASV and the ASV taxonomic identity

description: Supplementary data S4 of the paper "Competition between microbial species in freshwaters? Diatom metabarcoding shows that environmental filtering and mass effect are stronger in a large lake."
DOI: 10.15454/pa1cw6
title: Synthetic dataset used for validating srnadiff

description: This dataset contains all the mapped reads generated to validate the tool srnadiff on a synthetic dataset, where the "truth" is known. Samples 1 to 6 are supposed to be one condition, and samples 7 to 12 are the other condition. The file "diffVal.bed" contains the differentially expressed regions.
DOI: 10.15454/pw4f9p
title: RPG complété 2019 département 93

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 93. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/qvfy62
title: Minimal Inhibitory Concentration (MIC) of Carvacrol

description: This document describes the minimal inhibitory concentration of the carvacrol (antimicrobial compound) that will be used to enhance the conservation of falafel. This table is in connection with the deliverable 3.2. The objective of the deliverable 3.2 was to identify and characterize the active functionalities, namely antimicrobial compounds and oxygen scavengers, and the intelligent functionalities, namely the RFID based biosensor, to be included in packaging in order to improve and control the storage of targeted products packaged with the new PHBV packaging. To achieve the active functionalites objective (regarding antimicrobial compounds), the best anti-microbial molecules were selected depending on their Minimum Inhibitory Concentration (MIC), their Admissible Daily Intake (ADI) and odor threshold value (if any). The quantity to be added in the packaging material was calculated thanks to the modeling. Analysis of the literature and the study of the exposure assessment have permitted to select the carvacrol for falafel. The carvacrol is a molecule found in several aromatic plants and more specifically in the essential oil of oregano, thyme, marjoram and summer savory. Several articles show an antimicrobial effect of carvacrol, included microorganisms that belong to the Gram-positive bacteria, Gram-negative bacteria, molds and yeasts. The minimum inhibitory concentration (MIC) of carvacrol depends on the microorganisms’ target. In this present table, we choose to gather MIC values of carvacrol in vapor phase because the molecule is expected to be released in the headspace packaging in its volatile form. Indeed, carvacrol is a volatile molecule which evaporates easily and its vapor phase has shown antimicrobial activity against food-born bacteria and fungi.