cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/azns3a
title: Floristic surveys and environmental data of gaps and undisturbed forests

description: These data were taken within the framework of the project "Optimisation des travaux sylvicoles post-tempête". Details on the project are available online at https://www6.nancy.inrae.fr/silva/Equipes-de-recherche/ForeSTree/Projets-Recherche/Post-tempete-2017-2020 . The file "data_flore" present exhaustive floristic surveys carried out in 2002 (G02) and 2018 (G18) in 139 20m-diameter plots installed in forest openings created by the 1999 storms in France. For each plot, environmental data (temperature, elevation, surface area...) are also available. In 2018, floristic surveys were also conducted in 139 20m-diameter plots installed in undisturbed forest (UF18) close to each studied opening. The file "EcoPlant_VI_temperature" present species indicator value for temperature from EcoPlant database. The calculation method is described in the following article: "Gégout, J.C. (2006). Distribution et caractère bioindicateur des espèces végétales forestières françaises vis-à-vis du sol et du climat. Ecole Nationale du Génie Rural des Eaux et des Forêts (ENGREF), Nancy. Habilitation à Diriger les Recherches de l’Institut Polytechnique de Lorraine, spécialité : Sciences Agronomiques. 109 p."
DOI: 10.15454/bbiwc9
title: Pratiques culturales et problèmes malherbologiques en semis direct sous couvert. Enquête sur un réseau d'agriculteurs en Bourgogne-Franche-Comté: 2018-2019

description: Les données présentées dans ce document décrivent les pratiques culturales et les problèmes malherbologiques enquêtés sur 176 parcelles en agriculture de conservation de la région Bourgogne-Franche-Comté (et du département de la Haute Marne). Les données ont été obtenues par le biais d’un questionnaire en ligne soit en 2018 (90 parcelles), soit en 2019 (86 parcelles). Les parcelles étaient, l’année où les données ont été demandées, soit en culture de blé tendre (Triticum aestivum L., 134 parcelles) soit en culture de soja (Glycine max L., 42 parcelles).
DOI: 10.15454/8kcnlu
title: RSSI measurements on B3-EM001-SC4 RAIN transponder

description: RSSI measurements on B3-EM001-SC4 RAIN transponder and associated environmental data
DOI: 10.15454/9puypn
title: High-frequency acquisition of stream chemical data on ORACLE observatory

description: Observational data from ionic chromatography and physico-chemical probes. All data is measured at high-frequency. Data have been collected during CRITEX/EQUIPEX project on the ORACLE observatory (INRAE). These data are free available on the BDOH database (https://doi.org/10.17180/obs.oracle).
DOI: 10.15454/aoatkg
title: Biomass of phytoplankton assemblages in Lake Geneva 1974-2010

description: Sampling has been continuously undertaken in the middle of the lake at the deepest point, once or twice a month. The studied environmental factors used in this study were selected based on previous analyses that emphasized their role on phytoplankton abundance: phosphorus concentration , water temperature , abundance of Daphnia sp. , and solar radiation (https://intranet.inra.fr/climatik_v2). Water temperature was measured with a thermometer from 1974 to 1998; a multiprobe was used after 1998. Dissolved phosphorus concentrations (P-PO43-) was measured at a series of discrete depths between the surface and the bottom of the lake, using colorimetric analyses and spectrophotometric assay according to a standardized protocol (AFNOR NF EN 1189). Water samples for estimating phytoplankton species and biomass were collected in the upper 10 m from 1974 to 2001; after 2001 in the top 18 m, using an integrating bell sampler. Phytoplankton identifications and cell counts were performed in sedimentation chambers under an inverted microscope. More than 400 cells were counted per samples. In this study, phytoplankton quantity was expressed in terms of biomass. Species biovolumes were derived from cell numbers and mean cell volumes using geometrical models. Finally, species biomass was computed considering a ratio of 1 µg per unit of volume. Daphnia sp. were sampled by a vertical tow from 50 m to the surface using a 200 µm plankton net. The zooplankton samples were preserved in a 5% buffered formaldehyde solution. Daphnia sp. were identified and individuals were enumerated in a 0.1ml sedimented zooplankton sub-sample. Abundances were given as the number of individuals per square meter. Phytoplankton functional groups were previously identified in Anneville et al. (2018).
DOI: 10.15454/aqjtbd
title: RPG complété 2018 département 91

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 91. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020
DOI: 10.15454/avzlia
title: RPG complété 2019 département 31

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 31. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/ay4lmt
title: BRC “Egg Parasitoids Collection” (EP-Coll)

description: The BRC “Egg Parasitoids Collection” (EP-Coll) aims to collect, characterize, maintain, investigate and share egg parasitoids’ strains, these organisms being useful for biological control, applied entomology and evolutionary ecology.
DOI: 10.15454/a15akv
title: Following the Adaptive Path of Fruit Tree Domestication using Population Genomics : the Case of Apricots

description: In this paper, we generated four high-quality genome assemblies, for the first time anchored on genetic maps for apricots, and we sequenced the genomes of 578 accessions from natural populations their whole range (Central Asia and China) and from the two main cultivated populations (European and Chinese cultivated apricots). Withe these data and other available data, we investigated the population structure and divergence history of apricot across Eurasia, as well as the domestication history of cultivated apricots and the selection footprints in genomes. Population structure inferences and approximate Bayesian computation indicated that Chinese and European apricots formed two differentiated gene pools with relatively high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow between wild and cultivated populations. We further detected genomic footprints of selection (i.e., selective sweeps and recurrent changes in amino-acids) in the two groups of cultivated apricots. As expected given the large effective population sizes and outcrossing in fruit trees, we found a relatively low proportion of the genome affected by selection. Different genomic regions showed footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits. Selection footprints appeared more abundant in European apricots, with a hotspot on chromosome 4, while admixture was much more pervasive in Chinese cultivated apricots. In both cultivated groups, the genes affected by selection had predicted functions involved in the perennial life cycle, fruit quality and disease resistance, and/or colocalized with previously mapped genomic regions associated with these functions.
DOI: 10.15454/atyobo
title: History of land uses over the period 2013-2019 in the Kervidy-Naizin watershed (Brittany, France)

description: The dataset provides the representation of an agricultural landscape located in the Kervidy-Naizin watershed (Brittany, north-western France). Data describe the landscape mosaic (in vector format) and the history of land covers over the period 2013-2019. Part of this landscape belongs to the long-term environmental research observatory AgrHys led by the French National Research Institute for Agriculture, Food and the Environment (INRAE, UMR SAS, Rennes) since 1993.
DOI: 10.15454/bgsmue
title: Slakestable : R package to explore raw data from the Slakes app

description: Le package "slakestable" permet de formater rapidement les données brutes issues de l'application pour smartphone "Slakes" (Fajardo et al., 2016). La fonction "tablecourbe" permet de créer une unique table contenant les coefficients a, b, c issues de l'ajustement sur la Gompertz des données brutes, ainsi que le SI600 pour chaque agrégat. Il est possible de concaténer les données par site.localisation par une moyenne ou une médiane avant ou après l'ajustement de l'équation de la Gompertz, deux tables indépendantes sont créées. Il est possible de les rassembler à l'aide de la fonction "jointurefeuilles".
DOI: 10.15454/bpjvvy
title: RPG complété 2019 département 56

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 56. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/cj09mo
title: RPG complété 2018 département 78

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 78. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/9sso46
title: RPG complété 2019 département 84

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 84. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/9x2dya
title: Case Study Interviews

description: For the development of the generic assessment framework in WP1, a collaborative work together with WP4, WP5 was done in order to gather information and issues in the six FAIRCHAIN Case Studies. For this objective, a structured process of guideline-based interviews in two stages was carried out with each case study. The documentation of these interviews is available on the FAIRCHAIN-Sharepoint. 1.Interview Stage: Austria: 15th Jan. 2021; Belgium: 19th Jan. 2021; France: 15th Jan. 2021 ; Greece: 19th Jan. 2021; Sweden: 25th Jan. 2021; Switzerland: 26th Jan. 2021 2.Interview Stage: Austria: 24th June 2021; Belgium: 11th June 2021; France: 20th April 2021; Greece: 7th of May 2021; Sweden: 3th of June 2021; Switzerland: 7th of May 2021
DOI: 10.15454/a96tw6
title: PlantSyntenyViewer Cucurbitaceae submission file

description: Submission file of Cucurbitaceae botanic family (22 proto-chromosomes) in PlantSyntenyViewer
DOI: 10.15454/aabgo7
title: Data for: Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality

description: This dataset supports the study of Bensadoun et al. about multi-trait genomic prediction of bread making quality. It includes genotypes and phenotypes of the winter wheat lines.
DOI: 10.15454/chhyix
title: Experimental data of Series #8: Initiation of the trapping of large wood

description: Series 8: These data describe blockage probabilities of logs passing under a flexible barrier. Each probability Pblockage is computed after 30 repetitions of introducing a log in a flume with a given slope (S, values = 2%, 4% or 6%), under a given discharge (Q, range: 1.5 l/s - 6.8 l/s) and with a flexible barrier having a given bottom clearance (z1, values = 10 mm, 15 mm or 20 mm). Each log has a given diameter (exact value: Dlog, class: Dlw) and length (exact value: Llog, class: Llw). The log mean density is assumed to be 770 kg/m3 (range of variation: 745 - 830 kg/m3).
DOI: 10.15454/dacdjm
title: Annotation data about Multi Criteria Assessment Methods used in Animal Genetics : the French National Institute for Agricultural Research (INRA-GA) experience

description: This data article contains annotation data characterizing Multi Criteria Assessment Methods proposed in the scientific literature by INRA researchers belonging to the Animal Genetics department. Those researchs aim to understand the genetic determinism of the traits observed in farm animals and more generally to gain knowledge in animal integrative biology. In addition methods and tools are developed for the genetic improvement and conservation of farm animals.
DOI: 10.15454/ah6u4a
title: Enabling reusability of plant phenomic datasets with MIAPPE 1.1 - Supplementary dataset iBET

description: Spreadsheet file for the iBET cork oak dataset, accompanying the Enabling reusability of plant phenomic datasets with MIAPPE 1.1 paper
DOI: 10.15454/bdwvvv
title: DMP of the e-DIP ANR project - Dynamics and impacts of microplastics in soils

description: DMP for the data related to the ANR project Environmental Dynamics and Impacts of contaminant cocktails originating from Plastics in soil ecosystems.
DOI: 10.15454/bjfuev
title: R code for the statistical analysis for: Spatial variations, origins, and risk assessments of polycyclic aromatic hydrocarbons in French soils

description: We provide here a R script embebed in a R markdown file to conduct the statistical analysis of the article published in soil discuss journal.
DOI: 10.15454/brbk8x
title: Life Cycle Assessment of fructo- and galacto-oligosaccharides (FOS and GOS) produced by synthesis or hydrolysis

description: This dataset presents Life Cycle Assessment (LCA) of the production of FOS and GOS by enzymatic synthesis from glucose (to get FOS) or lactose (to get GOS) and hydrolytic production from extraction of yacon potato (to get FOS) or chickpea (to get GOS). A cradle-to-gate approach was considered in the two scenarios under assessment (the phases of use and/or final disposal of FOS/GOS were not considered). The functional unit was defined as 100 g of FOS/GOS produced. LCAs were performed using data collected at the laboratory scale, supplemented with data from Ecoinvent database. SimaPro was used for the LCA modeling with the midpoint impact EF2.0 characterization method. For each scenario (FOS produced by synthesis, FOS produced by hydrolysis, GOS produced by synthesis, GOS produced by hydrolysis), the Life Cycle Inventory (LCI) and the Life Cycle Impact Assessment (LCIA) are provided.
DOI: 10.15454/bynehb
title: Oviposition Preference and Larval Performance of Drosophila suzukii (Diptera: Drosophilidae), Spotted-Wing Drosophila: Effects of Fruit Identity and Composition

description: A better understanding of the factors affecting host plant use by spotted-wing drosophila (Drosophila suzukii) could aid in the development of efficient management tools and practices to control this pest. Here, proxies of both preference (maternal oviposition behavior) and performance (adult emergence) were evaluated for 12 different fruits in the form of purees. The effect of the chemical composition of the fruits on preference and performance traits was then estimated. We synthesized the literature to interpret our findings in the light of previous studies that measured oviposition preference and larval performance of D. suzukii. We show that fruit identity influences different parts of the life cycle, including oviposition preference under both choice and no-choice conditions, emergence rate, development time, and number of emerging adults. Blackcurrant was always among the most preferred fruit we used, while grape and tomato were the least preferred fruits. Larvae performed better in cranberry, raspberry, strawberry, and cherry than in the other fruits tested. We found that fruit chemical compounds can explain part of the effect of fruit on D. suzukii traits. In particular, oviposition preference under choice conditions was strongly influenced by fruit phosphorus content. In general, the consensus across studies is that raspberry, blackberry, and strawberry are among the best hosts while blackcurrant, grape and rose hips are poor hosts. Our results generally confirm this view but also suggest that oviposition preferences do not necessarily match larval performances. We discuss opportunities to use our results to develop new approaches for pest management.
DOI: 10.15454/c3xh6h
title: New insights into homoeologous copy number variations in the hexaploid wheat genome

description: Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.
DOI: 10.15454/dbtalb
title: Etude 4pour1000 : Procédure d'extrapolation et agrégation des sorties de STICS et PaSim

description: Procédure d’extrapolation des sorties des modèles STICS et PaSim pour les calculs économiques à l’échelle régionale. • Les variations de rendement, d’intrants, d’opérations culturales induites par les pratiques servent ensuite à calculer les coûts de mise en œuvre des pratiques par région et à compléter leur bilan GES. • Permet d’agréger l’assiette des pratiques au niveau régional. • Permet d’agréger le stockage additionnel de carbone et les émissions de N2O à l’échelle régionale. Cette procédure permet d’assurer la représentativité des surfaces simulées des cultures, par rapport aux surfaces issues des données statistiques publiques (SAA, Agreste), à l’échelle régionale. Son principe est expliqué dans le rapport de l’étude : Stocker du carbone dans les sols français : https://www.inrae.fr/sites/default/files/pdf/Rapport%20Etude%204p1000.pdf Lire le fichier metadata.xlsx pour l’ordre de mise en œuvre des scripts et les fichiers de données en entrée et en sortie
DOI: 10.15454/dolrjo
title: Protective ability of oligosaccharides to preserve lactic acid bacteria (LAB) during freezing, freeze-drying and storage

description: This study concerns the evaluation of the protective ability of oligosaccharides (FOS produced by enzymatic synthesis from sucrose) to preserve three lactic acid bacteria (Lactobacillus delbrueckii ssp bulgaricus CFL1, Lactobacillus plantarum WCFS1, and Carnobacterium maltaromaticum CNCM I-3298) during freezing, freeze-drying at pilot scale, and two weeks of storage of freeze-dried samples at 25°C. The dataset includes, for each of the three strains: i) the fermentation conditions (temperature, pH, and base consumption); ii) the stabilization conditions (freezing temperature and containers, freeze-drying recipe and parameters monitored during the cycle); iii) the quantification of the acidifying activity (using the CinAc system, AMS, Frepillon, France) and viability (using the plate count method) before and after freezing, after freeze-drying, and after storage.
DOI: 10.15454/dwg2ib
title: RPG complété 2019 département 28

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 28. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/aovoo2
title: 70 highly validated SNP markers for Quercus ilex

description: 70 highly validated SNP markers for Quercus ilex developped from ddRAD-Seq data following Garcia et al., 2018. PCR primer sequences and single base extension primers for MassArray analysis are provided.
DOI: 10.15454/au8ezi
title: Fish eDNA metabarcoding from aquatic biofilm samples: methodological aspects - Fish reference barcoding library

description: These data supplement the article “Fish eDNA metabarcoding from aquatic biofilm samples: methodological aspects” Sinziana F. Rivera, Frédéric Rimet, Valentin Vasselon, Marine Vautier, Isabelle Domaizon, Agnès Bouchez submitted to Molecular Ecology Resources journal. ----------------------------------------- The directory contains a curated fish reference library targeting a 163–185 bp of the mitochondrial 12S rRNA gene. The reference library contains 272 DNA sequences from 12 orders, 17 families, 19 genera and 126 fish species. ----------------------------------------- “Mifish_12S_272seqs.tax”: text-based file containing the taxonomic affiliation of each nucleotide sequences from the reference library ----------------------------------------- “Mifish_12S_272seqs.fasta”: text-based file containing all the nucleotide sequences from the reference library
DOI: 10.15468/dl.4vd5u6
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((8.79456 41.35803,9.39661 41.32288,9.77454 42.82141,9.42078 43.109,8.27161 42.57971,8.79456 41.35803))",
 "HasGeospatialIssue is false",
 "TaxonKey is Reynoutria japonica Houtt."
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180659-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kkmd5q
title: Occurrence Download

description: A dataset containing 6464 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Persea americana Mill."
 ]
}

 The dataset includes 6464 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036071-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nzp2sf
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Oreophryne biroi (Méhely, 1897)"
 ]
}

 The dataset includes 29 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020474-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.244fmf
title: Occurrence Download

description: A dataset containing 12289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Hyla japonica Günther, 1859",
 "TaxonKey is Hyla suweonensis Kuramoto, 1980",
 "TaxonKey is Hyla immaculata Boettger, 1888"
 ]
 }
 ]
}

 The dataset includes 12289 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180649-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.