cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/5blymj
title: Viral metagenomic data of crop and wild plant/weed species in horticultural contexts: analysis of viral diversity, prevalence and stability over a two-year period

description: Using purified double-stranded RNAs (dsRNAs) and high-throughput sequencing (HTS) on a 454 pyrosequencing platform, we analyzed the metavirome associated with crops and surrounding weeds/wild plants in horticultural contexts in southwestern France. A total of 165 libraries were prepared and sequences. One additional file provides the samples identity and metadata.
DOI: 10.15454/bbfrww
title: Measured and estimated tree dimensions of maritime pine (Pinus pinaster) and birch (Betula pendula) in the tree diversity experiment ORPHEE at the end of 2014

description: The ORPHEE experiment is located 40km south of Bordeaux (44°440 N, 00° 460 W) and belongs to the worldwide Tree Diversity Network (TreeDivNet). The experimental plantation was established in January 2008 on a clear cut of former maritime pine stands on a sandy podzol. Eight blocks were established, with 32 plots in every block. Each plot contained 10 rows of 10 trees planted 2 m apart, resulting in 100 trees within a plot of 400 m². The total initial stand density was therefore 2500 trees per hectare in each plot. Each plot was planted with one to five species. Only maritime pine (Pinus pinaster/Ppin) and silver birch (Betula pendula/Bpen) were considered in this data set. For this study, we have selected 14 plots per blocks. The present data set is composed by data collected in 2014 (7 years-old) on the target trees at the center of the plots in order to avoid edge effects (measured planting locations = 36). The total height was measured on living trees using a graduate pole. We also measured circumferences at 1.30m height on 7 randomly chosen pines and 7 randomly chosen birches per plot. We estimated missing tree heights and circumferences and tree volumes by: - Using height-circumference relationships to estimate the circumferences of trees that have not been measured in 2014 by mean of separate generalized additive models for each stand composition and tree density. - Using the generic model developed by Deleuze et al. (2014) to aboveground tree volumes. We assigned a minimum volume of 0.01m3/ha to the few trees below 1.30m in height (corresponding to the minimum volume found in the data set). - Eventually we estimated dimensions of dead trees by averaging diameter, height and volume of living trees in the plot.
DOI: 10.15454/behoqk
title: Sea lamprey nests promote the diversity of benthic macroinvertebrate assemblages

description: Dataset and script for the analysis of the data used in the paper entitled "Sea lamprey nests promote the diversity of benthic macroinvertebrate assemblages". The habitat heterogeneity hypothesis states that increased habitat heterogeneity promotes species diversity through increased availability of ecological niches. We aimed at describing the local-scale effects of nests of the sea lamprey Petromyzon marinus L. as ecosystem engineer on macroinvertebrate assemblages. We hypothesized that increased streambed physical heterogeneity caused by sea lamprey spawning would modify invertebrate assemblages and specific biologic traits and promote reach-scale diversity. We sampled thirty lamprey nests of the Nive River in three zones: the unmodified riverbed (control) and zones corresponding to the nest: the area excavated (pit) and the downstream accumulation of pebbles and cobbles (mound). The increase habitat heterogeneity created by lamprey was traduced by biological heterogeneity with a reduced density of invertebrates (1160 to 6540 individuals per m² in control, 680 to 6460 individuals per m² in pit and 1980 to 6240 individuals per m² in mound) and number of taxa (23.5 ± 3.9 taxa for control, 18.6 ± 3.9 taxa in pit and 21.2 ± 4.5 taxa for mound) in the pit compared to other zones. However the overall taxa diversity in nest increased with 82 ± 14 taxa compared to the 69 ± 8 taxa estimated in control zone. Diversity indices were consistent with the previous results indicating a loss of alpha diversity in pit but a higher beta diversity between a pit and a mound than between two control zones, especially considering Morisita index accounting for taxa abundance. Trait analysis showed high functional diversity within zones with a reduced proportion of collectors, scrapers, shredders, litter/mud preference and small invertebrates in mound, while the proportion of "slabs, blocks, stones and pebbles" preference and largest invertebrates increased. Pit presented the opposite trend, while control had globally intermediate trait proportions. Our results highlight important effects on species and functional diversity due to habitat heterogeneity created by a nest-building species, what can ultimately influence food webs and nutrient processes in river ecosystems.
DOI: 10.15454/ercvzr
title: 1D 1H-NMR profiling of wheat samples

description: NMR metabolomic profiling of wheat samples recorded on three sites (JEOL400, Bruker 500 and Bruker 600 MHz) - To be used with NMRProcFlow (https://nmrprocflow.org)
DOI: 10.15454/7x7zrm
title: Oak Provenances database

description: The Oak provenance database contains passport data of Quercus petraea and Quercus robur provenances and provenance tests established in Europe. Passport data comprise geographic data of the source stands of provenances and of the provenance tests. Additional information on seed collections in the source stands and on the plantation protocol and experimental design of provenance tests are also available. The database was constructed and populated during the FAIROAK project (1996-1999) supported by the EU (http://www.pierroton.inra.fr/Fairoak/) by partners of FAIROAK hosting oak provenance tests. It does not contain all provenance tests and provenances present in Europe. The database was upgraded within the EVOLTREE network of excellence.
DOI: 10.15454/838u9l
title: Long-term and large-scale Quercus petraea population survey conducted in provenance tests installed in France

description: Provenance tests are invaluable resources in forest genetics and ecology. They were originally established for seed sourcing research, but they are now also used for monitoring and predicting population responses to environmental changes. They have also excited considerable interest for conservation purposes. We provide here a data resource for a multisite large-scale long-term provenance test on sessile oak (Quercus petraea (Matt.) Liebl.) set up in the late 1980s in France, containing also a few Q. robur provenances as well.. The experimental layout comprises a range-wide collection of 124 provenances (109 Q.petraea and 15 Q. robur) planted at four experimental sites covering 90 ha in total. The dataset includes individual tree assessments of traits of functional, ecological and economic importance. The data are stored within the « Oak provenance » data base : Oak provenances
DOI: 10.15454/8dqxk5
title: Phenotypic, genotypic and transcriptomic data of 241 Populus nigra (from the Sybiopop project)

description: This dataset includes all the files produced in the Sybiopop project.
DOI: 10.15454/9z4ps3
title: Capex ontology

description: In many agri-food chains, the food quality is often managed using the know-how based on the experience. The global quality enhancement may come from the sharing of the collective know-how. Capex ontology has been designed as a core ontology to represent potential causal relationships between situations of interest which permit to link a quality/default to an action to maintain/solve it. Current version is expressed using the Conceptual Graph ontological formalism. It will be expressed in OWL/RDF in the very next future. Current applications concern food processing but this core ontology may be used in any production sector.
DOI: 10.15454/annpot
title: Assessment of CO2 solubility coefficient in semi-hard cheese related to ripening conditions - CO2 solubility in semi-hard cheese in relation to moisture content

description: value unavailable
DOI: 10.15454/e1ji8u
title: A dataset of the chemical composition and near-infrared spectroscopy measurements of raw cattle, poultry and pig manure

description: The dataset is composed of chemical analysis results and the NIR spectra of 490 solid animal organic waste products that were collected in 2 campaigns conducted in 2018 and 2019. The sampling was designed to capture the large diversity of animal species (mainly cattle, pigs and poultry), type of farming and storage modes). Compositional parameters (dry matter, organic matter, total and ammonium nitrogen, phosphorus, potassium, calcium and magnesium contents) were analyzed according to French AFNOR standards. Samples were scanned using a Q-interline AgriQuant B8 equipped with a patented spiral sampler, which aggregates the heterogeneity of the sample. This dataset covers a wide range of variability in the composition of solid animal manure, and is of great interest to chemometricians and agronomists in search of references on the fertilizing value of these products.
DOI: 10.15454/agu4qe
title: WIDEa: a Web Interface for big Data exploration, management and analysis

description: WIDEa is R-based software aiming to provide users with a range of functionalities to explore, manage, clean and analyse "big" environmental and (in/ex situ) experimental data. These functionalities are the following, 1. Loading/reading different data types: basic (called normal), temporal, infrared spectra of mid/near region (called IR) with frequency (wavenumber) used as unit (in cm-1); 2. Interactive data visualization from a multitude of graph representations: 2D/3D scatter-plot, box-plot, hist-plot, bar-plot, correlation matrix; 3. Manipulation of variables: concatenation of qualitative variables, transformation of quantitative variables by generic functions in R; 4. Application of mathematical/statistical methods; 5. Creation/management of data (named flag data) considered as atypical; 6. Study of normal distribution model results for different strategies: calibration (checking assumptions on residuals), validation (comparison between measured and fitted values). The model form can be more or less complex: mixed effects, main/interaction effects, weighted residuals.
DOI: 10.15454/bb0wjn
title: Sporangia size and number relationship for Phytophthora infestans isolates

description: Phenotypic data (sporangia size and sporangia number) of P. infestans isolates obtained in three infection experiments conducted under controlled conditions.
DOI: 10.15454/bujusx
title: Time series dataset of dissolved oxygen, water temperature and Secchi depths profiles in Lakes Annecy and Geneva

description: Data description : Data are in situ profiles of dissolved oxygen concentrations, water temperature, Secchi depths and total phosphorus concentrations recorded in Lakes Geneva and Annecy. The dataset consists in monthly to bi-monthly profiles for the periods 1957 to 2016 and 1966 to 2016 for Lakes Geneva and Annecy respectively. Data acquisition : Temperature data were collected from the deepest point in the lakes. Temperature measurements were measured manually using thermometers and multiparameters probes. In Lake Geneva, water temperature was measured manually with a thermometer until 1990 from discrete depths of 5 to 10 meter intervals through 50 meter depth and approximately 50-meter intervals for the rest of the water column. After 1990 various multiparameter probes were used for temperature measurements, Meerestechnik Elektronik (1991-2001), CTD 90 (2002-2007), CTD 90M (2008-2011, 2013), and RBR (2012). In Lake Annecy, various multiparameter probes, including Meerestechnik Elektronik (1991-2001), CTD 90 (2003-2005), CTD 90M (2008-2011, 2013), and RBR (2012) were used for temperature measurements at depth intervals between 0.01 and 1.8 meters. Temperature profiles were measured in Lake Bourget at depth intervals between 0.01 and 10 meters using various multiparameter probes, including ISMA probe DNTC (1984-1985), Meerestechnik Elektronik ECO 236 (1986-1998), CTD SBE 19SeaCAT Profiler (1992-2002), and CTD SBE 19plus V2 SeaCAT (2003-2013).
DOI: 10.15454/8il3lj
title: Températures Aquapôle INRAE

description: Petit fleuve côtier de 39 km de long, la Nivelle est une rivière à migrateurs (saumon, alose, truites de mer) et ses populations sont suivies depuis le début des années 80. Ce Dataset présente un classeur Excel qui décrit les relevés de températures qui sont effectués quotidiennement sur l’Aquapôle de l’INRAE depuis 1984. Les données acquises depuis la mise en place de ce suivi long terme proviennent du même site de collecte sur l’Aquapôle (canal d’amené de la pisciculture), en revanche le type d’enregistreur a changé au cours du temps : enregistreur de type Jules richard (données papier) de 1984 à 2002, puis enregistreurs Vemco et Tidbit entre 2002 et 2008. Depuis 2008 les enregistrements se font à nouveau avec des thermo-enregistreurs Vemco dont la fiabilité et la faible dérive des enregistreurs a fait ses preuves. Le présent document donne pour chaque jour la température mini et maxi relevée ainsi que la moyenne des 24 mesures qui sont enregistrées quotidiennement.
DOI: 10.15454/agbw7g
title: données lidar acquises par drone sur site de Puechabon (34)

description: Acquisitions Lidar par drones des sites d’études SentyMed , juin 2021. Télépilotes unité TETIS, Montpellier : Samuel Alleaume : samuel.alleaume@inrae.fr Audrey Jolivot : audrey.jolivot@cirad.fr Capteur : Yellowscan, Surveyor • Centrale GNSS-inertielle : Applanix APX-15 UAV • Lidar : Velodyne VLP16 (Puck) : Longueur d’onde:905 nm / 300 000 pulses par seconde (300 kHz) / 2 échos par pulse / Angle de vue : 360 deg • Précision : 4cm Vecteur : drone DJI Matrice 600 Pro
DOI: 10.15454/axy7fv
title: Replication Data for: Nguyen et al. Reduction in PLANT DEFENSIN 1 results in increased resistance to pathogens and zinc toxicity

description: Datasets for replication of the figures in the paper by Nguyen et al.
DOI: 10.15454/criudy
title: R scripts and datas for the analysis of Lepidoptera feeding bioassays

description: Rscripts, raw datas, and documentation associated to the statistical analysis of the data produced by the Sanane Lepidoptera feeding bioassay.
DOI: 10.15454/dzm5bl
title: RPG complété 2018 département 39

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 39. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/ekgzgv
title: Species-level leaf trait data (ECOPICS)

description: Leaf traits for 11 plant species at 11 altitudinal levels at Massif de Belledonne, France
DOI: 10.15454/akeo5g
title: Survey data on European organic multi-species livestock farms

description: While there is increasing evidence of the sustainability benefits of diversified systems in the organic cropping sector, this has been much less investigated with organic livestock farming. To fill this knowledge gap, we surveyed a sample of 128 European organic multi-species livestock farms located across seven countries – Austria, Belgium, France, Germany, Italy, Sweden and Switzerland – and covering a large range of livestock species combinations. We recorded 1574 variables as raw data out of which we calculated 107 indicators describing farm structure, management and several sustainability dimensions: resource use efficiency and conservation, animal, land and work productivities, animal and human welfare. After technical validation of the data, we withdrew 26 farms and the database covers 102 farms. This database is well suited to unveil relationships between various dimensions of organic multi-species livestock farm sustainability and their structure and management. It can help reveal sustainable strategies for organic multi-species livestock farming systems, and levers or barriers to their development. Scripts: https://forgemia.inra.fr/mix-enable/mix-enable_indicators/
DOI: 10.15454/ar5pml
title: RPG complété 2018 département 66

description: RPG complété 2018. Complète le RPG campagne 2018 pour le département 66. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2020.
DOI: 10.15454/bebb7u
title: Terminologie pour la recherche d’information du département Phase

description: TriPhase est un thésaurus couvrant largement le domaine de la physiologie animale et de l'élevage conçu par l'INRA.
DOI: 10.15454/bmgbz8
title: Suivi pluri annuel de la croissance de châtaigniers à double fin (production de bois et de fruits) sur un dispositif expérimental à Saint Caprais (46)

description: Le jeu de données présenté a été produit dans le cadre d’une étude portant sur les possibilités de la gestion de vergers "fruits et bois",ici dans le cas des châtaigniers. L'objectif principal de cette étude est de déterminer,pour deux clones d'arbres hybrides Castanea sativa x Castanea crenata,les méthodes techniques pour obtenir (du même arbre) des noix à court terme et du bois de qualité à long terme,selon les modes de tailles. Les modes de tailles ont été testées sur des arbres âgés de trois à huit ans dans un essai situé dans le sud-ouest de la France. Le jeu de données présenté ici concerne les données de croissance en diamètre et en hauteur à différents niveaux dans l’arbre.
DOI: 10.15454/bpn57s
title: Base de Données Géographique des Sols de France à 1/1 000 000 version 3.2.8.0, 10/09/1998

description: The Soil Geographical Data Base of France at Scale 1:1,000,000 is part of the European Soil Geographical Data Base of Europe. It is the resulting product of a collaborative project involving all the European Union and neighbouring countries. It is a simplified representation of the diversity and spatial variability of the soil coverage for France. The methodology used to differentiate and name the main soil types is based on the terminology of the F.A.O. legend for the Soil Map of the World at Scale 1:5,000,000. This terminology has been refined and adapted to take account of the specificities of the landscapes in Europe. It is itself founded on the distinction of the main pedogenetic processes leading to soil differentiation. The database contains a list of Soil Typological Units (STU). Besides the soil names they represent, these units are described by variables (attributes) specifying the nature and properties of the soils: for example the texture, the water regime, etc. The geographical representation was chosen at a scale corresponding to the 1:1,000,000. At this scale, it is not feasible to delineate the STUs. Therefore they are grouped into Soil Mapping Units (SMU) to form soil associations and to illustrate the functioning of pedological systems within the landscapes. Harmonisation of the soil data from the member countries is based on a dictionary giving the definition for each occurrence of the variables. Considering the scale, the precision of the variables is weak. Furthermore these variables were estimated over large areas by expert judgement rather than measured on local soil samples. This expertise results from synthesis and generalisation tasks of national or regional maps published at more detailed scales, for example 1:50,000 or 1:25,000 scales. Delineation of the Soil Mapping Units is also the result of expertise and experience. The spatial variability of soils is very important and is difficult to express at global levels of precision. Quality indices of the information (purity and confidence level) are included with the data in order to guide usage.
DOI: 10.15454/eobum0
title: 3D data from T-LiDAR describing tree trunks with bark singularities, and corresponding manual measurements

description: This dataset contains 3D data coming from T-LiDAR describing tree trunks of different species, and singularities of the bark surface potentially linked to internal wood defects. Hand-made characterization of the singularities is also provided. The dataset is structured in training data for establishing Random Forests classification of the defects and trunk data for evaluation purposes on oak and beech trees
DOI: 10.15468/dl.82bqqx
title: Occurrence Download

description: A dataset containing 70370989 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84"
 ]
}

 The dataset includes 70370989 records from 4052 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003418-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k2fbdw
title: Occurrence Download

description: A dataset containing 817 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chlorophyceae",
 "HasCoordinate is true",
 "Country is one of (Germany)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 817 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221904-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzfmzw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euglenophyceae",
 "HasCoordinate is true",
 "Country is one of (Germany)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221934-210914110416597/datasets/export for details.
DOI: 10.15468/dl.x5xysp
title: Occurrence Download

description: A dataset containing 7905 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parietaria pensylvanica Muhl. ex Willd."
 ]
}

 The dataset includes 7905 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036511-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7367r8
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mediophyceae",
 "HasCoordinate is true",
 "Country is one of (Germany)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 95 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0221943-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.we4bua
title: Occurrence Download

description: A dataset containing 12273 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trifolium tomentosum L."
 ]
}

 The dataset includes 12273 records from 267 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021207-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgjq47
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helicops hagmanni Roux, 1910"
 ]
}

 The dataset includes 353 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0277751-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.