cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15454/aiq9ws
title: French RMQS soil profile and monitoring dataset with related management practices data

description: This dataset corresponds to a datamart produced by the WP2 team of the Landmark H2020 project. 2 tables provided by France are available: One table of fact-gathering the results of the chemical and physical analyses of the soil profiles and monitoring. One table of fact-gathering the results of the cultural management practices related to soil data. Both tables are connected with the same id attribute. To link soil data to management practices, you just need to use the "profile_id" of the soil table and the "management_id" of the management table. For soil data, the same id may come more than one time if multiple layers are described. Moreover, the names of the crops have been coded into the management table with the "Eurostat Handbook for Annual Crop Statistics (Regulation (EC) No 543/2009, Commission Delegated Regulation (EU) 2015/1557 and ESS agreement for Annual Crop Statistics) - Revision 2017 - (Released 9 February 2017)". All the codes and their meaning are into the table "eurostat_crops_list".
DOI: 10.15454/brkov3
title: Observatoire National des Anomalies Bovines

description: L'Observatoire vise à détecter précocement l’émergence d’anomalies génétiques dans les élevages afin d'aider les Organismes de Sélection raciaux à gérer ces anomalies dans les populations. Ses objectifs principaux sont 1) d'organiser la gestion de l’information et du matériel biologique correspondant, 2) approfondir les connaissances scientifiques en matière d’étiologie et d’épidémiologie des anomalies congénitales 3) transmettre les savoirs faire pour la gestion des anomalies sur le terrain. L’ONAB a été créé sous l’instance du Ministère chargé de l’Agriculture et regroupe les différents acteurs concernés : INRAE, Institut de l’Elevage, Groupements Techniques Vétérinaires, Ecoles vétérinaires de Nantes, Toulouse, Alfort, et Lyon, Allice et entreprises adhérentes, Races de France et Organismes de Sélection raciale, Contrôle de Performances. La coordination est assurée par Cécile Grohs (INRAE) et Coralie Danchin (Institut de l’Elevage), en collaboration avec Françoise Dion (vétérinaire, Races de France).
DOI: 10.15454/d3odjm
title: Colisa, the collection of ichthyological samples.

description: The collection of ichthyological samples, Colisa, results from the merging of historical samples collected by 3 INRA units (U3E in Rennes, ECOBIOP in Saint Pée sur Nivelle and CARRTEL in Thonon les Bains) and AFB-INRA Pole Gest’Aqua. These samples come from long term monitoring and research activities conducted by these units and from a national catch declaration scheme (angling and professional fishery). It consists of more than 200000 scales or other tissue samples of fish from 26 species collected in France over 50 years. Beyond age and growth, these samples, carrying DNA, allow genetic characterization of individuals or populations. Via microchemistry, they alos allow to characterize the trophic status and the environmental conditions of life of animals. The conservation of these tissues allow to investigate retrospective changes (global and local). Colisa is a part of BRC4env, one of the 5 specialized pillars of the French Research Infrastructure "Agricultural Resources for Research" (AgroBRC-RARe, http://www.enseignementsup-recherche.gouv.fr/cid99437/ressources-agronomiques-pour-la-recherche-rare.html) federating BRCs: animals as CRB-Anim, plant as CRB-Plantes, micro-organisms as CIRM, environmental resources as BRC4Env, and forests as CRB-Forets. BRC4Env includes BRCs and collections hosted by INRA, IRD, CIRAD, CNRS, technical and higher education institutions. (2018-09-20).
DOI: 10.15454/e2dfnj
title: Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France

description: To ensure methodological reproducibility the datasets used in "Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France", Rmd and bash files used to perform all analyses used in the article, are stored here. Please start by reading 0_README.html
DOI: 10.15454/fqo7va
title: GestCO2, heat, carbon and water budgets of a broiler batch (ROSS 308): observations and associated modelling equations

description: Models of heat production of broilers are used to design the thermal equipment to optimize climate control. The reference models are now around fifteen years old. Daily values of heat productions are deduced from the live weight of broilers and do not integrate the diversity of livestock systems and the genetic progress's evolution. Animal welfare and environmental issues now require simulations at an hourly time step or even shorter. Our objective is to propose an hourly model of heat, carbon dioxide and water vapor productions incorporating the zootechnical parameters specific of a commercial batch of broilers. To update the reference equations, we measured the heat fluxes of two lots of 4580 chickens, during 33 days, in conditions similar to commercial farming. Both breeding rooms were equipped with sensors for continuous recording of hygrometry, temperature, CO2 concentration, lighting duration, ventilation rate and heating. The usual zootechnical data enabled us to calculate the balance of water and carbon mass. We propose a new model design for heat production. The main parameters of the allometric relationship are calibrated with the nocturnal phases because of the observed stability of fluxes. Over the total duration of the batch, within a 24-hour cycle, heat outputs can vary between -1 W animal-1 and + 50 % of the night heat output. Since we cannot explain the kinetics during the daytime periods, we propose to border the total heat production. The value of energy conversion to CO2 has been updated to 0,197 L CO2 h-1 W-1. When indoor temperature remains near the temperature setpoint, diurnal evaporation increases when indoor hygrometry decreases.
DOI: 10.15454/aknf4q
title: High throughput phenotyping of seeds from Beta vulgaris genotypes

description: Dataset obtain by high throughput phenotyping of seed morphology, germination and seedling heterotrophic growth traits on a sugar beet population of genotypes.
DOI: 10.15454/ew0ehv
title: RPG complété 2019 département 24

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 24. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/fg261f
title: Diversity matters in wheat mixtures : a genomic survey of the impact of genetic diversity on the performance of twelve way Durum wheat mixtures grown in two contrasted and controlled environments

description: Phenotypic and genotypic data on 96 populations of Durum wheat
DOI: 10.15454/gaxtx6
title: Physico-chemical parameters of river water in Scorff and its tributaries (Morbihan county - France)

description: The data consist of physico-chemical parameters of river raw water in Scorff and its tributaries, collected since 1999. The parameters are water temperature (°C), hydrogen potential (pH), conductivity, turbidity, nitrates (NO3-), ammonium (NH4+) and ortophosphates (PO4 ---). This data is collected as part of the French Environmental Research Observatory (ERO) on Diadromous Fish in Coastal rivers (DiaPFC). ORE DiaPFC is a research infrastructure dedicated to the study of diadromous fish populations under the influence of anthropic pressure (e.g. agriculture) and environmental changes (e.g. climate). The Scorff River is a small coastal river in southern Brittany (France). The main river is 78.6km long, including a 15km estuary. The mean gradient is 3.6%, annual mean discharge is 5m3/s and the drainage basin area has an area of 480km2
DOI: 10.15454/ha6v6y
title: Biochem-Env: a platform of biochemistry for research in environmental and agricultural sciences

description: Biochemical indicators are potent tools to assess ecosystem functioning under anthropic and global pressures. Nevertheless, additional work is needed to improve the methods used for the measurement of these indicators, and for a more relevant interpretation of the obtained results. To face these challenges, the platform Biochem-Env aims at providing innovative and standardized measurement protocols, as well as database and information system favoring result interpretation and opening. Its skills and tools are also offered for expertise, consulting, training, and standardization. In addition, the platformis a service of a French Research Infrastructure for Analysis and Experimentation on Ecosystems (AnaEE-France), for research in environmental and agricultural sciences.
DOI: 10.15454/aif6tx
title: PO2 Biorefinery Ontology

description: This work presents a domain ontology based on the Process and Observation Ontology PO2 (http://agroportal.lirmm.fr/ontologies/PO2), dedicated to the representation of biorefinery applications. The objective was to establish a common vocabulary to describe different biorefinery projects aiming to produce bio-composite packaging: Chercheur d’avenir region Languedoc-Roussillon MALICE, H2020 NoAW, FP7 EcoBioCAP and H2020 Resurbis. The domain ontology's classes are separated in different main aspects: measured attributes (measured characteristics or process controlled parameters), components, material, observations and steps.
DOI: 10.15454/bqhgr9
title: 1D 1H-NMR profiling of 8 fleshy fruits (mixed-stage samples)

description: 1D 1H-NMR metabolomic profiling of 8 fleshy fruit species, including three herbaceous species, eggplant, pepper and cucumber, three tree species, apple, peach and clementine, and two vines, kiwifruit and grape. “stage-mixture sample”, dedicated to the identification of major soluble compounds, was constituted as a mixture of an equal amount of all the stages of development harvested. Profil métabolomique 1D 1H-RMN de 8 espèces de fruit charnu, provenant de trois herbacées, aubergine, poivron et concombre, trois espèces d'arbre, pomme, pêche et clémentine, et deux espèces de lianes, kiwi et raisin. Par “stage-mixture sample” est entendu un échantillon constitué d'un mélange en quantité égale de chaque stade de développement de cette espèce de fruit récoltée; cet échantillon a servi à l'identification des composés majeurs solubles.
DOI: 10.15454/budu7e
title: RPG complété 2019 département 30

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 30. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/d7epfw
title: eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva

description: Supplementary tables of the article“eDNA metabarcoding from aquatic biofilms allows studying spatial and temporal fluctuations of fish communities from Lake Geneva” Rivera, S.F., Vasselon, V., Bouchez. A. Rimet, F.
DOI: 10.15454/d9ijwr
title: Raw data - resistance Iledher under multiinfection

description: Raw experimental data on resistance of potato cultivar Iledher to Globodera pallida under multiinfections
DOI: 10.15454/dpfu1t
title: Scripts used to compute temporal calibration parameters of leaf growth

description: Scripts to be used in R-cran and COPASI
DOI: 10.15454/ds6vik
title: NLGenomeSweeper

description: NLGenomeSweeper is a command line bash pipeline that searches a genome for NBS-LRR (NLR) disease resistance genes based on the presence of the NB-ARC domain using the consensus sequence of the Pfam HMM profile (PF00931) and class specific consensus sequences built from Vitis vinifera. This pipeline can be used with a custom NB-ARC HMM consensus protein sequence(s) built for a species of interest or related species for greater power, separately for each type of NBS-LRR (TNLs, CNLs, NLs) and combine them into a single fasta file for use. This pipeline shows high specificity for complete genes and structurally complete pseudogenes. However, candidate regions are identified but may not necessarily represent functional genes and does not itself do gene prediction. A domain identification step is also included and the output in gff3 format can be used for manual annotation of NLR genes. Therefore, it is primarily for the identification of NLR genes for a genome where either no annotation exists or a large number of genes are expected to be absent due to repeat masking and difficulties in annotation. For many genomes this may be the case. (2019-08-26)
DOI: 10.15454/gxlrhg
title: European climate indicators datasets

description: This dataset corresponds to a datamart produced by the WP2 team of the Landmark H2020 project. A specific request consists in the computation of a limited number of climate indicators for each grid cells and needed to run the dexi models. They are calculated for each year. Those indicators was calculated for 2 periods: 1990 to 2016 1997 to 2016
DOI: 10.15454/hx3cz8
title: Performance of a non-invasive methodology for assessing oxygen diffusion in liquid and solid food products - Oxygen diffusivity of water for temperature ranging from 10 to 40°C

description: value unavailable
DOI: 10.15454/bl3gym
title: Impaired cell growth in ammonium stress explained by modelling the energy cost of vacuole expansion in tomato leaves

description: Research project "CAMTV" : Cell growth, Ammonium stress, Modelling the energy cost, Tomato leaves, Vacuole expansion. Collaboration between the University of the Basque Country (UPV/EHU) and UMR 1332 Biologie du fruit et Pathologie. Research subject: Impaired cell growth in ammonium stress explained by modelling the Energy cost of vacuole expansion in tomato leaves. Authors: Théo Poucet, Bertrand Beauvoit, María Begoña González-Moro, Cécile Cabasson, Pierre Pétriacq, Amélie Flandin, Yves Gibon, Daniel Marino, Martine Dieuaide-Noubhani. Théo Poucet's PhD thesis submitted to the doctoral school of Agrobiología Ambiental from the University of the Basque Country (UPV/EHU) and the doctoral school of Science de la Vie et de la Santé (speciality: Plant biology) from the University of Bordeaux the 10th July 2020. Beginning of the project: October 2016 - End of the project: July 2020. Fundings: This research was financially supported by the Basque Government (IT-932-16) and, the Spanish Government (BIO2017-84035-R cofunded by FEDER). Analytics were supported by MetaboHUB (ANR-11-INBS-0010) and PHENOME (ANR-11-INBS-0012) projects.
DOI: 10.15454/bncxyb
title: Statistiques sommaires issues du RMQS sur les données agronomiques et en éléments traces des sols français de 0 à 50 cm

description: Ce jeu de données fournit des statistiques sommaires sur les concentrations en éléments traces et propriétés pédologiques issues des résultats d'analyses du RMQS pour deux profondeurs. Le réseau RMQS repose sur le suivi de 2200 sites répartis uniformément sur le territoire français (métropole et outre-mer), selon une maille carrée de 16 km de côté. L’évaluation et le suivi de la qualité des sols sont fondés sur l’analyse de propriétés physiques, chimiques et biologiques des sols, associée à la recherche des sources de contamination diffuse et à la connaissance de l’historique de l’occupation et des pratiques de gestion de chaque site. L’ensemble des prélèvements, mesures et observations réalisés sur un site est détaillé dans le Manuel du Réseau de Mesures de la Qualité des Sols. La première campagne de prélèvement en métropole s'est déroulée de 2000 à 2009. Le RMQS couvre également les départements d'Outre-mer : après un déploiement en 2006-2007 aux Antilles, la mise en place du RMQS se poursuit actuellement à la Réunion, à Mayotte et en Guyane. La base de données produite comprend les résultats d’analyses issus de 2171 sites de métropole, répartis sur 2146 cellules et correspondant à la première campagne RMQS (2000 -2009). Les sites recouvrent diverses occupations (grandes cultures, prairies permanentes, forêts , vignes et vergers, milieux peu anthropisés, parcs urbains). Les résultats d’analyses ont été réalisés sur les échantillons composites constitués à partir des prélèvements de la surface d’échantillonnage tels que décrit dans le manuel (25 échantillons élémentaire prélevés à la tarière selon 2 couches de prélèvements (0-30 cm ou bien couche travaillée en sols cultivés et 30-50 cm).
DOI: 10.15454/ermty9
title: RPG complété 2019 département 51

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 51. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/h4p5u3
title: Lefebvre et al. 2020 : manuscript and associated data

description: Publication "Physicochemical characterization of Populus nigra seeds and impact of genetic variability on germination and early seedling growth" submited to PCI Forest and Wood Sciences
DOI: 10.15454/cdukml
title: Data and scripts of the article: Predicting the dynamics of enteric methane emissions based on intake kinetic patterns in dairy cows fed diets containing either wheat or corn

description: This data set contains the data and scripts of the article “Predicting the dynamics of enteric methane emissions based on intake kinetic patterns in dairy cows fed diets containing either wheat or corn” • Table_DataFeed.xls: filtered data of Lucerne consumption (wet mass) • Table_PCA: values of variables used in the principal component analysis Files to use the Scilab_scripts • model_methane.sci: script to estimate the model parameters for a given animal • DryMatterFeed.sci: script with the values of dry matter of the feeds • conc_XXXYYY.txt: time and weights of concentrate consumption for the animal XXX with the diet YYY • WMI_XXX_YYY.txt: wet mass intake of the animal XXX with the diet YYY • methane_XXX_YYY.txt: methane production of the animal XXX with the diet YYY (2021-10-06)
DOI: 10.15454/cgg7hw
title: Does physical inactivity induce significant changes in human gut microbiota? New answers using the dry immersion hypoactivity model.

description: Ensemble des données physiologiques et métagénomiques utilisés au cours de l'étude associée au CPP Est III: 02 October, 2018, n° ID RCB 2018-A01470-55) et l'autorité sanitaire française (ANSM: August 13, 2018, ClinicalTri-als.gov Identifier: NCT03915457). Essai clinique référencé sur ClinicalTrialsGov (NCT03915457).
DOI: 10.15454/d4jtkb
title: Genotyping of DNA pools of 166 maize landraces with 50K illumina array

description: Genotyping datasets of 166 maize landraces and 327 lines published in Arca et al., (2023) in Plant Biotechnology Journal entitled "Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next generation varieties". 1) Raw fluorescent Intensity dataset 50K array used for allelic frequency prediction at 23,412 SNPs 2) Allelic frequencies matrix of allele B for 166 maize landraces at 23,412 SNPs obtained by applying two step approach described in Arca et al., 2021, Frontiers in Plant Science (doi:10.3389/fpls.2020.568699) on raw fluorescent intensity dataset with a predictive model calibrated with datasets and scripts from this paper (doi: 10.15454/GANJ7J) 3) Allelic frequencies matrix of allele B for 327 inbred lines from a diversity panel (CK lines panel) at 23,412 SNPs retrieved from genome studio. 4) Modified Roger's Distance (MRD) between 166 maize landraces and 327 inbred lines estimated from genotyping data (Rogers, 1973).
DOI: 10.15454/hhy2z2
title: NIAS-db

description: NIAS-db 1.0 is an open-source software in R, developed with the Shiny framework and the Chromium Portable v16.0.3153.0 web browser (32-bit) for exploring databases of theoretical oligoesters and phenolic oligomers. NIAS-db 1.0 is freely available under the GPLv3 license. It is packed as an executable file of 1.0 GB. It runs out of the box without need for computer skills or administrative rights, when installed in a folder in which the user has full read/write access (not necessarily C/Program files). Once installed, the uncompressed database reaches 10.0 GB. The NIAS-db Windows command file available at the folder root launches the interface. Queries can be performed from either the neutral chemical formula or the monoisotopic mass with a mass tolerance (mDa).
DOI: 10.15468/dl.bz2nfx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasCoordinate is TRUE",
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON ((-153.86758206721046 56.55030733904814, -154.01452237642974 56.55075813462369, -154.12984669902082 56.50816106194378, -153.95391819575624 56.50357382722663, -153.86758206721046 56.55030733904814))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035109-250525065834625/datasets/export for details.
DOI: 10.15454/dpbmbw
title: Agri-Food Experiment Ontology

description: The Agri-Food Experiment Ontology (AFEO), a new ontology network was developed based on two existing ontology resources, i.e., OAE (Ontology for Agriculture Experiment) and OFPE (Ontology for Food Processing Experiment). It contains 136 concepts which cover various viticultural practices, and winemaking products and operations.
DOI: 10.15454/efk56h
title: RPG complété 2019 département 35

description: RPG complété 2019. Complète le RPG campagne 2019 pour le département 35. (contient les parcelles agricoles hors RPG) Données géographiques (vectorielles, shapefile), parcellaires. Sources : IGN, OSO/Cesbio. Traitements : INRAE US ODR, 2021.
DOI: 10.15454/eqp1bv
title: Etude 4pour1000 : Données modèle BANCO

description: Données et sorties du modèle d'allocation coût efficace de l’effort de stockage BANCO
DOI: 10.15454/fkdgtg
title: CowNflow: A dataset on nitrogen flows and balances in dairy cows fed maize forage or herbage-based diets

description: Diet and animal characteristics have a significant impact on the nitrogen (N)-use efficiency by dairy cows. A dataset was built that compiles 28 N-balance experiments with Holstein dairy cows from 1983-2019, corresponding to 414 individual N flows, on a wide range of diets and animal characteristics. This dataset is composed of six Microsoft® files that correspond to six levels of information. The main file, “CowNflow_6_Cows_measurements” reports individual weekly measurements of dry matter intake, daily faeces and urine excretion, milk production and composition, cows characteristics, and chemical composition of diets, faeces, urine and milk. These raw data were used to calculate the N-balance, N-use efficiency and nutrients' in vivo total-tract digestibility. The experiments, conducted under standardised conditions, had multiples aims and offered a wide range of diets, including maize forage or herbage-based diet. The other five Excel files provide supplementary information at larger scales and describe experiment characteristics, experimental treatments, offered feeds along with their chemical composition, ingredients composition of compound feeds and cow characteristics.