cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3ndzqb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Eugenia uniflora",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014336-220831081235567/datasets/export for details.
DOI: 10.15468/dl.a65usf
title: Occurrence Download

description: A dataset containing 325925 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Epilobium palustre L., Epilobium collinum C.C.Gmel., Epilobium confusum Hausskn., Epilobium tournefortii Michalet, Epilobium obscurum Schreb., Epilobium parviflorum Schreb.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 325925 records from 577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0240079-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6gfp3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-80.3725888000000026 40.9700618000000034, -80.3725888000000026 40.9706391900000000, -80.3725888000000026 40.9715630299999987, -80.3725888000000026 40.9721404200000023, -80.3725888000000026 40.9726408300000031, -80.3725888000000026 40.9731797299999982, -80.3725888000000026 40.9739111000000022, -80.3718160899999958 40.9739111000000022, -80.3713137400000051 40.9739111000000022, -80.3702317399999941 40.9739111000000022, -80.3695361599999956 40.9739111000000022, -80.3685315999999972 40.9739111000000022, -80.3685315999999972 40.9731412399999968, -80.3685315999999972 40.9724483700000022, -80.3685315999999972 40.9717939900000019, -80.3685315999999972 40.9710241300000035, -80.3685315999999972 40.9700618000000034, -80.3697680199999951 40.9700618000000034, -80.3706954499999995 40.9700618000000034, -80.3713137400000051 40.9700618000000034, -80.3720865899999950 40.9700618000000034, -80.3725888000000026 40.9700618000000034))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1932",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Observation, Specimen, Machine Observation)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099613-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pgpfgs
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "TaxonKey is Aphelandra macrophylla Leonard"
 ]
}

 The dataset includes 110 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0369205-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.143025
title: Ostracon hiératique Ifao - ODM 1220_nu_2009_02609

description: Référence : nu_2009_02609<br />Site : Deir el-Médina<br />Secteur : Grand puits<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143026
title: Ostracon hiératique Ifao - ODM 1220_nu_2009_02610

description: Référence : nu_2009_02610<br />Site : Deir el-Médina<br />Secteur : Grand puits<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143027
title: Ostracon hiératique Ifao - ODM 1220_nu_2009_02611

description: Référence : nu_2009_02611<br />Site : Deir el-Médina<br />Secteur : Grand puits<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143028
title: Ostracon hiératique Ifao - ODM 1245_nu_2009_02612

description: Référence : nu_2009_02612<br />Site : Deir el-Médina<br />Secteur : Temple ptolémaïque<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143029
title: Ostracon hiératique Ifao - ODM 1246_nu_2009_02613

description: Référence : nu_2009_02613<br />Site : Deir el-Médina<br />Secteur : Grand puits<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143030
title: Ostracon hiératique Ifao - ODM 1246_nu_2009_02614

description: Référence : nu_2009_02614<br />Site : Deir el-Médina<br />Secteur : Grand puits<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143031
title: Ostracon hiératique Ifao - ODM 1240_nu_2009_02615

description: Référence : nu_2009_02615<br />Site : Deir el-Médina<br />Secteur : TT_290 (Arinefer)<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143032
title: Ostracon hiératique Ifao - ODM 1243_nu_2009_02617

description: Référence : nu_2009_02617<br />Site : Deir el-Médina<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143033
title: Ostracon hiératique Ifao - ODM 1244_nu_2009_02618

description: Référence : nu_2009_02618<br />Site : Deir el-Médina<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.143034
title: Ostracon hiératique Ifao - ODM 1241_nu_2009_02619

description: Référence : nu_2009_02619<br />Site : Deir el-Médina<br />Type : photographie<br />
DOI: 10.15468/dl.8u8j59
title: Occurrence Download

description: A dataset containing 5724 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pogostemon Desf."
 ]
}

 The dataset includes 5724 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0205436-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vy6zrz
title: Occurrence Download

description: A dataset containing 5974 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diospyros kaki L.f."
 ]
}

 The dataset includes 5974 records from 221 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095033-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gcrmu8
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Nothofagus moorei (F.Muell.) Krasser",
 "Year 2017-2022"
 ]
}

 The dataset includes 67 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175914-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bbzy7c
title: Occurrence Download

description: A dataset containing 13342170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "Year 1986-2023"
 ]
}

 The dataset includes 13342170 records from 1641 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0102729-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15454/0cnfws
title: Bioinformatic and statistical scripts for "Fort et al. 2020. Maternal effects shape seed fungal communities in Quercus petraea, New Phytologist"

description: This dataset contains R-scripts to analyse the diversity and composition of seed fungal communities (Fort et al. 2020. Maternal effects shape seed fungal communities in Quercus petraea. New Phytologist, https://doi.org/10.1111/nph.17153). The bioinformatic script was applied to raw sequences after paired-end sequences were joined using PEAR v0.9.10 (Zhang et al., 2014). Raw sequences are available at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA551388. The metadata and ASV tables are provided so that the statistical analysis scripts can be applied without running the bioinformatic steps. Scripts used to fit HMSC models (Ovaskainen et al., 2017) are provided.
DOI: 10.15454/0dcigo
title: Datasets for the "srnadiff" article.

description: The dataset contains all the BAM files in order to reproduce the results given in the article.
DOI: 10.15454/1.469094224299365e12
title: Environment Ontology for Livestock

description: The EOL ontology describes environmental conditions of livestock breeding. It includes feeding modalities, the structure of breeding systems and their environment.
DOI: 10.15454/1.4821558812795176e12
title: W4M00006_BPA-MMusculus

description: Study Metabolic shifts induced in vivo after perinatal exposure to low doses of BPA in CD-1 mice were assessed. In this study conducted by the ToxAlim-MeX team and the Tufts University school of medicine (Boston, MA, USA) in collaboration with the AXIOM-MetaToul-MetaboHUB platform, aqueous brain extracts from twenty-four 21-day-old pups whose mothers were exposed to either 0.025µg or 0.25µg BPA/kg BW/day during gestation and lactation were analyzed by NMR Spectroscopy. Dataset The dataset contains 24 Bruker files preprocessed using the TopSpin software (Bruker): Fourier Transformation was applied to free induction decays, then all the NMR spectra were phased and the baselines were corrected and calibrated with the TopSpin software. Workflow The workflow consists in the following steps: fixed-size bucketing (0.01ppm), normalization by the total intensity of the spectrum, Pareto scaling, PCA to detect outliers, OPLS-DA modeling of BPA dose, univariate hypothesis testing of significant variations with BPA dose (FDR &lt; 0.05) for discriminant buckets (OPLS-DA VIP &gt; 0.8), and metabolite annotation with the NMR Annotation tool. Comments Please note that this pairwise comparison was not presented in the publication by Cabaton et al. (2013).
DOI: 10.15454/1.4894016754286177e12
title: Vocabulary for analysis and experimentation on terrestrial and aquatic ecosystems

description: The anaeeThes thesaurus aims at providing a controlled vocabulary for the semantic description of the study of continental ecosystems and their biodiversity. It has been developed within the framework of the AnaEE-France infrastructure through an iterative process combining both top down and bottom up approaches: import of concepts from other thesauri and collection of concepts used in the AnaEE data bases and/or modeling platforms. The thesaurus consists of concepts handled in different main thematic areas:Abiotic (atmosphere, climate, hydrosphere, litosphere, …); Biotic (animals, plants, micro-organisms, biodiversity, …); Chemical compounds; Experimentation and observation (instrument, method, protocol, measurement, quality, infrastructure …); Ecosystems (type, structure, functioning …); Modeling (formalism, platform, type of model, computer language …); Disciplines (disciplinary and scientific fields); Unit (units of the international system, inherited from the OBOE–standards ontology). anaeeThes contains 12 top concepts. It contains nearly 3320 concepts, of which about 1500 are also offered in French. 360 concepts are inherited from the OBOE-standards ontology, while 748 concepts about soils and their characteristics were created using the « Référentiel pédologique 2008 – AFES» and « World reference base for soil resources 2006 – FAO ». Approximately 400 concepts are mapped to Agrovoc and 280 to Gemet thesauri. Approximately 480 concepts have a definition.The hierarchy offers up to 8 depth levels. Although the headings of the first and second levels are now stable, it is still evolving, especially on the issue of translation and mapping/alignment.
DOI: 10.15454/1.4502762931471938e12
title: Multi-scale Multi-step ontology

description: The Multi-scale Multi-step ontology (MS²O) is an ontology to describe transformation processes. IMPORTANT : MS²O is obsolete. Please use Process and Observation Ontology (https://doi.org/10.15454/XSVVBW) instead
DOI: 10.15454/1.5009072354498936e12
title: A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

description: Abstract:The dataset comprises 12X.v2 grapevine reference genome assembly and its VCost.v3 gene annotation in Genbank format. The 12X.v2 chromosome assembly is based on the scaffolds of the grapevine reference genome build (FN594950-FN597014, EMBL release 102; Vitis vinifera cv. PN40024). The data set is provided in support of the data paper: “A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)” by Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Mohellibi N, Guichard C, Choisne N, Rombault S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Ruztenholtz C, Morgante M, Le Paslier M-C, Brunel D, Adam-Blondon A-F (Genomic Data, 2017, https://doi.org/10.1016/j.gdata.2017.09.002)
DOI: 10.15454/2dvozs
title: A single bout of ultra-endurance exercise reveals early signs of muscle aging in master athletes

description: Middle-aged (37Y) and older master (50Y) highly-trained athletes performed a 24-h treadmill run (24TR). Vastus lateralis muscle biopsies were collected before and after the run and assessed for proteomics, fiber morphometry, intramyocellular lipid droplets (LD), mitochondrial oxidative activity, extracellular matrix (ECM) and micro-vascularisation. Before 24TR, muscle fiber type morphometry, intramyocellular LD, oxidative activity, ECM and micro-vascularisation were similar between master and middle-aged runners. For 37Y runners, 24TR was associated with ECM thickening, increased capillary tortuosity, and 89% depletion of LD in type-I fibers. In contrast for 50Y runners, 24TR did not alter ECM and capillarization and poorly depleted LDs. Moreover, impaired SDH activity and functional class scoring of proteomes suggested reduced oxidative phosphorylation exclusively in 50Y muscle post-24TR. Collectively, our data support that middle-aged and master endurance athletes exhibit distinct transient plasticity in response to a single bout of ultra-endurance exercise, which may constitute early signs of muscle aging for master athletes.
DOI: 10.15454/2vz16d
title: Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication.

description: Different Variant data set combining genotypic data data from the newly sequenced strains and data from available genomes sequences obtained at SGD. Data at vcf format or at hapmap format (.ped files).
DOI: 10.15454/4gnnos
title: Statistiques spatio-temporelles par petite région agricole des teneurs en ETM et de propriétés pédologiques issues d’observations collectées dans le cadre du programme BDETM

description: L’ADEME a financé deux programmes de collecte d’analyses de sols en éléments traces métalliques. Ces deux campagnes ont été réalisées par l’Inra. La première collecte, effectuée en 1997 et 1998, a permis de recueillir des analyses pour plus de 11 000 sites provenant principalement d’une trentaine de départements métropolitains.La nouvelle collecte s’est déroulée de novembre 2008 à janvier 2010. Elle a été réalisée selon les mêmes principes que la première mais avec de plus grands moyens informatiques. Elle inclut toutes les données déjà rassemblées et traitées en 1998 et contient plus de 73 400 sites. La répartition à l’échelon national est bien meilleure que dans le cas de la première collecte de 1998 : il n’y a qu’un seul département pour lequel aucune donnée n’a pu être recueillie. L’immense majorité des analyses récoltées provient de plans d’épandages de boues d’épuration et dans une moindre mesure de programmes scientifiques.Les analyses concernent 7 ETM mesurés avec deux méthodes (extraction à l’eau régale ou HF) : cadmium, chrome, cuivre, mercure, nickel, plomb, zinc. Elle a permis de collecter également 5 propriétés pédologiques : la texture (argile, limons, sables), le carbone organique, la CEC et le pH dans l’eau.Un ensemble de statistiques sont calculées sur des sous populations par tranche temporelle de 10 ans et par PRA. Attention, il est important de noter qu’il n’a pas été fait de distinction quant à la méthode d’extraction dans le calcul des statistiques.
DOI: 10.15454/52j8ys
title: Data on cow activity in relation to health and welfare

description: This dataset contains hours per hours the activity level of cows on four farms. These data were used in Wagner et al. 2021. The dataset contains 4 files, one for each farm. Files are structured as follows: cow working id; date; hour (integer); the time (s) spent 'walking' during one hour (the cow is positioned 'in alleys'); the time (s) spent 'resting’ during one hour (the cow is in a resting area (typically cubicles)); the time (s) spent 'eating' during one hour (the cow is positioned at the feeding table); the activity level (unitless), which is the weighted sum of the time spent in each activity (with the following weights: -0.23 for resting, +0.16 for in alleys, and +0.42 for eating). Due to the weights, the hourly activity level can range from -828 (i.e. -0.23*3600) to 1512 (i.e. 0.42*3600); finally, for each of the 11 types of events, a boolean is provided, for the question "is there this type of event on this hour ?" (i.e. 1 means this type of event were reported for this hour; 0 means that this type of event were not reported for this hour). Note that in fact daily events are reported here at hourly scale. There are 11 types of events: oestrus; calving; lameness includes all types of lameness and issues on claw or leg; mastitis includes all types of mastitis; Event LPS is specific to experimentation as it is for administered lipopolysaccharide (LPS) in the mammary gland on one day to induce inflammation; Event acidosis stands for subacute ruminal acidosis; Event labelled 'other_disease’, which contains all other diseases such as colic, diarrhea, ketosis, milk fever or other infectious disease; Event accidents contains all types of accidents such as retained placenta or vaginal laceration; Event disturbance is mild intervention on animal (e.g. late feeding, alarm test, animal tied for injection, claw trimming, drying of the cow) and other issues on the day but that did not concerned management changes; Event mixing is for when cows were mixed or moved to another park. Event labelled ‘management_changes’ contains marginal management such as ration changes or bed filling. This event is reported in the dataset, but is not considered as influent on the animal behaviour; A final Boolean sum up the information on whether this hour is considered as normal (i.e. if all the booleans (without considering the management changes one) are equal to 0 then this hour can be considered as normal, then the boolean is set to 1). Dataset 2 was also used in Wagner et al., 2020 https://doi.org/10.1016/j.compag.2020.105233 and in Wagner et al., 2020, https://doi.org/10.1007/978-3-030-59491-6_32
DOI: 10.15454/2ydsbl
title: Leaf microbiome data for European cultivated grapevine (Vitis vinifera L.) during downy mildew (Plasmopara viticola) epidemics in three wine-producing regions in France

description: Grapevine downy mildew (Plasmopara viticola) is a major disease of European cultivated grapevine (Vitis vinifera L.) against which a large amount of synthetic pesticides are used. Developing microbial biocontrol of P. viticola could reduce the use of pesticides in viticulture and preserve human and environmental health. To achieve this goal, it is necessary to better understand the interactions between P. viticola and the vine foliar microbiome. Here we present metabarcoding datasets describing the bacterial and fungal communities from more than 500 leaf samples collected during powdery mildew epidemics in three major wine-producing regions in France. The microbiome of both healthy tissues and disease lesions was characterized. P. viticola abundance was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata describing sampling sites and tissue health condition and the code used for bioinformatic and descriptive statistical analysis.
DOI: 10.15454/9rucep
title: A dataset of 9.896 single nuclear polymorphisms for 112 wild grapes, obtained with the GrapeReSeq 18K Vitis chip

description: The dataset, comprising 9.896 SNPs for 112 wild grapes (Vitis vinifera subsp. sylvestris), is made available here in support of the paper : Ramos-Madrigal J, Wiborg Runge AK, Bouby L, Lacombe T, Samaniego-Castruita JA, Adam-Blondon AF, Figueiral I, Hallavant C, Martínez-Zapater JM, Schaal C, Töpfer R, Petersen B, Sicheritz-Pontén T, This P, Bacilieri R, Gilbert MTP, Wales, 2019. Palaeogenomic insights into the origins of French grapevine diversity. Submitted to Nature Plants, 2019. These 9.869 SNPs are a subset of the 10.207 SNPs for cultivated grapes previously published by Le Paslier et al, 2018 (https://doi.org/10.15454/1.4861359557068474E12). Plant material was harvested in two grapevine collections (FAO WIEWS instcode FRA139 and DEU098), respectively: A) France, “INRA Domaine de Vassal, Marseillan-Plage” (http://www6.montpellier.inra.fr/vassal) ; and B) Germany, “JKI Geilweilerhof, Siebeldingen” (http://www.deutsche-genbank-reben.julius-kuehn.de/)
DOI: 10.15454/c4qoet
title: Raw data - resistance Robijn - multiinfections

description: Experimental data on resistance to late blight in potato cv Robijn under multiinfections
DOI: 10.15454/1.4382637738008071e12
title: Wheat Trait and Phenotype Ontology

description: Wheat Trait and Phenotype Ontology is an ontology of wheat traits and environmental factors that affect these traits. They include resistance to disease, development nutrition, bread quality, etc. Environmental factors include biotic and abiotic factors.
DOI: 10.15454/15rxtu
title: Microprung 16S

description: 16S sequence fasta file of the 103 samples of the Microprung study and associated metadata
DOI: 10.15454/1afkz2
title: Enabling reusability of plant phenomic datasets with MIAPPE 1.1 - Supplementary dataset INRA Wheat

description: This is a subset of the dataset "Winter wheat (Triticum aestivum L) phenotypic data from the multiannual, multilocal field trials of the INRA Small Grain Cereals Network." (doi:10.15454/1.4489666216568333E12). It is an ISA-Tab archive for the INRA wheat dataset, accompanying the Enabling reusability of plant phenomic datasets with MIAPPE 1.1 paper