cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17049350
title: tidyexposomics Data Bundle

description: This bundle contains curated datasets used in the vignettes and ontology annotation workflows of the tidyexposomics Bioconductor package. The data are derived from the ISGlobal Exposome Data Challenge 2021 (Maitre et al., Environment International, 2022; DOI: 10.1016/j.envint.2022.107422). The original challenge datasets are available on Figshare, Project 98813 (licensed under CC-BY 4.0) and on GitHub (isglobal-exposomeHub/ExposomeDataChallenge2021). Please cite the original study and data creators when using this bundle.

This Zenodo record provides a processed version of the challenge data to support reproducibility of examples within tidyexposomics. It is not a replacement for the full dataset and users requiring complete data should consult the original repositories.

Contents



omics_list.zip: multi-omics matrices (gene expression, DNA methylation, metabolomics).

fdata.zip: feature-level metadata corresponding to each omic dataset.

meta.zip: sample-level metadata.

annotated_cb.zip: annotated codebook for exposure variables.

chebi.zip: snapshot of the Chemical Entities of Biological Interest (ChEBI) ontology (retrieved 2025-06-19).

ecto.zip: snapshot of the Environmental Conditions, Treatments, and Exposures (ECTO) ontology (retrieved 2025-06-19).

hpo.zip: snapshot of the Human Phenotype Ontology (HPO) (retrieved 2025-06-19).


Citation

If you use this data bundle, please cite both:



The original ISGlobal Exposome Data Challenge paper (Maitre et al., 2022, Env. Int. DOI: 10.1016/j.envint.2022.107422).

This Zenodo record (DOI provided by Zenodo).
DOI: 10.17026/dans-zvs-97et
title: Proefsleuvenonderzoek Wijk en Aalburg Maasdijk 207 Proefsleuvenonderzoek aan de Maasdijk 207 te Wijk en Aalburg in de gemeente Aalburg

description: &lt;p&gt;In het noordelijk gelegen terreindeel komt onder de laag recent geroerde/verstoorde grond van minimaal 85 tot 110 cm dik een oude woongrond voor die qua kleuring en textuur in drie lagen is onder te verdelen. Aangetroffen vondstmateriaal, voornamelijk in de vorm van gebruiksaardewerk en bouwkeramiek, geeft aan dat het onderste deel van de oude woongrond aan het einde van de Late-Middeleeuwen (14e/15e eeuw) is ontstaan en doorloopt in de Nieuwe tijd. Onder de oude woongrond komen kronkelwaardafzettingen (Cg-horizont) voor die gesedimenteerd zijn tijdens de actieve fase van de meandergordel/stroomgordel van Biesheuvel - Hamer. Op de overgang van de oude woongrond naar de natuurlijke en onverstoorde bodemopbouw zijn een aantal sporen aangetroffen in de vorm van twee kuilen en waarschijnlijk twee paalkuilen. Vondstmateriaal uit deze sporen geven een datering in de 17e tot 18e eeuw. Beschikbaar kaartmateriaal geeft aan dat er in de directe omgeving van het plangebied historische bewoning aanwezig was dan wel nog aanwezig is langs de Maasdijk en op de hoek van de straten Spijk en Den Oudert. Op basis van de aangetroffen sporen kan niet met zekerheid worden aangegeven of dat deze behoren tot een op zichzelf staande structuur/houten constructie die buiten de de proefsleuf doorloopt (zowel in noordelijke als in zuidelijke richting), of dat het sporen betreffen die tot de periferiezone behoren van het ten noorden aangrenzende historische erf aan de Maasdijk. Van het van nature gevormde bodemprofiel, in de vorm van een kalkhoudende ooivaaggrond die in het oostelijk gelegen terreindeel is aangetroffen, zijn geen restanten meer aangetroffen. Aangezien in het oostelijk gelegen terreindeel wel een natuurlijk bodemprofiel is aangetroffen en de top van de C-horizont zich op een diepte van circa 1 m +NAP bevindt, zal bewerking door menselijke activiteiten, en daarmee de vorming van een oude woongrond, reiken tot in de oorspronkelijke top van de C-horizont. In het oostelijk gelegen terreindeel is, in overeenstemming met de resultaten van het archeologisch vooronderzoek, geen woongrond aangetroffen. Het aanwezige bodemprofiel is afgezien van de huidige bouwvoor intact en betreft een ooivaaggrond, gevormd in de top van oeverwalafzettingen die eveneens gesedimenteerd zijn tijdens de actieve fase van de meandergordel/stroomgordel van Biesheuvel - Hamer. Archeologische resten dan wel sporen zijn echter niet aangetroffen.&lt;/p&gt;
DOI: 10.17026/dans-zpr-jyp8
title: Archeologische begeleiding Almkerk Provincialeweg Noord Waterberging RWB 2 Archeologische begeleiding aan de Provincialeweg Noord Waterberging RWB 2 te Almkerk in de gemeente Woudrichem

description: &lt;p&gt;Er zijn geen sporenclusters waargenomen waaruit kan worden opgemaakt dat binnen het plangebied (grotere) structuren aanwezig zijn. De ontginningsgreppels uit de 19e -20e eeuw (Nieuwe tijd C) zijn niet zeldzaam en vanwege de beperkte hoeveelheid sporen enhet ontbreken van vondstmateriaal is de informatie waarde laag. De ensemblewaarde is laag omdat er geen bijzondere contextwaarde is aangetroffen waardoor er sprake is van meerwaarde.&lt;br&gt;De aangetroffen ontginningsgreppels hebben geen directe relatie met uit de omgeving bekende archeologische en historische locaties. Ze sluiten wel aan op de ontwikkeling zoals is weergegeven op historisch kaartmateriaal vanaf het begin van de 19e eeuw. Vanwege de beperkte informatiewaarde is de representativiteit van de ontginningsgreppels op laag gewaardeerd.&lt;/p&gt;
DOI: 10.15468/dl.9rpbpz
title: Occurrence Download

description: A dataset containing 9018 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago arborea",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9018 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032568-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6vyw9h
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago arborea",
 "Country is Morocco",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032570-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abty26
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago arborea",
 "Country is Malta",
 "HasCoordinate is true"
 ]
}

 The dataset includes 50 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032569-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.96panm
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Distichodus microps, Distichodus mossambicus, Distichodus nefasch, Distichodus noboli, Distichodus notospilus, Distichodus petersii, Distichodus rostratus, Distichodus rufigiensis, Distichodus schenga, Distichodus sexfasciatus, Dundocharax bidentatus, Eugnathichthys eetveldii, Eugnathichthys macroterolepis, Ichthyborus besse, Ichthyborus monodi, Ichthyborus ornatus, Ichthyborus quadrilineatus, Mesoborus crocodilus, Microstomatichthyoborus bashforddeani, Microstomatichthyoborus katangae, Monostichodus elongatus, Hemistichodus lootensi, Monostichodus lootensi, Hemistichodus mesmaekersi, Monostichodus mesmaekersi, Hemistichodus vaillanti, Nannaethiops unitaeniatus, Nannocharax altus, Hemigrammocharax angolensis, Nannocharax angolensis, Nannocharax ansorgii, Nannocharax brevis, Nannocharax elongatus, Nannocharax fasciatus, Nannocharax fasciolaris, Nannocharax gracilis, Nannocharax hollyi, Nannocharax intermedius, Nannocharax latifasciatus, Nannocharax lineomaculatus, Hemigrammocharax lineostriatus, Nannocharax lineostriatus, Nannocharax luapulae, Hemigrammocharax machadoi, Nannocharax machadoi, Nannocharax macropterus, Nannocharax maculicauda, Nannocharax micros, Hemigrammocharax minutus, Nannocharax minutus, Hemigrammocharax monardi, Nannocharax monardi, Hemigrammocharax multifasciatus, Nannocharax multifasciatus, Nannocharax niloticus, Nannocharax occidentalis, Hemigrammocharax ocellicauda, Nannocharax ocellicauda, Nannocharax ogoensis, Nannocharax parvus, Nannocharax procatopus, Nannocharax pteron, Nannocharax reidi, Nannocharax rubrolabiatus, Nannocharax schoutedeni, Nannocharax seyboldi, Nannocharax taenia, Hemigrammocharax uniocellatus, Nannocharax uniocellatus, Hemigrammocharax wittei, Nannocharax wittei, Neolebias ansorgii, Neolebias axelrodi, Neolebias gossei, Neolebias gracilis, Neolebias kerguennae, Neolebias lozii, Neolebias philippei, Neolebias powelli, Neolebias spilotaenia, Neolebias trewavasae, Neolebias trilineatus, Neolebias unifasciatus, Paradistichodus dimidiatus, Paraphago rostratus, Phago boulengeri, Phago intermedius, Phago loricatus, Xenocharax crassus, Hepsetus cuvieri, Hepsetus kingsleyae, Hepsetus lineatus, Hepsetus occidentalis, Hepsetus odoe, Alosa agone, Alosa algeriensis, Alosa alosa, Alosa fallax, Congothrissa gossei, Ethmalosa fimbriata)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((1.1382 20.0599,-7.8618 20.0599,-7.8618 11.0599,1.1382 11.0599,1.1382 20.0599))"
 ]
}

 The dataset includes 62 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032574-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t5tse6
title: Occurrence Download

description: A dataset containing 3225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Copaifera langsdorffii"
 ]
}

 The dataset includes 3225 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032573-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29594515
title: Design and Analysis of Randomized Trials to Estimate Spatio-Temporally Heterogeneous Treatment Effects

description: In this article, we consider randomized trial design to evaluate interventions with spatially or spatio-temporally heterogeneous effects. A common approach in this setting is the cluster randomized trial. In many cases, clusters are constituted as discrete subdivisions of a contiguous area of interest. However, cluster trials designed in this way may suffer from issues of spillover and may fail to capture the relevant spatial and temporal effects. We define possible randomization schemes and consider the identifiability of the causal effects of the intervention and the required trial design assumptions. We develop mixed model and dose response function specifications that satisfy the required assumptions. We show that the dose response functions are identifiable under certain randomization schemes and compare the performance of estimators in a simulation-based study. We demonstrate that obtaining valid inference may be difficult in these settings but that design-based estimators of confidence intervals and <i>p</i>-values generally perform well. Finally, we present design examples, including a re-analysis of data from a trial of an interventions to reduce the risk of malaria. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.29594515.v2
title: Design and Analysis of Randomized Trials to Estimate Spatio-Temporally Heterogeneous Treatment Effects

description: In this article, we consider randomized trial design to evaluate interventions with spatially or spatio-temporally heterogeneous effects. A common approach in this setting is the cluster randomized trial. In many cases, clusters are constituted as discrete subdivisions of a contiguous area of interest. However, cluster trials designed in this way may suffer from issues of spillover and may fail to capture the relevant spatial and temporal effects. We define possible randomization schemes and consider the identifiability of the causal effects of the intervention and the required trial design assumptions. We develop mixed model and dose response function specifications that satisfy the required assumptions. We show that the dose response functions are identifiable under certain randomization schemes and compare the performance of estimators in a simulation-based study. We demonstrate that obtaining valid inference may be difficult in these settings but that design-based estimators of confidence intervals and <i>p</i>-values generally perform well. Finally, we present design examples, including a re-analysis of data from a trial of an interventions to reduce the risk of malaria. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.29594515.v1
title: Design and analysis of randomized trials to estimate spatio-temporally heterogeneous treatment effects

description: In this article, we consider randomized trial design to evaluate interventions with spatially or spatio-temporally heterogeneous effects. A common approach in this setting is the cluster randomized trial. In many cases, clusters are constituted as discrete subdivisions of a contiguous area of interest. However, cluster trials designed in this way may suffer from issues of spillover and may fail to capture the relevant spatial and temporal effects. We define possible randomisation schemes and consider the identifiability of the causal effects of the intervention and the required trial design assumptions. We develop mixed model and dose response function specifications that satisfy the required assumptions. We show that the dose response functions are identifiable under certain randomisation schemes and compare the performance of estimators in a simulation-based study. We demonstrate that obtaining valid inference may be difficult in these settings but that design-based estimators of confidence intervals and p-values generally perform well. Finally, we present design examples, including a re-analysis of data from a trial of an interventions to reduce the risk of malaria.
DOI: 10.6084/m9.figshare.29473599
title: Kernel Density Estimation with Polyspherical Data and its Applications

description: A kernel density estimator for data on the polysphere Sd1×⋯×Sdr, with r,d1,…,dr≥1, is presented in this article. We derive the main asymptotic properties of the estimator, including mean square error, normality, and optimal bandwidths. We address the kernel theory of the estimator beyond the von Mises–Fisher kernel, introducing new kernels that are more efficient and investigating normalizing constants, moments, and sampling methods thereof. Plug-in and cross-validated bandwidth selectors are also obtained. As a spin-off of the kernel density estimator, we propose a nonparametric <i>k</i>-sample test based on the Jensen–Shannon divergence that is consistent against alternatives with non-homogeneous densities. Numerical experiments illuminate the asymptotic theory of the kernel density estimator and demonstrate the superior performance of the <i>k</i>-sample test with respect to parametric alternatives in certain scenarios. Our smoothing methodology is applied to the analysis of the morphology of a sample of hippocampi of infants embedded on the high-dimensional polysphere (S2)168 through skeletal representations (<i>s</i>-reps). Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.6084/m9.figshare.29473599.v2
title: Kernel Density Estimation with Polyspherical Data and its Applications

description: A kernel density estimator for data on the polysphere Sd1×⋯×Sdr, with r,d1,…,dr≥1, is presented in this article. We derive the main asymptotic properties of the estimator, including mean square error, normality, and optimal bandwidths. We address the kernel theory of the estimator beyond the von Mises–Fisher kernel, introducing new kernels that are more efficient and investigating normalizing constants, moments, and sampling methods thereof. Plug-in and cross-validated bandwidth selectors are also obtained. As a spin-off of the kernel density estimator, we propose a nonparametric <i>k</i>-sample test based on the Jensen–Shannon divergence that is consistent against alternatives with non-homogeneous densities. Numerical experiments illuminate the asymptotic theory of the kernel density estimator and demonstrate the superior performance of the <i>k</i>-sample test with respect to parametric alternatives in certain scenarios. Our smoothing methodology is applied to the analysis of the morphology of a sample of hippocampi of infants embedded on the high-dimensional polysphere (S2)168 through skeletal representations (<i>s</i>-reps). Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.
DOI: 10.17026/dans-xrd-wm4e
title: Proefsleuvenonderzoek Dussen Persleiding trace Sleeuwijk - Dussen Proefsleuvenonderzoek aan de Persleiding trace Sleeuwijk - Dussen te Dussen in de gemeente Werkendam

description: &lt;p&gt;Tijdens het proefsleuvenonderzoek zijn zeven vindplaatsen aangetroffen, waaronder vier greppels,een duiker, een vermoedelijke vlonder of steiger en een oude woongrond. Twee van de vindplaatsen werden behoudenswaardig geacht: de woongrond en de vlonder/steiger. De beide behoudenswaardige vindplaatsen zijn, na overleg met de bevoegde overheid, opgegraven. De behoudenswaardige archeologische resten zijn geborgen en worden ex situ behouden. Hiermee heeft het onderzochte terrein haar archeologische waarde verloren en kunnen de werkzaamheden doorgang vinden.&lt;/p&gt;
DOI: 10.6084/m9.figshare.29473599.v1
title: Kernel density estimation with polyspherical data and its applications

description: A kernel density estimator for data on the polysphere Sd1×⋯×Sdr, with r,d1,…,dr≥1, is presented in this paper. We derive the main asymptotic properties of the estimator, including mean square error, normality, and optimal bandwidths. We address the kernel theory of the estimator beyond the von Mises–Fisher kernel, introducing new kernels that are more efficient and investigating normalizing constants, moments, and sampling methods thereof. Plug-in and cross-validated bandwidth selectors are also obtained. As a spin-off of the kernel density estimator, we propose a nonparametric <i>k</i>-sample test based on the Jensen–Shannon divergence that is consistent against alternatives with non-homogeneous densities. Numerical experiments illuminate the asymptotic theory of the kernel density estimator and demonstrate the superior performance of the <i>k</i>-sample test with respect to parametric alternatives in certain scenarios. Our smoothing methodology is applied to the analysis of the morphology of a sample of hippocampi of infants embedded on the high-dimensional polysphere (S2)168 through skeletal representations (<i>s</i>-reps).
DOI: 10.15468/dl.vr9zyk
title: Occurrence Download

description: A dataset containing 20041 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Coronilla scorpioides"
 ]
}

 The dataset includes 20041 records from 441 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032571-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5067/seabass/pvst_gloc/data001
title: PVST_GLOC
DOI: 10.17026/dans-z2j-6svz
title: Proefsleuvenonderzoek Groenlo Mattelierstraat 19 Proefsleuvenonderzoek aan de Mattelierstraat 19 te Groenlo in de gemeente Oost Gelre

description: &lt;p&gt;De opgraving heeft sporen opgeleverd die doen vermoeden dat de locatie in de periode 1100 - 1500 onderdeel is geweest van een (achter)erf van een woonperceel. De vindplaats bestaat uit een cluster paalkuilen, twee waterputten en een kuil. Een gebouwstructuur is niet te herkennen in de paalkuilen. Door het ontbreken van een (hoofd)gebouw kunnen geen gedetailleerde uitspraken worden gedaan omtrent de vindplaats. Wel lijkt sprake te zijn van een abrupt einde aan het relatief intensieve gebruik van de locatie in de 15e eeuw. Sporen uit latere periodes zijn, tot in de Nieuwe tijd C, niet aangetrof-fen. Vermoedelijk is na de 15e eeuw enkel sprake geweest van gebruik als tuin/kleinschalig agrarisch gebruik. Dit is in overeenstemming met het latere gebruik zoals weergegeven op kaartmateriaal uit de 16e en de 19e eeuw.&lt;/p&gt;
DOI: 10.15468/dl.3m5tfb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemigrapsus sanguineus",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032577-250827131500795/datasets/export for details.
DOI: 10.15468/dl.rnv83f
title: Occurrence Download

description: A dataset containing 31828 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemigrapsus sanguineus",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 31828 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032576-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2n3gy3
title: Occurrence Download

description: A dataset containing 3638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hemigrapsus sanguineus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3638 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032578-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/dans-xyv-fz7k
title: Proefsleuvenonderzoek Sambeek Grotestraat 40 Proefsleuvenonderzoek aan de Grotestraat 40 te Sambeek in de gemeente Boxmeer

description: &lt;p&gt;Op basis van de resultaten is het niet waarschijnlijk dat zich binnen het geplande bouwvlakken of het gehele kavel een archeologische vindplaats bevindt, zonder dat daar tijdens het proefsleuvenonderzoek aanwijzingen zijn aangetroffen. Econsultancy adviseert zodoende om geen verder onderzoek uit te voeren en het plangebied vrij te geven voor verdere ontwikkeling.&lt;/p&gt;
DOI: 10.15468/dl.dk98ju
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago arborea",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 103 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032579-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.