cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ku24mw
title: Occurrence Download

description: A dataset containing 3540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Penaeus monodon",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 3540 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022997-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fd5gp
title: Occurrence Download

description: A dataset containing 3813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Schizachyrium scoparium",
 "Year 2023-2024"
 ]
}

 The dataset includes 3813 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022998-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adm3pp
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mikania neurocaula"
 ]
}

 The dataset includes 102 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022999-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/4497il
title: PAN-00178076 - monochrome glass bead barrel/spherical shaped (antique)

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00178076&lt;/p&gt;
description: Modified: 2025-08-07T17:05:36+02:00
DOI: 10.25345/c5f766m4q
title: MassIVE MSV000100078 - To Understand The Role Of Clinical Translation In Leukemia Using AML Patient Biopsies
title: AML stem cells were isolated from the Human Bone Marrow biopsies and were subjected to either untreated control or treated with ACC1 inhibitor 12.5uM, FSP1 inhibitor 12,5uM or in Synergistic combination of ACC1[12,5]+FSP1[6,25uM]. CD34- stem cells were isolated from healthy human bone marrow served as negative control. The synergistic combination displayed genes related to cholesterol synthesis and ferrinitinophagy
DOI: 10.15468/dl.bwttp6
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "GbifRegion is Latin America and the Caribbean",
 "Geometry POLYGON((-74.41442 10.08625,-73.20429 10.08625,-73.20429 11.40828,-74.41442 11.40828,-74.41442 10.08625))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Crocodylia"
 ]
}

 The dataset includes 173 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023000-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d43fcj
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "OccurrenceStatus is Present",
 "TaxonKey is Ralstonia pseudosolanacearum"
 ]
}

 The dataset includes 75 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023001-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qgp2k2
title: Occurrence Download

description: A dataset containing 1586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Perna perna",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 1586 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023003-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/icqhb2
title: PAN-00114684 - coin/coin-related, Victorinus (269-271)/Tetricus I (271-274), antoninianus

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00114684&lt;/p&gt;
description: Modified: 2025-08-26T08:46:02+02:00
DOI: 10.15468/dl.njnm7c
title: Occurrence Download

description: A dataset containing 4253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mobula birostris"
 ]
}

 The dataset includes 4253 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023002-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g6znt3
title: Occurrence Download

description: A dataset containing 27296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DecimalLatitude is -25.8629073673544,-25.7718944452895",
 "DecimalLongitude is 28.3413023644203,28.439414982272"
 ]
}

 The dataset includes 27296 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023004-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60520/ieda/114151
title: Supporting chemical information for "Two slowly cooled and chemically diverse basalt clasts identified in ANGSA core 73001"

description: Dataset corresponds to electron microprobe mineral analyses collected for two Apollo 17 basalts. Data were collected at the University of Arizona using the Cameca SX-100 electron microprobe.
description: Wilbur Z. E., Tatsch A., Barnes J. J., Stadermann A. C., Eckley A., Erickson T. M., Gross J., Shearer C. K., Zeigler R. A., McCubbin F. M., & the Angsa Science Team. (2025). Two slowly cooled and chemically diverse basalt clasts identified in ANGSA core 73001. Journal of Geophysical Research: Planets, 130(9), e2025JE009113.
DOI: 10.25574/25655
title: Chandra X-ray Observatory ObsId 25655

description: 2022 Fall Semester - Calibration Observations of Cas A
DOI: 10.15468/dl.hsmj4d
title: Occurrence Download

description: A dataset containing 1085 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Clavipanurgus, Dasyhesma, Bathanthidium, Aglae, Hemirhiza, Elaphropoda, Eulonchopria, Chlerogella, Rhathymus)"
 ]
}

 The dataset includes 1085 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023005-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/2liean
title: PAN-00114263 - coin/coin-related, Septimius Severus (193-211), denarius

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00114263&lt;/p&gt;
description: Modified: 2025-08-26T08:27:56+02:00
DOI: 10.15468/dl.ym67c3
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mikania premnifolia"
 ]
}

 The dataset includes 101 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023008-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kfhskg
title: Occurrence Download

description: A dataset containing 973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Perna viridis",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 973 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023007-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8cg6m
title: Occurrence Download

description: A dataset containing 363608 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hoplostethus atlanticus"
 ]
}

 The dataset includes 363608 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022973-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vbzh2x
title: Occurrence Download

description: A dataset containing 381271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trachurus trachurus"
 ]
}

 The dataset includes 381271 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022971-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dd.er6y43
title: WSP_GBIF_Collector_21490984

description: Generated from API search results. Project 21490984 - FRTP
DOI: 10.17026/ar/v1w9ri
title: PAN-00037160 - copper alloy nail with round flat head

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00037160&lt;/p&gt;
description: Modified: 2025-08-07T15:20:30+02:00
DOI: 10.15468/dl.x35bqa
title: Occurrence Download

description: A dataset containing 7988 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Photis longicaudata",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 7988 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023009-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17787643
title: Database of geological properties for the EU porous reservoir gas storage sites

description: This dataset accompanies HyDRA Deliverable D4.1: Database and Site Characterisation for Underground Hydrogen Storage in Porous Reservoirs and provides the first harmonised, pan-European geological database focused on porous-rock sites relevant to underground hydrogen storage (UHS).

The resource integrates data for 134 porous reservoir gas storage sites across Europe, including depth, temperature, pressure, lithology, porosity, permeability, salinity, depositional environment, formation names, basin definitions, operational status, and well information. The dataset supports microbial–geochemical risk assessment, laboratory experiment design, and strategic site selection for hydrogen storage.

Contents





Excel spreadsheet containing the HYDRA porous-reservoir attribute database, including:





Site identifiers, operator and location data




Working gas capacity and storage status




Reservoir depth, temperature, and pressure (sourced or derived)




Lithology and harmonised lithology categories




Porosity, permeability, salinity




Depositional environment, basin, formation




Number of wells and operational notes






GIS shapefiles providing spatial layers for:





Reservoir depth




Temperature and pressure




Lithology and lithology category




Porosity and permeability




Salinity




Basin and formation




Site status and operator






Supporting documentation summarising the methodology, harmonisation rules, normalisation procedures, data sources, assumptions, and limitations used to compile the dataset - please note due to limited data availability, many properties are unknown.



Purpose and Use

The dataset provides the geological baseline required to:





characterise the range of conditions present in European porous-rock storage sites,




identify representative lithologies and reservoir conditions for laboratory H₂–rock–fluid–microbe experiments,




support EU-wide screening of UHS potential,




inform microbial and geochemical risk assessments,




develop boundary conditions for reactive transport and geomechanical modelling.



It serves as a FAIR, reusable resource for researchers, industry operators, regulators, and stakeholders evaluating the suitability of porous reservoirs for hydrogen storage.

Provenance and Funding

This dataset was developed under the HyDRA Project – Diagnostic Tools and Risk Protocols to Accelerate Underground Hydrogen Storage, funded by the Clean Hydrogen Partnership and European Union (Grant Agreement No. 101192337). https://hydrahydrogen.eu/ 

Authors:Katriona Edlmann, Lubica Slabon, Ciaran Hemming, Andrew Kilpatrick (University of Edinburgh)

Citation

Please cite both the Zenodo record and HyDRA Deliverable D4.1 when using this dataset.
DOI: 10.5281/zenodo.17787644
title: Database of geological properties for the EU porous reservoir gas storage sites

description: This dataset accompanies HyDRA Deliverable D4.1: Database and Site Characterisation for Underground Hydrogen Storage in Porous Reservoirs and provides the first harmonised, pan-European geological database focused on porous-rock sites relevant to underground hydrogen storage (UHS).

The resource integrates data for 134 porous reservoir gas storage sites across Europe, including depth, temperature, pressure, lithology, porosity, permeability, salinity, depositional environment, formation names, basin definitions, operational status, and well information. The dataset supports microbial–geochemical risk assessment, laboratory experiment design, and strategic site selection for hydrogen storage.

Contents





Excel spreadsheet containing the HYDRA porous-reservoir attribute database, including:





Site identifiers, operator and location data




Working gas capacity and storage status




Reservoir depth, temperature, and pressure (sourced or derived)




Lithology and harmonised lithology categories




Porosity, permeability, salinity




Depositional environment, basin, formation




Number of wells and operational notes






GIS shapefiles providing spatial layers for:





Reservoir depth




Temperature and pressure




Lithology and lithology category




Porosity and permeability




Salinity




Basin and formation




Site status and operator






Supporting documentation summarising the methodology, harmonisation rules, normalisation procedures, data sources, assumptions, and limitations used to compile the dataset - please note due to limited data availability, many properties are unknown.



Purpose and Use

The dataset provides the geological baseline required to:





characterise the range of conditions present in European porous-rock storage sites,




identify representative lithologies and reservoir conditions for laboratory H₂–rock–fluid–microbe experiments,




support EU-wide screening of UHS potential,




inform microbial and geochemical risk assessments,




develop boundary conditions for reactive transport and geomechanical modelling.



It serves as a FAIR, reusable resource for researchers, industry operators, regulators, and stakeholders evaluating the suitability of porous reservoirs for hydrogen storage.

Provenance and Funding

This dataset was developed under the HyDRA Project – Diagnostic Tools and Risk Protocols to Accelerate Underground Hydrogen Storage, funded by the Clean Hydrogen Partnership and European Union (Grant Agreement No. 101192337). https://hydrahydrogen.eu/ 

Authors:Katriona Edlmann, Lubica Slabon, Ciaran Hemming, Andrew Kilpatrick (University of Edinburgh)

Citation

Please cite both the Zenodo record and HyDRA Deliverable D4.1 when using this dataset.
DOI: 10.6084/m9.figshare.30763049
title: Holocene reef growth R project for Macedo and van Woesik

description: This code was used for the analysis for "Growth rates for coral reefs peaked at 25 °C through the Holocene" by Tonya Macedo and Robert van Woesik. <br>Overview:Main dataset: "Holocene_Reef_Growth_Final.csv" is the final dataset used for modeling, containing 1,890 samples. Main goals:Use a GLMM in INLA to determine fixed effects for coral growth rates during the Holocene. Use deep learning to evaluate non-linear relationships between variables of interest and coral reef growth rates through the Holocene. Reproduce figures from the publication or generate new figures with new data. Main scripts: Holocene_INLA_GLMM.RSets up model formulasFits modelsCompares and visualizes INLA model resultsHolocene_Deep_Learning.RSets up the H2O deep learning environmentFits 30 models using 6 different deep learning configurationsCompares and visualizes model resultsHolocene_Figures.qmdReproduces the figures used in the manuscriptUsage guidance:Each script is set up so that it can be run standalone. There is no order that the scripts need to be run. The project uses the here package for reproducible file paths, no need to set working directory.The repository is organized so that it can be cloned and executed as an R project.
DOI: 10.6084/m9.figshare.30763049.v1
title: Holocene reef growth R project for Macedo and van Woesik

description: This code was used for the analysis for "Growth rates for coral reefs peaked at 25 °C through the Holocene" by Tonya Macedo and Robert van Woesik. <br>Overview:Main dataset: "Holocene_Reef_Growth_Final.csv" is the final dataset used for modeling, containing 1,890 samples. Main goals:Use a GLMM in INLA to determine fixed effects for coral growth rates during the Holocene. Use deep learning to evaluate non-linear relationships between variables of interest and coral reef growth rates through the Holocene. Reproduce figures from the publication or generate new figures with new data. Main scripts: Holocene_INLA_GLMM.RSets up model formulasFits modelsCompares and visualizes INLA model resultsHolocene_Deep_Learning.RSets up the H2O deep learning environmentFits 30 models using 6 different deep learning configurationsCompares and visualizes model resultsHolocene_Figures.qmdReproduces the figures used in the manuscriptUsage guidance:Each script is set up so that it can be run standalone. There is no order that the scripts need to be run. The project uses the here package for reproducible file paths, no need to set working directory.The repository is organized so that it can be cloned and executed as an R project.
DOI: 10.5281/zenodo.17789447
title: Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

description: This Zenodo record provides all processed datasets, MAGPIE inputs, and analysis scripts associated with the MAGPIE manuscript (Williams et al).

 

AbstractRecent developments in spatially resolved -omics have enabled the joint study of gene expression, metabolite levels and tissue morphology, offering greater insights into biological pathways. Integrating these modalities from matched tissue sections to probe spatially-coordinated processes, however, remains challenging.Here we introduce MAGPIE, a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections.We show MAGPIE’s generalisability and scalability on spatial multi-omics data from multiple tissues, combining Visium with MALDI and DESI mass spectrometry imaging. MAGPIE was also applied to new multimodal datasets generated with a specialised sampling strategy to characterise the metabolic and transcriptomic landscape in an in vivo model of drug-induced pulmonary fibrosis and to link small-molecule co-detection with endogenous lung responses.MAGPIE demonstrates the refined resolution and enhanced interpretability that spatial multimodal analyses provide for studying tissue injury especially in pharmacological contexts, and delivers a modular, accessible workflow for data integration

The repository is designed to enable reproducibility of integrative multi-omics analyses performed in the manuscript and facilitate extended analysis of the new and previously published datasets.

 



 

1. MAGPIE Inputs


The file magpie_inputs.zip contains separate folders for each dataset used in the manuscript. Each folder includes:





MSI data in a peak-by-pixel table (MSI_intensities) along with (x,y)-coordinates and other metadata (MSI_metadata) and (if available) an MSI H&E image (MSI_HE)

Visium Space Ranger outputs (from outs/ folder)




These inputs are ready to be used directly with the MAGPIE pipeline (see the MAGPIE GitHub repository).

 





 

2. Analysis scripts and processed data


The figure_notebooks.zip file contains qmd files and rendered htmls showing how the manuscript figures were generated and data/ which contains processed semla objects and other saved outputs used by these scripts. 

 

For more details on the contents of this record, see README.md