cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17472788
title: Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa - Revision 2

description: Raw data, supplemental datasets and intermediate files generated for the manuscript 'Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa' - REVISION 2.

 

Code for the analysis can be found in https://github.com/VishnuRaghuram94/SEPI .

 

Link to publication : https://doi.org/10.1099/mgen.0.001633

 

---- Changelog ----

2.0.2: 



Alignment information for plasmid CP146619.1 was missing from Dataset_S15 and has now been included


2.0.1: 



Added another table (S10) - Non-redundant PLSDB AMRFinder results

Fix error in table S10 (now table S11) - initially had uploaded the wrong BLAST results from an earlier date, now updated with results from Oct 6th 2025


2.0.0:



Increased number of publicly available genomes used from 229 to 465. All relevant tables updated accordingly. 

Added new table with fastq read mapping against plasmid reference sequences

Added new table with results from ISEScan (Insertion element search)

BEAST results removed


1.0.0: 



First release
DOI: 10.5281/zenodo.18543127
title: ADC target profiling in NSCLC: Generalizable AI separates TROP-2 and cMET phenotypes

description: This dataset accompanies the paper "ADC target profiling in NSCLC: Generalizable AI separates TROP-2 and cMET phenotypes" and provides comprehensive clinicopathological, molecular, and expression data for a cohort of resected non-small cell lung cancer (NSCLC) patients.

Contents:



Patient Data Table (cohort_data.csv)



QC flags (tumor content, rejection criteria for cMET/TROP-2)

Clinical characteristics (age, sex, smoking status, ECOG)

Tumor characteristics (histological subtype, grade, diameter)

Pathological staging (pTNM, UICC 8th edition)

Molecular pathology (mutation status for EGFR, KRAS, ALK, ROS1, TP53, and others)

Survival outcomes (OS)

AI-derived H-scores for:



TROP-2 (membranous)

TROP-2 (cytoplasmic)

cMET (membranous)



AI-derived cell phenotype counts per patient



TMA Spot Images



Immunohistochemistry-stained tissue microarray (TMA) spots for TROP-2 and cMET

Linked via case_uuid to the patient data table
DOI: 10.5281/zenodo.18494664
title: ADC target profiling in NSCLC: Generalizable AI separates TROP-2 and cMET phenotypes

description: This dataset accompanies the paper "ADC target profiling in NSCLC: Generalizable AI separates TROP-2 and cMET phenotypes" and provides comprehensive clinicopathological, molecular, and expression data for a cohort of resected non-small cell lung cancer (NSCLC) patients.

Contents:



Patient Data Table (cohort_data.csv)



QC flags (tumor content, rejection criteria for cMET/TROP-2)

Clinical characteristics (age, sex, smoking status, ECOG)

Tumor characteristics (histological subtype, grade, diameter)

Pathological staging (pTNM, UICC 8th edition)

Molecular pathology (mutation status for EGFR, KRAS, ALK, ROS1, TP53, and others)

Survival outcomes (OS)

AI-derived H-scores for:



TROP-2 (membranous)

TROP-2 (cytoplasmic)

cMET (membranous)



AI-derived cell phenotype counts per patient



TMA Spot Images



Immunohistochemistry-stained tissue microarray (TMA) spots for TROP-2 and cMET

Linked via case_uuid to the patient data table
DOI: 10.5281/zenodo.18543605
title: NextStat Replication Bundle: replication-rerun-prod-doi-18542624

description: Replication bundle for a published NextStat public benchmark snapshot. Includes rerun artifacts, snapshot_comparison.json, and a (draft) signed report template.

Published snapshot DOI: 10.5281/zenodo.18542624
Published snapshot URL: https://zenodo.org/records/18542624
Replication bundle sha256: 228287839063bbcdc2e411370cf8addbb2eef58a37b051ff33f000732f5087a8
description: Fill in the published snapshot DOI/URL and include sha256 of the replication bundle archive.
DOI: 10.5281/zenodo.18543606
title: NextStat Replication Bundle: replication-rerun-prod-doi-18542624

description: Replication bundle for a published NextStat public benchmark snapshot. Includes rerun artifacts, snapshot_comparison.json, and a (draft) signed report template.

Published snapshot DOI: 10.5281/zenodo.18542624
Published snapshot URL: https://zenodo.org/records/18542624
Replication bundle sha256: 228287839063bbcdc2e411370cf8addbb2eef58a37b051ff33f000732f5087a8
description: Fill in the published snapshot DOI/URL and include sha256 of the replication bundle archive.
DOI: 10.5281/zenodo.18543588
title: METABOLIK SINDROMLI  BEMORLARDA ODONTOGEN FLEGMONALARNI SUN'IY INTELLEKT YORDAMIDA DAVOLASHNI REJALASHTIRISH
DOI: 10.5281/zenodo.18543589
title: METABOLIK SINDROMLI  BEMORLARDA ODONTOGEN FLEGMONALARNI SUN'IY INTELLEKT YORDAMIDA DAVOLASHNI REJALASHTIRISH
DOI: 10.6084/m9.figshare.31229737
title: Epigenome-wide association meta-analysis summary statistics for circulating adiponectin (RODAM and AADM study)

description: This dataset contains summary statistics from epigenome-wide association study (EWAS) meta-analyses of circulating adiponectin conducted in West African populations from the RODAM and AADM studies.The Excel file includes multiple sheets:<b>Description</b>: overview of the dataset and explanation of all included sheets and variables.<b>Adiponectin_RODAM_AADM_T2D</b>: meta-analysis summary statistics combining RODAM and AADM cohorts across type 2 diabetes (T2D) status.<b>Adiponectin_RODAM_T2D_cases_controls</b>: cohort-specific meta-analysis results for the RODAM study, stratified by T2D status.<b>Adiponectin_AADM_T2D_cases_controls</b>: cohort-specific meta-analysis results for the AADM study, stratified by T2D status.For each CpG site, summary statistics include effect direction (Z-score), raw p-values, false discovery rate (FDR)-adjusted p-values, chromosome, genomic position, and gene annotation where applicable.Individual-level data are not included due to ethical and privacy restrictions. These summary statistics support the findings reported in the associated eBioMedicine manuscript.
DOI: 10.6084/m9.figshare.31229737.v1
title: Epigenome-wide association meta-analysis summary statistics for circulating adiponectin (RODAM and AADM study)

description: This dataset contains summary statistics from epigenome-wide association study (EWAS) meta-analyses of circulating adiponectin conducted in West African populations from the RODAM and AADM studies.The Excel file includes multiple sheets:<b>Description</b>: overview of the dataset and explanation of all included sheets and variables.<b>Adiponectin_RODAM_AADM_T2D</b>: meta-analysis summary statistics combining RODAM and AADM cohorts across type 2 diabetes (T2D) status.<b>Adiponectin_RODAM_T2D_cases_controls</b>: cohort-specific meta-analysis results for the RODAM study, stratified by T2D status.<b>Adiponectin_AADM_T2D_cases_controls</b>: cohort-specific meta-analysis results for the AADM study, stratified by T2D status.For each CpG site, summary statistics include effect direction (Z-score), raw p-values, false discovery rate (FDR)-adjusted p-values, chromosome, genomic position, and gene annotation where applicable.Individual-level data are not included due to ethical and privacy restrictions. These summary statistics support the findings reported in the associated eBioMedicine manuscript.
DOI: 10.5281/zenodo.18540296
title: Comparative genomics of different haplotypes in Ditylenchus destructor provides insights into their host preferences

description: Comparative Genomics of Different Haplotypes in Ditylenchus destructor Provides Insights into Their Host Preferences. Numerical source data for graphs and charts can be found in Supplementary Data 1–7.
DOI: 10.5281/zenodo.18540295
title: Comparative genomics of different haplotypes in Ditylenchus destructor provides insights into their host preferences

description: Comparative Genomics of Different Haplotypes in Ditylenchus destructor Provides Insights into Their Host Preferences. Numerical source data for graphs and charts can be found in Supplementary Data 1–7.
DOI: 10.5281/zenodo.18543691
title: STATE SUPPORT FOR SMALL AND MEDIUM BUSINESS DEVELOPMENT IN UZBEKISTAN: AN ANALYSIS OF PROGRAMS AND INITIATIVES FOR ENTREPRENEURSHIP PROMOTION
DOI: 10.5281/zenodo.18543690
title: STATE SUPPORT FOR SMALL AND MEDIUM BUSINESS DEVELOPMENT IN UZBEKISTAN: AN ANALYSIS OF PROGRAMS AND INITIATIVES FOR ENTREPRENEURSHIP PROMOTION
DOI: 10.5281/zenodo.18543627
title: Alcancía

description: Réplica de una alcancía producida en Fajalauza. La pieza no esta cocida. Presenta una morfología que presenta un cono en la parte superior adosado a un cilindro que da paso al cuerpo. Este es piriforme y tiene una abertura, necesaria para su uso. La base es plana.

Cronología: Contemporánea

Fotografías y modelo: (http://sketchfab.com/ibarramedinaA)

Este modelo forma parte de CEGRAM (Proyecto PID2022-140442NA-I00 financiado por MICIU/AEI/10.13039/501100011033/ y por FEDER, UE) e iCERAAM (Proyecto de Innovación docente: Ceramoteca medieval y moderna. Un instrumento docente y de divulgación. ICERAMM (PIB Tipo A nº 24-199), financiado por la Universidad de Granada)
DOI: 10.5281/zenodo.18543626
title: Alcancía

description: Réplica de una alcancía producida en Fajalauza. La pieza no esta cocida. Presenta una morfología que presenta un cono en la parte superior adosado a un cilindro que da paso al cuerpo. Este es piriforme y tiene una abertura, necesaria para su uso. La base es plana.

Cronología: Contemporánea

Fotografías y modelo: (http://sketchfab.com/ibarramedinaA)

Este modelo forma parte de CEGRAM (Proyecto PID2022-140442NA-I00 financiado por MICIU/AEI/10.13039/501100011033/ y por FEDER, UE) e iCERAAM (Proyecto de Innovación docente: Ceramoteca medieval y moderna. Un instrumento docente y de divulgación. ICERAMM (PIB Tipo A nº 24-199), financiado por la Universidad de Granada)
DOI: 10.5281/zenodo.17853530
title: Dataset for "Unified analysis of spatially-coupled absorption and saturation dynamics in multi-pass pumped thin-disk lasers"

description: This dataset includes relevant data and figures associated with the manuscript "Unified analysis of spatially-coupled absorption and saturation dynamics in multi-pass pumped thin-disk lasers".
DOI: 10.5281/zenodo.17853529
title: Dataset for "Unified analysis of spatially-coupled absorption and saturation dynamics in multi-pass pumped thin-disk lasers"

description: This dataset includes relevant data and figures associated with the manuscript "Unified analysis of spatially-coupled absorption and saturation dynamics in multi-pass pumped thin-disk lasers".
DOI: 10.15468/dl.p2bqt6
title: Occurrence Download

description: A dataset containing 12015 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Italian rotifer records"
 ]
}

 The dataset includes 12015 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002369-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5vnstd
title: Occurrence Download

description: A dataset containing 23638 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Great Crested Newt presence records determined from Class Licence return documents 2013-2018"
 ]
}

 The dataset includes 23638 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002385-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pegjgn
title: Occurrence Download

description: A dataset containing 1839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Austria",
 "Geometry POLYGON((8.92266 45.36599,17.81887 45.36599,17.81887 48.9444,8.92266 48.9444,8.92266 45.36599))",
 "HasGeospatialIssue is false",
 "TaxonKey is Triturus carnifex"
 ]
}

 The dataset includes 1839 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002384-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g4gqr6
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidepecreum eoum"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002386-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjv9pt
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centauropsis fruticosa"
 ]
}

 The dataset includes 65 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002371-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjg5xc
title: Occurrence Download

description: A dataset containing 38865 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alternanthera philoxeroides",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil)"
 ]
 }
 }
 ]
}

 The dataset includes 38865 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002389-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jb2c2k
title: Occurrence Download

description: A dataset containing 1482 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnolia stellata"
 ]
}

 The dataset includes 1482 records from 192 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002388-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wfmz6
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lithocarpus echinophorus"
 ]
}

 The dataset includes 30 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002390-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7y4qmw
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Equus kiang kiang"
 ]
}

 The dataset includes 174 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002391-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e6ts9n
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carabus hungaricus"
 ]
}

 The dataset includes 329 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002367-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmqehp
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Castanopsis wattii"
 ]
}

 The dataset includes 52 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002387-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhhk2d
title: Occurrence Download

description: A dataset containing 36515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 36515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002376-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufw3y6
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CatalogNumber is one of (PC0781481, PC0781460, PC0796887)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002374-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tsw55v
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Magnolia rabaniana"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002366-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmdxer
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gibbula turbinoides",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 329 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002368-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q8jgyt
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mallotus roxburghianus"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002382-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcqceh
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "OccurrenceStatus is Present",
 "TaxonKey is Elephas maximus"
 ]
}

 The dataset includes 224 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002392-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2bs42
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mangifera khasiana"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002393-260208012135463/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.29899274
title: Dataset of typical terminal lake and surrounding oasis outlines in arid/semi-arid endorheic basins based on remote sensing data

description: Terminal lakes and surrounding oases are critical investigating water resource sustainability in arid and semi-arid endorheic basins. However, comprehensive long-term datasets for monitoring these remain scarce. Based on optical remote sensing imagery and land use data, we constructed a dataset using a combination of optical remote sensing indexes and manual corrections, covering 1985 to 2022 and showcasing outlines of typical terminal lakes and surrounding oases in arid/semi-arid endorheic basins. Encompassing the terminal lakes and surrounding oases of 12 inland rivers worldwide, this dataset achieves the verification accuracy of the terminal lakes and oases being 89.18% and 87.53% respectively, and the kappa coefficients being 0.8569 and 0.8614 respectively (as verified against Google Earth historical images). It provides researchers with a valuable tool for analyzing long-term deformation and area variations in these terminal lakes and surrounding oases. Furthermore, it facilitates the identification of sustainable development strategies in these basins, especially in the context of the combined impacts of climate change and human activities.
DOI: 10.6084/m9.figshare.29899274.v1
title: Dataset of typical terminal lake and surrounding oasis outlines in arid/semi-arid endorheic basins based on remote sensing data

description: Terminal lakes and surrounding oases are critical investigating water resource sustainability in arid and semi-arid endorheic basins. However, comprehensive long-term datasets for monitoring these remain scarce. Based on optical remote sensing imagery and land use data, we constructed a dataset using a combination of optical remote sensing indexes and manual corrections, covering 1985 to 2022 and showcasing outlines of typical terminal lakes and surrounding oases in arid/semi-arid endorheic basins. Encompassing the terminal lakes and surrounding oases of 12 inland rivers worldwide, this dataset achieves the verification accuracy of the terminal lakes and oases being 89.18% and 87.53% respectively, and the kappa coefficients being 0.8569 and 0.8614 respectively (as verified against Google Earth historical images). It provides researchers with a valuable tool for analyzing long-term deformation and area variations in these terminal lakes and surrounding oases. Furthermore, it facilitates the identification of sustainable development strategies in these basins, especially in the context of the combined impacts of climate change and human activities.
DOI: 10.3929/ethz-c-000787224
title: Dataset for Article "Controlling the sign of optical forces using metaoptics"
DOI: 10.15468/dl.99zvja
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Observatoire Pelagis - Reseau National Echouage (French stranding network) strandings 1934-2020, EOD – eBird Observation Dataset, Réseau National Echouages de mammifères marins - Observations de mammifères marins du Réseau National d'Echouages en Métropole, iNaturalist Research-grade Observations)",
 "GadmGid is FRA.10.1_1",
 "Geometry POLYGON((-1.3955 45.97395,-1.39138 45.97395,-1.39138 45.97687,-1.3955 45.97687,-1.3955 45.97395))",
 "OccurrenceStatus is Present",
 "Year 2016-2026"
 ]
}

 The dataset includes 147 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002398-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.