cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.uqbh55
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Barbodes katolo)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045932-250827131500795/datasets/export for details.
DOI: 10.15468/dl.xrxe6s
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Ecuador",
 "HasCoordinate is true"
 ]
}

 The dataset includes 122 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045933-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mbseg7
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Equatorial Guinea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045934-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ucr8v5
title: Occurrence Download

description: A dataset containing 405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 405 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045935-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17086215
title: Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum
title: Coordinated cellular responses for quantitative disease resistance involve a calcium-associated switch in transcriptional noise

description: Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum (24hpi).

sc_jones2025.Rds and sc_jones2025.RData are identical R objects that can be loaded using either readRDS or load (as preferred). The data is stored as a SingleCellExperiment object which can easily be converted to other common formats (e.g. Seurat).

Minimal steps to load the dataset in R are:

if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("SingleCellExperiment")

load("sc_jones2025.RData") # creates object sc_jones2025
# or
sc_jones2025 <- readRDS("sc_jones2025.Rds")

library(SingleCellExperiment)

colData(sc_jones2025)
rowData(sc_jones2025)
reducedDimNames(sc_jones2025)

colData contains cluster and celltype assignments for each nucleus under e.g. cluster_l1 and cluster_l1_celltypes, for the level 1 clusters.

The main datasets used in the manuscript are accessible by:

reducedDim(sc_jones2025, "HARMONY")
reducedDim(sc_jones2025, "HARMONY.TSNE")reducedDim(sc_jones2025, "CNMF")

assay(sc_jones2025, "counts")
assay(sc_jones2025, "logcounts")
assay(sc_jones2025, "normcounts")

 

For those not using R or if compatibility issues arise, these main datasets and associated column and row data are also included as tsv files in sc_jones2025_tsvs.zip. Tables can be joined by either the "gene" or "cell" columns.
DOI: 10.5281/zenodo.17086216
title: Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum
title: Coordinated cellular responses for quantitative disease resistance involve a calcium-associated switch in transcriptional noise

description: Processed single nucleus data of Arabidopsis thaliana leaves infected by Sclerotinia sclerotiorum (24hpi).

sc_jones2025.Rds and sc_jones2025.RData are identical R objects that can be loaded using either readRDS or load (as preferred). The data is stored as a SingleCellExperiment object which can easily be converted to other common formats (e.g. Seurat).

Minimal steps to load the dataset in R are:

if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("SingleCellExperiment")

load("sc_jones2025.RData") # creates object sc_jones2025
# or
sc_jones2025 <- readRDS("sc_jones2025.Rds")

library(SingleCellExperiment)

colData(sc_jones2025)
rowData(sc_jones2025)
reducedDimNames(sc_jones2025)

colData contains cluster and celltype assignments for each nucleus under e.g. cluster_l1 and cluster_l1_celltypes, for the level 1 clusters.

The main datasets used in the manuscript are accessible by:

reducedDim(sc_jones2025, "HARMONY")
reducedDim(sc_jones2025, "HARMONY.TSNE")reducedDim(sc_jones2025, "CNMF")

assay(sc_jones2025, "counts")
assay(sc_jones2025, "logcounts")
assay(sc_jones2025, "normcounts")

 

For those not using R or if compatibility issues arise, these main datasets and associated column and row data are also included as tsv files in sc_jones2025_tsvs.zip. Tables can be joined by either the "gene" or "cell" columns.
DOI: 10.6084/m9.figshare.30086668
title: Metabolic plasticity supports a flexible nutritional symbiosis in Cardiocondyla ants

description: Insects have repeatedly evolved intimate nutritional symbioses that become fixed and indispensable. Yet in some ant lineages, a notable exception has emerged—ancient nutritional symbionts are maintained in a flexible manner, with complete losses observed at both the individual and colony level in natural populations. How such labile symbioses are regulated to ensure their long-term persistence in host lineages remains an evolutionary puzzle. Here, we use <i>Cardiocondyla obscurior</i>, which hosts the vertically-transmitted symbiont <i>Cand.</i> <i>Westeberhardia</i> <i>cardiocondylae </i>yet shows natural losses, to uncover the regulatory dynamics and functional role of this flexible symbiosis. Using symbiont-removal, dietary, and multi-omics assays, we show that <i>Westeberhardia</i> primarily provisions shikimate-derived nutrients, notably tyrosine and folate, and contributes to colony resilience under protein starvation. RNA in situ hybridisation localises expression of key biosynthetic genes to <i>Westeberhardia</i>-harbouring bacteriocytes. Yet strikingly, in the absence of the symbiont, ants adapt by upregulating host genes to derive tyrosine from external sources. This context-dependent plasticity extends to symbiont regulation: ants appear to modulate symbiont density in response to nutritional demands, potentially through sugar metabolism and transport pathways. Together, our findings suggest that host metabolic versatility may explain how ants are able to maintain an ancient, yet labile, nutritional symbiosis.
DOI: 10.6084/m9.figshare.30086668.v1
title: Metabolic plasticity supports a flexible nutritional symbiosis in Cardiocondyla ants

description: Insects have repeatedly evolved intimate nutritional symbioses that become fixed and indispensable. Yet in some ant lineages, a notable exception has emerged—ancient nutritional symbionts are maintained in a flexible manner, with complete losses observed at both the individual and colony level in natural populations. How such labile symbioses are regulated to ensure their long-term persistence in host lineages remains an evolutionary puzzle. Here, we use <i>Cardiocondyla obscurior</i>, which hosts the vertically-transmitted symbiont <i>Cand.</i> <i>Westeberhardia</i> <i>cardiocondylae </i>yet shows natural losses, to uncover the regulatory dynamics and functional role of this flexible symbiosis. Using symbiont-removal, dietary, and multi-omics assays, we show that <i>Westeberhardia</i> primarily provisions shikimate-derived nutrients, notably tyrosine and folate, and contributes to colony resilience under protein starvation. RNA in situ hybridisation localises expression of key biosynthetic genes to <i>Westeberhardia</i>-harbouring bacteriocytes. Yet strikingly, in the absence of the symbiont, ants adapt by upregulating host genes to derive tyrosine from external sources. This context-dependent plasticity extends to symbiont regulation: ants appear to modulate symbiont density in response to nutritional demands, potentially through sugar metabolism and transport pathways. Together, our findings suggest that host metabolic versatility may explain how ants are able to maintain an ancient, yet labile, nutritional symbiosis.
DOI: 10.15468/dl.3pd32g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Iraq",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045936-250827131500795/datasets/export for details.
DOI: 10.34740/kaggle/dsv/13010019
title: Mahanagar Yatayat Transport Dataset
DOI: 10.15468/dl.6rqxrk
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045938-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kkhnmd
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Sao Tome and Principe",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045937-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfb39q
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arius madagascariensis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045939-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3eqgwu
title: Occurrence Download

description: A dataset listing the 8319 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Plantae [GBIF Backbone Taxonomy])",
 "GadmGid is one of (COL.9_2)",
 "StateProvince is one of (Caquetá)"
 ]
 }
 ]
}

 The dataset's 8319 records were derived from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045915-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15264491
title: Normalized GEFS Week 3 Forecasts and ERA5 VPD Labels for ML

description: Machine Learning dataset from 2000-2019, specifically used to train UNET neural networks, containing the following training data processed to a CONUS-like domain, 10.5 to 59.5 latitude and -159.5 to -60.5 longitude, on half degree resolution from 11 ensemble members of 6-hourly GEFS data and vapor pressure deficit (VPD) labels created on the same domain from ERA5.

Training data are from years: 2000, 2001, 2003-2006, 2009-2012, 2016, 2017, and 2019

Validation data are from years: 2002, 2008, 2014, and 2018

Blind testing data are from years 2007, 2013, and 2015

The input data are created from week 4 forecasting data produced by the GEFS initialized on the first Wednesdays of the year. Input data included in this dataset are:



'soilw'   # Weekly mean volumetric soil moisture content @ bgrnd_depth

'pwat'    # Weekly mean precipitable water

'2t'      # Weekly mean 2 metre temperature

't'       # Weekly mean temperature at pressure (note two values at 850mb and 200mb)

sine of the number of the week of the year


Finally, the files are normalized by z-score normalization by pressure height (or surface) and variable. They are then saved into npy matrices sized [99, 199, 6] in the above order for NN training purposes. The VPD labels are the coresponding weekly mean VPD per gridcell derived form ERA5 data, and stored in npy files sized [99, 199, 1] for NN label purposes, intended to represent "observed" vpd on the corresponding week three forecast. They have an identical name to the input but are stored in the label directory. The zip files has been zipped in a way that contains subdirectories directories storing the npy files and identical data-label names as the following:

naming example - nn_dataset_YYYY_week_WW_ens_E_f_3.npy

where YYYY = year (2019)

where WW = week (1 through up to 48)

where E = GEFS ensemble number (0-10)

where f_3 means forecast week three (0-4 included in initial GEFS dataset)

Directories are named to divide npy files into:



training data

training labels

validation data

validation labels

testing data

testing labels


Lastly, an additional file called "norm_inference_vars" is concluded and contains the validation and testing input variable datasets standard deviations and means.
DOI: 10.5281/zenodo.17086907
title: Normalized GEFS Week 3 Forecasts and ERA5 VPD Labels for ML

description: Machine Learning dataset from 2000-2019, specifically used to train UNET neural networks, containing the following training data processed to a CONUS-like domain, 10.5 to 59.5 latitude and -159.5 to -60.5 longitude, on half degree resolution from 11 ensemble members of 6-hourly GEFS data and vapor pressure deficit (VPD) labels created on the same domain from ERA5.

Training data are from years: 2000, 2001, 2003-2006, 2009-2012, 2016, 2017, and 2019

Validation data are from years: 2002, 2008, 2014, and 2018

Blind testing data are from years 2007, 2013, and 2015

The input data are created from week 4 forecasting data produced by the GEFS initialized on the first Wednesdays of the year. Input data included in this dataset are:



'soilw'   # Weekly mean volumetric soil moisture content @ bgrnd_depth

'pwat'    # Weekly mean precipitable water

'2t'      # Weekly mean 2 metre temperature

't'       # Weekly mean temperature at pressure (note two values at 850mb and 200mb)

sine of the number of the week of the year


Finally, the files are normalized by z-score normalization by pressure height (or surface) and variable. They are then saved into npy matrices sized [99, 199, 6] in the above order for NN training purposes. The VPD labels are the coresponding weekly mean VPD per gridcell derived form ERA5 data, and stored in npy files sized [99, 199, 1] for NN label purposes, intended to represent "observed" vpd on the corresponding week three forecast. They have an identical name to the input but are stored in the label directory. The zip files has been zipped in a way that contains subdirectories directories storing the npy files and identical data-label names as the following:

naming example - nn_dataset_YYYY_week_WW_ens_E_f_3.npy

where YYYY = year (2019)

where WW = week (1 through up to 48)

where E = GEFS ensemble number (0-10)

where f_3 means forecast week three (0-4 included in initial GEFS dataset)

Directories are named to divide npy files into:



training data

training labels

validation data

validation labels

testing data

testing labels


Lastly, an additional file called "norm_inference_vars" is concluded and contains the validation and testing input variable datasets standard deviations and means.
DOI: 10.15468/dl.dn6gae
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hibiscus rosa-sinensis",
 "Country is Singapore",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045942-250827131500795/datasets/export for details.
DOI: 10.15468/dl.8nwm3s
title: Occurrence Download

description: A dataset containing 199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "TaxonKey is Allium sativum"
 ]
}

 The dataset includes 199 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045941-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wdztd
title: Occurrence Download

description: A dataset containing 209385007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-60.19447 28.38359,-147.10858 13.99047,-176.36679 -41.16484,-176.36679 -76.19335,-131.61893 -76.39722,-67.93929 -74.90575,-47.28643 -66.16519,-57.61287 -52.31225,-60.19447 28.38359))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 1901-2025"
 ]
}

 The dataset includes 209385007 records from 9788 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045887-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jbvat8
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Ecuador",
 "TaxonKey is Coursetia dubia (Kunth) DC."
 ]
}

 The dataset includes 89 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048071-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wqeysx
title: Occurrence Download

description: A dataset containing 7364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ganoderma lucidum (Curtis) P.Karst."
 ]
}

 The dataset includes 7364 records from 256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0228579-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxxu5n
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is New species and records of the Pericoma trifasciata group from Croatia (Diptera: Psychodidae)"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001944-230828120925497/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpug2n
title: Occurrence Download

description: A dataset containing 4722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "MediaType is Image",
 "TaxonKey is Melilotus officinalis (L.) Pallas"
 ]
}

 The dataset includes 4722 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038363-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.usykqf
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diplodactylus capensis Doughty, Oliver & Adams, 2008"
 ]
}

 The dataset includes 37 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0282460-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhj4ep
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Canavalia saueri Fantz"
 ]
}

 The dataset includes 20 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118043-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cow5u6
title: Occurrence Download

description: A dataset containing 958 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Felis chaus Schreber, 1777"
 ]
}

 The dataset includes 958 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008598-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eyj7nu
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vicia caucasica Ekutim.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180419-220831081235567/datasets/export for details.
DOI: 10.15468/dl.s4uths
title: Occurrence Download

description: A dataset containing 2004137 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Accipiter nisus (Linnaeus, 1758)"
 ]
}

 The dataset includes 2004137 records from 2185 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0118024-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jyr1vj
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Silene gigantea L."
 ]
}

 The dataset includes 176 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024955-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bmxbdg
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Achillea chrysocoma Friv."
 ]
}

 The dataset includes 80 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012122-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w6ujtg
title: Occurrence Download

description: A dataset containing 10423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microtus longicaudus (Merriam, 1888)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10423 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001197-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.