cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xrusp1
title: Occurrence Download

description: A dataset containing 5794 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Dichelachne crinita (L.f.) Hook.f."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5794 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012663-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pivmc1
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gagea peduncularis Wall."
 ]
}

 The dataset includes 23 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007103-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/ds/5000332
title: EngineBench
DOI: 10.15468/dl.fvurux
title: Occurrence Download

description: A dataset containing 16640 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Luciobarbus graellsii (Steindachner, 1866)"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 16640 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014413-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ul14tb
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uganda",
 "HasCoordinate is true",
 "TaxonKey is Pseudospondias microcarpa (A.Rich.) Engl.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012663-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u8qtw7
title: Occurrence Download

description: A dataset containing 68352 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alces alces (Linnaeus, 1758)"
 ]
}

 The dataset includes 68352 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008911-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3lcrk7
title: Occurrence Download

description: A dataset containing 23085 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1900-2018",
 "HasCoordinate is true",
 "TaxonKey is Bidens frondosa L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 23085 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014413-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0rvvsx
title: Occurrence Download

description: A dataset containing 53445 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungal Specimens of National Museum of Nature and Science (TNS)"
 ]
}

 The dataset includes 53445 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012663-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gdsxje
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Congo",
 "Year 1911-2013",
 "HasCoordinate is true",
 "TaxonKey is Autranella congolensis (De Wild.) A.Chev.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001855-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cokp3a
title: Occurrence Download

description: A dataset containing 12459 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Dichelachne micrantha (Cav.) Domin"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 12459 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012664-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eyjdd8
title: Occurrence Download

description: A dataset containing 526418 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is USGS Nonindigenous Aquatic Species database"
 ]
}

 The dataset includes 526418 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069065-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0utaie
title: Occurrence Download

description: A dataset containing 109125 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fish collection of National Museum of Nature and Science"
 ]
}

 The dataset includes 109125 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012664-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8pnhxq
title: Occurrence Download

description: A dataset containing 5592 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Riqueza de especies y biodiversidad edáfica de una zona de humedales del Parque Nacional Arrecife de Puerto Morelos, Quintana Roo, México",
 "Geometry POLYGON((-87.20650449560841 20.578545479309923,-86.60602206037251 20.578545479309923,-86.60602206037251 21.179027914545834,-87.20650449560841 21.179027914545834,-87.20650449560841 20.578545479309923))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5592 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058825-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cqysbg
title: Occurrence Download

description: A dataset containing 424 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The types of Phasmida in the Natural History Museum, London, UK"
 ]
}

 The dataset includes 424 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014414-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8n4e4h
title: Occurrence Download

description: A dataset containing 140434 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 {
 "or" : [
 "Issue is Coordinate rounded",
 "Issue is Geodetic datum assumed WGS84"
 ]
 },
 "Year 1960-2019",
 "HasCoordinate is true",
 "TaxonKey is Polygala L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 140434 records from 485 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012664-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13625631
title: Single-cell and spatial transcriptomics of stricturing Crohn's disease

description: This folder contains the spatial transcriptomics data + code. This code was generated by members of the Smillie Lab @ MGH and Harvard Medical School.



github.tar.gz: spatial analysis code and data

anndata.h5ad: anndata object (scanpy)

V*tar.gz: raw spatial transcriptomics files


The github.tar.gz folder contains everything you need to reproduce the spatial transcriptomics figures. It is structured as follows:



1.BayesPrism: code for running BayesPrism on spatial data

2.SparCC: code for running SparCC on spatial data

3.Lasso: code for running lasso regression on spatial data

4.Analysis: code for reproducing all figures in the paper

4.Analysis/1.analysis.r: script to reproduce all figures in the paper ***

code: code library containing all necessary functions

load_data.r: code to load the single-cell and spatial datasets

sco.rds: single-cell analysis object (10X Chromium) formatted as an R list

vis.rds: spatial analysis object (10X Visium) formatted as an R list


All scripts are numbered. You need to run everything in order. For convenience, we include the output files for 1.BayesPrism, 2.SparCC, and 3.Lasso, allowing you to skip straight to the analysis code in 4.Analysis.

To reproduce all figures in the paper, you need to do the following:



Edit your PROJECT_FOLDER in the header of load_data.r

Install the packages listed at the top of load_data.r

Go to the 4.Analysis directory, start an interactive R session, and type:> source('1.analysis.r')


This will load the beginning of the 1.analysis.r script (until the stop() statement on line 68). You can run the code in two different ways:



You can step through the code line by line in your interactive R session (starting at line 68)

Alternatively, remove the stop() statement from the script, then run the code start to finish


If you encounter any errors, try to debug them using a combination of Google+ChatGPT. If you still have trouble, please contact the Smillie Lab.

Note: the single-cell and spatial code are also available on GitHub. However, the spatial analysis requires large files that cannot be hosted on GitHub. Therefore, it is better to download the code + files from Zenodo. The GitHub link is provided below:

https://github.com/LJ-Kong/fibrosis_scRNA_stRNA
DOI: 10.5281/zenodo.13625632
title: Single-cell and spatial transcriptomics of stricturing Crohn's disease
DOI: 10.5281/zenodo.14509802
title: Single-cell and spatial transcriptomics of stricturing Crohn's disease

description: This folder contains the spatial transcriptomics data + code. This code was generated by members of the Smillie Lab @ MGH and Harvard Medical School.



github.tar.gz: spatial analysis code and data

anndata.h5ad: anndata object (scanpy)

V*tar.gz: raw spatial transcriptomics files


The github.tar.gz folder contains everything you need to reproduce the spatial transcriptomics figures. It is structured as follows:



1.BayesPrism: code for running BayesPrism on spatial data

2.SparCC: code for running SparCC on spatial data

3.Lasso: code for running lasso regression on spatial data

4.Analysis: code for reproducing all figures in the paper

4.Analysis/1.analysis.r: script to reproduce all figures in the paper ***

code: code library containing all necessary functions

load_data.r: code to load the single-cell and spatial datasets

sco.rds: single-cell analysis object (10X Chromium) formatted as an R list

vis.rds: spatial analysis object (10X Visium) formatted as an R list


All scripts are numbered. You need to run everything in order. For convenience, we include the output files for 1.BayesPrism, 2.SparCC, and 3.Lasso, allowing you to skip straight to the analysis code in 4.Analysis.

To reproduce all figures in the paper, you need to do the following:



Edit your PROJECT_FOLDER in the header of load_data.r

Install the packages listed at the top of load_data.r

Go to the 4.Analysis directory, start an interactive R session, and type:> source('1.analysis.r')


This will load the beginning of the 1.analysis.r script (until the stop() statement on line 68). You can run the code in two different ways:



You can step through the code line by line in your interactive R session (starting at line 68)

Alternatively, remove the stop() statement from the script, then run the code start to finish


If you encounter any errors, try to debug them using a combination of Google+ChatGPT. If you still have trouble, please contact the Smillie Lab.

Note: the single-cell and spatial code are also available on GitHub. However, the spatial analysis requires large files that cannot be hosted on GitHub. Therefore, it is better to download the code + files from Zenodo. The GitHub link is provided below:

https://github.com/LJ-Kong/fibrosis_scRNA_stRNA
DOI: 10.13140/rg.2.2.24940.69769
title: Background image
DOI: 10.13140/rg.2.2.18334.66889
title: 51 Annals of Clinical Prosthodontics Cross Sectional Survey Awareness of COVID-19 among dental professionals working at Karnataka state government hospitals and its impact on dental health services of patients -A cross-sectional survey
DOI: 10.13140/rg.2.2.36212.88961
title: Systems Thinking Vs. Transmodern ontoepistemology AKA 5 levels of mind - work in progress
DOI: 10.13140/rg.2.2.32228.30088
title: General Bulletin 21-03-05
DOI: 10.34740/kaggle/dsv/13444392
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.xbxpug
title: Occurrence Download

description: A dataset containing 14383 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Africa, Asia, Europe)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aedes aegypti (Linnaeus, 1762)"
 ]
}

 The dataset includes 14383 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000025-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t6vnsg
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Tanzania, United Republic of",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vigna friesiorum var. angustifolia Verdc."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000026-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5pv6bk5s
title: MassIVE MSV000097113 - Hematopoietic stem cell derived conditioned media metabolomics
title: Metabolomic data of conditioned media derived from culturing hematopoietic stem cells.
DOI: 10.25424/cmcc-75s8-a308
title: Statistical Downscaling through Empirical Quantile Mapping for an ensemble of Global Climate Models over Italy
title: SD-EQM_GCMs_IT over Italy

description: This dataset, SD-EQM_GCMs_IT (Statistical Downscaling through Empirical Quantile Mapping for an ensemble of Global Climate Models over ITaly), provides high-resolution (~5.5 km) climate information specifically tailored to Italy. It consists of statistically downscaled data derived from an ensemble of CMIP6 (Coupled Model Intercomparison Project Phase 6; https://wcrp-cmip.org/cmip6/) Global Circulation Models (GCMs) through the bias-correction technique known as Empirical Quantile Mapping (EQM; e.g., Piani et al., 2010; Lafon et al., 2013), covering the period from 1985 to 2100, for two different scenarios: SSP1-2.6 and SSP3-7.0 (O’Neill et al., 2013). The SD-EQM technique has been applied to the selected CMIP6 GCMs, using as reference the Copernicus European regional reanalysis (CERRA; Schimanke et al., 2021) at ~5.5 km resolution. CERRA has been chosen as a reference dataset in order to reach the highest atmospheric horizontal resolution possible over Italy, using a reanalysis as reference. The dataset offers daily values for key climate variables, including mean, maximum, and minimum temperature, mean surface wind speed, mean relative humidity and accumulated precipitation.
DOI: 10.5281/zenodo.10688434
title: Data  repository for study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate"

description: Data for the study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate".

hindcasting_analysis



figures of the hindcasting exercise in the main text

raw_data



   raw model output data for



baseline scenario -- agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_regions=AgrimateEU28_start=2000-01-01.nc

production failure scenario --  agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc

production failure and export restriction scenario -- agrimate_baseline=2007-2009_export_restrictions=2007-2011_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc






multibreadbasket_analysis



figures of the multibreadbasket analysis in the main text

raw_data



   raw model output data for



simulations under historical climatic conditions with <number> as an identifier  -- agrimate_his-<number>.nc

simulations under +2°C projection with <number> as an identifier  -- agrimate_2p0-<number>.nc





processed_data



processed output data to easier/faster plot




sensitivity_analysis



raw data and graphics as in main_output for different model parameters as given in Table F.1
DOI: 10.5281/zenodo.10688435
title: Data  repository for study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate"

description: Data for the study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate".

main_output



comparison_FAO_crop_baseline=2007-2009_start=2000-01-01.pdf -- Graphic for model perfomance in comparison with FAOSTAT data

egypt_dynamics_baseline=2007-2009_start=2000-01-01.pdf -- Graphic for model dynamics of purchaser of Egypt

russia_dynamics_baseline=2007-2009_start=2000-01-01.pdf -- Graphic for model dynamics for supplier of Russia 

data



   raw model output data for



baseline scenario -- agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_regions=AgrimateEU28_start=2000-01-01.nc

production failure scenario --  agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc

production failure and export restriction scenario -- agrimate_baseline=2007-2009_export_restrictions=2007-2011_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc






sensitivity_analysis



raw data and graphics as in main_output for different model parameters as given in Table F.1
DOI: 10.5281/zenodo.14022965
title: Data  repository for study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate"

description: Data for the study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate".

hindcasting_analysis



figures of the hindcasting exercise in the main text

raw_data



   raw model output data for



baseline scenario -- agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_regions=AgrimateEU28_start=2000-01-01.nc

production failure scenario --  agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc

production failure and export restriction scenario -- agrimate_baseline=2007-2009_export_restrictions=2007-2011_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc






multibreadbasket_analysis



figures of the multibreadbasket analysis in the main text

raw_data



   raw model output data for



simulations under historical climatic conditions with <number> as an identifier  -- agrimate_his-<number>.nc

simulations under +2°C projection with <number> as an identifier  -- agrimate_2p0-<number>.nc





processed_data



processed output data to easier/faster plot




sensitivity_analysis



raw data and graphics as in main_output for different model parameters as given in Table F.1
DOI: 10.5281/zenodo.14870541
title: Data  repository for study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate"

description: Data for the study "Understanding agricultural market dynamics in times of crisis: the dynamic agent-based model Agrimate".

hindcasting_analysis



figures of the hindcasting exercise in the main text

raw_data



   raw model output data for



baseline scenario -- agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_regions=AgrimateEU28_start=2000-01-01.nc

production failure scenario --  agrimate_baseline=2007-2009_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc

production failure and export restriction scenario -- agrimate_baseline=2007-2009_export_restrictions=2007-2011_extra_regions=(Egypt=EGY)_production_anomalies=FAOsince-2005_regions=AgrimateEU28_start=2000-01-01.nc






multibreadbasket_analysis



figures of the multibreadbasket analysis in the main text

raw_data



   raw model output data for



simulations under historical climatic conditions with <number> as an identifier  -- agrimate_his-<number>.nc

simulations under +2°C projection with <number> as an identifier  -- agrimate_2p0-<number>.nc





processed_data



processed output data to easier/faster plot




sensitivity_analysis



raw data and graphics as in main_output for different model parameters as given in Table F.1
DOI: 10.15468/dl.k65jam
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "Geometry POLYGON((10.64872 44.87952,12.87464 44.87952,12.87464 45.76950,10.64872 45.76950,10.64872 44.87952))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tulipa sylvestris L."
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000027-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4atp92
title: Occurrence Download

description: A dataset containing 3517603 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Belgium",
 "Month is one of (May, June, July)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2000-2025"
 ]
}

 The dataset includes 3517603 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000016-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.