cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ss2vnf
title: Occurrence Download

description: A dataset containing 22370 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calotropis procera",
 "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 22370 records from 281 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059604-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17980723
title: Code and data for "Transformers Improve Streamflow Prediction in Karst Watersheds by Capturing Long-Term Memory Effect of Storage"

description: This repository contains code and data for Choi et al. (under review).

Author: Seohye ChoiLast modified: 12/18/2025

# Code

Transformer-RR.ipynb: Jupyter notebook for finetuning, training, validation, and interpretative analysis of a simplified Transformer model, using datasets described below. 

LSTM-RR.ipynb: Jupyter notebook for finetuning, training, and validation of a baseline LSTM model, using datasets described below.  

# Data

karst.mat: Inputs and target variables for training and validation, compiled for nine snow-dominated karst watersheds in the Western U.S. The first dimension represents each watershed in the following order:

1. Little Bighorn River2. Salina Creek3. Steptoe Creek4. Lamoille Creek5. Mission Cr. ab Reservoir6. Cache Creek7. Logan River8. Red Butte Creek9. Blacksmith Fork

non_karst.mat: Inputs and target variables for training and validation, compiled for nine snow-dominated non-karst watersheds in the Western U.S. The first dimension represents each watershed in the following order:

1. Halfmoon Creek2. Black Gore Creek3. Andrews Creek4. Minam River5. Rock Creek6. Bobtail Creek7. Lake Fork8. Stillwater Fork9. Headwater Weber River

For both datasets, the third dimension represents 1. Streamflow (m/d),2. Liquid water input (i.e., snowmelt plus rain (m)),3. PET (mm).

# Reference

Choi, S., Tennant, H., Hill, D., Neilson, B., Newell, D., Ashmead, N., McNamara, J., & Xu, T. Transformers Improve Streamflow Prediction in Karst Watersheds by Capturing Long-Term Memory Effect of Storage. Under Review.
DOI: 10.5281/zenodo.17980722
title: Code and data for "Transformers Improve Streamflow Prediction in Karst Watersheds by Capturing Long-Term Memory Effect of Storage"

description: This repository contains code and data for Choi et al. (under review).

Author: Seohye ChoiLast modified: 12/18/2025

# Code

Transformer-RR.ipynb: Jupyter notebook for finetuning, training, validation, and interpretative analysis of a simplified Transformer model, using datasets described below. 

LSTM-RR.ipynb: Jupyter notebook for finetuning, training, and validation of a baseline LSTM model, using datasets described below.  

# Data

karst.mat: Inputs and target variables for training and validation, compiled for nine snow-dominated karst watersheds in the Western U.S. The first dimension represents each watershed in the following order:

1. Little Bighorn River2. Salina Creek3. Steptoe Creek4. Lamoille Creek5. Mission Cr. ab Reservoir6. Cache Creek7. Logan River8. Red Butte Creek9. Blacksmith Fork

non_karst.mat: Inputs and target variables for training and validation, compiled for nine snow-dominated non-karst watersheds in the Western U.S. The first dimension represents each watershed in the following order:

1. Halfmoon Creek2. Black Gore Creek3. Andrews Creek4. Minam River5. Rock Creek6. Bobtail Creek7. Lake Fork8. Stillwater Fork9. Headwater Weber River

For both datasets, the third dimension represents 1. Streamflow (m/d),2. Liquid water input (i.e., snowmelt plus rain (m)),3. PET (mm).

# Reference

Choi, S., Tennant, H., Hill, D., Neilson, B., Newell, D., Ashmead, N., McNamara, J., & Xu, T. Transformers Improve Streamflow Prediction in Karst Watersheds by Capturing Long-Term Memory Effect of Storage. Under Review.
DOI: 10.15468/dl.rxz9yh
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tapes conspersus, Paphia guttulata, Tapes adspersa, Tapes dorsatus, Tapes turgida, Tapes turgidula, Tapes watlingi, Venus dorsata, Venus litterata conspersa, Venus ovulaea, Venus turgida)",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 112 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059606-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkbzqv
title: Occurrence Download

description: A dataset containing 7510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cinnamomum verum",
 "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 7510 records from 211 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059607-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fsede
title: Occurrence Download

description: A dataset containing 102905 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ramphastos toco",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-180 -90, 180 -90, 180 90, -180 90, -180 -90))"
 ]
}

 The dataset includes 102905 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059589-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v3sfzz
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tapes literatus, Paphia nocturna, Tapes aspersa, Tapes distinguenda, Venus adspersa, Venus compunctata, Venus deshayesii sulphurea, Venus deshayesii sulphurea, Venus literata, Venus litterata, Venus litterata maculosa, Venus litterata nebulosa, Venus litterata punctata, Venus litterata nebulosa, Venus litterata punctata, Venus punctifera, Venus radiata, Venus radiata)",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 31 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059608-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2rdcvg
title: Occurrence Download

description: A dataset containing 155532625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 155532625 records from 12084 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059472-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5uxhh9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys garmani (Meek, 1897)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.628 -23.023,35.6007 -22.9702,35.6007 -23.165,35.628 -23.023))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035804-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15639247
title: Datasets of "Caught in the spotlight: glow-worm larvae reduce their activity under blue and white, but not red light"
DOI: 10.5281/zenodo.15639246
title: Datasets of "Caught in the spotlight: glow-worm larvae reduce their activity under blue and white, but not red light"
DOI: 10.15468/dl.ug6hfh
title: Occurrence Download

description: A dataset containing 4501 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Iran (Islamic Republic of)",
 "OccurrenceStatus is Present",
 "StateProvince is Markazi"
 ]
}

 The dataset includes 4501 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035805-250525065834625/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.26825533
title: UDCA OVCAR

description: Primary data for a paper.
DOI: 10.6084/m9.figshare.26825533.v1
title: UDCA OVCAR

description: Primary data for a paper.
DOI: 10.15468/dl.k58efz
title: Occurrence Download

description: A dataset containing 1067 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus schottkyana Rehder & E.H.Wilson"
 ]
}

 The dataset includes 1067 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035806-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12129183
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.15468/dl.mm6gxb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys garmani (Meek, 1897)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035807-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15637793
title: MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations - Test Cases

description: MDPath Test Cases Dataset

This repository contains the molecular dynamics (MD) simulation data used in the manuscript:

"MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations"

Contents

The dataset includes post-processed topology files (.pdb) and trajectory files (.dcd) for each system analyzed in the study. Simulations were conducted for 200 ns and repeated in triplicate for statistical robustness. 

Each simulation subdirectory is organized by:    - Protein target    - Functional state (e.g., active/inactive)    - Bound ligand

Replicate runs are labeled numerically (1, 2, 3) in the filenames, corresponding to:    - rep<number>_protein_state_ligand_top.pdb: topology file of the system    - rep<number>_protein_state_ligand_traj.dcd: trajectory file of the system

Directory Structure

MDPath_test_cases/├── MOR/│   ├── active_DAMGO/│   └── inactive_alvimopan/├── AA2a/│   ├── active_adenosine/│   └── inactive_caffine/├── ABL1/├── ß2/│   ├── active_salbutamol/│   ├── inactive_carazolol/│   └── active_salbutamol_truncated_ICL2/└── README

Example File Naming

For the MOR/active_DAMGO system:- 1_MOR_active_DAMGO_top.pdb: Topology file for replicate 1- 1_MOR_active_DAMGO_traj.dcd: Trajectory file for replicate 1- 2_MOR_active_DAMGO_top.pdb: Topology file for replicate 2- ...

Usage

These data files can be used to:- Reproduce the analyses in the manuscript- Perform additional studies based on this data
DOI: 10.5281/zenodo.15637794
title: MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations - Test Cases

description: MDPath Test Cases Dataset

This repository contains the molecular dynamics (MD) simulation data used in the manuscript:

"MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations"

Contents

The dataset includes post-processed topology files (.pdb) and trajectory files (.dcd) for each system analyzed in the study. Simulations were conducted for 200 ns and repeated in triplicate for statistical robustness. 

Each simulation subdirectory is organized by:    - Protein target    - Functional state (e.g., active/inactive)    - Bound ligand

Replicate runs are labeled numerically (1, 2, 3) in the filenames, corresponding to:    - rep<number>_protein_state_ligand_top.pdb: topology file of the system    - rep<number>_protein_state_ligand_traj.dcd: trajectory file of the system

Directory Structure

MDPath_test_cases/├── MOR/│   ├── active_DAMGO/│   └── inactive_alvimopan/├── AA2a/│   ├── active_adenosine/│   └── inactive_caffine/├── ABL1/├── ß2/│   ├── active_salbutamol/│   ├── inactive_carazolol/│   └── active_salbutamol_truncated_ICL2/└── README

Example File Naming

For the MOR/active_DAMGO system:- 1_MOR_active_DAMGO_top.pdb: Topology file for replicate 1- 1_MOR_active_DAMGO_traj.dcd: Trajectory file for replicate 1- 2_MOR_active_DAMGO_top.pdb: Topology file for replicate 2- ...

Usage

These data files can be used to:- Reproduce the analyses in the manuscript- Perform additional studies based on this data
DOI: 10.15468/dl.en9gc6
title: Occurrence Download

description: A dataset containing 70181 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cupressus L."
 ]
}

 The dataset includes 70181 records from 1028 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035786-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trzyz8
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys capensis Tschudi, 1838",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.0251 -31.3959,30.5701 -30.7329,30.5701 -28.5786,25.5395 -28.5786,25.5395 -32.9007,28.2048 -32.9007,28.5753 -32.6569,29.4902 -31.7517,30.0251 -31.3959))"
 ]
}

 The dataset includes 486 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035808-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14236827
title: Single cell RNA-sequencing counts of mucosal biopsies from ulcerative colitis patients

description: Mucosal biopsy samples were obtained from patients during routine ileocolonoscopy at the Department of Gastroenterology and Hepatology of the Amsterdam UMC between December 2020 and April 2021. Patients were aged ≥16 years with an established diagnosis of ulcerative colitis (UC) determined through endoscopy and histopathology, where disease activity was scored by a trained gastroenterologist using the Mayo Endoscopic Score (MES) and the Ulcerative Colitis Endoscopic Index of Severity (UCEIS). In total, we acquired samples from 10 UC patients: 5 inflamed UC (MES≥1), 5 non-inflamed UC (MES=0). Exclusion criteria were ongoing malignancy, a history of colonic dysplasia, or colonic surgery. Control samples were obtained from resection specimens acquired from 4 patients with no established diagnosis of UC (CD, suspicion of rectum carcinoma, trans-anal total mesorectal excision or hemicolectomy), which were obtained from the biobank of the Amsterdam UMC.Raw reads were aligned to GRCh38 using Cellranger (v7.0.0) (10X Genomics) generating unique molecular identifiers (UMIs) were obtained. Samples were imported separately, processed, and analysed in the R programming environment (v4.2.1) using Seurat (v4.3.0) 43,44. UMI counts were normalized by SCTransform (v) using default parameters.
DOI: 10.5281/zenodo.14236828
title: Single cell RNA-sequencing counts of mucosal biopsies from ulcerative colitis patients

description: Mucosal biopsy samples were obtained from patients during routine ileocolonoscopy at the Department of Gastroenterology and Hepatology of the Amsterdam UMC between December 2020 and April 2021. Patients were aged ≥16 years with an established diagnosis of ulcerative colitis (UC) determined through endoscopy and histopathology, where disease activity was scored by a trained gastroenterologist using the Mayo Endoscopic Score (MES) and the Ulcerative Colitis Endoscopic Index of Severity (UCEIS). In total, we acquired samples from 10 UC patients: 5 inflamed UC (MES≥1), 5 non-inflamed UC (MES=0). Exclusion criteria were ongoing malignancy, a history of colonic dysplasia, or colonic surgery. Control samples were obtained from resection specimens acquired from 4 patients with no established diagnosis of UC (CD, suspicion of rectum carcinoma, trans-anal total mesorectal excision or hemicolectomy), which were obtained from the biobank of the Amsterdam UMC.Raw reads were aligned to GRCh38 using Cellranger (v7.0.0) (10X Genomics) generating unique molecular identifiers (UMIs) were obtained. Samples were imported separately, processed, and analysed in the R programming environment (v4.2.1) using Seurat (v4.3.0) 43,44. UMI counts were normalized by SCTransform (v) using default parameters.
DOI: 10.5281/zenodo.15624420
title: Datasets for the CIKM resource paper "A Semantically Enriched Mobility Dataset with Contextual and Social Dimensions"
DOI: 10.15468/dl.jug7de
title: Occurrence Download

description: A dataset containing 358 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Carabid beetles in Southern Dolomites from 1983 to 1996"
 ]
}

 The dataset includes 358 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035810-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.836p44
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Kazakhstan",
 "TaxonKey is Aegilops crassa Boiss. ex Hohen."
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035809-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ngvtd8
title: Occurrence Download

description: A dataset containing 4501 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Iran (Islamic Republic of)",
 "OccurrenceStatus is Present",
 "StateProvince is Markazi"
 ]
}

 The dataset includes 4501 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035812-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fw8fau
title: Occurrence Download

description: A dataset containing 38191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((5.05952 51.56407,5.3002 51.56407,5.3002 51.69064,5.05952 51.69064,5.05952 51.56407))",
 "Issue is Coordinate rounded",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 38191 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035811-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqncf2
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sclerophrys capensis Tschudi, 1838",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((30.5701 -24.0715,25.5395 -24.0715,25.5395 -28.5786,30.5701 -28.5786,30.5701 -24.0715))"
 ]
}

 The dataset includes 247 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035813-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j37neg
title: Occurrence Download

description: A dataset containing 512992 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Accipitridae",
 "Year 2015-2025"
 ]
}

 The dataset includes 512992 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035799-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r8mwmp
title: Occurrence Download

description: A dataset containing 328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus delavayi Franch."
 ]
}

 The dataset includes 328 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035814-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/5770
title: HisGermaNER
DOI: 10.15468/dl.qtjwnn
title: Occurrence Download

description: A dataset containing 834 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aethina tumida Murray, 1867"
 ]
}

 The dataset includes 834 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035815-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.