cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4866e9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anastrepha obliqua",
 "Country is Dominican Republic",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026181-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16914394
title: Martyn et al. (2025) Variant-EFFECTS Evaluator for GAME API

description: This Evaluator requests expression predictions for sequences in THP-1 monocytes and Jurkat T cells. It then computes the log2 fold change (log2FC) between alternate and reference sequence predictions, and evaluates performance by calculating the Pearson correlation between the measured and predicted log2FC values.



Included in Engreitz_evaluator.sif :



Scripts to process the data and connect to predictors in the GAME API

Scripts to parse the returned predictions and calculate performance metrics

All software dependencies


/evaluator_data folder contents:



/Jurkat



all_jurkat_sequences.tsv: SPDI ID; Reference Sequence; Alternate Sequence. ~2000 bp long sequence (depending on indel size)

all_Jurkat.tsv: concatenated variants from individual variant files in SPDI format. 332 total variants.



/THP1



all_THP1_sequences.tsv: SPDI ID; Reference Sequence; Alternate Sequences. ~2000 bp long sequence (depending on indel size)

all_THP1.tsv : concatenated variants from individual variant files in SPDI format. 392 total variants.



/SPDI_toseq



instructions.tsv : How to run the Rscript to pull sequences from SPDI IDs (hg38)

.yaml to create the conda enviroment for the Rscript 



parse_Engreitz_data.py

File Specification_VariantEffectsFiles.png: Details about information in the variant files


How to run:

apptainer run --containall -B /path_to/evaluator_data/:/evaluator_data -B /path_to/prediction_folder/:/predictions Engreitz_evaluator.sif HOST PORT /predictions

Notes:



The main evaluator script (Engreitz_evaluator.py)will read in the *_sequences.tsv files from their respective folders and send two seperate requests to the connected Predictor

Duplicated SPDI ID sequences are only sent to the Predictors once to minimize duplicated computation and the values are merged with the measured values to calculate the correlation



Additional information can be found on GitHub: Genomic API for Model Evaluation

Original Publication can be found here: Martyn et al. (2025)
DOI: 10.15468/dl.buax88
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhabdalestes rhodesiensis)",
 "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 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026182-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k43yku
title: Occurrence Download

description: A dataset containing 2429 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-70.09809 -33.46449,-73.3134 -33.55001,-73.56994 -37.2955,-70.11519 -38.62952,-69.49949 -33.65262,-70.09809 -33.46449))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pteroptochos castaneus",
 "Year 1970-2025"
 ]
}

 The dataset includes 2429 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026183-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aqtyrf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anastrepha obliqua",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026184-250811113504898/datasets/export for details.
DOI: 10.25574/25116
title: Chandra X-ray Observatory ObsId 25116

description: Unveiling a new phenomenon: disk-wind collisions
DOI: 10.15468/dl.twtxxq
title: Occurrence Download

description: A dataset containing 20209 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachysylvia semibrunnea"
 ]
}

 The dataset includes 20209 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026185-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tts2s7
title: Occurrence Download

description: A dataset containing 1218884 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-06-25",
 "EventDate is less than or equal to 2025-07-25",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 1218884 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026173-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mgh7w5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bryconamericus tenuis)",
 "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 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026188-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xth34m
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Poland",
 "TaxonKey is Metcalfa pruinosa"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026187-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yu59n4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Antigua and Barbuda",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026189-250811113504898/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12820423
title: Balochi Language to English Translation Dataset
DOI: 10.5281/zenodo.16888005
title: Dataset from a Study on the Effects of Circuit Connectivity in a Biophysical Thalamocortical Model

description: This link provides the datasets used to re-run the analysis and generate the figures of the paper "Closed-Loop Connectivity Best Supports Angular Tuning and Sleep Dynamics in a Biophysical Thalamocortical Circuit Model. JVS Moreira, FS Borges, Z Atherton, SR Crandall, C Varela, S Dura-Bernal".

The idea is that the data can be analyzed without re-running the model, since it requires access and setup on an HPC environment.

We also provide a version of the dataset in which the output of the analysis is already included, in case the user doesn't want to re-run the analysis.

For more information on how to set up the dataset within the model code, refer to the file 'README_paper_002_data.md' included in this repository.

For more information on how to download/install/run the model and set up the code for analyzing the data, refer to the source publication and to the repository linked there (see more info in the 'README' files in the repository).

 



For further information, please contact: salvador.dura-bernal@downstate.edu and/or joao.moreira@downstate.edu.
DOI: 10.5281/zenodo.16888006
title: Dataset from a Study on the Effects of Circuit Connectivity in a Biophysical Thalamocortical Model

description: This link provides the datasets used to re-run the analysis and generate the figures of the paper "Closed-Loop Connectivity Best Supports Angular Tuning and Sleep Dynamics in a Biophysical Thalamocortical Circuit Model. JVS Moreira, FS Borges, Z Atherton, SR Crandall, C Varela, S Dura-Bernal".

The idea is that the data can be analyzed without re-running the model, since it requires access and setup on an HPC environment.

We also provide a version of the dataset in which the output of the analysis is already included, in case the user doesn't want to re-run the analysis.

For more information on how to set up the dataset within the model code, refer to the file 'README_paper_002_data.md' included in this repository.

For more information on how to download/install/run the model and set up the code for analyzing the data, refer to the source publication and to the repository linked there (see more info in the 'README' files in the repository).

 



For further information, please contact: salvador.dura-bernal@downstate.edu and/or joao.moreira@downstate.edu.
DOI: 10.15468/dl.ygw2jg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Bahamas",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026190-250811113504898/datasets/export for details.
DOI: 10.15468/dl.fqx4ku
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gasterosteus crenobiontus)",
 "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/0026193-250811113504898/datasets/export for details.
DOI: 10.15468/dl.v9pnvf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Belize",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026196-250811113504898/datasets/export for details.
DOI: 10.15468/dl.v5qnrf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Barbados",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026195-250811113504898/datasets/export for details.
DOI: 10.15468/dl.zcfs2t
title: Occurrence Download

description: A dataset containing 40952 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Valeriana montana"
 ]
}

 The dataset includes 40952 records from 223 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026192-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e237306
title: High School Longitudinal Study (HSLS) (source: NCES)

description: The High School Longitudinal Study of 2009 (HSLS:09) is a nationally representative, longitudinal study of more than 21,000 9th graders in 944 schools who will be followed through their secondary and postsecondary years. The study focuses on understanding students' trajectories from the beginning of high school into postsecondary education, the workforce, and beyond. What students decide to pursue when, why, and how are crucial questions for HSLS:09, especially, but not solely, in regards to science, technology, engineering, and math (STEM) courses, majors, and careers.High School Longitudinal Study of 2009 (HSLS:09) Features
 Nationally representative, longitudinal study of 23,000+ 
9th graders from 944 schools in 2009, with a first follow-up in 2012 and
 a second follow-up in 2016Students followed throughout secondary and postsecondary yearsSurveys of students, their parents, math and science teachers, school administrators, and school counselorsA new student assessment in algebraic skills, reasoning, and problem solving for 9th and 11th grades10 state representative datasets
 HSLS:09 Data Collection Waves
 Base Year (2009)First Follow-up (2012)2013 Update (2013)High School Transcripts (2013-2014)Second Follow-up (2016)Postsecondary Transcripts (2017-18)
DOI: 10.3886/e237306v1
title: High School Longitudinal Study (HSLS) (source: NCES)

description: The High School Longitudinal Study of 2009 (HSLS:09) is a nationally representative, longitudinal study of more than 21,000 9th graders in 944 schools who will be followed through their secondary and postsecondary years. The study focuses on understanding students' trajectories from the beginning of high school into postsecondary education, the workforce, and beyond. What students decide to pursue when, why, and how are crucial questions for HSLS:09, especially, but not solely, in regards to science, technology, engineering, and math (STEM) courses, majors, and careers.High School Longitudinal Study of 2009 (HSLS:09) Features
 Nationally representative, longitudinal study of 23,000+ 
9th graders from 944 schools in 2009, with a first follow-up in 2012 and
 a second follow-up in 2016Students followed throughout secondary and postsecondary yearsSurveys of students, their parents, math and science teachers, school administrators, and school counselorsA new student assessment in algebraic skills, reasoning, and problem solving for 9th and 11th grades10 state representative datasets
 HSLS:09 Data Collection Waves
 Base Year (2009)First Follow-up (2012)2013 Update (2013)High School Transcripts (2013-2014)Second Follow-up (2016)Postsecondary Transcripts (2017-18)
DOI: 10.15468/dl.sxvqwv
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gila nigra)",
 "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 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026199-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7rppv9
title: Occurrence Download

description: A dataset containing 23646 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepus californicus"
 ]
}

 The dataset includes 23646 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026198-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xvunph
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Central African Republic",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026200-250811113504898/datasets/export for details.
DOI: 10.15468/dl.7z5d9c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026201-250811113504898/datasets/export for details.
DOI: 10.5066/p13dg5ca
title: Daily predictions of water temperature for streams across the contiguous United States (1979-2021)

description: This model application data release provides the data processing and model code used to generate predictions of daily stream water temperature across the contiguous United States from 1979-2021. We used a recurrent graph convolutional network (RGCN) algorithm to make daily stream temperature predictions. Stream water temperature observations, along with forcing data consisting of daily meteorological information, a stream distance matrix, and static stream characteristics were used to predict daily stream temperature summaries (minimum, mean, and maximum) for 57,810 stream segments across the contiguous United States. This model application data release is organized as follows:

data_processing_code.zip contains the instructions and code needed to assemble inputs to the model. This directory contains a README.txt file that describes all major processing steps and outputs of this code.
model_code.zip contains code to process the outputs from data_processing_code.zip into model-ready data structures and implements the modeling algorithm. This directory contains a README.txt file that describes all model-ready input files, major processing steps, and an overview of the modeling steps.
national_temperature_metadata.xml describes the top-level files contained in this model application data release (model outputs and supporting reach-level metadata).
The model outputs are contained in a Parquet database, where chunks of data are stored in regional and subregional (HUC2 and HUC4) nested folders titled huc2={HUC2 ID}.zip}. Each HUC2 can be downloaded separately.
data_access_pattern.R gives an example of how to extract and use the stream temperature predictions in this data release.
reach_metadata.csv contains reach-level metadata that describes how the reach was used in the model (training or testing) and how the reach was classified (groundwater, atmospheric, reservoir, thermoelectric) for evaluation purposes.


The methods and results from this modeling effort are described in: Diaz, J., Oliver, S.K., Gorski, G. 2025. Evaluation of daily stream temperature predictions across the contiguous United States using a spatiotemporal aware machine learning algorithm. Environmental Modelling & Software, https://doi.org/10.1016/j.envsoft.2025.106655.
DOI: 10.7910/dvn/qn75gf
title: County smoking rate and mean BMI from BRFSS

description: Yearly county interpolated series of smoke rate and mean BMI. The variables are derived from the public-use annual BRFSS Behavioral Risk Factor Surveillance System data files from the CDC. &lt;br&gt;
&lt;br&gt;
The public-use annual BRFSS data files are meant for state-level analysis. Prior to 2012, the public files contain county codes.
description: Filenames of sources:

├── 1999
│ ├── CDBRFS99.XPT
│ ├── codebook_99.pdf
│ └── overview_99.pdf
├── 2000
│ ├── CDBRFS00.XPT
│ ├── codebook_00.pdf
│ └── overview_00.pdf
├── 2001
│ ├── CDBRFS01.XPT
│ ├── codebook_01.pdf
│ └── overview_01.pdf
├── 2002
│ ├── cdbrfs02.xpt
│ ├── codebook_02.pdf
│ └── overview_02.pdf
├── 2003
│ ├── cdbrfs03.xpt
│ ├── codebook_03.pdf
│ └── overview_03.pdf
├── 2004
│ ├── CDBRFS04.XPT
│ ├── codebook_04.pdf
│ └── overview_04.pdf
├── 2005
│ ├── CDBRFS05.XPT
│ ├── codebook_05.pdf
│ └── overview_05.pdf
├── 2006
│ ├── CDBRFS06.XPT
│ ├── codebook_06.pdf
│ └── overview_06.pdf
├── 2007
│ ├── CDBRFS07.XPT
│ ├── codebook_07.pdf
│ └── overview_07.pdf
├── 2008
│ ├── CDBRFS08.XPT
│ ├── codebook08.pdf
│ └── overview_08.pdf
├── 2009
│ ├── CDBRFS09.XPT
│ ├── codebook_09.pdf
│ └── overview_09.pdf
├── 2010
│ ├── CDBRFS10.XPT
│ ├── codebook_10.pdf
│ └── overview_10.pdf
├── 2011
│ ├── codebook11_llcp.pdf
│ ├── LLCP2011.XPT
│ └── overview_11.pdf
├── 2012
│ ├── codebook12_llcp.pdf
│ ├── LLCP2012.XPT
│ └── overview_2012.pdf
DOI: 10.15468/dl.xjcdxs
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-113.53235 37.15088,-113.47076 37.15088,-113.47076 37.19468,-113.53235 37.19468,-113.53235 37.15088))",
 "HasCoordinate is true",
 "TaxonKey is Asclepias erosa"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026203-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tjgqw3
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caprichromis liemi)",
 "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 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026202-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpwmu5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Congo",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026204-250811113504898/datasets/export for details.
DOI: 10.34740/kaggle/ds/7895310
title: BHaM: Biomechanics Hand Modeling Dataset
DOI: 10.15468/dl.dyg4p6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maconellicoccus hirsutus",
 "Country is Côte d’Ivoire",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026205-250811113504898/datasets/export for details.
DOI: 10.15468/dl.uxrsrq
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Poland",
 "TaxonKey is Metcalfa pruinosa"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026206-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.