cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.cvh5mq
title: Occurrence Download

description: A dataset containing 876638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Dolichonyx oryzivorus"
 ]
}

 The dataset includes 876638 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016130-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffum2v
title: Occurrence Download

description: A dataset containing 1786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyperus blepharoleptos"
 ]
}

 The dataset includes 1786 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016210-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hg3699
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus nigriceps"
 ]
}

 The dataset includes 24 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016211-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17155651
title: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

description: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

Overview

Relative binding free energy benchmarks of the openff-2.2.1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.2.1_elf10`: simulations using OpenFF 2.2.1 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.2.1_nagl`: simulations using OpenFF 2.2.1 and AshGC v0.1rc3 charges  * `openff-2.2.1_am1bcc`: simulations using OpenFF 2.2.1 and AM1BCC charges calculated using ambertools. Please note that these charges were not assigned to the input conformer, but rather a conformer that was generated at charge assignment time via RDKit through the OpenFF toolkit.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.

Plots

dG (MLE-derived using cinnabar) and ddG plots are present for each system under the `plots` folder.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff
DOI: 10.15468/dl.k9zsa6
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus poecilochromus"
 ]
}

 The dataset includes 25 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016212-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqp56q
title: Occurrence Download

description: A dataset containing 145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gymnotus anguillaris)",
 "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 145 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016213-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ztagjm
title: Occurrence Download

description: A dataset containing 457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Abies pinsapo"
 ]
}

 The dataset includes 457 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016214-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17150786
title: Example data and R scripts for PTL.PRS

description: This record provides a minimal, reproducible toy dataset and companion R scripts to exercise the PTL.PRS package end-to-end (training and evaluation), using both individual-level genotypes and summary-statistics–based pseudo-tests.

What’s included





Scripts





example_script.RBasic workflow: trains with PTL_PRS_train and evaluates on individual-level test data.




example_script_pseudotest_multiSeeds.RBatch workflow: runs PTL_PRS_run across multiple random seeds and evaluates using summary statistics (reports pseudo-R²).






Genetic data (toy)





Target panel: 1000 Genomes Phase 3 — South Asian (SAS).




Chromosome: 22 only.




Variant counts: 16,210 SNPs in the source PRS; 613,839 SNPs in SAS PLINK files (chr22 subset used here).




PLINK bundles:





1kg_SAS_chr22 — main SAS PLINK set (chr22).




1kg_SAS_ref — reference subset (200 samples), PLINK-formatted.








Phenotypes & summaries





601 total target samples





200 reference → PLINK: 1kg_SAS_ref




300 train/validation → phenotype file; derived summary stats: tr_val.summaries




101 test → randomly generated binary phenotype (0/1); phenotype file (sample indices from FAM): test_ped.txt








Source PRS





t2d_prscs_EUR.pgs (example score file used as the starting PRS)
DOI: 10.5281/zenodo.17150787
title: Example data and R scripts for PTL.PRS

description: This record provides a minimal, reproducible toy dataset and companion R scripts to exercise the PTL.PRS package end-to-end (training and evaluation), using both individual-level genotypes and summary-statistics–based pseudo-tests.

What’s included





Scripts





example_script.RBasic workflow: trains with PTL_PRS_train and evaluates on individual-level test data.




example_script_pseudotest_multiSeeds.RBatch workflow: runs PTL_PRS_run across multiple random seeds and evaluates using summary statistics (reports pseudo-R²).






Genetic data (toy)





Target panel: 1000 Genomes Phase 3 — South Asian (SAS).




Chromosome: 22 only.




Variant counts: 16,210 SNPs in the source PRS; 613,839 SNPs in SAS PLINK files (chr22 subset used here).




PLINK bundles:





1kg_SAS_chr22 — main SAS PLINK set (chr22).




1kg_SAS_ref — reference subset (200 samples), PLINK-formatted.








Phenotypes & summaries





601 total target samples





200 reference → PLINK: 1kg_SAS_ref




300 train/validation → phenotype file; derived summary stats: tr_val.summaries




101 test → randomly generated binary phenotype (0/1); phenotype file (sample indices from FAM): test_ped.txt








Source PRS





t2d_prscs_EUR.pgs (example score file used as the starting PRS)
DOI: 10.15468/dl.2zxfxj
title: Occurrence Download

description: A dataset containing 69548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerastoderma edule",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 69548 records from 251 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016145-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7rvebf
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Museu Paraense Emílio Goeldi - Ophidia Collection, AMNH Herpetology Collections, Field Museum of Natural History (Zoology) Amphibian and Reptile Collection, University of Florida Herpetology, NMNH Extant Specimen Records (USNM, US), The reptiles and amphibians collection (RA) of the Muséum national d'Histoire Naturelle (MNHN - Paris), University of Michigan Museum of Zoology, Division of Reptiles & Amphibians, Colección de Reptiles del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-R), Natural History Museum (London) Collection Specimens)",
 "HasCoordinate is true",
 "TaxonKey is Lachesis muta (Linnaeus, 1766)"
 ]
}

 The dataset includes 140 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289626-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fcvh4
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lemyra flammeola (Moore, 1877)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 38 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196135-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sm889g
title: Occurrence Download

description: A dataset containing 9597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tapirus terrestris (Linnaeus, 1758)",
 "Year 2000-2023"
 ]
}

 The dataset includes 9597 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0262909-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myfhn7
title: Occurrence Download

description: A dataset containing 353644 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scutellaria L."
 ]
}

 The dataset includes 353644 records from 1478 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0289630-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qk3chb
title: Occurrence Download

description: A dataset containing 38757 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is University of Jena, Herbarium Haussknecht - Herbarium JE"
 ]
}

 The dataset includes 38757 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0196141-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gjzeuu
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ipomoea paraguariensis Peter"
 ]
}

 The dataset includes 56 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0254013-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aug6yk
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aneurus macrotylus",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0224386-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yykesk
title: Occurrence Download

description: A dataset containing 127515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-78.24005 3.476,-76.93624 3.476,-76.93624 4.3765,-78.24005 4.3765,-78.24005 3.476))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 127515 records from 299 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0262900-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ah5hdg
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex kitaibeliana Degen ex Bech."
 ]
}

 The dataset includes 270 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000749-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mvwnfa
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum paucidentatum Moldenke"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000609-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6b6cgj
title: Occurrence Download

description: A dataset containing 293 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Lygisaurus curtus (Boulenger, 1897)"
 ]
}

 The dataset includes 293 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000593-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7w27bu
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex kabanovii V.I.Krecz."
 ]
}

 The dataset includes 36 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000606-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2n4pb
title: Occurrence Download

description: A dataset containing 375 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Uta squamata Dickerson, 1919"
 ]
}

 The dataset includes 375 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000620-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fju5ak
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Lerista flammicauda Storr, 1985"
 ]
}

 The dataset includes 53 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000633-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ek5hz8
title: Occurrence Download

description: A dataset containing 308576 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cacatua sanguinea Gould, 1843",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 308576 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000631-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fakg5a
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex karlongensis Kük."
 ]
}

 The dataset includes 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000654-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p3esbm
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Enyalioides cofanorum Duellman, 1973"
 ]
}

 The dataset includes 22 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000602-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2z877r
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum pauciflorum Moldenke"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000618-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vajhwk
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alsophila setulosa (Copel.) R.M.Tryon"
 ]
}

 The dataset includes 7 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002287-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmaqjr
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nyctinomops aurispinosus (Peale, 1848)",
 "Country is Brazil"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011704-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whytmg
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum phyllomega Steud."
 ]
}

 The dataset includes 71 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000684-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4xv9nv
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clerodendrum peii Moldenke"
 ]
}

 The dataset includes 41 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000627-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkh9sm
title: Occurrence Download

description: A dataset containing 4418 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Acritoscincus duperreyi (Gray, 1838)"
 ]
}

 The dataset includes 4418 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000616-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q875xm
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cassipourea malosana (Baker) Alston"
 ]
}

 The dataset includes 625 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000670-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uav36s
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Uroplatus malahelo Nussbaum & Raxworthy, 1994"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000623-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ezc9av
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium microstictum (Dahlst. & Enander ex Zahn) Dahlst. & Enander ex Johanss."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024902-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzxr8h
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pachydactylus tsodiloensis Haacke, 1966"
 ]
}

 The dataset includes 38 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000662-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.