cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.gfbc79
title: Occurrence Download

description: A dataset containing 4158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Deutzia scabra Thunb.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 4158 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014169-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18176313
title: OpenFF 2.3.0rc2 Relative Binding Free Energy Benchmarks

description: Overview

Relative binding free energy benchmarks of the openff-2.3.0rc2 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc2_elf10`: simulations using OpenFF 2.3.0rc2 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc2_nagl`: simulations using OpenFF 2.3.0rc2 and AshGC v0.1rc3 charges

For additional validation, an extra 3 replica was run for the simulations using AshGC charges for all sets. Results have been collated in separate files which are labelled with the tag `6replica` in their name.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can also be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

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  * 3 replica were originally run, and then a further 3 were added to the `6replica` files.


Changelog

Version 3

This upload adds recalculated results for the elf10 benchmarks. Unfortunately due to an oversight, previous versionsused am1bcc charges instead of am1bcc-elf10.
DOI: 10.5281/zenodo.17402653
title: OpenFF 2.3.0rc2 Relative Binding Free Energy Benchmarks

description: Overview

Relative binding free energy benchmarks of the openff-2.3.0rc2 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc2_elf10`: simulations using OpenFF 2.3.0rc2 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc2_nagl`: simulations using OpenFF 2.3.0rc2 and AshGC v0.1rc3 charges

For additional validation, an extra 3 replica was run for the simulations using AshGC charges for all sets. Results have been collated in separate files which are labelled with the tag `6replica` in their name.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can also be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

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  * 3 replica were originally run, and then a further 3 were added to the `6replica` files.


Changelog

Version 3

This upload adds recalculated results for the elf10 benchmarks. Unfortunately due to an oversight, previous versionsused am1bcc charges instead of am1bcc-elf10.
DOI: 10.15468/dl.jprkkj
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003891-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zkde32
title: Occurrence Download

description: A dataset containing 4776 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidoscelis costatus (Cope, 1878)"
 ]
}

 The dataset includes 4776 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113345-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e7hxk0
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012853-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhhs83
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013282-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fslprr
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012401-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjhffh
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amitus fuscipennis MacGown & Nebeker, 1978"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113348-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbjie9
title: Occurrence Download

description: A dataset containing 507 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "StateProvince is misiones",
 "TaxonKey is Melastomataceae"
 ]
}

 The dataset includes 507 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026405-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nlmlo4
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013888-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gdpqje
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arcoscalpellum portoricanum (Pilsbry, 1907)"
 ]
}

 The dataset includes 103 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113375-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brtqec
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012821-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.quckmk
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002928-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rw9tz4
title: Occurrence Download

description: A dataset containing 392 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Podocarpus nubigenus Lindl."
 ]
}

 The dataset includes 392 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113355-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hzdsdc
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-21.18164 -4.41101,48.81126 -4.41101,48.81126 28.90753,-21.18164 28.90753,-21.18164 -4.41101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "InstitutionCode is tnhc",
 "InstitutionCode is cumv",
 "InstitutionCode is fishbase",
 "InstitutionCode is uf"
 ]
 },
 "TaxonKey is Hemichromis letourneuxi Sauvage, 1880"
 ]
}

 The dataset includes 10 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086173-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rryn9y
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003884-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfwm3c
title: Occurrence Download

description: A dataset containing 222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrophyllia cornigera (Lamarck, 1816)"
 ]
}

 The dataset includes 222 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0135464-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tj7xjg
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.51092 1.62972,0.3156 1.62972,0.3156 9.26023,-10.51092 9.26023,-10.51092 1.62972))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "InstitutionCode is tnhc",
 "InstitutionCode is fishbase"
 ]
 },
 "TaxonKey is Hemichromis guttatus Günther, 1862"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086170-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tokdap
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012918-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcpqey
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013293-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c7kse3
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arctides antipodarum Holthuis, 1960"
 ]
}

 The dataset includes 72 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113389-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdqgei
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013034-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.prjery
title: Occurrence Download

description: A dataset containing 444969497 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 444969497 records from 1771 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019007-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/lsq-f68-r4k
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lkk-nr6-jt2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vze-rjk-t8r
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cmq-68t-fbz
title: Orchestia Leach, 1814

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eh1-gfn-vet
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.rxrx2x
title: Occurrence Download

description: A dataset containing 1133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tamarix ramosissima Ledeb.",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1133 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104167-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/506-xx5-1gt
title: Euchirella speciosa Grice & Hulsemann, 1968

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6f0-sh1-v2w
title: Candona (Candona) Baird, 1845

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.yhz8ff
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tamarix ramosissima Ledeb.",
 "Country is Argentina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104166-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/7wj-rmn-mfa
title: Euchirella messinensis messinensis (Claus, 1863)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0rp-3pc-2j6
title: Candona (Candona) Baird, 1845

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lbs-war-qhy
title: Orchestia gammarellus (Pallas, 1766)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4c5-qw7-atz
title: Ilyodromus Sars, 1894

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8am-6ve-72s
title: Cyprois marginata (Straus, 1821)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cyl-py3-n45
title: Euchirella splendens Vervoort, 1963

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h2x-0bx-8s9
title: Marinogammarus marinus (Leach, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fe7-wdc-21w
title: Metopa alderi (Spence Bate, 1857)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lxn-7gg-72h
title: Britorchestia brito (Stebbing, 1891)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rda-p8r-712
title: Heterocypris salina (Brady, 1868)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m5b-r55-dbd
title: Bathyporeia pelagica (Spence Bate, 1857)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qr2-7dq-b8x
title: Bathyporeia elegans Watkin, 1938

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/psm-yx8-lfq
title: Ilyocypris gibba (Ramdohr, 1808)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tbx-3pb-w5k
title: Cypridopsis vidua (Mueller, 1776)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/534-0ds-g51
title: Bathyporeia pelagica (Spence Bate, 1857)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k3h-hkz-z5t
title: Ilyocypris gibba (Ramdohr, 1808)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kfc-xq6-05s
title: Euchirella rostrata (Claus, 1866)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8dm-w8f-grg
title: Candona (Candona) Baird, 1845

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9t8-xhn-d93
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.v3zjku
title: Occurrence Download

description: A dataset containing 3151620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((-112.41 22.58,-91.84 22.58,-91.84 32.25,-112.41 32.25,-112.41 22.58))",
 "HasCoordinate is true",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 3151620 records from 617 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0104126-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/m1r-9l1-k66
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gtx-k1n-lg7
title: Isocypris G.W. Müller, 1908

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lqp-jca-0en
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0d7-9jk-f58
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fp7-b5g-bdk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5xs-8h5-byp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rye-hp5-z3v
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gb9-y9d-7vm
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yl5-j83-keb
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cwy-xl0-14l
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yzl-qc9-je0
title: Eucypris Vavra, 1891

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/84y-pxv-22j
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.