cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57745/n3jvph
title: slice01559.tif

description: :unav
DOI: 10.13145/bacdive120440.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57745/gzk0mc
title: slice00842.tif

description: :unav
DOI: 10.57745/nfpyii
title: slice01796.tif

description: :unav
DOI: 10.13145/bacdive120441.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57745/k8wsoi
title: slice00361.tif

description: :unav
DOI: 10.57745/xi9gsc
title: slice01151.tif

description: :unav
DOI: 10.13145/bacdive120442.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57745/hvldwh
title: slice01443.tif

description: :unav
DOI: 10.57745/p1vprn
title: slice00986.tif

description: :unav
DOI: 10.13145/bacdive120443.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57745/f2iuxg
title: slice00564.tif

description: :unav
DOI: 10.57745/ovglqt
title: slice01449.tif

description: :unav
DOI: 10.13145/bacdive120444.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.57745/6kcbbr
title: slice00167.tif

description: :unav
DOI: 10.57745/opp4gz
title: slice01737.tif

description: :unav
DOI: 10.57745/lcvzjm
title: slice01394.tif

description: :unav
DOI: 10.57745/rr0fzh
title: slice00994.tif

description: :unav
DOI: 10.13145/bacdive120445.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.v9uzup
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Atrichum angustatum (Brid.) Bruch & Schimp.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 195 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0232245-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ck2uqb
title: Occurrence Download

description: A dataset containing 1108 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chlorella vulgaris Beij."
 ]
}

 The dataset includes 1108 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027475-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.28rhps
title: Occurrence Download

description: A dataset containing 280 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Echeveria nodulosa (Baker) Ed.Otto"
 ]
}

 The dataset includes 280 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015215-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jvnaf7
title: Occurrence Download

description: A dataset containing 2200 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "Year 2020-2023",
 "GadmGid is one of (COL.15.42_2)"
 ]
 }
 ]
}

 The dataset includes 2200 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027493-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4m8qe
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "TaxonKey is Oscaecilia polyzona (Fischer, 1880)"
 ]
}

 The dataset includes 25 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0423821-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3eyvhe
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Indocypraea montana (Blume) Orchard"
 ]
}

 The dataset includes 157 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034190-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ck6qzu
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vernonia bontocensis Merr."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028729-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wcxhn
title: Occurrence Download

description: A dataset containing 627 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Berberis aristata DC."
 ]
}

 The dataset includes 627 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034213-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7u8jhs
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tarentola boehmei Joger, 1984"
 ]
}

 The dataset includes 92 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285477-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3pz2yy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Epinotia emarginana (Walsingham, 1879)",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Poland",
 "Country is Poland"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0369328-210914110416597/datasets/export for details.
DOI: 10.15468/dl.u9y2sw
title: Occurrence Download

description: A dataset containing 2151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acacia leptocarpa A.Cunn. ex Benth.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2151 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113951-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7axprp
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is MEX",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Anaxyrus californicus (Camp, 1915)"
 ]
}

 The dataset includes 169 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0428857-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d83pwj
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanilla palembanica Teijsm. & Binn."
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027459-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aa5ns9
title: Occurrence Download

description: A dataset containing 5228 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coloeus dauuricus (Pallas, 1776)"
 ]
}

 The dataset includes 5228 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0384865-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4y9qnk
title: Occurrence Download

description: A dataset containing 2795 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calanthe triplicata (Willemet) Ames"
 ]
}

 The dataset includes 2795 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113956-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vqwdcv
title: Occurrence Download

description: A dataset containing 622585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.5495 43.82723,3.98111 43.83584,4.04236 43.95068,4.00504 44.18324,3.761 44.21769,3.32747 44.24449,3.17435 44.05978,3.3112 43.86646,3.5495 43.82723))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 622585 records from 798 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0120222-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6k8wyt
title: Occurrence Download

description: A dataset containing 5417 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Occurrence evidence)",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Continent derived from country, Continent derived from coordinates, Occurrence status inferred from individual count, Collection match none, Institution match fuzzy, Institution match none, Institution collection mismatch, Collection match fuzzy)",
 "TaxonKey is Avicennia germinans (L.) L."
 ]
}

 The dataset includes 5417 records from 277 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017286-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4tt4ua
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Betaproteobacteria",
 "HasCoordinate is true",
 "Country is one of (Portugal)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0232255-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mw8y95
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Halophila johnsonii Eiseman"
 ]
}

 The dataset includes 47 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0113961-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehpvmy
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allobates goianus (Bokermann, 1975)"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285455-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrv4vc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laetmogonidae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017259-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nuwrz
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia parva N.E.Br."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0206124-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdnjgh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acinetasteridae",
 "Continent is one of (North America, South America)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017261-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rxbk34
title: Occurrence Download

description: A dataset containing 13700 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mosquito Alert Dataset"
 ]
}

 The dataset includes 13700 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0384850-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3zfmwk
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tolpis ×grossii Talavera"
 ]
}

 The dataset includes 38 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017292-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpc3gu
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cordylus machadoi Laurent, 1964"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285458-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tkhcju
title: Occurrence Download

description: A dataset containing 475 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tolpis laciniata (Sch.Bip. ex Webb & Berthel.) Webb & Berthel."
 ]
}

 The dataset includes 475 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017295-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dk6mh8
title: Occurrence Download

description: A dataset containing 1363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (Bangladesh, Cambodia, Fiji, India, Malaysia, Northern Mariana Islands, Marshall Islands, Myanmar, New Caledonia, Papua New Guinea, Philippines, Samoa, Solomon Islands, Thailand, Tonga, Tuvalu, Vanuatu, Viet Nam)",
 "OccurrenceStatus is Present",
 "TaxonKey is Casuarina equisetifolia L.",
 "Year 1900-2025"
 ]
}

 The dataset includes 1363 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030305-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5c6xf
title: Occurrence Download

description: A dataset containing 6486137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is France",
 "Geometry POLYGON((1.95275 51.30254,0.84115 50.35262,-0.72818 49.84931,-2.03595 49.93356,-2.10134 48.91282,-2.886 49.12723,-5.23999 48.74063,-5.1746 47.56284,-3.21294 47.16423,-2.16673 46.17715,-2.03595 44.61617,-2.95139 43.15534,-0.5974 42.19388,3.3913 41.60987,4.17596 42.77254,6.07223 42.67647,7.70694 42.48388,7.96849 41.21757,9.53782 41.21757,10.12631 41.90255,9.60321 43.39338,8.23005 42.96424,8.23005 44.47637,8.03388 46.71779,8.55699 48.17692,9.27626 48.95578,8.23005 49.76491,6.13761 50.39432,4.17596 51.22071,1.95275 51.30254))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 2021-2025"
 ]
}

 The dataset includes 6486137 records from 1501 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053179-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17155650
title: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

description: 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.

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 alsos 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
DOI: 10.5281/zenodo.17936667
title: OpenFF 2.2.1 Relative Binding Free Energy Benchmarks

description: 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.

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 alsos 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