cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13883722
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

1000 conformer test set, version "nc_1000_v1":

This provides a curated hdf5 file for a subset eof the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile  includes 1000 total conformers for 100  unique molecules.

Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit number>:



Link to the source code at this commit: <add link to commit>

Link to the script file used to generate the dataset: <add link to commit>


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.5281/zenodo.13883727
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

Full dataset, version "full_dataset_v1":

This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile  includes 1,107,018 total conformers for 18,782  unique molecules.

Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit number>:



Link to the source code at this commit: <add link to commit>

Link to the script file used to generate the dataset: <add link to commit>


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.5281/zenodo.14264431
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

Full dataset, version "full_dataset_v2":

This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile  includes 1,107,018 total conformers for 18,782  unique molecules.

Changes: Fixed tagging issue for scf_dipoleWhen applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit number>:



Link to the source code at this commit: <add link to commit>

Link to the script file used to generate the dataset: <add link to commit>


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.5281/zenodo.14264561
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

Full dataset restricted to elements H, C, N, O, F, Cl, S, version "full_dataset_v2_HCNOFClS":

This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This subset is limited to molecules containing any of the following 7 elements: H, C, N, O, F, Cl, and S.  This datafile  includes 996941 total conformers for 16560 unique molecules.

Changes: Fixed tagging issue for scf_dipoleWhen applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit number>:



Link to the source code at this commit: <add link to commit>

Link to the script file used to generate the dataset: <add link to commit>


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.5281/zenodo.14269058
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

1000 conformer test set restricted to elements H, C, N, O, F, Cl, S, version "nc_1000_v2_HCNOFClS":

This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This subset is limited to molecules containing any of the following 7 elements: H, C, N, O, F, Cl, and S.  This datafile  includes 1000 total conformers for 10 unique molecules.

Changes: Fixed tagging issue for scf_dipoleWhen applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit <add commit number>:



Link to the source code at this commit: <add link to commit>

Link to the script file used to generate the dataset: <add link to commit>


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.5281/zenodo.14269264
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

1000 conformer test set, version "nc_1000_v2":

This provides a curated hdf5 file for the SPICE 1 OpenFF dataset (Open Force Field initiative default level of theory) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This datafile  includes 1000 total conformers for 10 unique molecules.

Changes: Fixed tagging issue for scf_dipoleWhen applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module




 


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated using B3LYP-D3BJ/DZVP level of theory, using Psi4 1.4.1.This is the default theory used for force field development by the Open Force Field Initiative.  



This includes the following collections from the MolSSI qcarchive (these are also included in the standard SPICE 1 dataset):



"SPICE Solvated Amino Acids Single Points Dataset v1.1",

"SPICE Dipeptides Single Points Dataset v1.2",

"SPICE DES Monomers Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset v1.0",

"SPICE PubChem Set 1 Single Points Dataset v1.2",

"SPICE PubChem Set 2 Single Points Dataset v1.2",

"SPICE PubChem Set 3 Single Points Dataset v1.2",

"SPICE PubChem Set 4 Single Points Dataset v1.2",

"SPICE PubChem Set 5 Single Points Dataset v1.2",

"SPICE PubChem Set 6 Single Points Dataset v1.2",



This does not include the following collections (which are part of the standard SPICE 1 dataset):





"SPICE Ion Pairs Single Points Dataset v1.1",

"SPICE DES370K Single Points Dataset Supplement v1.0",



Citations:

Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6
DOI: 10.15468/dl.yk5rg9
title: Occurrence Download

description: A dataset containing 277342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eristalis tenax (Linnaeus, 1758)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 277342 records from 662 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010323-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc110591162
title: Persepolis Fortification Aramaic Text 246, PFAT 246

description: [Text Description:] Administrative text with seal PFATS 0032; illeg ❧ [Text or Publication Number Note:] PFAT 246, Bowman 246 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFATS 0032 on obverse, reverse; illeg. on bottom edge.
DOI: 10.25549/jrbm-c91-640
title: Kankai ibun, vol. 6, 1807

description: Kankai ibun, [1807], volume 6 = Description and travel of circumnavigation of seas, [1807], volume 6 = 環海 異聞 六 文化 4. Volume six of a manuscript by Gentaku Ōtsuki and Kōkyō Shimura who drew from four Japanese fishermen the story of their voyage around the world during repeated interviews. The Kankai Ibun is an account of their journey when they were sent off-course en route to the capital, Edo. The fishermen were rescued by a Russian ship and taken to late 18th / early 19th century Europe and, most especially, Russia.; The cargo ship, Wakamiyamaru, left from the port of Ishimaki in Sendai-han, today’s Miyagi Prefecture, in Japan carrying rice and lumber with 16 crew members for Edo, today’s Tokyo, on November 27th, 1793. Shipwrecked and drifted in the Pacific Ocean for half a year, they finally landed in one of the islands of the Andreanof Islands, a part of the Aleutian Islands on May 10th, 1794. They were transferred to Irkutsk by Russians where they stayed until the spring of 1803. They were then called in by Alexander I of Russia to St. Petersburg where they stayed from April to June in 1803, and from where they started their journey back home. They were included in the Rezanov mission on the first Russian global circumnavigation by a ship Nadezhda. It took them 16 months to reach the port of Nagasaki, Japan in September, 1804 since they left in June, 1803. Of the sixteen, five crewmen got on board. Four returned home in Sendai; one, who had become an interpreter, returned to Russia with Rezanov.
DOI: 10.25549/inscriptifact-ouc110594646
title: Persepolis Fortification Anepigraphic Tablet 0844.105, PFAnep 0844.105

description: [Text Description:] Administrative text with seal PFUTS 0031 ❧ [Text or Publication Number Note:] PFAnep 0844.105, PFUT 0844-105 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Non-Text ❧ [Physical Object Description:] Clay tablet with seal impression PFUTS 0031 on obverse, reverse, bottom edge.
DOI: 10.25549/inscriptifact-ouc110596177
title: Persepolis Fortification Aramaic Text 331, PFAT 331

description: [Text Description:] Administrative text with seal PFATS 0326. ❧ [Text or Publication Number Note:] PFAT 331, Bowman 331 ❧ [Excavation Description:] Found during Oriental Institute's excavations in Spring, 1933, near the northeastern corner of the stone platform of Persepolis, in two small rooms of a bastion in the fortification wall ❧ [Medium:] Clay ❧ [Script Note:] Aramaic ❧ [Physical Object Description:] Clay tablet with ink inscription. Seal impression PFATS 0326 on reverse. ❧ [Physical Object Note:] Damage on round edge.
DOI: 10.15468/dl.w2wc5v
title: Occurrence Download

description: A dataset containing 50286 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is NEFSC Right Whale Aerial Survey"
 ]
}

 The dataset includes 50286 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011746-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cjhzgw
title: Occurrence Download

description: A dataset containing 4084535 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4084535 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011744-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8dh3aq
title: Occurrence Download

description: A dataset listing the 30291 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 "TaxonKey is Fungi"
 ]
}

 The dataset's 30291 records were derived from 344 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018466-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npj82x
title: Occurrence Download

description: A dataset containing 2741 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Material citation",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "Geometry POLYGON((-0.02782 61.01835,-2.15643 60.66355,-3.70661 60.40267,-6.90134 59.28421,-8.45031 57.66471,-10.67694 55.58841,-11.54824 53.7411,-11.161 51.38792,-6.61091 49.35062,-2.93212 50.03945,0.55305 50.41106,2.39244 51.68899,2.58606 52.5803,0.94029 53.85546,0.26262 54.53508,-0.51187 55.36896,-0.60868 56.45406,-0.22144 57.35269,-2.25445 58.22984,-0.8023 58.9363,-0.02782 61.01835))",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "License is CC-BY 4.0",
 "License is CC-BY-NC 4.0",
 "License is CC0 1.0",
 "License is Pending",
 "License is Incompatible"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Erica vagans L."
 ]
}

 The dataset includes 2741 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0407463-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dved9u
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Singapore, Malaysia, Indonesia)",
 "OccurrenceStatus is Present",
 "TaxonKey is Aetomylaeus nichofii (Bloch & Schneider, 1801)",
 "Year 2000-2024"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011910-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.