cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/fq1-mhn-8r5
title: †Praebulimina Hofker, 1953

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h0b-b5v-40r
title: Dorothia caribaea Cushman, 1936

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h9c-ghq-arc
title: Discorbis Lamarck, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n9z-ckd-sjk
title: Pyrgo clypeata (d'Orbigny, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qkq-94n-2nt
title: Frondicularia sagittula van den Broeck, 1876

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z2q-6g4-2h5
title: Cytherelloidea (Cytherelloidea) Alexander, 1929

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.jkcuu3
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Drymonema dalmatinum",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022592-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/4w1-56b-bpk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gzg-v93-4sr
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g1l-g34-ef5
title: Lenticulina calcar (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fnf-lq5-7lw
title: Ehrenbergina trigona Goës, 1896

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y13-15a-y1b
title: †Marginotruncana Hofker, 1956

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s8c-3ez-2nc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z8b-sxs-9hn
title: Apodemus sylvaticus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8fz-x77-hqv
title: †Eggerellina mariae Ten Dam, 1950

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eq2-e2w-gtv
title: Dentalina Risso, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rvv-nmb-m1z
title: †Citharina plumoides (Plummer, 1927)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j06-34l-jy3
title: Dicerorhinus Gloger, 1841

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ykb-3x4-6ef
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/670-mkg-drx
title: Duvalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9f2-r66-vzp
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dte-43j-y1h
title: Massilina secans (d'Orbigny, 1826)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wnt-ydl-659
title: †Acrocythere pumila Plumhoff, 1963

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mw4-9vx-t1d
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nye-t43-3z7
title: Neorotalia gaimardi (d'Orbigny in Fornasini, 1908)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y6a-k6w-tqz
title: Teschenites

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g4e-1v4-txv
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r82-7n5-4hw
title: Amphistegina radiata (Fichtel & Moll, 1798)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7fz-3h9-dzv
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1tw-4fq-q5w
title: Liebusella soldanii (Jones & Parker, 1860)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ggt-gnt-b6t
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ah6-2y1-1jf
title: Reussella mortenseni Hofker, 1956

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/88n-ngq-e61
title: Miliolinella Wiesner, 1931

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/avf-dc9-jqb
title: Lenticulina calcar (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.pk335z
title: Occurrence Download

description: A dataset containing 2600 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyanidiophyceae"
 ]
}

 The dataset includes 2600 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011025-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12178522
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

Full dataset, version full_dataset_v0:

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.

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 c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice114_openff.py 


 

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.12192219
title: modelforge curated dataset: SPICE 1 OpenFF

description: Curated SPICE 1 OpenFF Dataset:

1000 conformer test set, version "nc_1000_v0":

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.

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 c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice114_openff.py 


 

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.12208395
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_v0_HCNOFClS":

This provides a curated hdf5 file for a subset of 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 100  unique molecules.

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 c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice114_openff.py 


 

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.12209421
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_v0_HCNOFClS":

This provides a curated hdf5 file for a subset of 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.

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 c5c7153:



Link to the source code at this commit: https://github.com/choderalab/modelforge/tree/c5c7153e06172fe8e6f25015250ecb5db05655cc

Link to the script file used to generate the dataset: https://github.com/choderalab/modelforge/blob/c5c7153e06172fe8e6f25015250ecb5db05655cc/modelforge/curation/scripts/curate_spice114_openff.py 


 

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.13883653
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_v1_HCNOFClS":

This provides a curated hdf5 file for a subset of 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: 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.13883717
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_v1_HCNOFClS":

This provides a curated hdf5 file for a subset of 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 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