adds the dataset card

README.md

@@ -0,0 +1,309 @@
+---
+license:
+  - pddl
+license_link: https://opendatacommons.org/licenses/pddl
+tags:
+  - pubchem
+  - small-molecules
+  - InChI
+  - SMILES
+  - molecular-geometry
+  - molecular-properties
+  - chemical-properties
+  - cheminformatics
+annotations_creators:
+  - crowdsourced
+pretty_name: pubchem-04-18-2025
+size_categories:
+  - 100M<n<200M
+source_datasets:
+  - pubchem-compound
+  - pubchem-04-18-2025
+task_categories:
+  - tabular-regression
+  - other
+task_ids:
+  - tabular-single-column-regression
+viewer: false
+configs:
+  - config_name: pubchem-04-18-2025
+    data_files:
+      - split: train
+        path: "data/train/*.json"
+    default: true
+---
+
+# PubChem Dataset (version 04-18-2025)
+
+* **Important Note:** The current version of the PubChem dataset includes a new
+  entry, `PUBCHEM_SMILES`, which is equivalent to isomeric SMILES and contains
+  both stereochemical and isotopic information. This entry is set to replace
+  both `PUBCHEM_OPENEYE_CAN_SMILES` and `PUBCHEM_OPENEYE_ISO_SMILES` in the future.
+  For further details, please refer to the [PubChem documentation](https://pubchem.ncbi.nlm.nih.gov/docs/glossary#section=SMILES).
+
+## Table of Contents
+
+- [PubChem Dataset (version 04-18-2025)](#pubchem-dataset-version-04-18-2025)
+  - [Table of Contents](#table-of-contents)
+  - [Dataset Description](#dataset-description)
+    - [Dataset Summary](#dataset-summary)
+  - [Dataset Structure](#dataset-structure)
+    - [Data Instances](#data-instances)
+    - [Data Fields](#data-fields)
+    - [Data Splits and Configurations](#data-splits-and-configurations)
+  - [Dataset Creation](#dataset-creation)
+    - [Curation Rationale](#curation-rationale)
+    - [Source Data](#source-data)
+      - [Initial Data Collection and Normalization](#initial-data-collection-and-normalization)
+    - [Personal and Sensitive Information](#personal-and-sensitive-information)
+  - [Considerations for Using the Data](#considerations-for-using-the-data)
+    - [Social Impact of Dataset](#social-impact-of-dataset)
+  - [Additional Information](#additional-information)
+    - [Dataset Curators](#dataset-curators)
+    - [Licensing Information](#licensing-information)
+    - [Citation Information](#citation-information)
+    - [Contributions](#contributions)
+
+## Dataset Description
+
+- **Homepage:** https://pubchem.ncbi.nlm.nih.gov
+- **Paper:** https://doi.org/10.1093/nar/gkac956
+- **Point of Contact:** [Sunghwan Kim]([email protected])
+- **Point of Contact:** [Mohammad Mostafanejad]([email protected])
+- **Point of Contact:** [MolSSI-AI Hub]([email protected])
+
+### Dataset Summary
+
+[PubChem](https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information
+resource that serves a wide range of use cases. It is an open chemistry
+database at the National Institutes of Health (NIH). "Open" means that you can
+put your scientific data in PubChem and that others may use it. Since the launch
+in 2004, PubChem has become a key chemical information resource for scientists,
+students, and the general public. Each month our website and programmatic
+services provide data to several million users worldwide.
+
+PubChem mostly contains small molecules, but also larger molecules such as
+nucleotides, carbohydrates, lipids, peptides, and chemically-modified
+macromolecules. PubChem collects information on chemical structures,
+identifiers, chemical and physical properties, biological activities, patents,
+health, safety, toxicity data, and many others.
+
+## Dataset Structure
+
+### Data Instances
+
+An example of a data instance is as follows:
+
+```json
+{
+'PUBCHEM_COMPOUND_CID': '12',
+'PUBCHEM_COMPOUND_CANONICALIZED': '1',
+'PUBCHEM_CACTVS_COMPLEXITY': 104.0,
+'PUBCHEM_CACTVS_HBOND_ACCEPTOR': 4,
+'PUBCHEM_CACTVS_HBOND_DONOR': 4,
+'PUBCHEM_CACTVS_ROTATABLE_BOND': 0,
+'PUBCHEM_CACTVS_SUBSKEYS': 'AAADcYBgOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAACASAkAAwBoAAAgCAACBCAAACAAAgIAAAiAAGiIgJJyKCERKAcAElwBUJmAfAYAQAAQAACAAAQAACAAAQAACAAAAAAAAAAA==',
+'PUBCHEM_IUPAC_OPENEYE_NAME': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_CAS_NAME': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_NAME_MARKUP': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_NAME': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_SYSTEMATIC_NAME': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_TRADITIONAL_NAME': 'benzene-1,2,3,5-tetrol',
+'PUBCHEM_IUPAC_INCHI': 'InChI=1S/C6H6O4/c7-3-1-4(8)6(10)5(9)2-3/h1-2,7-10H',
+'PUBCHEM_IUPAC_INCHIKEY': 'RDJUHLUBPADHNP-UHFFFAOYSA-N',
+'PUBCHEM_XLOGP3_AA': None,
+'PUBCHEM_EXACT_MASS': 142.02660867,
+'PUBCHEM_MOLECULAR_FORMULA': 'C6H6O4',
+'PUBCHEM_MOLECULAR_WEIGHT': 142.11,
+'PUBCHEM_SMILES': 'C1=C(C=C(C(=C1O)O)O)O',
+'PUBCHEM_OPENEYE_CAN_SMILES': 'C1=C(C=C(C(=C1O)O)O)O',
+'PUBCHEM_OPENEYE_ISO_SMILES': 'C1=C(C=C(C(=C1O)O)O)O',
+'PUBCHEM_CACTVS_TPSA': 80.9,
+'PUBCHEM_MONOISOTOPIC_WEIGHT': 142.02660867,
+'PUBCHEM_TOTAL_CHARGE': 0,
+'PUBCHEM_HEAVY_ATOM_COUNT': 10,
+'PUBCHEM_ATOM_DEF_STEREO_COUNT': 0,
+'PUBCHEM_ATOM_UDEF_STEREO_COUNT': 0,
+'PUBCHEM_BOND_DEF_STEREO_COUNT': 0,
+'PUBCHEM_BOND_UDEF_STEREO_COUNT': 0,
+'PUBCHEM_ISOTOPIC_ATOM_COUNT': 0,
+'PUBCHEM_COMPONENT_COUNT': 1,
+'PUBCHEM_CACTVS_TAUTO_COUNT': 15,
+'PUBCHEM_COORDINATE_TYPE': [1, 5, 255],
+'PUBCHEM_BONDANNOTATIONS': [5,
+6,
+8,
+...,
+8],
+'COORDS': [4.269000053405762,
+2.0,
+0.0,
+...,
+0.0],
+'ATOMIC_INDICES': [1, 2, 3, ..., 16],
+'ATOMIC_SYMBOLS': ['O',
+'O',
+'O',
+...,
+'H'],
+'ATOMIC_NUMBERS': [8, 8, 8, ..., 1],
+'ATOMIC_FORMAL_CHARGES': [0, 0, 0, ..., 0],
+'BOND_ORDERS': [1,
+5,
+1,
+...,
+1],
+'PUBCHEM_XLOGP3': '0.8',
+'PUBCHEM_NONSTANDARDBOND': None,
+'PUBCHEM_REFERENCE_STANDARDIZATION': None
+}
+```
+
+### Data Fields
+
+| Field                             | Description                                                            |
+| --------------------------------- | ---------------------------------------------------------------------- |
+| PUBCHEM_COMPOUND_CID              | PubChem Compound ID                                                    |
+| PUBCHEM_COMPOUND_CANONICALIZED    | Canonicalized form of the compound computed by OEChem 2.3.0            |
+| PUBCHEM_CACTVS_COMPLEXITY         | Complexity of the compound computed by Cactvs 3.4.8.18                 |
+| PUBCHEM_CACTVS_HBOND_ACCEPTOR     | Number of hydrogen bond acceptors computed by Cactvs 3.4.8.18          |
+| PUBCHEM_CACTVS_HBOND_DONOR        | Number of hydrogen bond donors computed by Cactvs 3.4.8.18             |
+| PUBCHEM_CACTVS_ROTATABLE_BOND     | Number of rotatable bonds computed by Cactvs 3.4.8.18                  |
+| PUBCHEM_CACTVS_SUBSKEYS           | Substructure keys computed by Cactvs 3.4.8.18                          |
+| PUBCHEM_IUPAC_OPENEYE_NAME        | IUPAC name of the compound computed by OEChem 2.3.0                    |
+| PUBCHEM_IUPAC_CAS_NAME            | CAS name of the compound                                               |
+| PUBCHEM_IUPAC_NAME_MARKUP         | IUPAC name markup                                                      |
+| PUBCHEM_IUPAC_NAME                | IUPAC name computed by Lexichem TK 2.7.0                               |
+| PUBCHEM_IUPAC_SYSTEMATIC_NAME     | IUPAC systematic name                                                  |
+| PUBCHEM_IUPAC_TRADITIONAL_NAME    | IUPAC traditional name                                                 |
+| PUBCHEM_IUPAC_INCHI               | InChI of the compound computed by InChI 1.0.6                          |
+| PUBCHEM_IUPAC_INCHIKEY            | InChI key of the compound computed by InChI 1.0.6                      |
+| PUBCHEM_XLOGP3_AA                 | XLogP3 with atom additive model computed by XLogP3 3.0                 |
+| PUBCHEM_EXACT_MASS                | Exact mass of the compound computed by PubChem 2.2                     |
+| PUBCHEM_MOLECULAR_FORMULA         | Molecular formula of the compound computed by PubChem 2.2              |
+| PUBCHEM_MOLECULAR_WEIGHT          | Molecular weight of the compound computed by PubChem 2.2               |
+| PUBCHEM_SMILES                    | Isomeric SMILES (deposited or) computed by OEChem 2.3.0                |
+| PUBCHEM_OPENEYE_CAN_SMILES        | Canonical SMILES of the compound computed by OEChem 2.3.0              |
+| PUBCHEM_OPENEYE_ISO_SMILES        | Isomeric SMILES of the compound computed by OEChem 2.3.0               |
+| PUBCHEM_CACTVS_TPSA               | Topological polar surface area computed by Cactvs 3.4.8.18             |
+| PUBCHEM_MONOISOTOPIC_WEIGHT       | Monoisotopic weight of the compound computed by PubChem 2.2            |
+| PUBCHEM_TOTAL_CHARGE              | Total charge of the compound computed by PubChem                       |
+| PUBCHEM_HEAVY_ATOM_COUNT          | Number of heavy atoms in the compound computed by PubChem              |
+| PUBCHEM_ATOM_DEF_STEREO_COUNT     | Number of defined stereo centers in the compound computed by PubChem   |
+| PUBCHEM_ATOM_UDEF_STEREO_COUNT    | Number of undefined stereo centers in the compound computed by PubChem |
+| PUBCHEM_BOND_DEF_STEREO_COUNT     | Number of defined stereo bonds in the compound computed by PubChem     |
+| PUBCHEM_BOND_UDEF_STEREO_COUNT    | Number of undefined stereo bonds in the compound computed by PubChem   |
+| PUBCHEM_ISOTOPIC_ATOM_COUNT       | Number of isotopic atoms in the compound computed by PubChem           |
+| PUBCHEM_COMPONENT_COUNT           | Number of components in the compound computed by PubChem               |
+| PUBCHEM_CACTVS_TAUTO_COUNT        | Number of tautomers of the compound computed by Cactvs 3.4.8.18        |
+| PUBCHEM_COORDINATE_TYPE           | Coordinate type                                                        |
+| PUBCHEM_BONDANNOTATIONS           | Bond annotations                                                       |
+| COORDS                            | Cartesian coordinates of the molecular geometry                        |
+| ATOMIC_INDICES                    | Atomic indices                                                         |
+| ATOMIC_SYMBOLS                    | Atomic symbols                                                         |
+| ATOMIC_NUMBERS                    | Atomic numbers                                                         |
+| ATOMIC_FORMAL_CHARGES             | Atomic formal charges                                                  |
+| BOND_ORDERS                       | Bond orders                                                            |
+| PUBCHEM_XLOGP3                    | XLogP3 computed by XLogP3 3.0                                          |
+| PUBCHEM_NONSTANDARDBOND           | Non-standard bond                                                      |
+| PUBCHEM_REFERENCE_STANDARDIZATION | Reference standardization                                              |
+
+### Data Splits and Configurations
+
+The dataset has only one `train` split and one configuration/subset:
+
+- `pubchem-04-18-2025` (default)
+
+## Dataset Creation
+
+### Curation Rationale
+
+The present version of PubChem dataset has been extracted from its original
+ftp repository, transformed into a dictionary and stored in the `.json`
+format.
+
+### Source Data
+
+The link to the original PubChem dataset FTP repository can be found
+[here](https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/)
+
+#### Initial Data Collection and Normalization
+
+Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale),
+no data modification has been performed on the PubChem dataset.
+
+### Personal and Sensitive Information
+
+The PubChem dataset does not involve any personal or sensitive information.
+
+## Considerations for Using the Data
+
+### Social Impact of Dataset
+
+The PubChem dataset paves the way for applications in drug discovery and materials science, among others.
+
+## Additional Information
+
+### Dataset Curators
+
+- **Sunghwan Kim**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Jie Chen**, National Center for Biotechnology Information, National Library
+  of Medicine, National Institutes of Health, Department of Health and Human
+  Services, Bethesda, MD, 20894 USA
+- **Tiejun Cheng**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Asta Gindulyte**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Jia He**, National Center for Biotechnology Information, National Library of
+  Medicine, National Institutes of Health, Department of Health and Human
+  Services, Bethesda, MD, 20894 USA
+- **Siqian He**, National Center for Biotechnology Information, National Library
+  of Medicine, National Institutes of Health, Department of Health and Human
+  Services, Bethesda, MD, 20894 USA
+- **Qingliang Li**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Benjamin A Shoemaker**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Paul A Thiessen**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Bo Yu**, National Center for Biotechnology Information, National Library of
+  Medicine, National Institutes of Health, Department of Health and Human
+  Services, Bethesda, MD, 20894 USA
+- **Leonid Zaslavsky**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Jian Zhang**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+- **Evan E Bolton**, National Center for Biotechnology Information, National
+  Library of Medicine, National Institutes of Health, Department of Health and
+  Human Services, Bethesda, MD, 20894 USA
+
+### Licensing Information
+
+[Free Public Domain License](https://www.ncbi.nlm.nih.gov/home/about/policies/#data)
+
+### Citation Information
+
+```tex
+@article{Kim:2022:D1373,
+    author = {Kim, Sunghwan and Chen, Jie and Cheng, Tiejun and Gindulyte, Asta and He, Jia and He, Siqian and Li, Qingliang and Shoemaker, Benjamin A and Thiessen, Paul A and Yu, Bo and Zaslavsky, Leonid and Zhang, Jian and Bolton, Evan E},
+    title = "{PubChem 2023 update}",
+    journal = {Nucleic Acids Research},
+    volume = {51},
+    pages = {D1373-D1380},
+    year = {2022},
+    doi = {10.1093/nar/gkac956}
+}
+```
+
+### Contributions
+
+- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)