Transformations in PubChem - Full Dataset
Authors/Creators
- 1. LCSB, Uni Luxembourg
- 2. NCBI/NLM/NIH
- 3. University of Amsterdam
Description
This is an archive of the data contained in the "Transformations" section in PubChem for integration into patRoon and other workflows.
For further details see the ECI GitLab site: README and main "tps" folder.
Credits:
Concepts: E Schymanski, E Bolton, J Zhang, T Cheng;
Code (in R): E Schymanski, R Helmus, P Thiessen
Transformations: E Schymanski, J Zhang, T Cheng and many contributors to various lists!
PubChem infrastructure: PubChem team
Acknowledgements: ECI team who contributed to related efforts, especially: J. Krier, A. Lai, M. Narayanan, T. Kondic, P. Chirsir, E. Palm, Bashir Mayahi. All contributors to the NORMAN-SLE transformations!
March 2025 released as v0.2.0 since the dataset grew by >3000 entries! Nov 2025 updated to new SMILES fields.
The stats are:
# 21 Mar. 2026
Unique Transformation Entries: 11260
Unique Reactions by CID: 9371
Unique Reactions by IK: 9358
Unique Reactions by IKFB: 8790
Unique NORMAN-SLE Compounds by CID: 8426
Unique ChEMBL Compounds by CID: 1418
Unique Compounds (all) by CID: 9483
Unique Predecessors (all) by CID: 3813
Unique Successors (all) by CID: 7501
Range of XlogP Differences: -12.5,10
Range of Mass Differences: -957.97490813,820.227106427
Notes
Files
PubChem_all_transformations_wExtraInfo.csv
Additional details
Related works
- Is derived from
- Dataset: https://pubchem.ncbi.nlm.nih.gov/ (URL)
- Is supplement to
- Publication: 10.1186/s13321-018-0277-8 (DOI)
- Software: https://fairtps.lcsb.uni.lu/ (URL)
- Publication: 10.1021/acsenvironau.5c00314 (DOI)