🧪 BChemLookup

An Open Science Initiative for Mapping Common Chemical Abbreviations

Welcome to the Beilstein Chemical Lookup Collection – an open, community-driven resource dedicated to collecting and standardizing chemical abbreviations and shorthand notations used in structure drawing, reaction schemes, and synthetic chemistry.

This open-science repository aims to gather, curate, and share a comprehensive set of chemical lookups. In chemical drawings or reaction schemes, it's common to use abbreviated labels to represents (larger) substructures:

Abbreviation	Meaning	SMILES/SMARTS	Notes
Ph	Phenyl	c1ccccc1	Benzene ring
Bn	Benzyl	c1ccccc1CH2	Common protecting group
tBu	tert-Butyl	C(C)(C)C	Often used as steric bulk
Boc	tert-Butoxycarbonyl	OC(C)(C)C=O	Amine protecting group
Et	Ethyl	CC	Alkyl chain

This project aims to collect, normalize, curate and publish these mappings as open source structured data and human readable.

Goals

• Create comprehensive lists of chemical abbreviations used in:
  • Academic literature
  • Chemical drawing software
  • Reaction databases
• Provide machine-readable formats for use in parsers, renderers, and other cheminformatics tools
• Identify ambiguities, overloads, and regional variations
• Enable community contribution and review for open data curation

What is in this repository

• abbreviations.smi – a machine-readable dictionary for structural group abbreviations on chemical drawings

  • It is a two-column, tab separated text file, the first column contains the abbreviation and the second column holds the corresponding SMILES, using an asterisk (*) to indicate the attachment point
  • The initial abbreviations list contains the most common abbreviations found in the Beilstein Journal of Organic Chemistry articles. The abbreviations are translated and reviewed into structures and SMILES by our chemical experts.

  Abbreviation	SMILES
  C	*c1ccc(F)cc1
  –OCH2O–	*OCO*
  MeO	CO[*]

Contributing

We believe the best resource is a community-built one, so you are welcome to contribute. To contribute:

1. Fork this repository
2. Add or update entries
3. Submit a pull request
4. Optionally open an issue for discussion if a term is ambiguous or unclear

We really appreciate your help in keeping things nice and tidy by only modifying one list in each pull request.

Please check for potential copyright infringements and ensure that the data provided is suitable to be included in a CC0-licensed work before contributing. Please include in the commentary section of the pull request a short description or common use of your changes and state the source of the data.

License

All data in this repository is released under the CC0 1.0 Universal license. Use it freely in research, software, education, or commercial applications.

Acknowledgments

This project is inspired by the needs of the cheminformatics community, and we thank the many open-source projects that aim to make chemical knowledge more FAIR (Findable, Accessible, Interoperable, Reusable).
We would like to express our gratitude to Nicole Jung and her team from KIT for their inspiring talks and discussions.

Feedback?

Open an issue or contact the maintainers: open-source@beilstein-institut.de.