wikidata-chemistry-curation

Curating chemistry in Wikidata

© 2025 Egon Willighagen , Adriano Rutz

License: CC-BY-SA 4.0 International

This book is written in Markdown with additional instructions that are preprocessed.

Wishes, comments, and pull requests can be send to this GitHub repository.

Contents

1. Introduction
   
2. Wikidata property constraints
   2.1. Single value
   2.2. Uniqe value
   
3. Models of chemistry
   3.1. Model and guidance
   3.1.1. Wikidata guidelines
   3.2. Shape expressions
   3.2.1. Chemical elements
   
4. Wikidata-based curation approaches
   4.1. Wikidata items without SMILES
   4.2. Polymers without CXSMILES
   4.3. Functional groups without CXSMILES
   
5. Cheminformatics-based curation
   5.1. Chemistry Development Kit-based
   5.1.1. Unparsable SMILES
   5.2. RDkit-based
   
6. Comparing against databases
   6.1. Chemical Entities of Biological Interest (ChEBI)
   6.2. Common Chemistry
   6.3. DrugBank
   6.4. DSSTox
   6.5. HMDB
   6.6. KNApSAcK
   6.7. nmrshiftdb2
   6.8. NP Atlas
   6.9. PubChem
   6.10. SureChEMBL
   6.11. SwissLipids
   6.12. Unique Ingredient Identifier (UNII)
   
7. Adding additional information
   7.1. Adding chemical compounds
   7.2. Melting points
   7.3. Boiling points
   

Index

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