PRA3006-SPARQL

Using SPARQL to query Life Science Databases

Ammar Ammar  0000-0002-8399-8990, Marvin Martens  0000-0003-2230-0840, Egon L. Willighagen  0000-0001-7542-0286

© 2021-2026 The Authors

License: CC-BY-SA 4.0 International

This book is written in Markdown with additional instructions that are preprocessed. Part of the content is based on previous workshops, funded by various projects funded by the European Commission.

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

Contents

1. Introduction
   1.1. SPARQL query language
   1.2. This book
   
2. List of Databases
   2.1. Other useful resources
   2.2. Literature data
   
3. Biology
   3.1. Biological entities
   3.1.1. Genes
   3.1.2. Proteins
   3.1.3. Small compounds
   
4. Generic queries
   4.1. Listing all classess
   4.2. Listing all items of some class
   4.3. Listing all properties of some class
   
5. AOP-Wiki
   5.1. Entities
   5.2. Data model
   5.3. Example queries
   5.3.1. Counting key events
   
6. ChEMBL
   6.1. Entities
   6.2. Data model
   6.3. Exercises
   6.3.1. ChEMBL sources
   6.3.2. Counting assays
   6.3.3. Binding affinities
   6.3.4. Assays and UniProt IDs
   
7. PubChem RDF
   7.1. Entities
   7.2. Data model
   
8. UniProtKB
   8.1. Entities
   8.2. Example queries
   
9. Wikidata
   9.1. Entities
   9.2. Data model
   9.3. Example queries
   9.3.1. Proteins
   9.3.2. Chemicals
   
10. WikiPathways
    10.1. Entities
    10.2. Data model
    10.3. Example queries
    10.3.1. Asking information for a specific pathway
    10.3.2. A lipid pathway
    10.3.3. A federated SPARQL query
    

Index

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