"Analysis and Design of Biological graph databases"

Antonio Mora, Huang Xiaowei, Mei Songqing

Part 1. Basics.

1. Introduction. What are graph databases? What is Neo4J?
2. Biological graph databases: GREG, Reactome, and others.
3. Installing Neo4J and using GREG-minimum.

Part 2. Introduction to Biological Databases using Cypher.

4. Basics of Cypher.
5. Retrieving GREG's nodes and relationships using Cypher.
6. Queries by property.
7. Single-relationship queries.
8. Multiple-relationship queries.

Part 3. Network analysis applied to biological databases.

9. Shortest paths.
10. Clustering and community detection.
11. Centralities.
12. Network alignment.
13. Link prediction.

Part 4. Machine Learning and Graph Databases.

Extra.

1. Cypher commands.
2. R and Neo4J.