Example A: Pathway visualization
- Visualizes gene expression data from Lesch Nyhan Disease patient on the Purine metabolism pathway from WikiPathways
- Dataset: GSE24345
- Pathway: https://www.wikipathways.org/instance/WP4792
- R script
Example B: Pathway enrichment analysis
- Identifies affected pathways in dataset
- Dataset: GSE24345
- Pathway collection: WikiPathways human pathway collection
- R script
Example A: Network Extension
- Extends the Purine metabolism pathway from WikiPathways with known drug-target interactions from DrugBank
- Pathway: https://www.wikipathways.org/instance/WP4792
- Drug-target database: DrugBank (https://www.drugbank.ca/)
- R script
Prerequisits: Beginners tutorial on SPARQL
- Provides basic explanation on RDF, SPARQL and building queries.
- Follow the tutorial here.
Example A: Mapping chemical IDs with BridgeDb
Example B: Performing SPARQL query with InChIKey
Example C: Performing SPARQL query with neutralised InChIKey
Example D: Additiona; SPARQL queries for chemical compounds