Databases used in this project

UniProt

Two primary sections: 1. Swiss-Prot/ Reviewed: Manually annotated records 2. TrEMBL/ Unreviewed: Computationally annotated records Subset of UniProtKB —> Proteomes data set

Allows search via:

  • BLAST (local alignment)
  • Multiple sequence alignment
  • ID Mapping
  • ‘Peptide search’ for 3 or more residues

Reactome Pathway Database

  • Compilation of many sources of data including Kegg, UniProt, NCBI, Ensemble, etc.
    • Manually curated, open-source, peer-reviewed
  • Neo4J representation exists. Integrated with Spring Data Neo4j
  • Tutorial on extracting different data types/building reactome cypher queries: https://reactome.org/dev/graph-database/extract-participating-molecules

Drugbank

  • Comprehensive free database of drugs and drug targets
  • Well maintained
  • 13k+ drug entries, 5k+ protein sequences (drug targets/enzymes/etc)
  • Data base can be downloaded here
    • Free for non-commercial use
    • Contains sub databases to download as well (structures, protein identifiers, target sequences, etc.)