Pathway databases: making chemical and biological sense of the genomic data flood

Chem Biol. 2013 May 23;20(5):629-35. doi: 10.1016/j.chembiol.2013.03.018.


Pathway databases are a means to systematically associate proteins with their functions and link them into networks that describe the reaction space of an organism. Here, the Reactome Knowledgebase provides a convenient example to illustrate strategies used to assemble such a reaction space based on manually curated experimental data, approaches to semiautomated extension of these manual annotations to infer annotations for a large fraction of a species' proteins, and the use of networks of functional annotations to infer pathway relationships among variant proteins that have been associated with disease risk through genome-wide surveys and resequencing studies of tumors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Protein*
  • Genomics / methods*
  • Humans
  • Knowledge Bases*
  • Metabolic Networks and Pathways*
  • Mutation
  • Protein Interaction Maps*
  • Proteome / genetics
  • Proteome / metabolism*


  • Proteome