WholeCellKB: model organism databases for comprehensive whole-cell models

Nucleic Acids Res. 2013 Jan;41(Database issue):D787-92. doi: 10.1093/nar/gks1108. Epub 2012 Nov 21.


Whole-cell models promise to greatly facilitate the analysis of complex biological behaviors. Whole-cell model development requires comprehensive model organism databases. WholeCellKB (http://wholecellkb.stanford.edu) is an open-source web-based software program for constructing model organism databases. WholeCellKB provides an extensive and fully customizable data model that fully describes individual species including the structure and function of each gene, protein, reaction and pathway. We used WholeCellKB to create WholeCellKB-MG, a comprehensive database of the Gram-positive bacterium Mycoplasma genitalium using over 900 sources. WholeCellKB-MG is extensively cross-referenced to existing resources including BioCyc, KEGG and UniProt. WholeCellKB-MG is freely accessible through a web-based user interface as well as through a RESTful web service.

Publication types

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

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Chromosomes, Bacterial
  • Databases, Genetic*
  • Genes, Bacterial
  • Internet
  • Models, Biological*
  • Mycoplasma genitalium / genetics*
  • Mycoplasma genitalium / growth & development
  • Mycoplasma genitalium / metabolism
  • RNA, Bacterial / metabolism
  • Software
  • User-Computer Interface


  • Bacterial Proteins
  • RNA, Bacterial