title: Representation and inference of cellular architecture for metabolic reconstruction and modeling.
abstract: Metabolic modeling depends on accurately representing the cellular locations of enzyme-catalyzed and transport reactions. We sought to develop a representation of cellular compartmentation that would accurately capture cellular location information. We further sought a representation that would support automated inference of the cellular compartments present in newly sequenced organisms to speed model development, and that would enable representing the cellular compartments present in multiple cell types within a multicellular organism.
  
  
  
  We define the cellular architecture of a unicellular organism, or of a cell type from a multicellular organism, as the collection of cellular components it contains plus the topological relationships among those components. We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures. We provide software for visualizing cellular architectures to verify their correctness and software for editing cellular architectures to modify or correct them. We also developed a representation that records the cellular compartment assignments of reactions with minimal duplication of information.
  
  
  
  The Cell Component Ontology is freely available. The Pathway Tools software is freely available for academic research and is available for a fee for commercial use.
  
  
  
  pkarp@ai.sri.com
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.affiliation: Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D000465:Algorithms; D003585:Cell Biology; D002468:Cell Physiological Phenomena; D003196:Computer Graphics; D008962:Models, Theoretical; D012984:Software