title: Metannogen: annotation of biological reaction networks.
abstract: BACKGROUND
  Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse and merging of existing models which concern present-day systems biology research more often. Two types of tools for the reconstruction of biological networks currently exist: (i) several sophisticated programs support graphical network editing and visualization. (ii) Data management systems permit reconstruction and curation of huge networks in a team of scientists including data integration, annotation and cross-referencing. We seeked ways to combine the advantages of both approaches.
  
  
  RESULTS
  Metannogen, which was previously developed for network reconstruction, has been considerably improved. From now on, Metannogen provides sbml import and annotation of networks created elsewhere. This permits users of other network reconstruction platforms or modeling software to annotate their networks using Metannogen's advanced information management. We implemented word-autocompletion, multipattern highlighting, spell check, brace-expansion and publication management, and improved annotation, cross-referencing and team work requirements. Unspecific enzymes and transporters acting on a spectrum of different substrates are efficiently handled. The network can be exported in sbml format where the annotations are embedded in line with the miriam standard. For more comfort, Metannogen may be tightly coupled with the network editor such that Metannogen becomes an additional view for the focused reaction in the network editor. Finally, Metannogen provides local single user, shared password protected multiuser or public access to the annotation data.
  
  
  BACKGROUND
  Metannogen is available free of charge at: http://www.bioinformatics.org/strap/metannogen/ or http://3d-alignment.eu/metannogen/.
  
  
  BACKGROUND
  christoph.gille@charite.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Biochemistry, Computational Systems Biochemistry Group, Universitätsmedizin Berlin (Charité), Reinickendorfer Strasse 61, D-13347 Berlin, Germany. christoph.gille@charite.de
authors.forename: Christoph
authors.initials: C
authors.lastname: Gille
authors.forename: Katrin
authors.initials: K
authors.lastname: Hübner
authors.forename: Andreas
authors.initials: A
authors.lastname: Hoppe
authors.forename: Hermann-Georg
authors.initials: HG
authors.lastname: Holzhütter
mesh_terms: D001686:Biological Phenomena; D003628:Database Management Systems; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012985:Software Design