Specifications for static pathway models:
- gene list file
1. FEATURE ID
     This is an internal id given to each CDS, sequentially numbered in the 
    order of appearance in the genome database.
2. Gene to Protein Match Level
     Level 1 is match with annnotation reference, Level 2 is by homology 
    search, and Level 3 is by orthology search. 
3. Database Reference
     In Level 1 and 2, SWISS-PROT entry id. In Level 3, EC number identified 
    by COG id in the KEGG Orthology database.
4. E-value
     E-value for Level 2. Always 0 for Levels 1 and 3.
5. COG ID
     COG ID obtained through orthology search, only available for Level 3.

- reaction list file
 The reaction list is divided into pathways in FASTA like format, begining 
 with a line like the following: 
>MAP00010 Glycolysis / Glucogenesis
where MAP00010 is the pathway id in KEGG database followed by the 
name  of the pathway.
End of the pathway list is specified by two slashes.(//)
Each reaction is described with the following fields:
1.  Gene name
     Name of the gene coding for the enzyme responsible for the reaction.
    If the reaction is filled in during the pathway check step, the name 
    starts with 'unknown-'.
2. dynamic or static
    Define whether the reaction is dynamic (d) or static(s) for the selection
    of simulation methods.
3. reaction
    Stoicheometric reaction equation. Metabolites are represented by KEGG
    compound ID.
4. localization
    Protein localization of the enzyme.
5. EC number
     EC number of the enzyme
6. reaction mechanism
     specific enzyme reaction mechanism where available
7. reversibility
     reversibility of the enzyme reaction.



- pathway view
 The pathway view visualizes the extracted pathway information by connecting
the metabolites as nodes and enzymes as edges. For this purpose we are
using the software "Visualizing protein-protein interaction" by Mrowka,R.
(Bioinformatics 2001 17-7:669-671)

See http://www.charite.de/bioinformatics/interaction/index.html this website
for details of the software.



- genome-scale model matrix
 The genome-scale model matrix is the entire stoichiometric matrix of the 
automatically generated models in csv (comma separated values format). 
This matrix can be used for metabolic flux analysis. The rows are the 
metabolites and the columns are the reactions.



 
Contact Kazuharu Arakawa <gaou@sfc.keio.ac.jp> for questions.
(C) 2004 Institute for Advanced Biosciences, Keio University