From owner-metabolic-reg@net.bio.net Sat Sep 18 14:32:00 1999
Path: biosci!glaxowellcome.co.uk!gzz78923
From: gzz78923@glaxowellcome.co.uk ("Goryanin, Igor I")
Newsgroups: bionet.metabolic-reg
Subject: Universal format for storing  pathways and models
Date: 18 Sep 1999 08:32:24 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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Dear all,

I completely agree with Herbert about the importance to have Portable Metabolic Standard format.
But, it is not clear to me the advantage of introducing new pbm binary format.
I would like to remind that I've already included parsers for (KEGG, WIT, Scamp files) to DBsolve.
http://websites.ntl.com/~igor.goryanin
Existing SCAMP cmd files automatically parsable for 99%.
WIT (MPW) already has  e-circuits like format for storing and retrieve pathways in HTML (SGML).
KEGG has easy readable underlying ASCII format (LIGAND DB).
Personally, I would prefer XML for human and browser readable exchange format. XML becomes very popular in scientific community. All browsers and editors will support XML in near future. Parsers for XML have been written and are freely available. XML subsets for mathematics and general modeling are being developed.
For my  opinion WIT and  KEGG will remain the main sources of original pathway information in genome related  
areas. So, it would be great if we could invite (Selkov & Kanehisa) to take part in our discussions.
For storing all available information about enzymes/pathways ASCII EMP format http://www.empproject.com has been developed at least 10 years ago.

All the best,

Igor Goryanin






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