From owner-metabolic-reg@net.bio.net Sat Sep 18 23:03:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!demos!news.stack.serpukhov.su!not-for-mail From: "Alex Sel'kov" Newsgroups: bionet.metabolic-reg Subject: Re: Universal format for storing pathways and models Date: Sun, 19 Sep 1999 03:11:03 +0400 Organization: Not organized Lines: 51 Message-ID: <937692632.667327@sirius.shome.eu.org> References: <40EF164E4C27D31192760000F847DF32519954@ukz206.ggr.co.uk> NNTP-Posting-Host: sirius.stack.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Cache-Post-Path: sirius.shome.eu.org!unknown@lamb.empproject.com X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) "Goryanin, Igor I" wrote in message news:40EF164E4C27D31192760000F847DF32519954@ukz206.ggr.co.uk... > 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 can' agree. From my point of view we actually don't need any kind of "format for storing" as declared in subject. We really need good abstract model. Which language may be used for describing such model (BNF, SGML or XML DTD, relational - you name it) much less significent. Actual represntation of data have no importance at all, because I can convert anything from one format to another using billion availiable standard tools. > 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. XML have some nice features from developers point of view (avaliable parsers, tools, class libraries e.t.c). But, again, XML is only one of possible presentation formats and nothing else. You can't assemble a car if you spend half of your life discussing most useful color for screwdriver handle. Igor, I can easely add XML representation of our records but I don't think that this can make your life much better :) > 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. Hmm, our native format is an interesting example - it's old, ugly and simply nightmare for programmers (you must forgot about context-free grammar, LL e.t.c.). Fortunately last years we works mostly with relational representaion. I think that RAW interface to SQL server with our data and a good manual describing our data model much more suitable for your tasks. But If you want to play with standalone views or subsets I can easy generate valid SGML or XML representaion of our data. You can ever send me your favorite DTD, tags e.t.c. :) Regards, as .