P.
At 10:34 02/02/2004 +0100, E.L. Willighagen wrote:
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On Monday 02 February 2004 10:17, Peter Murray-Rust wrote: > At 22:23 01/02/2004 +0100, Egon Willighagen wrote: > >dadml://pdb/?1CRN > > > >or dadml://any/pdbid?1CRN > > > >The second will try any mirror that can return information based on the > >pdbid... > > Presumably someone enters these mirrors and keeps their addresses and > templates up to date.
Yes. The nice thing about the DADML system is, that the maintainance can be done by website developers, much like the real domain name server system...
> Is there a cascade - if mirror 1 fails does mirror2 > get called? And what is returned - the actual file? > > If so we have something like: > > User -> PDBCode -> server > server -> munged URL (format1)-> mirror1 -> success/error > success -> PDB file -> user > failure > server -> munged URL (format2)-> mirror2 -> success/error > and so on > > is this the model?
Yes, more or less. A HTTP 404 is easily detected, but the system can also detect things like a returned webpage which states that no information is available...
> >The DADML system also support retrieving information in other formats, not > >just chemical/x-pdb or chemical/x-cml, but also text/html etc.. > >I'm not sure if we want to be able to do that sort of things too, so for > > now it only supports reading chemical formats... > > The attraction of chemical/x-* is that the information contained within > each is (relatively?!) consistent and structured. For an arbitrary web site > producing HTML the structure could be anything and a separate parser has to > be written for each. (For example we have written parsers for 2 of the main > sites offering small molecule information and they obviously are completely > different.
DADML does not deal with interpretation of the returned format... the cdk.internet.dadml.DADMLReader does a bit... it can read molecules from chemical/x-mdl-mol and chemical/x-cml and others... actually, it completely disregards the MIME system, and just uses the cdk.io.ReaderFactory and looks at the contents of the stream...
> Moreover the structure of the pages changes regularly. For > example the *text/html* on the RCSB site will be completely different from > that on the EBI site even though the actual PDB file is presumably the same > or closely related. It is the consistency of chemical/x-* that makes it > useful for machines to parse.
Sofar the DADML has only been used to read clear chemical formats, and display
HTML as is... without any interpretation step... It would be very nice to
have a web service at WWMM that accepts an URL or DADML URI
(dadml://nist-html/cas/50-00-0) and converts the HTML into a CML stream...
Something like: dadml://wwmm-nist-bridge/cas/50-00-0
Egon
- -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6
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Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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