Re: [Jmol-developers] Standard syntax for pulling from remote databases

[E.L. W. <eg...@sc...>]

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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.=20

Yes. The nice thing about the DADML system is, that the maintainance can be=
=20
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=20
detect things like a returned webpage which states that no information is=20
available...

> >The DADML system also support retrieving information in other formats, n=
ot
> >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 si=
te
> 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 ma=
in
> sites offering small molecule information and they obviously are complete=
ly
> different.=20

DADML does not deal with interpretation of the returned format... the=20
cdk.internet.dadml.DADMLReader does a bit... it can read molecules from=20
chemical/x-mdl-mol and chemical/x-cml and others... actually, it completely=
=20
disregards the MIME system, and just uses the cdk.io.ReaderFactory and look=
s=20
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 sa=
me
> 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 disp=
lay=20
HTML as is... without any interpretation step... It would be very nice to=20
have a web service at WWMM that accepts an URL or DADML URI=20
(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

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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