From: Peter Murray-R. <pm...@ca...> - 2004-02-01 15:05:15
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At 12:01 31/01/2004 +0100, Miguel Howard wrote: > > I am sure you know that Egon has done something like this in CDK/JCP. > >While I was aware of the RSS and plug-in work, I did not make the >association between the two ... Thanks! > > > So it's important to keep consistency... > >Agreed. > > > I favour the use of symbolic addresses which are set in configuration > > files - e.g. in user.dir and which can be overruled specifically by the > > user if required. > >I have been thinking about this in the context of script development and >deployment of web applications. I hadn't yet thought about how this would >be configured for the application. > >But I agree with you. This should be part of the user preferences for the >application. > > > > I would then favour a URL-like syntax wherever > > possible > >At first I thought about something like > > load pdb://1crn > >Which would route to the appropriate cgi on your chosen pdb mirror. > >But then I decided that it was probably 'illegal' and/or a bad idea to >just make up a new protocol called 'pdb' In CML we use namespace prefixes. We are increasingly using them as data prefixes. So in CMLReact we may use an attribute like: <identifier name="pdb:1crn"/> This identifies an identifier (1crn) and the namespace it belongs to. It is important to differentiate names and addresses. This is a fundamental and very difficult problem. Objects can have both: ISBN-0123456 identifies the book but does not tell you where to buy it http://www.xml-cml.org/index.html tells you where to find the CML home page but does not identify *what* it is. As the PDB codes are globally agreed IDs they should be kept as such and pdb:1crn. Thus would identify a code as belonging to namespace pdb. Unfortunately and irreversibly the W3C resolves namespace prefixes with URIs (sic). These are usually of the form: http://www.some.where/foo This is a NAME and need not be a valid address. Note that the prefix is arbitrary and is dereferenced as: <identifier xmlns:pdb="http://www.rcsb.org/pdb" name="pdb:1crn"/> Here http://www.rcsb.org/pdb is a globally agreed name. As yet I don't think there is an agreed set of names. However this is something that IUPAC is starting to work on. So then there is a requirement for resolving addresses. Perhaps something like (all names are fictitious): <serverList name="http://www.rcsb.org/pdb"> <server address="http://www.rcsb.org/data/pdb"/> <server address="http://www.ebi.ac.uk/MSD/pdb"/> </server> This doesn't absolutely require XML syntax - properties could perhaps be used. >It is now clearly obvious that I need to talk with Egon :-) Always an excellent idea P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |