Re: [cml/ccml-discuss] [BlueObelisk-discuss] Proposition on new XML elements for CML

[Peter Murray-R. <pm...@ca...>]

On Sat, Mar 20, 2010 at 8:52 AM, Egon Willighagen <
ego...@gm...> wrote:

> Hi Sam,
>
> On Fri, Mar 12, 2010 at 4:09 PM, Sam Adams <se...@ca...> wrote:
> > <atom elementType="O">
> >   <atomType dictRef="cml:mol2">O.co2</atomType>
> >   <atomType dictRef="cml:mmff94">O=CO</atomType>
> > </atom>
>
> I always understood that the dictRef was a deep link... not pointing
> to a particular dictionary, but to the matching entry in the
> dictionary... I would have expected something like:
>
> <atom elementType="O">
>   <atomType dictRef="mol2:Oco2">O.co2</atomType>
>   <atomType dictRef="mmff94:Oco2">O=CO</atomType>
> </atom>
>
Essentially the dictRef value

(mol2:bar)

is equivalent to a URI

http://www.foo.com/mol2#bar

The world is split between whether a URI is purely a name or whether it is
also an address. I was inducted to the W3C philosophy that names and
addresses are separate. Tim wishes to conflate them. I am now relaxed about
this. So you can interpret

  <atomType xmlns:mmff94="http://mmff94.org/dict"
dictRef="mmff94:Oco2">O=CO</atomType>
either as a statement that

"there is a defined uniqueId in the mmff94 namespace
(http://mmff94.org/dict) with
value Oco2. There may or may not be an accessible dictionary entry but there
should be at least the concept of one"

 or
"there is a dictionary at http://mmff94.org/dict
with an entry
http://mmff94.org/dict#Oco2
and this is of the form <cml:entry id="Oco2">...</cml:entry>
"

I think the the latter is most useful if we can manage it.

I absolutely agree that the BO should try to support and systematize this.
All the Chem4Word material (code, schemas, dictionaries) etc. will be Open
Source/Data/Standard. They may not always be robust but it's best endeavour.

Where there are existing BO dictionaries then Chem4Word will be informed by
them.

P.


-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069