[Kalzium] [feature request]oxidation numbers

[Egon Willighagen]

Hi all,

On Wed, Sep 1, 2010 at 10:38 PM, LucaTringali <TRINGALINVENT at libero.it> wrote:
> I think it could be useful to add oxidation numbers in the other element's
> informations (when you click on an element).

I'm mostly dormant on the list, but I think it is time for me to jump
in here... since there was talk about conceptual problems anyway, and
the fact that I am making the releases of the BODR [0] data used by
Kalzium...

* Things like oxidation state, boiling point and melting point are not
*element* properties.

Now, to do this properly, the BODR data actually has to be fixed.
Carsten contributed a lot of data from Kalzium to it, and BODR does
not make a proper distinction between element and substance yet...

Here's the thing where we should go (in pseudo triple format):

element:C bodr:hasSubstance substance:Graphite.
substance:Graphite: bodr:hasBoilingPoint "450.0"^^xsd:float. (made up
actual value)

Likewise, the melting point.

Now, the oxidation state is a property of an 'atom', not of an
element... or in cheminformatics terms, a property of an 'atom type'.
One element can actually have multiple oxidation states, thought that
particularly happens for the transition metals... So:

element:C bodr:hasAtomType atomtype:C.something.
atomtype:C.something bodr:hasOxidationState "IV".

I'll try to get back on this very soon...

Egon

0.http://blueobelisk.sourceforge.net/wiki/index.php/DataRepository#Blue_Obelisk_Data_Repository_.28BODR.29

-- 
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers