Hi Egon,
A minor point:
You've created URIs such as http://pubchem.ncbi.nlm.nih.gov/#297 and
http://pubchem.ncbi.nlm.nih.gov/#cid
Generally, it is considered better to mint URIs in a namespace you
control or with which you have an agreement. Have you worked with
Pubchem and do they sanction these URIs?
The downside of using URIs that are controlled by someone else is
that you preclude the possibility of supplying meaningful behavior
upon dereferencing these URIs. So according the the current
recommendations, it is desirable that for a # uri, if one
dereferences the URI before the #, with content negotiation set to
ask for rdf, then one retrieves some rdf within which one would find
further statements about the URI in question.
However if you ask:
wget -S --header='Accept: application/rdf+xml' http://
pubchem.ncbi.nlm.nih.gov/
You will see that you don't get rdf/xml. Changing that would require
the cooperation of pubchem, hence my advised practice.
Similarly, the property iupac:inchi is an html page about inchis, but
is used in your rdf as a property name. There are two issues here. 1)
What sort of thing is iupac:inchi? We generally want to have a URI
denote a single thing 2) Same issue as with pubchem. If you
dereference http://www.iupac.org/inchi/ you won't get information
about the property, like its domain and range.
There are reasonable alternatives to convey the same information -
I'd be glad to discuss them if you are interested in doing so.
Certainly the links to blog posts about the compounds are a unique
and valuable contribution!
Regards,
-Alan
On Aug 2, 2007, at 7:39 AM, Egon Willighagen wrote:
Hi all,
I played a bit with RDF for molecular data a bit this week, and now
have a RDF provider service (try methane [1]), which is written in
PHP, uses XSLT to create a HTML frontend (*). It works for any
molecule/InChI, but depends on 'plugins' to set up any other than the
implied properties (i.e. reproduce the InChI). The methane example
mentioned shows some information extracted from Chemical blogspace
[2], but I plan to write other plugins too, e.g. for PubChem,
ChemSpider and other databases.
I have written up some thoughs at [3], and would much like to hear
your opinions and comments.
Looking forward to hearing from you,
kind regards,
Egon Willighagen
http://chem-bla-ics.blogspot.com/
*) FireFox 2.0.0.6 and IE pick up the declared stylesheet, but
Konqueror/Linux does not.
1.http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4
2.http://cb.openmolecules.net/
3.http://chem-bla-ics.blogspot.com/2007/07/rdf-ing-molecular-
space.html
