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Re: RDF for molecules, using InChI

From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 18 Aug 2007 10:32:36 +0200
Message-ID: <6aeb064b0708180132n4c24ade4y2639d5136a411832@mail.gmail.com>
To: "Eric Neumann" <eneumann@teranode.com>
Cc: public-semweb-lifesci@w3.org

Hi Eric,

On 8/17/07, Eric Neumann <eneumann@teranode.com> wrote:
>  Thanks for the pointer-- is there a list of all the molecules you store
> something about?

Not at this moment. That would be a rather lengthy RDF doc. The number
of molecules of which something is know is currently in the order of
10M. I have not taken up the challenge of hosting that.

> I've noticed your server will handle any InchI string it
> receives, though CIDs and other annotations will not be returned.

Correct. I looks up information from other sources, so the 'service'
is more like a relay or aggregator than a database.

> Since one
> can determine the molecular weight from InchI, would it make sense to
> include such a feature?

Yes. One thing I am interesting in, is using SPARQL to find incorrect
data in databases. And it happens to occur that databases show one
InChI (e.g. of salts), but derive properties of only one fragment...
that will show up in the MW.

>  Finally, I see you point to Pubchem CIDs and Pubchem uses InchIs as well,
> so is there any way to include all compounds PC refers to as well?

Yes, I do plan to write a relay for PubChem. I will make these scripts
open source asap, but been busy with project reports and grant
proposals the last two weeks.


Received on Saturday, 18 August 2007 08:32:39 UTC

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