Comments on: We Need an InChIKey Resolver and We Need It Now http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html Building Community for Chemists Tue, 21 May 2013 16:16:29 +0000 hourly 1 http://wordpress.org/?v=3.5 By: Egon Willighagen http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-128560 Egon Willighagen Tue, 30 Dec 2008 14:01:18 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-128560 The proper URL for the JChemPaint website is:

http://jchempaint.sourceforge.net/

Antony, can you please update the link in this blog item?

]]> By: Antony Williams http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18636 Antony Williams Wed, 13 Feb 2008 02:29:01 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18636 Alf, Thanks for the comments. Yes, I think ChemSpider, as is, offers a certain level of InChIKey resolving. That said, I know that we are likely only half way there. There are quality issues we need to resolve with the entire process, we need to improve the workflows for deposition as well as some of the checking procedures and reporting of structural issues during deposition. We also need to build web services to facilitate deposition from other services. There’s a lot of work to be done. Also, we need to address the issue of 24/7 uptime and reduce dependency on Internet Service Providers and a support system of only two servers and one backup.

There are definitely InChIStrings floating around which are not on ChemSpider yet and we are working on a crawler to find them and deposit them. We would also like people to deposit structures via our structure deposition system described here: http://www.chemspider.com/docs/Single_Structure_Depositions_on_ChemSpider.pdf

]]> By: alf http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18561 alf Tue, 12 Feb 2008 18:39:27 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18561 ChemSpider is already an excellent InChIKey resolver, inasmuch as all a resolver has to do is reverse lookup of InChI strings from InChI keys.

If the only problem is that there are InChI strings floating around that aren’t in ChemSpider, then that’s a separate problem – it means people aren’t depositing their structures in the right repositories, doesn’t it?

]]> By: David Bradley http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18502 David Bradley Tue, 12 Feb 2008 12:22:10 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18502 I’d much prefer there to be a single, simple system that, as a journalist, I could use without having to worry about all the technicalities, like DOI…

…incidentally, CrossRef just published a WordPress plugin that can help youdo DOI look ups and paste citations in blog posts

http://www.sciencebase.com/science-blog/search-and-cite-for-science-bloggers.html

Perhaps a plugin like this that worked with Chemspider would allow Inchikey and Inchi to become transparently interchangeable and so more widely useful. Like I say I haven’t gone into the tech of any of this, just want to be able to start working with a simple solution ;-)

db

]]> By: Alan McNaught http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18471 Alan McNaught Tue, 12 Feb 2008 09:09:43 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18471 Tony

The InChI team welcomes enthusiastically the initiative from ChemSpider to look for ways of providing an InChIKey resolver service; we’re grateful to you for starting the ball rolling. We had hoped that the chemical information community would pick up the idea of developing InChI/InChIKey look-up facilities; indeed this would represent an enormous increase in accessibility for web-based chemical information. IUPAC itself is not best constituted to develop this kind of service. Sorry we didn’t get round to expressing our support earlier.

]]> By: Richard http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18379 Richard Mon, 11 Feb 2008 16:37:27 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18379 Q> Are the InChIStrings and Keys associated with Project Prospect available as an aggregate anywhere by the way?

A> Not yet…

]]> By: Rajarshi http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18374 Rajarshi Mon, 11 Feb 2008 16:06:07 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18374 Martin, yes that’s what I had in mind. I’ve been looking at Nutch (http://lucene.apache.org/nutch/) as a candidate crawler. It’s pretty featureful, but for the purposes of an InChI crawler, the problem is much simpler than generic web crawling – no need to make text indices of the page contents. Rather, it boils down to simply identifying InChI’s on the page and storing the (link, InChI) tuple in a DB (and generate an InChI key as well)

Of course I have not worked with web crawlers before, so my view might be naive!

]]> By: Antony Williams http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18368 Antony Williams Mon, 11 Feb 2008 15:13:33 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18368 Posted on behalf of Martin Walker, one of our advisory group.

I think a InChIString crawler could be a big part of the solution (though it fails if people post ONLY the InChIKey). It could record every InChIString it finds on the Internet (along with the link – to enhance the service), and then generate an InChIKey for that InChIString. It would be designed so that anyone searching for the InChIKey via a DOI-type lookup would be directed to an entry that would list, InChIKey and InChIString, as well as relevant links and ideally an automatically generated structure as well. I think ChemSpider could probably operate such a service very well, once the server was bought and the software written.

I know someone briefly mentioned a crawler, is this what they had in mind?
Is this a reasonable suggestion? I even have a great name for it – “ChemSpider” – oh dear, that domain’s been taken already…..

]]> By: Antony Williams http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18367 Antony Williams Mon, 11 Feb 2008 15:12:55 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18367 Richard, yes it is a good practice. But not everyone is doing it. SO maybe the request is this easy. Post them together. But, I don’t think this will ever happen exhaustively though we can wait and see.

Are the InChIStrings and Keys associated with Project Prospect available as an aggregate anywhere by the way?

]]> By: Richard http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html/comment-page-1#comment-18364 Richard Mon, 11 Feb 2008 14:56:07 +0000 http://www.chemspider.com/blog/we-need-an-inchikey-resolver-and-we-need-it-now.html#comment-18364 Isn’t it just good practice for anyone publishing an InChIKey to publish the InChI in the same place? As the InChIKey is a fix for a particular problem (text search engines) why promote its general use beyond its capabilities? Find InChIKey, use InChI !

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