Comments on: Gathering Physicochemical Data Onto ChemSpider

By: Antony Williams

Antony Williams — Tue, 27 Oct 2009 20:31:32 +0000

J.Med Chem 1969, Vol.12, p.692 has the logP of toluene as 2.11 which is even outside of that predictive spread. BAsed on my experiences of working with large pharma companies the accurate and reproducible determination of logP is challenging. I would say that Toluene is well characterized at this point and a settled value of around 2.75 +/- 0.1 is accepted. The “estimate” of 2.23 is good enough for binning but is not a prediction. But its way better that the AlogP value.

By: Soaring Bear

Soaring Bear — Tue, 27 Oct 2009 19:40:10 +0000

>with the thorough work reported in the publication above is it necessary to build yet another logP prediction algorithm?

For the toluene example mentioned, 2.65 – 2.23 = 0.42 which on the log scale is huge. So although this new work is impressive, it is not the last word. Until we can better quantify the variables of solubility, and the biochemical relevance, there will be more of such thorough efforts.

By: Antony Williams

Antony Williams — Tue, 27 Oct 2009 15:55:25 +0000

If drawing structures is fun you should have played in the digitonin curation (http://www.chemspider.com/blog/a-request-for-a-crowdsourced-investigation-of-digitonin.html) I will summarize that situation today. I don’t think it’s over yet…

Why not go ahead and get the data deposited into Bioclipse now. If I get any data then I’ll direct it to you for now. Let me know the URL for the NMR entry and I can try it out and then the LogP one later.

Afterwards we can move the data into ChemSpider, if there is any. We’re in the middle of delivering a development sprint so can’t hack up the form etc right now.

We’ll be chatting with numerous publishers about harvesting data and maybe THomson when the time is right.

By: Egon Willighagen

Egon Willighagen — Tue, 27 Oct 2009 06:40:41 +0000

Hi Antony,

I would even be interested in doing some data extraction from literature… I have done this for NMR data too, and drawing chemical structures is just fun. So, if people know a nice paper that reports experimental LogP values…

The next question would be, how I could enter this into ChemSpider… I either need a webform, but alternatively I could hack up a CML editor for Bioclipse to hold: 1. the chemical structure, 2. the InChI, 3. the experimental LogP value, and 4. the literature from which the data was taken. Such an editor is available in Bioclipse for submitting assigned NMR spectra with the matching molecular structure, and bibliography too.

BTW, it is rather interesting to observe that the paper you published with the 96k data points is about comparing the modeling methods, which is rather meaningless and can be done by any student, whereas the (scientific) value in that paper is in the aggregation of the data. However, the latter is practically impossible to get awarded.

Antony, when does ChemSpider step up and have there data entries indexed, so that enlisting experimental (curated, Open) data from a paper actually causes a citation of that paper? I believe that’s the kind of incentive we need to solve the lack of data moving from literature into databases. Can we please start talking to Thomson about this possibility?

Egon