Comments from chemspider

Chemspider writes: –

Name: Monkey at Development | E-mail: | URI: | IP: | Date: April 24, 2007
Peter, good catch – thanks for reporting. I’ve put a notice that properties are calculated for the main component only. Hopefully this is it. Please keep reporting all problems which you’ll find – as you might seen this is the beta version and only with public comments and feedback we can improve it and make it useful.

This doesn’t solve it. There are several broken parts.

  • for CaCO3 the system created H2CO3 and calculated that
  • What is the point of calculating logP for a sodium Ion?
  • there is no point in calculating logP for calcium carbonate. It’s insoluble in water and octanol

To calculate meaningless stuff is to give the message that quality is unimportant. I have blogged on this today

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4 Responses to Comments from chemspider

  1. I’d say it solves it 80-90% – it warns about it. And this is the most of what we currently can do about tens of millions chemical compounds discovered and reported to the moment. As you said Wiki has 23k chemical compounds purified. This IS great. But this was done by 100’s (or 1000’s) chemists worldwide. Now we calculate: 10M / 23k * 100 (chemists) = ~50000 (chemists) to purify 10M compounds from PubChem (sorry, I missed decimals..along with thousands). Or 10M * 1-5 hours = ~500 years of calculations (as you blogged today). No doubt Condor system will be happy. Happy machine is running machine.
    PubChem is great, legacy, The Only, trusted or untrusted (yes, all “strange” compounds like NaCl dimer come from there). It all depends on the point of view. But the point is that PubChem will never be purified. It already fulfils its purpose – it links small molecules to biological data. And this is all it was created for. And you can’t do anything with this. Conserved domain.
    So, solution is either curate PubChem (or Pubchem + new coming compounds from all depositors) dataset or “MOPAC it” and “carefully compare experiment with theory” and “create protocols” and only then “make the results Open, of course”. The idea behind ChemSpider is to instrument the first way. Namely – provide infrastructure to facilitate 10M+ dataset (semi-automatical, human-assisted) purification. And I don’t see how it contradicts to anything else. We’ll gladly accept the data which you’ve received and put them as one of the sources for data curation and judgement. Or you already have such system which is able to handle 10M compounds? Please don’t consider PubChem – it’s conserved domain as I said. There never will be PubChem Wiki.
    Still want to address this:
    > 1. for CaCO3 the system created H2CO3 and calculated that
    > 2. What is the point of calculating logP for a sodium Ion?
    It does not, please look at here:
    Also you can try to predict different properties for Na+ at this page: Sorry, you have to draw it first.
    > 3. there is no point in calculating logP for calcium carbonate. It’s insoluble in water and octanol
    I also thought it does not dissolve… but my teacher in 7th grade said – it is. Especially when you remember about pH in biological systems… but that’s not about logP, it’s about logD, which is also listed for many compounds in ChemSpider database. Predicted. And waiting for feedback and curation.
    P.S. ChemSpider is in beta state and is desperately requiring feedback and comments… but..please let’s skip comments like “zoo must be closed!”. They are not constructive, they are “verdictive” and it’s too early for that in my opinion. Cheerz.

  2. Greg Pearl says:

    calcium carbonate is poorly soluble, which is not the same as insoluble. So the carbonate ion will protonate, at which point the logP prediction is valid. If you want to learn more about logP predictions or obtain a free logP calculation see

  3. Pingback: ChemSpider Blog » Blog Archive » Do Monkeys know about Calcium Carbonate?

  4. Pingback: ChemSpider Blog » Blog Archive » Monkeys and Calcium Carbonate. Should ChemZoo Close its Gates?

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