Conspiracy theories are fun. Most of us have seen a movie or read a book regarding some form of conspiracy theory – whether it’s something that is in our distant history, some interpretation of what happened on 9/11 (and there are no shortages of those) or some view on industrial espionage. They are fun. What is surprising is how many of them turn out to be true. There is a new conspiracy theory in our own domain and it relates to the InChI, the International Chemical Identifier. How does that story go?

I use Google Alerts to keep my eye on what is being said on the web about ChemSpider. It’s also how we keep track of what people think should be uploaded to ChemSpider using the loadtochemspider tag. So it was that I was made aware of an article mentioning ChemSpider. Later that day two people pointed me to the same article. Daniel Pollock at Outsell had published an article on March 30th 2009 entitled “Chemical Bonding InChI by InChI”. He discussed the InChI Resolver and the efforts to raise enthusiasm for the InChI. He also discussed the efforts of both Nature Publishing Group and the Royal Society of Chemistry to proliferate the use of InChIs. ChemSpider is a user and producer of InChIs. We like them..and also acknowledge they are not perfect. The mainstream chemistry software vendors like them. The cheminformatics domain has embraced them. Societies see InChI as an enabling standard. The InChI subcommittee continues to expand with participants. InChIs are added to many online databases now. InChI has arrived, warts and all, and we should be working together now to support its enhancements and use it to integrate information. Any publisher or producer in the domain of chemistry publishing and chemistry related information should be embracing the opportunities InChI offers – if not now then for sure in the future. There won’t be much choice because information will become increasingly available and interconnected and groups ignoring the InChI will become less relevant. It’s taken a decade for InChI to gain traction..but now momentum is increasong quickly.

Daniel’s article went on to comment on the present level of acceptance for InChI by the American Chemical Society and CAS and stated “However, given that CAS has been criticised for its proprietary approach in the past, and took until April 2008 to release a web based version of its flagship SciFinder database, in Outsell’s opinion we may have to wait a while yet.”  Overall I thought that Daniel’s article was well-written and balanced and concluded with “Meanwhile, whilst we can see the reaction of the big chemistry publishers and abstraction services, we can reflect on a sobering question: why is it taking government and voluntary contributions to build an industry standard? Surely that should have be the territory of the information providers? In chemistry it seems, as everywhere, the web changes everything.” Good question.

I’d like to recommend that you go and read the article. Why not? Well, the article is not there anymore. It’s been withdrawn!  While the first article was, in my opinion quite balanced, the retraction puzzles me. It states “in the Implications section we published information about Chemical Abstract Service’s highly-regarded SciFinder product that was incorrect, and we did not cite a sufficiently balanced set of references in developing our argument.” In the original article there is one mention of SciFinder and it says “and took until April 2008 to release a web based version of its flagship SciFinder database”.  One statement, one reference..back to CAS’s own press release.

The retraction also stated “Further, it is our practice to avoid speculating about an organization’s stance on a topic without reaching out to the organization for on-the-record research briefings. Overall, the tone of the piece could be taken to single out CAS as being late in responding to the trends, and in our view the research and analysis did not support it.” I’ll interpret this as “no one spoke to CAS”. Ok…that’s fair comment. Someone should have spoken to CAS about this article and asked for their opinion. Maybe some questions might be: 1) It appears that InChI is already changing the way that chemistry related information can be linked for the benefit of the community. What are your observations and thoughts? 2) InChI has been around for over a decade and I am interested to know whether ACS and CAS will embrace the perceived value of InChI and the potential benefits to the community and include in either ACS articles or integrate into the CAS registry? 3) You recently released the CommonChemistry.org website and it is an interesting shift towards Openness by CAS. Congratulations. It would be an ideal opportunity to allow integration via InChIs. What type of feedback have you received from the community? 4) It would appear that the ongoing growth in informational resources such as PubChem, ChEBI, ChemSpider, Google Scholar, Wikipedia and many other rich resources can impact the business model of CAS. InChI-integrated resources and efforts such as the InChI Resolver  allows connection of such resources in a seamless manner and will lead to a web-centric view of chemistry resources. How does CAS expect to respond to this potential threat?5) There are LOTS more questions that I believe the community would like to ask. Who in the scientific reporting community would get an audience with CAS to ask such questions?

Conspiracy theories are already moving around the community. The majority of people I have discussed this with believe that the retraction was likely forced by CAS and as Stuart Cantrill from Nature Chemistry points out in his blog “Outsell now say that the original article wasn’t balanced and that the ‘tone of the piece could be taken to single out CAS as being late in responding to the trends’. Surely readers could make that judgement for themselves?”.

I say decide for yourself. The article is in the Google Archives here. Welcome to the power of the web. Now then…can the removal of THAT article from the Google Archives be enforced? Hmm…..

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12 Responses to “Conspiracy Theories and InChIs – Why was the Article Removed?”

  1. Egon Willighagen says:

    The Google Archives link only points to the Google *cache*. As far as I know, it will get overwritten the next time the page gets indexed. So, better hurry and make a PDF snapshot of the page!

  2. Bill Town says:

    I completely agree with your summary and I too would like to hear the CAS response to your questions.

    Bill

  3. Antony Williams says:

    Egon..fortunately I grabbed myself a copy of the article just in case…

  4. Rich Apodaca says:

    Although the Outsell article doesn’t mention it, there are reasonable technical arguments for CAS avoiding use of InChIs, among them:

    - no specification necessary for creating independent implementations;
    - single implementation with an open source license that has come under legitimate criticism;
    - fails to generate unique identifier for many common molecules (e.g., ferrocene, (R)- and (S)- BINAP);
    - InChI itself is problematically long (breaks HTML layouts, for example) for even medium-sized molecules;
    - InChIKey has no mechanism for backward-compatibility with newer versions that may fix bugs or add features to the existing implementation;
    - the “final” version has only very recently been available.

    These may have played a role in the article’s retraction as well. Isn’t it possible that Outsell simply recognized its piece was somewhat one-sided, decided that it didn’t reflect well on on organization in the business of selling thorough research, and pulled it for the reasons they cited?

  5. Antony Williams says:

    Rich, Thanks for the comments.

    There are a myriad of technical arguments against InChIs. You have listed some of them. There are a lot more including support of polymers, organometallics, host-guest complexes, excited states, Markush structures, and so on. I’ve seen you support InChI on your blog previously and then of late have entered into the discussions regarding FlexMol and CML…it’s interesting to watch the discussions between yourself and Peter Murray-Rust in this domain and interested parties should watch.

    InChI is not perfect. It is the BEST available vendor-neutral international standard that is presently being used by publishers, online databases and cheminformatics vendors to connect and integrate information. Despite its warts it has high value. The development is not over and the InChI developers and subcommittee acknowledge that. The InChI trust are working hard to set up a system that will sustain development costs and effort. I encourage you to participate and bring your ideas and challenges to the committee and sit in!

    The acceptance of InChI might be political or technical or a combination of both. We don’t know as there is no commentary from CAS on either aspect. Are you aware of ANY commentary suggesting that it is political or technical. And if so what are your judgments of the other publishers and database groups who are supporting it even with its imperfections?

    It IS possible that the Outsell article was one-sided. That said I don’t read it that way and everyone else who has discussed it with me by phone or email seems to agree. Do you think it was one-sided?

  6. Unilever Centre for Molecular Informatics, Cambridge - Conspiracy and chemistry and an invitation to lunch « petermr’s blog says:

    [...] and chemistry and an invitation to lunch Antony Williams (Chemspider) and Stuart Cantrill (Nature) have recently blogged about what the blogosphere is seeing as [...]

  7. Antony Williams says:

    These comments were made by Steve Heller (one of our advisory group) on the CHMINF list and are useful to associate here

    “Just for the record…

    CAS manually covers all of chemistry and everything indexed is given a CAS Registry Number.

    InChI’s, generated locally (i.e., not in any central location) by individuals and/or individual organizations who care to generate them, can only be generated by a computer algorithm and cover only defined chemical structures (and currently does not cover all classes of chemicals).
    “Defined chemical structures” are, by definition, those chemicals whose structure one can draw. This leaves out many, many things covered by CAS, including, as Bob Buntrock points out below, gasoline. Thus InChI’s and the corresponding InChIKey’s are not a replacement or alternative.

    Steve”

  8. Rich Apodaca says:

    Tony,

    “I’ve seen you support InChI on your blog previously and then of late have entered into the discussions regarding FlexMol and CML…it’s interesting to watch the discussions between yourself and Peter Murray-Rust in this domain and interested parties should watch.”

    I neither support or oppose InChI; this shouldn’t be that kind of discussion. Like any technology, InChI has it uses and limitations, and I’ve discussed both for over three years now.

    Pointing out InChI’s limitations doesn’t make me an opponent any more than explaining its utility makes me a supporter.

    In my reading, the Outsell piece implied that CAS were behind the times in not already generating and storing InChIs in its databases. But there are other plausible explanations that the Outsell piece (and the other discussions I had seen) didn’t even consider, some of which I outlined in my comments above and here:

    http://depth-first.com/articles/2009/04/10/why-chemical-abstracts-service-might-not-want-to-use-inchi

    It may be tempting to attribute what CAS and Outsell are doing or not doing to some conspiracy theory. But this is ultimately not productive and only obscures the most important question: for which applications is InChI well-suited and for which is it not?

    IMO, that’s a discussion that needs to take place – before CAS (or anyone else) rush out to InChI-fy their cheminformatics systems.

    (BTW, I’m still getting an error to the effect of ‘page not found’ after posting comments to your blog).

  9. will says:

    It does look as though things have happened behind the scenes however…

    There is no real evidence (afaik) to suggest that CAS tried to get the article pulled. Even if they did, Outsell would not have to oblige and responsibility would still not lie with CAS.

    CAS are not the CIA or the KGB (again, afaik).

    Equally, so what if the article was ‘unbalanced’? Is it bad practise to publish an article that is positive about InChI? This would surely be useful anyway.

    And someone could always post another pointing out its negative aspects, again it would be fine for such an article not to be balanced (whatever that is) for the same reason.

  10. Antony Williams says:

    Will…the “conspiracy theories” have continued. Other than the “Data” that an article was written and then withdrawn we don’t know anything else. I’ll stand by my judgment that the article was fine as written. And I think my questions would be interesting to have answered so that the stories regarding what CAS are thinking/saying about InChI could be silenced. People wouldn’t have to make up what CAS are thinking…they could simply state it.

  11. Antony Williams says:

    Rich..I agree that conspiracy theories are not productive.

    I suggested that you be invited to join the InChI committee and I hope you join us.

  12. Joerg Kurt Wegner says:

    I agree with Rich, it is a pity to see InChI under this light and (low) level of niveau. I would wish, more companies would do a serious comparison of InChIs and CAS. We need a fair and high-level comparison, no strange theories.

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