Open Notebook – reflections and conclusion

Posted on October 25, 2007 by pm286

Jean-Claude and Bill are right to point out that in the last week it has been inappropriate to use the term “Open Notebook Science” and I shall no longer use it in conjunction with the NMR work that Nick, Henry, Christoph and I have been working on. Nick and I have, however, been doing fully conformant Open Notebook Science for months in the CrystalEye project. In this project the aims are transparent -the robots collect crystallographic data every day and pass it through an elaborate and tested set of validation procedures so that we feel extremely confident of the accuracy and precision of the data. Every night the robots transform the data, collect statistics, add chemistry and create indexes – we feel justified in believing that it is among the best heterogeneous scientific knowledge bases. There is no “insider knowledge” – everyone has access to the data as soon as it comes off the machine. The entries and the statistics are available to all and anyone can use the data without our explicit blessing. So we know what Open Notebook is and we practice it. The data are labelled Open Data and I have explained why. And, although not required, the code is Open Source and distributed as soon as it is robust.
We had hoped to use the same model for the NMR project. We have been preparing the software so it would write to the web directly. This has not proved easy. Meanwhile we have set out our project aims very clearly. We have also defined our protocol for analysing variance in some detail.
The science is going well – we are on track according to our schedule. But the Open Notebook isn’t working out. Although the community at large is interested, their interests are highly varied and in several places inconsistent. The community does not seem to wish to support our project aims – that’s fine – but it doesn’t make it easy to have a large virtual collaborative project.
We shall continue on the project, one of whose purposes is to investigate the hypothesis that QM calculations can be used to evaluate the quality of NMR spectra to a useful level. We shall continue to post results – hopefully with the same frequency as up-to-now. Since we shall have had a few hours to analyse the results before posting we cannot call them “Open Notebook” but we hope they will have pedagogic value and we also invite constructive criticism.

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5 Responses to Open Notebook – reflections and conclusion

  1. ChemSpiderMan says:
    October 26, 2007 at 12:01 am

    Peter, I asked previously about how to obtain an SDF file of the structures on CrystalEye so that we could link to CrystalEye records via ChemSPider. This was based on my question to the community at
    http://www.chemspider.com/blog/?p=191
    Your comment was that the data was Open but that an SDF was not available and we should scrape the data. I was looking at this possibility today. I was pleasantly surprised to see a number of the journals listed included ACS journals and Elsevier journals (http://wwmm.ch.cam.ac.uk/crystaleye/summary/index.html). There has been a lot of traffic of late about their Open Access policies but now I see that they are supporting your Open Data efforts. This is excellent. I would like confirmation that they are aware of the Open Data posted from their journals before we scrape them. Are they aware? I want to make sure I am respecting all parties. Thanks

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  2. pm286 says:
    October 26, 2007 at 7:54 am

    (1) All data come from Free sources – i.e. visible without a subscription. Some journals (Acta Crystallographica and RSC for example) do not copyright the data. Others like ACS add copyright notices. It is our contention, and Elsevier has agreed for its own material, that facts are not copyrightable. We have therefore extracted and transformed facts and mounted these. Where the original material (CIF) does not carry copyright we mount it on our pages – where it does we do not, but we have the transformed data. In those cases it would be possible to recreate the original CIF data in semantic form ,but not the exact typographical layout which contains meaningless whitespace.
    I am not aware that ACS or Elsevier have ever made statements of any kind about our Open Data efforts.
    You may scrape anything, must you must honour the source and the metadata and you should add the Open Data sticker. If you scrape the link (simplest) you may simpy point to our site. If you scrape more data you should ensure that the integrity of the data is maintined and that if it is re-used the re-used data should still clearly show our metadata.

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  3. ChemSpiderMan says:
    October 26, 2007 at 4:29 pm

    Thanks for the fast comments Peter. I know you are very busy on the NMR project.
    I’ll check with the ACS about their stance before I trigger their potential ire if we scrape data linking back to their articles.
    Of course the source will be honored.
    We are only intending to grab the InChis and deduplicate into ChemSpider or add new records. All structures are Open as you know and can be downloaded. We will also grab the journal article title and the DOI. All Open. I will have to figure out whether to add the Open Data sticker or not since not everything on a page is classed as Open Data. it is free access but not Open Data. I am working on the policy based on discussions with Peter Suber. The conversation with him was very valuable.
    All other details from the pages, the CIF etc, will not be grabbed. The intention is to drive attention to CrystalEye as a project and connect us all.

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  4. Pingback: ChemSpider Blog » Blog Archive » Why We Can’t Publish Scraped CrystalEye Data Yet….And Science Commons Declare a Protocol for Implementing Open Access Data

  5. Pingback: Good Science Takes Time: 16 months to examine NMR Prediction Performance at The ChemConnector Blog by Antony Williams - Observations and Musings for the Chemistry Community By Antony Williams, Freelance Scientist

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