{"id":13248,"date":"2015-01-15T14:05:19","date_gmt":"2015-01-15T14:05:19","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13248"},"modified":"2023-09-16T19:48:19","modified_gmt":"2023-09-16T18:48:19","slug":"a-convincing-example-of-the-need-for-data-repositories-fair-data","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13248","title":{"rendered":"A convincing example of the need for data repositories. FAIR Data."},"content":{"rendered":"
\n

Derek Lowe in his In the Pipeline blog<\/a> is famed for spotting unusual claims in the literature and subjecting them to analysis. This one is entitled\u00a0Odd Structures, Subjected to Powerful Computations<\/a>. He looks at this image below, and finds the structures represented there might be a mistake, based on his considerable experience of these kinds of molecules. I expect he had a gut feeling within seconds of seeing the diagram.<\/p>\n

\"\"<\/p>\n

Indeed, so, you will now find that the authors have apparently acknowledged<\/a> a mistake[1]<\/a><\/span>. My interest piqued, I went to the article, and immediately tracked down the supplementary information<\/a>. Surely, if these molecules had been subjected to powerful computation<\/em><\/strong><\/span>, this supporting information should contain coordinates of some kind that would allow a correlation\u00a0with the 2D structural representation shown above. I have just returned from FORCE2015<\/a>, a three-day event in Oxford. From the detailed agenda, you can see that a lot of the conference centered around what is called FAIR Data<\/a>. FAIR stands for:<\/p>\n

    \n
  1. Findable<\/span><\/li>\n
  2. Accessible<\/span><\/li>\n
  3. Interoperable<\/span><\/li>\n
  4. Re-usable<\/span><\/li>\n<\/ol>\n

    So I then set out to find if the supplementary information<\/a> WAS FAIR. Well, check for yourself (unlike the narrative article, the data should be accessible outside of the paywall, i.e.<\/em> you should not need a subscription to access it). It is certainly big, running out to 45 pages, in the form of a paginated PDF file (the norm). The table of contents does not refer to data as such, but it does quote\u00a025\u00a0figures, from which you might just be able to extract some data. But no molecules as such! So:<\/p>\n

      \n
    1. No data is findable, although the \u00a0PDF which might contain it is reasonably so.<\/li>\n
    2. The data is not easily accessible,<\/li>\n
    3. let alone interoperable (thus many of the charts were probably created using spreadsheet software, but the source files for these are not available),<\/li>\n
    4. and not-reusable (certainly not without loss and possible error in any attempt at capture).<\/li>\n<\/ol>\n

      I think it fair to say that the data for these powerful computations are not FAIR<\/strong>. Had we had at least some coordinates (the computations involved molecular mechanics based dynamics simulations, which certainly involve manipulating atom coordinates in some form) then the structures shown in the figure above could be checked, and perhaps even the apparent error would have been quickly spotted.<\/p>\n

      Derek does not make the point about FAIR data (to be fair, he was not at FORCE2015) and so I will make the case. If you are reporting a computational model or simulation, there is no excuse for not supplying FAIR data to accompany it. If the data is FAIR it will<\/strong> be inter-operable and re-usable. And this will instantly allow anyone to check e.g.<\/em> the structures above. You would not need to have Derek’s vast experience and instinct (although having it is also helps). And of course we might presume that there were 2-3 referees that also looked at the article, and presumably none of them requested FAIR data.<\/p>\n

      Oh, if you are interested in my take on FAIR data, I gave a talk about\u00a0<\/a>that at FORCE2015, which you are welcome to view; I hope it constitutes a FAIR talk!<\/p>\n

      \n

      Acknowledgments<\/h4>\n

      This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n

      References<\/h2>\n
      1. K.J. Kohlhoff, D. Shukla, M. Lawrenz, G.R. Bowman, D.E. Konerding, D. Belov, R.B. Altman, and V.S. Pande, \"Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways\", Nature Chemistry<\/i>, vol. 6, pp. 15-21, 2013. https:\/\/doi.org\/10.1038\/nchem.1821<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        Derek Lowe in his In the Pipeline blog is famed for spotting unusual claims in the literature and subjecting them to analysis. This one is entitled\u00a0Odd Structures, Subjected to Powerful Computations. 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FAIR Data. - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13248\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A convincing example of the need for data repositories. FAIR Data. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Derek Lowe in his In the Pipeline blog is famed for spotting unusual claims in the literature and subjecting them to analysis. This one is entitled\u00a0Odd Structures, Subjected to Powerful Computations. 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His point is that orally taken drugs have to survive acid (green below) encountered in the stomach,\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":28290,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28290","url_meta":{"origin":13248,"position":3},"title":"Au-pseudocarbyne – a unusual example of a twelve coordination by carbon.","author":"Henry Rzepa","date":"February 1, 2025","format":false,"excerpt":"Derek Lowe tells the story of \"carbyne\", a potential further allotrope of carbon, comprising linear chains of carbon atoms, C-C\u2261C-C\u2261C-C. Whether such a molecule can exist on its own has long been the the topic of speculation. Now a report has appeared of a \"pseudocarbyne\", stabilised by gold atoms. The\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":25726,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25726","url_meta":{"origin":13248,"position":4},"title":"Derek Lowe asks “What’s a Journal For?” – Knowledge graphs?","author":"Henry Rzepa","date":"October 21, 2022","format":false,"excerpt":"What's a Journal For? This debate has been raging ever since preprint servers were introduced as far back as 1991! Indeed, during my recent submission of a journal article, one of the questions asked was whether the article was already deposited in such a preprint server (in a positive sense,\u2026","rel":"","context":"In \"Interesting chemistry\"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=interesting-chemistry"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":25486,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486","url_meta":{"origin":13248,"position":5},"title":"Octafluorocubane radical anion – where does the extra electron sit?","author":"Henry Rzepa","date":"August 29, 2022","format":false,"excerpt":"Derek Lowe reports the story that the recently synthesized octafluorocubane can absorb one electron to form a radical anion - an electron in a cube. So I thought it would be fun to compute exactly where that electron sits! 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