{"id":10998,"date":"2013-09-15T18:01:44","date_gmt":"2013-09-15T17:01:44","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10998"},"modified":"2021-08-15T09:19:09","modified_gmt":"2021-08-15T08:19:09","slug":"a-two-publisher-model-for-the-scientific-article-narrativeshared-data","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10998","title":{"rendered":"A two-publisher model for the scientific article: narrative+shared data."},"content":{"rendered":"
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I do go on rather a lot about enabling or\u00a0hyper-activating<\/a>[1]<\/a><\/span> data.<\/em> So do others[2]<\/a><\/span>. Why is sharing data important?<\/p>\n

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  1. Reproducibility is a cornerstone in science,<\/li>\n
  2. To achieve this, it is important that scientific research be\u00a0open and transparent.<\/li>\n
  3. Openly available research data is central to achieving this. It is estimated that less than 20% of the data collected in chemistry is made available in any open manner.<\/li>\n
  4. RCUK (the UK research councils) wish increased transparency of publicly funded research and availability of its outputs<\/em>\u2021<\/sup><\/li>\n<\/ol>\n

    But it’s not all hot air, honestly. Peter Murray-Rust and I had started out on a journey to improve reproducibility, openness and transparency in (inter alia<\/em>) scientific publishing in 1994. In 2001 we published an example of a data-rich article[3]<\/a><\/span> based on CML, and by 2004 the concept had evolved into something Peter termed a\u00a0datument<\/a>[4]<\/a><\/span>. Some forty such have now been crafted.[5]<\/a><\/span><\/p>\n

    In 2009, the journal Nature Chemistry<\/em> was starting up, and I approached them with the idea of an interactive data exploratorium<\/a>\u00a0on the premise that a new journal might be receptive to new ways of presenting science. It was accepted and published[6]<\/a><\/span> and was followed in 2010 by a second variation<\/a>.[7]<\/a><\/span> In both cases, these activated-figures were sent to the journal as part of the submission process, and hosted by them (they still are). You can even access them without a subscription to the journal!<\/p>\n

    Move on to 2012, when David Scheschkewitz had some very exciting silicon chemistry to report, we collaborated on some computational modelling, and sent the resulting article to Nature Chemistry <\/em>for publication. This included the usual interactive table reporting the modelling and its data. However, it transpired that the production workflows for Nature Chemistry<\/em> had been streamlined and I was informed that interactive tables could no longer be accepted. This time, we<\/strong> (i.e.\u00a0<\/em>the authors) would have to solve the issue of how to host and present the data ourselves.<\/p>\n

    I was very keen that\u00a0this table be treated with equal weight to the article itself (citable in its own right) and that it not be downgraded to supporting information (ESI). My objection to ESI is that it is often poorly structured by authors, i.e.<\/em> it is not prepared in a form which allows the data to be re-used, either by a perceptive human, or a logical machine. As a result it is often given little attention by referees<\/a>\u00a0(although bloggers seem to do a far better job<\/a>) and furthermore can end up being lost behind a pay wall (the two Nature Chem<\/em> interactive objects noted above can<\/strong> be openly accessed, but only if you know that they exist). So I determined that:<\/p>\n

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    1. The table should be immediately accessible by non-experts, but not through any convoluted processes of downloading a file, expanding it and finding the correct document within the resulting fileset to view in the correct program, which is how normal ESI is handled.<\/li>\n
    2. The table and the data it contained within should be capable of acting as a scientific tool, forming what could be the starting point for a new investigation if appropriate.<\/li>\n<\/ol>\n

      To solve this issue, some lateral and quick thinking was needed. The solution was a two-component model in which the original article is treated as a “narrative<\/em>“, intertwingled<\/a> with a second, but nevertheless distinct component, the “data<\/em>“. This data would follow the principles of the Amsterdam Manifesto<\/a>;\u00a0it would itself be citable. The two components would become symbiotes (a datument). The narrative[8]<\/a><\/span> could cite this data and the data could back-link to the narrative. The data would inherit trust (i.e.<\/em> peer review) from that applied to the narrative and the latter would inherit a date stamp and integrity from the data host (in this case Figshare<\/a>[9]<\/a><\/span>).*<\/sup><\/p>\n

      The data itself can have two layers, presentation [9]<\/a><\/span>\u00b6<\/sup> using a combination of software (Jmol or JSmol for chemistry) which are used to invoke<\/a> the\u00a0“raw” data. That data itself is citable[10]<\/a><\/span> (this is just a single example, resident as it happens on a different repository). The reader can choose use\u00a0just the presentation layer<\/a>\u00a0or the underlying data.<\/p>\n

      The data object can be embedded in other pages; here it is below. The data sources for this table are themselves citable[11]<\/a><\/span>.<\/p>\n

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