Imperial College London

Henry Rzepa

I do go on rather a lot about enabling
or [hyper-activating](http://www.ch.imperial.ac.uk/rzepa/blog/?p=701 "(Hyper)activating the chemistry journal."){target="_blank"
rel="noopener"}\[cite\]10.1039/P29950000007\[/cite\] *data.* So do
others\[cite\]10.1038/nj7461-243a\[/cite\]. Why is sharing data
important?

1.  Reproducibility is a cornerstone in science,
2.  To achieve this, it is important that scientific research be open
    and transparent.
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.
4.  RCUK (the UK research councils) wish *increased transparency of
    publicly funded research and availability of its outputs*^‡^

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*) scientific publishing in 1994. In 2001 we published an
example of a data-rich article\[cite\]10.1039/b008780g\[/cite\] based on
CML, and by 2004 the concept had evolved into something Peter termed
a [datument](http://journals.tdl.org/jodi/index.php/jodi/article/view/130/128){target="_blank"
rel="noopener"}\[cite\]10.1186/1758-2946-5-6\[/cite\]. Some forty such
have now been crafted.\[cite\]10.6084/m9.figshare.797481\[/cite\]

In 2009, the journal *Nature Chemistry* was starting up, and I
approached them with the idea of an [interactive data
exploratorium](http://www.nature.com/nchem/journal/v1/n7/media/nchem.373_jmol.html){target="_blank"
rel="noopener"} on the premise that a new journal might be receptive to
new ways of presenting science. It was accepted and
published\[cite\]10.1038/nchem.373\[/cite\] and was followed in 2010 by
a [second
variation](http://www.nature.com/nchem/journal/v2/n5/media/nchem.596_jmol.html){target="_blank"
rel="noopener"}.\[cite\]10.1038/NCHEM.596\[/cite\] 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!

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* for publication.
This included the usual interactive table reporting the modelling and
its data. However, it transpired that the production workflows for
*Nature Chemistry* had been streamlined and I was informed that
interactive tables could no longer be accepted. This time, **we**
(*i.e. *the authors) would have to solve the issue of how to host and
present the data ourselves.

I was very keen that this 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.* 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](http://blog.chembark.com/2013/08/09/the-om-paper-vs-drinkels-phd-thesis/){target="_blank"
rel="noopener"} (although [bloggers seem to do a far better
job](http://justlikecooking.blogspot.co.uk/2013/08/cryptic-retraction-uncovered.html){target="_blank"
rel="noopener"}) and furthermore can end up being lost behind a pay wall
(the two *Nature Chem* interactive objects noted above **can** be openly
accessed, but only if you know that they exist). So I determined that:

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.
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.

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*",
[intertwingled](http://en.wikipedia.org/wiki/Intertwingularity){target="_blank"
rel="noopener"} with a second, but nevertheless distinct component, the
"*data*". This data would follow the principles of the [Amsterdam
Manifesto](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10972 "The Amsterdam Manifesto on Data Citation Principles"){target="_blank"
rel="noopener"}; it would itself be citable. The two components would
become symbiotes (a datument). The
narrative\[cite\]10.1038/nchem.1751\[/cite\] could cite this data and
the data could back-link to the narrative. The data would inherit trust
(*i.e.* 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](http://www.rsc.org/chemistryworld/2013/09/figshare-offer-institutional-university-data-platform){target="_blank"
rel="noopener"}\[cite\]10.6084/m9.figshare.744825\[/cite\]).^\*^

The data itself can have two layers, presentation
\[cite\]10.6084/m9.figshare.744825\[/cite\]^¶^ using a combination of
software (Jmol or JSmol for chemistry) which are used to
[invoke](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10972 "The Amsterdam Manifesto on Data Citation Principles"){target="_blank"
rel="noopener"} the "raw" data. That data itself is
citable\[cite\]http://dx.doi.org/10042/20409\[/cite\] (this is just a
single example, resident as it happens on a different repository). The
reader can choose use [just the presentation
layer](http://www.ch.imperial.ac.uk/rzepa/blog/?p=3154 "(re)Use of data from chemical journals."){target="_blank"
rel="noopener"} or the underlying data.

The data object can be embedded in other pages; here it is below. The
data sources for this table are themselves
citable\[cite\]10.6084/m9.figshare.96410\[/cite\].

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What are the advantages of such an approach? (the "what's in it for me"
question often asked by research students and their supervisors)

1.  Each of the components is held in an environment optimised for it
    and so can be presented to full advantage.
2.  The conventional narrative publisher does not necessarily also have
    to develop their own infrastructures for handling the data. They can
    choose to devolve that task to a "data publisher".
3.  The data publisher (Figshare in this case) makes the data open. One
    does not need an institutional subscription to access it.
4.  "Added value" for each component can be done separately. Thus most
    narrative publishers would not necessarily wish to develop
    infrastructures for validating it or subsequently mining such "big
    data". Indeed data mining of journals is prohibited by many
    publishers; it simply is either not possible or rendered so
    administratively difficult as to be impractical.
5.  Whilst a narrative article must clearly exist as a single instance
    (otherwise the authors would be accused of plagiarism), data can
    have multiple instances. Indeed, there exist protocols (SWORD) for
    moving data from one repository to another as the need arises.
    Publishing the same data in two or more locations is not currently
    considered plagiarism!
6.  The data component can be published as part of an article or say as
    part of a PhD thesis. This way, the creator of the data gets the
    advantages not of a date stamp associated with a narrative citation
    but of a much ***earlier*** stamp associated more closely with the
    actual creation of the data. That could easily and usefully resolve
    many disputes about who discovered what first, leaving the other
    issue of who interpreted what first to the narrative. I should
    mention that it is perfectly possible to "embargo" the data
    deposition so that it only becomes public when the narrative does
    (although you may choose not to do this).
7.  A data deposition cannot be modified, but a new version (which
    bidirectionally links back to the old one) can be published if say
    more data is collected at a future date.
8.  A whole infrastructure devoted just to enhancing the cited data can
    evolve; one that is unlikely to do so if the narrative publishers
    are the only stakeholders. For example, synthetic procedural data
    can be tagged using the excellent [chemical
    tagger.](http://chemicaltagger.ch.cam.ac.uk){target="_blank"
    rel="noopener"}
9.  It is relatively simple (=cheap) to build a pre-processor for
    publishing data, which for a research student can act as an
    electronic laboratory notebook, holding meta-data about the
    deposited/published data and the handles (doi) associated with each
    deposition. I have been using such [an environment
    now](http://www.ch.ic.ac.uk/rzepa/talks/opendata/){target="_blank"
    rel="noopener"} for about seven years as the e-notebook for this
    blog for example. Thus the task of preparing figures and tables for
    a publication (or a blog post) is greatly facilitated. The same
    system is also used by research students and undergraduates for
    their lab work.
10. I have [noted
    previously](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10736){target="_blank"
    rel="noopener"} how *e.g.* Google Scholar identifies data citations
    along with article citations in constructing an individual research
    profile. A researcher could become known for their published data as
    well as their published narratives. Indeed, it seems likely that the
    person who acquires and publishes the data, *i.e.* the research
    student, would then get accolades directly rather them all accruing
    to their supervisor.

But what can you, gentle reader of this blog, do to help? Well, ask if
your institution already has, or plans to create a data repository. It
can be local (we use DSpace) or "in-the-cloud" (*e.g.*
[Figshare](http://api.figshare.com/docs/){target="_blank"
rel="noopener"}). If not, ask why not! And if you are planning to submit
an article for publication in the near future, ponder how you might
better share its data.

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^‡^ As first circulated on 28 April, 2011. See   
[[http://www.epsrc.ac.uk/about/standards/researchdata/Pages/policyframework.aspx](http://www.epsrc.ac.uk/about/standards/researchdata/Pages/policyframework.aspx){target="_blank"
rel="noopener"}]{.small}

^†^The example given at the start of this
post\[cite\]10.1038/nchem.1751\[/cite\] contains only one table
processed in this manner; the actual synthetic procedures are still held
in more conventional SI.

^\*^This blog uses the excellent
[Kcite](http://knowledgeblog.org/kcite-plugin){target="_blank"
rel="noopener"} plugin to manage citations.

^¶^The good folks at Figshare were extremely helpful in converting this
deposition into an interactive presentation. Thanks guys!

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::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


I do go on rather a lot about enabling or hyper-activating[cite]10.1039/P29950000007[/cite]
<em>
 data.
</em>
So do others[cite]10.1038/nj7461-243a[/cite]. Why is sharing data important? Reproducibility is a cornerstone in science, To achieve this, it is important that scientific research be open and transparent. Openly available research data is central to achieving this.

Publicaciones de Rogue Scholar

A two-publisher model for the scientific article: narrative+shared data.