Imperial College London

Henry Rzepa

The [Amsterdam
manifesto](http://www.force11.org/AmsterdamManifesto){target="_blank"} espouses
the principles of citable open data. It is a short document, and it is
worth re-stating its eight points here:

1.  *Data should be considered citable products of research.*
2.  *Such data should be held in persistent public repositories.*
3.  *If a publication is based on data not included with the article,
    those data should be cited in the publication.*
4.  *A data citation in a publication should resemble a bibliographic
    citation and be located in the publication's reference list.*
5.  *Such a data citation should include a unique persistent identifier
    (a DataCite DOI recommended, or other persistent identifiers already
    in use within the community).*
6.  *The identifier should resolve to a page that either provides direct
    access to the data or information concerning its accessibility.
    Ideally, that landing page should be machine-actionable to promote
    interoperability of the data.*
7.  *If the data are available in different versions, the identifier
    should provide a method to access the previous or related versions.*
8.  *Data citation should facilitate attribution of credit to all
    contributors.*

The manifesto itself is dated  20 March 2013, but the principles above
go back far earlier, and most of the articles above have been
implemented in this blog for a little while now. But its best
illustrated with an example\[cite\]10.6084/m9.figshare.757728\[/cite\].
Here I have used the excellent wordpress extension
[Kcite](http://www.ch.imperial.ac.uk/rzepa/blog/?p=6341 "The blog post as a scientific article: citation management"){target="_blank"} to
adhere to **points 1-5 and 8** above. **Point 6** is the most
interesting perhaps, and it is illustrated below. If you click on the
graphic, it will load the log file associated with the calculation
described in the [previous
post](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10937 "VSEPR Theory: A closer look at chlorine trifluoride, ClF3."){target="_blank"}
to convert the data to a rotatable 3D model, using Jmol.

::: {#attachment_10948 .wp-caption .aligncenter style="width: 332px"}
![Click for
3D](http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2013/07/ClF3.jpg){.wp-image-10948
loading="lazy" decoding="async"
aria-describedby="caption-attachment-10948"
onclick="jmolInitialize('../Jmol/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load http://files.figshare.com/1134372/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');"
width="322" height="245"}

Click to load from Figshare
:::

This actually represents a departure from how I normally invoke data on
this blog. I have hitherto done it by uploading the data to the
WordPress uploads directory (it is thus in effect a local copy of the
data). Here in this post I have not done that; it's coming directly from
the citable data repository, using *e.g.*

`onclick="jmolInitialize('../Jmol/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load http://files.figshare.com/1134372/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');"`

Well, almost. The URL of the actual dataset
(`http://files.figshare.com/1134372/logfile.log`) is derived from the
doi (10.6084/m9.figshare.757728) by an internal process which has no
exposed algorithm. As it happens, the DSpace digital
repository\[cite\]http://hdl.handle.net/10042/24916\[/cite\] is a bit
better in this regard.

::: {#attachment_10948 .wp-caption .aligncenter style="width: 332px"}
![Click for
3D](http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2013/07/ClF3.jpg){.wp-image-10948
loading="lazy" decoding="async"
aria-describedby="caption-attachment-10948"
onclick="jmolInitialize('../Jmol/',true);jmolSetAppletColor('white');jmolApplet([450,450],'load https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24916/logfile.log;frame 27;vectors on;vectors 4;vectors scale 5.0; color vectors orange; vibration 10;animation mode loop;');"
width="322" height="245"}

Click to load from DSpace
:::

This is loaded using

` https://spectradspace.lib.imperial.ac.uk:8443/dspace/bitstream/handle/10042/24916/logfile.log;`

which is directly derived from the handle itself (although again that
algorithm has to be worked out by a human).

**Point 7** above is also implemented (sort of). If you look at the
Figshare repository, you will notice an additional link there which
points to the Dspace repository. As it happens, the two datasets are
identical (they are not different versions) and these semantics are
currently NOT handled well. You could probably work this out from the
date stamps of the two depositions (which are respectively **Published
on 29 Jul 2013 -- 05:58 (GMT)** and **2013-07-29T05:58:11Z** for
Figshare and DSpace respectively). 

Whereas the Amsterdam manifesto is here implemented on a blog post, I
think the grander aspiration is that the principles are to be followed
in ALL scientific publications. We are some way away yet from achieving
this. But watch this space for an upcoming example! 

So can I urge all scientists who care about data to promulgate the
principles of the Amsterdam manifesto, and wherever possible to practice
what they preach! 

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


The Amsterdam manifesto espouses the principles of citable open data.

Messaggi di Rogue Scholar

The Amsterdam Manifesto on Data Citation Principles