Imperial College London

Henry Rzepa

It is a sign of the times that one travels to a conference
well-connected. By which I mean email is on a constant drip-feed, with
venue organisers ensuring each delegate receives their WiFi password
even before their room key. So whilst I was at a conference [espousing
the benefits of open
science](http://www.ch.imperial.ac.uk/rzepa/blog/?p=18318), a
nice example of open collaboration was initiated as a result of a
received email.^‡^

Steven
Kirk [![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/orcid_16x16.gif){loading="lazy"
decoding="async" width="16"
height="16"}](https://orcid.org/0000-0002-0462-6962){target="_blank"
rel="noopener noreferrer"} contacted me with the following query: *Do
you know of any open-access database of calculated IRCs with coverage of
as broad a range of classes of chemical reactions as possible*? I
recollected that about six years ago, I was exploring the use of iTunesU
as a system for delivering course content in a rich-media format. I
produced animations for about 115 reactions (many of which as it happens
were taken from this blog, but quite a number were also unique to that
project) and placed them into iTunesU, and now sending
the URL <https://itunes.apple.com/gb/course/id562191342> to Steven.

I should at this point explain something of the structure of such an
iTunesU course.

1.  An essential feature is the course icon, seen below on the left.
    Since the course is hosted by Imperial College, it had to be an
    officially approved icon. I am sure you can believe me if I tell you
    that this took a month or so to obtain, with a fair bit of
    persistence required!
2.  I also had to get approval to place the iTunes app on all the
    teaching computers so that students could open the course. Believe
    me again when I tell you that I had to persuade the Apple lawyers in
    Cupertino to release a special license for this app to persuade our
    administrators here to install it on the Windows teaching clusters.
    Another few months had passed by.  
    ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/096-1024x619.jpg){.aligncenter
    .size-large .wp-image-18335 decoding="async" width="550"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/096-1024x619.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/096-300x181.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/096-768x464.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/096.jpg 2048w"
    sizes="(max-width: 1024px) 100vw, 1024px"}
3.  When creating an entry (using
    *e.g. *<https://itunesu.itunes.apple.com/coursemanager/> ) one has
    to specify values for various descriptors, also often called
    metadata. Thus any one entry has fields for **name** and
    **description**, with the **popularity** added by Apple. Only a few
    words are visible in the description field, which can be expanded in
    iTunes using the *i*
    button.![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/097-1024x89.jpg){.aligncenter
    .size-large .wp-image-18336 loading="lazy" decoding="async"
    width="450" height="39"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/097-1024x89.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/097-300x26.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/097-768x66.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/097.jpg 1456w"
    sizes="(max-width: 450px) 100vw, 450px"}
4.  Steven meanwhile had replied asking if the original data that was
    used to generate the IRC might be available. Specifically his second
    question was "*So the DOIs are only stamped into the animation's
    bitmaps, or are they also somewhere in the metadata?*". That
    little *i* button is not easy to spot, and there is no indication,
    in the event, of what information it might actually contain.
5.  Here it is expanded. The contents are unstructured text, into which
    I have placed the required
    DOI.![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/098.jpg){.aligncenter
    .size-full .wp-image-18337 decoding="async" width="540"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/098.jpg 718w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/05/098-300x236.jpg 300w"
    sizes="(max-width: 718px) 100vw, 718px"}
6.  The lesson here is that I had fortunately had the foresight to
    include a link to the IRC data in anticipation of just such a
    question from someone in the future. But black mark to Apple here;
    the text cannot be selected and copied into a clipboard! It is
    fairly unFAIR data, since it can only be inter-operated (the I of
    FAIR) by a human re-typing it by hand. And the human has also to
    recognise the pattern of a DOI; a machine could not obtain this
    information easily. Moreover Steven is a Linux user; he does not
    readily have access to the iTunes app on this operating system!
7.  Also, there were 115 such entries, and now the prospect was rearing
    that each would have to be hand processed. Moreover, because the
    text was unstructured, there was no guarantee that I would have
    adopted the same pattern for all 115 entries.
8.  Fortunately Steven was on the ball. I quote again: *it turns out
    iTunes isn't needed at all. A service I found on the web
    <http://picklemonkey.net/feedflipper-home/> takes an ITunes URL and
    converts it to an RSS feed. Opening this feed in Firefox and RSSOwl
    respectively let me save the feed as XML and HTML (both attached).*
9.  This is currently where we stand (Steven's first email was two days
    ago), but it's not finished yet. Depending on how assiduous I was
    five years ago, some DOIs to the data may be acquired from the list.
    Sometimes I simply wrote e.g. *See
    http://www.ch.imperial.ac.uk/rzepa/blog/?p=6816* knowing that the
    links to the data were there instead. I can already see that some
    descriptions have neither a DOI nor a link to the blog. More
    detective work will be needed, unfortunately.

How might the situation described above been avoided? Well, Apple in
iTunesU only provided in effect one metadata field, and this was an
unstructured one. Anything went in that field. Had they provided (or had
the course creator been able to configure it themselves) there might
have been another field entitled say "**data source**". This could
moreover been made a mandatory field and a structured one. Thus it might
have only accepted known types of persistent identifier, such as a DOI.
Further, the system could have checked that the DOI was actually
resolvable. Before you ask, I did log a "bug" with Apple asking this be
done, but nothing ever was. With such a tool to hand, I might have
achieved data sources for all the 115 entries. The resulting XML (as
generated above) could have been used to automate the retrieval of all
115 datasets describing this course. 

At this stage then, Steven can follow-up his interest in building a
reaction IRC library and analysing it. I will do all I can to encourage
Steven not to make the mistakes I did and to ensure that any further
data that is required to augment the library does not suffer the
problems above. On the other hand, I console myself that in two days,
much of the data for the course I created five years ago was
salvageable; I wonder how many other iTunesU courses there are for which
that can be said!

I will let (with some blushing) the final word be Steven's: *You are one
of the few chemists who has both pioneered and built the principles of
'open chemistry' into their actual scientific work. I visit your blog
occasionally knowing that there is a very high probability I could
download and tinker with the results of real calculations.*

------------------------------------------------------------------------

^‡^Might I assure all the speakers that I concentrated totally on their
talks rather than incoming emails!

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


It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key.

Rogue Scholar Beiträge

Conference report: an example of collaborative open science (reaction IRCs).