Imperial College London

Henry Rzepa

Living in London, travelling using [public
transport](http://www.ch.imperial.ac.uk/rzepa/blog/?p=14515) is often
the best way to get around. Before setting out on a journey one checks
the status of the network. Doing so today I came across this page: [our
open
data](https://tfl.gov.uk/info-for/open-data-users/our-open-data?intcmp=3668)
from Transport for London. 

1.  I learnt that by making TFL travel data openly available, some
    11,000 developers (sic!) have registered for access, out of which
    some 600 travel apps have emerged.
2.  The data is in XML, which makes it readily
    inter-operable.\[cite\]10.1021/ci990052b\[/cite\]
3.  This encourages crowd-sourced innovation.
4.  They have taken the trouble to [produce an
    API](https://api.tfl.gov.uk) (application programmable interface)
    which allows rich access to the data and information about
    *e.g.* [AccidentStats](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/AccidentStats "Open /AccidentStats in Swagger UI."){.endpoint},
    [AirQuality](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/AirQuality "Open /AirQuality in Swagger UI."){.endpoint},
    [BikePoint](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/BikePoint "Open /BikePoint in Swagger UI."){.endpoint},
    [Journey](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Journey "Open /Journey in Swagger UI."){.endpoint},
    [Line](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Line "Open /Line in Swagger UI."){.endpoint},
    [Mode](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Mode "Open /Mode in Swagger UI."){.endpoint},
    [Occupancy](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Occupancy "Open /Occupancy in Swagger UI."){.endpoint},
    [Place](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Place "Open /Place in Swagger UI."){.endpoint},
    [Road](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Road "Open /Road in Swagger UI."){.endpoint},
    [Search](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Search "Open /Search in Swagger UI."){.endpoint},
    [StopPoint](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/StopPoint "Open /StopPoint in Swagger UI."){.endpoint}[Vehicle](https://api.tfl.gov.uk/swagger/ui/index.html?url=/swagger/docs/v1#!/Vehicle "Open /Vehicle in Swagger UI."){.endpoint}.

Chemists could learn some lessons here! Of course, there are quite a few
chemical databases with APIs that are examples of open data, but the
"ESI" (electronic supporting information) sources which almost all
published articles rely upon to disseminate data are clearly struggling
to cope. Take for example this recent
article\[cite\]10.1021/jacs.6b13229\[/cite\], where much of the data has
been dropped into the inevitable PDF "*coffin*" and which is a
breathtaking **907** pages long. To give the authors their due, they
also provide 20 CIF files which ARE good sources of data. Rarely
commented on, but clearly missing from the information associated with
this (indeed most) articles is the **metadata** about the data. Thus the
metadata for these CIF files amounts to just *e.g.* **229**. To find out
the context, one has to scour the article (or the 907 pages of the ESI)
to identify compound **229** (I strongly suspect it's a molecule because
of the implied semantics of the term, not because its been explicitly
declared). You will not find the metadata at
e.g. [data.datacite.org](https://data.datacite.org/) which is one open
aggregator and global search engine based on deposited metadata.

I have commented
[elsewhere](http://www.ch.imperial.ac.uk/rzepa/blog/?p=15916) on this
blog that other types of data could also be enhanced in the manner that
CIF crystallographic files represent. For example the Mpublish NMR
project,^‡^ examples of which are shown
[here](http://www.ch.imperial.ac.uk/rzepa/blog/?p=16628), and for which
typical data AND[ its
metadata](https://data.datacite.org/10.14469/hpc/1053) can be seen at
DOI: [10.14469/hpc/1053](https://doi.org/10.14469/hpc/1053). I fancy
that if this method had been
adopted,\[cite\]10.1021/jacs.6b13229\[/cite\] those 907 pages might have
shrunk somewhat, although of course not entirely. But my hope is that
gradually the innovative chemistry community will find ways of
exhuming more and more data from the PDF coffin and in the process
reducing the paginated lengths of the PDF-based ESI further, perchance
eventually even to zero?

If you are yourself preparing an article and sweating over the ESI at
this very moment, do please take a look at the Mpublish method and how
perhaps it can help make your NMR data at least more useful to others.

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

^‡^I understand an article describing this project is in preparation. If
you cannot wait, this recent application of the Mpublish project has
some details.\[cite\]10.1186/s13321-017-0190-6\[/cite\]

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Living in London, travelling using public transport is often the best way to get around. Before setting out on a journey one checks the status of the network. Doing so today I came across this page: our open data from Transport for London.  I learnt that by making TFL travel data openly available, some 11,000 developers (sic!) have registered for access, out of which some 600 travel apps have emerged.

Messaggi di Rogue Scholar

A nice example of open data (in London).