Imperial College London

Henry Rzepa

In an era when [alternative
facts](https://en.wikipedia.org/wiki/Alternative_facts) and [fake
news](https://en.wikipedia.org/wiki/Fake_news) afflict us, the
[provenance of scientific
data](https://eos.org/opinions/the-importance-of-data-set-provenance-for-science)
becomes ever more important. Especially if that data is available as
open access and exploitable by others for both valid scientific reasons
but potentially also by those with other motives. Here I consider the
audit trail that might serve to establish data provenance in one typical
situation in chemistry, the acquisition of NMR instrumental data. 

Here I describe how such data is generated in my department; details may
vary elsewhere.

1.  The prospective user of the NMR service is allocated a service ID.
    In our case, that ID relates to the research group rather than to
    individual researchers. This ID is parochial, it does not reference
    any other information about the user in the institute. Only the
    service manager has the information to associate this ID with real
    users and this information is normally not distributed.
2.  When a sample is submitted, this ID is used to create a new folder
    containing the data as a sub-folder of the group ID and located on
    the NMR data servers.
3.  The dataset itself^‡^ contains a number of files that contain an
    audit trail (names such as audita.txt, auditp.txt) with the
    fields: ##AUDIT TRAIL=
    `$$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT). `Typically,
    none of these files have propagated the original user ID under which
    the data was collected; to do so would require a programmatic
    connection between the local authentication systems and the
    spectrometer software used, a connection that is normally missing.
    Thus the[ first break]{style="color: #ff0000;"} in the provenance
    trail.
4.  In principle other audit trails can be inferred from these files,
    such as the [unique identity of the
    instrument](http://www.ch.imperial.ac.uk/rzepa/blog/?p=17084)
    provided by its manufacturer. Further information such as *e.g.* the
    probe used to collect the data (probes can be readily changed over)
    or any calibration data used in setting up the instrument for the
    data collection are by and large not recorded. To my knowledge,
    although an instrument can have a unique serial number, such serial
    numbers of swappable components such as probes are not recorded by
    the collection software. Thus the [second
    break]{style="color: #ff0000;"} in the provenance trail.
5.  This data then needs to be processed by further software. In this
    case we use the [MestreNova
    system](http://mestrelab.com/resources/whats-new-in-mnova-11-0-0/)
    for this task. Each dataset has editable assigned properties; below
    I show those that can be associated with the spectrum (accessed with
    MestreNova using ***Edit/Properties***). All this comes from the
    information collected by the instrument. The user's identity can be
    inserted into the "title" field, the display of which is **off** by
    default. ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/073.jpg){.aligncenter
    .size-full .wp-image-17888 decoding="async" width="450"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/073.jpg 1008w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/073-300x99.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/073-768x253.jpg 768w"
    sizes="(max-width: 1008px) 100vw, 1008px"}
6.  There is also a section for parameters, a synonym for which might
    be **metadata** and accessed using this program from
    ***View/Tables/Parameter*s**. If **Author** was entered as a
    parameter in the dataset by the spectrometer software, the Mnova
    document would retrieve that information. Equally, an
    [ORCID](http://orcid.org/) identifier for the author entered at the
    time of data collection and thus stored in the dataset could be read
    by Mnova, stored and displayed if configured to do so. It would be
    fair to say however that this option is rarely if indeed ever
    systematically implemented by NMR instrument data collection
    software and so is never propagated to the data processing software
    (as highlighted in red below). Thus a
    third[ break]{style="color: #ff0000;"} in the provenance trail.  
    ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/077-389x1024.jpg){.aligncenter
    .size-large .wp-image-17910 decoding="async" width="300"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/077-389x1024.jpg 389w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/077-114x300.jpg 114w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/077.jpg 660w"
    sizes="(max-width: 389px) 100vw, 389px"}This is also an alternative
    and this time formal **metadata** field that can be populated, by
    default as shown below with the type of spectrum and nucleus. These
    properties are not controlled in the sense of only allowing those
    terms that are present in a specified dictionary. The jargon for
    such control is a **metadata schema.** This is not used here, since
    dissemination of this information is not intended; the software
    accepts whatever information it is given.   
    ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/074.jpg){.aligncenter
    .size-full .wp-image-17889 decoding="async" width="450"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/074.jpg 952w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/074-300x130.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/03/074-768x334.jpg 768w"
    sizes="(max-width: 952px) 100vw, 952px"} There are thus several
    opportunities to collect the identity of the experimenter and thus
    attribute provenance to the collected data, but this does very much
    depend on the will of researchers, institutions or publishers to
    enforce specific policies around this. [The fourth break in the
    provenance trail]{style="color: #ff0000;"}.
7.  The dataset can then be uploaded
    (DOI: [10.14469/hpc/1291](https://doi.org/10.14469/hpc/1291)), at
    which stage provenance can finally be added using the
    [ORCID](http://orcid.org/) credentials of the person publishing the
    dataset, who of course may or may not be the person who actually
    recorded the data! The full metadata for this specific collection
    can be seen
    at [data.datacite.org/10.14469/hpc/1291](https://data.datacite.org/10.14469/hpc/1291). Or
    to put it another way, this is the first point in the provenance
    chain where the metadata is controlled by a schema and is also
    discoverable in a standard programmatic manner, *i.e.* the preceding
    link. The provenance is now formally associated with the ORCID
    identifier using the [DataCite metadata
    schema](http://datacite%20metadata%20schema). You should be aware
    that a local policy^†^ is that access to the repository
    at <https://data.hpc.imperial.ac.uk> is only allowed
    by cross-authentication with <http://orcid.org/> using the user's
    ORCID. This identifier is then automatically propagated to the
    metadata held at
    *e.g.* [data.datacite.org/10.14469/hpc/1095](https://data.datacite.org/10.14469/hpc/1095).
    Currently however, none of any metadata originally recorded in
    either the instrumental file set or the processed MestreNova file is
    forwarded on to the metadata record held at DataCite; again [loss of
    information and potentially of
    provenance]{style="color: #ff0000;"}. 
8.  The peer-reviewed article resulting from the interpretation of this
    data however **can** be associated with the provenance introduced in
    the previous stage;
    see [data.datacite.org/10.14469/hpc/1267](https://data.datacite.org/10.14469/hpc/1267) 
    and the* IsReferencedBy* property. 

Now imagine if there was a common thread in all the stages of acquiring,
processing and publishing this scientific data based on the ORCID. 

1.  Providing an ORCID could be made an essential requirement of access
    to the instrument.
2.  This information would be propagated to the dataset ...
3.  by inclusion in one or more of the audit trail files.
4.  At this stage, further [persistent
    identifiers](http://www.ch.imperial.ac.uk/rzepa/blog/?p=17084)
    associated with the instrument manufacturer could be added, which
    help identify not only the instrument used, but sub-components such
    as the changeable probe. This would allow access to any calibration
    curves or probe sensitivity and other aspects.
5.  The ORCID and other relevant information could be picked up by the
    software used to convert the data into spectra and propagated into
    the metadata containers for this software ...
6.  where its use is controlled by a specified schema.
7.  At this stage, the ORCID and information such as the nucleus
    recorded, the sample temperature *etc* can be propagated on to the
    final metadata records.
8.  And the reader of the article describing this work would have a
    formally defined provenance audit trail they could follow back to
    the start of the experiment or forward to a published article. In
    this case, the data claims provenance (acquired from peer review)
    from the article, but it should also work in reverse with the
    article claiming provenance from the data on which it is based. The
    indexing of this bidirectional exchange is one of the exciting
    features that we should see emerging from CrossRef (holders of
    metadata about articles) and DataCite (holders of metadata about
    research data) in the near future.

We are clearly a little way from having the infrastructures described
above for establishing such data audit trails. To do so will require
cooperation from instrument manufacturers, at least in the example as
charted above, as well as researchers, institutions, publishers,
peer-reviewers and funding bodies. The first step would be to ensure
that all scientists who intend collecting, processing and publishing
data should claim an ORCID. That remark is directed specifically at
undergraduate, postgraduate and post-doctoral researchers, not just at
their supervisor or their PI (principal investigator). At a point when
the discussion about alternate facts and perhaps even alternate data
risks a general loss of confidence in science, we should be pro-active
in establishing trust in the scientific processes.

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

^‡^ You can see an example obtained by this process at DOI:
[10.14469/hpc/1095](http://doi.org/10.14469/hpc/1095)

^†^ This requirement is a strong driver for the uptake of ORCID amongst
our student population.

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


In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but potentially also by those with other motives.

Messages de Rogue Scholar

The provenance of scientific data – establishing an audit trail.