Imperial College London

Henry Rzepa

As data repositories start to flourish, it is reasonable to ask
questions such as *what sort of chemistry can be found there and how can
I find it?* Here I give an updated\[cite\]10.1515/ci-2016-3-408\[/cite\]
worked example of a digital repository search for chemical content and
also pose an important issue for the chemistry domain.

Firstly, I should say this search is restricted just to those data
repositories that submit indexing terms (metadata) to DataCite, which is
the agency that will be used to conduct the searches. Each type of
metadata is defined by a prefix or operator field (much in the same way
that an advanced Google search can be
[prefixed](http://www.googleguide.com/advanced_operators_reference.html)
with an operator, e.g. **author:**^♥^). I will use just two such
DataCite field prefixes^†^ here as exemplars (there are many more).

1.  **media:** This specifies the media type for the data being
    searched. For restriction to chemistry one takes advantage of the
    **chemical/x-** media type, as described
    previously.\[cite\]10.1021/ci9803233\[/cite\]
2.  **SubjectScheme:** This is a new declaration, as specified in the
    DataCite V4 metadata schema.\[cite\]10.5438/0012\[/cite\] The
    subject scheme in effect declares a subject-specific term, and is
    designed to be used by domains such as chemistry.

This latter is best illustrated by one specific example of a search
which I will dissect here:  
[[https://search.datacite.org/works?query=]{style="background-color: cornflowerblue;"}[media:chemical\\x\\gaussian\*]{style="background-color: lightpink;"}**+S**[ubjectScheme:inchikey]{style="background-color: darkturquoise;"}**+**[subject:XZYDALXOGPZGNV-UHFFFAOYSA-M]{style="background-color: deepskyblue;"}**+**[media:chemical\\x\\mnpub\*]{style="background-color: sandybrown;"}](https://search.datacite.org/works?query=media:chemical\/x\-gaussian*+subjectScheme:inchikey+subject:XZYDALXOGPZGNV-UHFFFAOYSA-M+media:chemical\/x\-mnpub*)^‡^

1.  [https://search.datacite.org/works?query=]{style="background-color: cornflowerblue;"}
    [queries the DataCite MDS](https://search.datacite.org/help.html)^†^
    (metadata store).
2.  [media:chemical\\x\\gaussian\*]{style="background-color: lightpink;"}
    defines a media type which contains the string
    [chemical/x-gaussian]{style="background-color: lightpink;"}, with
    the [\*]{style="background-color: lightpink;"} being a wild-card
    which allows any characters to follow this string. This now is
    specifying any data repository where **Gaussian** files have been
    deposited and assigned this media type.
3.  **+** represents a Boolean **AND** operator.
4.  [SubjectScheme:inchikey]{style="background-color: darkturquoise;"}
    restricts a subject search to a
    [subjectScheme]{style="background-color: darkturquoise;"} having the
    value [inchikey]{style="background-color: darkturquoise;"}, whilst
5.  [subject:XZYDALXOGPZGNV-UHFFFAOYSA-M]{style="background-color: deepskyblue;"}
    defines the value of the subject itself.
6.  [media:chemical/x-mnpub]{style="background-color: sandybrown;"}
    completes the search definition, this relating to the mandatory
    additional presence of an
    **Mpublish**\[cite\]10.1186/s13321-017-0190-6\[/cite\] file
    indicating (spectroscopic, probably NMR) data readable by the
    MestreNova program.

One hit with these restrictions has doi:
[10.14469/HPC/2635](http://doi.org/10.14469/HPC/2635) and clicking the
button on the landing page for this object labelled **metadata**
resolves to *e.g.*  
[[https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/2635]{.small}](https://data.datacite.org/application/vnd.datacite.datacite+xml/10.14469/hpc/1976),  
and downloads the metadata record for this object. Part of this record
looks a bit like:

![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/06/171-1024x196.jpg){.aligncenter
.size-large .wp-image-18503 loading="lazy" decoding="async" width="450"
height="86"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/06/171-1024x196.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/06/171-300x58.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/06/171-768x147.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/06/171.jpg 1252w"
sizes="(max-width: 450px) 100vw, 450px"}

This brings me to the important issue for the chemistry domain, which is
to agree upon a core set of **SubjectSchemes** for implementation
in data repositories with domain-specific chemical content. The two
subjects above, the InChI and the InChIKey seem obvious candidates for
inclusion. But how the list is extended and how the SubjectScheme is
specified are now matters for the community to discuss. Perhaps the
[IUPAC GoldBook](http://goldbook.iupac.org/) is one starting point for
the SubjectScheme URIs. Watch this space.

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

^‡^The \\ syntax indicates an ["escaped"
character](http://lucene.apache.org/core/4_0_0/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#Escaping_Special_Characters).
Thus in chemicalx\\gaussian a \\ ensured that the following / is treated
as part of the search string, and not as part of the search syntax.
Likewise **\\** ensures the minus character is part of the string and
not a syntactic negation. The current list of characters requiring
escaping is
`+ - & | ! ( ) { } [ ] ^ " ~ * ? : \ /`{style="background-color: lightyellow;"}

^†^ The documentation lists common fields, but there are far more
specified in V4 of their schema. The ones you see used here are not
(yet?) documented at <https://search.datacite.org/help.html>

^♥^ This [Google
page](http://www.googleguide.com/advanced_operators_reference.html) has
a rich plethora of powerful searches, which I suggest almost no-one
knows about!

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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"}
:::


As data repositories start to flourish, it is reasonable to ask questions such as
<em>
 what sort of chemistry can be found there and how can I find it?
</em>
Here I give an updated[cite]10.1515/ci-2016-3-408[/cite] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.

Messaggi di Rogue Scholar

How to search data repositories for FAIR chemical content and data: SubjectScheme