Imperial College London

Henry Rzepa

I do go on a lot about the importance of having modern access to data.
And so the appearance of this
article\[cite\]10.1038/sdata.2014.22\[/cite\] immediately struck me as
important. It is appropriately enough in the new journal *Scientific
Data*. The data contain computed properties at the B3LYP/6-31G(2df,p)
level for 133,885 species with up to nine heavy atoms, and the entire
data set has its own DOI\[cite\]10.6084/m9.figshare.978904\[/cite\]. The
data is generated by subjecting a molecule set to a number of validation
protocols, including obtaining relaxed (optimised) geometries at the
B3LYP/6-31G(2df,p) level. It would be good to replicate this set with
inclusion of a functional that also includes dispersion, and of course
making the coordinates all available in this manner greatly facilitates
this. The collection also includes data for *e.g.* 6095 constitutional
isomers of C~7~H~10~O~2~, which reminds me of an early, delightfully
entitled, article adopting such an approach in quantum
chemistry\[cite\]10.1021/jp057107z\[/cite\]. Such collections are an
important part of the process of validating computational
methods\[cite\]10.1007/s00894-005-0278-1\[/cite\] This way of publishing
data does raise some interesting discussion points.

1.  In this case, we have coordinates for 134 kilo molecules, but the
    individual molecules in this collection do not have formalised
    metadata. The InChI key is an example of such metadata, and means
    that the metadata can be specifically searched. Where you have a
    monolithic collection of 134k molecules, no such structured exposed
    metadata exists for individual entries and you will have to generate
    it yourself in order to search it.

2.  Each of the molecules in this collection is revealed (once you have
    downloaded the compressed archive as above and decompressed it into
    a 548 Mbyte folder) as separate XYZ files.^‡^ This syntax has the
    merit of being very simple, and can easily be processed by a human.
    Computed molecular properties in the form of metadata are missing
    from this particular (relatively ancient) format. To recover them,
    you would have to repeat the calculation.

3.  In fact the XYZ files in this example do seem to have
    **some** (unformalised) properties appended to the bottom of the XYZ
    file (the SMILES and InChI strings are recognizably there, shown as
    an example below

        27
        gdb 57483   2.68237 1.10148 0.98017 0.0557  94.95   -0.2958 0.073 ...
        C   -0.0805964233    1.5844710741    0.1983967506   -0.41097
        .........
        29.7376 87.1304 196.1576    216.856 ...
        CC(C)(C)C1CCCC1 CC(C)(C)C1CCCC1 
        InChI=1S/C9H18/c1-9(2,3)8-6-4-5-7-8/h8H,4-7H2,1-3H3 InChI=1S/C9H18/c1-9(2,3)8-6-4-5-7-8/h8H,4-7H2,1-3H3

    This of itself does raise some issues.

    1.  The title line (starting gdb) has extra numbers, but it is not
        immediately obvious what these are.
    2.  The XYZ file is no longer standard because extra information is
        appended, both to each atom line (the charge? shown above as
        ***-0.41097***) and to the bottom. Much software will not
        recognise this non-standard XYZ file, and is likely to discard
        the additional information. Thus I tried
        [wxMacMolPlt](https://code.google.com/p/wxmacmolplt/){target="_blank"}
        (a long time reader of XYZ files) with no success. [Human
        editing](http://www.ch.imperial.ac.uk/rzepa/blog/?p=12728 "Data nightmares: B40 and counting its π-electrons"){target="_blank"}
        of the file was required to remove the additional information
        before a sensible molecule loaded. Only at this point could one
        progress to (re)compute the molecular properties.
    3.  The extra information is not formally described. As a human^†^ I
        can recognise it as an atom coordinate list with appended
        charges (I think), to which is appended a  list of normal
        coordinate harmonic wavenumbers in units of cm^-1^, a SMILES and
        InChI as separate lines. That is really informed guesswork (a
        human is very good at such pattern recognition) but I cannot be
        absolutely certain, and a machine seeing this for the first time
        would certainly struggle.
    4.  The last lines contains repetitions of the SMILES and InChI
        strings. I am guessing that this is the connectivity determined
        before and after geometry optimisation (using quantum mechanics,
        bonds can indeed break or form during such a process) but I may
        be quite wrong about that. I have not tried to resolve this
        issue by actually reading the depths of the article, since the
        file itself really should carry such information.
    5.  The XYZ file itself carries no provenance, such as who created
        the file, which software and version was used to create it, the
        date of creation etc.

4.  An alternative approach is the one adopted here on this blog. Each
    individual molecule is assigned a DOI and its own metadata and
    provenance. It is presented to the user in a variety of syntactical
    forms, each designed for a different purpose, and each adopted for
    these needs. Thus the syntax and semantics of a CML file are clearly
    defined by a Schema, and this format can easily absorb additional
    information without "breaking the standard". It too can be scaled to
    134 kilo molecules\[cite\]10.1007/s00894-005-0278-1\[/cite\]
    although this does require a suitable container (repository) to
    handle this scale (and I am not entirely sure that DataCite would
    approve of the generation of 134 kiloDOIs).

Overall, this sort of data publication must be warmly welcomed by the
community, and I do hope that more chemistry data is routinely made
available in appropriate manner. The presentation in ready-to-reuse form
will no doubt improve as the value of such data becomes more fully
appreciated. And ultimately, humans need to be excluded from much of
this process (editing the 133,885 sets of XYZ coordinates as described
above is not for humans to do).

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

‡Your computer however might balk at opening a folder with 133,885 items
in it. Try this only on a very fast machine with lots of memory and
ideally an SSD!

^†^Contrary to some rumors, I do not hail from the planet Zog.

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


I do go on a lot about the importance of having modern access to data. And so the appearance of this article[cite]10.1038/sdata.2014.22[/cite] immediately struck me as important. It is appropriately enough in the new journal
<em>
 Scientific Data
</em>
. The data contain computed properties at the B3LYP/6-31G(2df,p) level for 133,885 species with up to nine heavy atoms, and the entire data set has its own DOI[cite]10.6084/m9.figshare.978904[/cite].

Messages de Rogue Scholar

Data galore! 134 kilomolecules.