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2018 ; 13
(6
): 470-481
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Caveat Usor: Assessing Differences between Major Chemistry Databases
#MMPMID29451740
Southan C
ChemMedChem
2018[Mar]; 13
(6
): 470-481
PMID29451740
show ga
The three databases of PubChem, ChemSpider, and UniChem capture the majority of
open chemical structure records with February 2018 totals of 95, 63, and 154
million, respectively. Collectively, they constitute a massively enabling
resource for cheminformatics, chemical biology, and drug discovery. As
meta-portals, they subsume and link out to the major proportion of public
bioactivity data extracted from the literature and screening center assay
results. Therefore, they not only present three different entry points, but the
many subsumed independent resources present a fourth entry point in the form of
standalone databases. Because this creates a complex picture it is important for
users to have at least some appreciation of differential content to enable
utility judgments for the tasks at hand. This turns out to be challenging. By
comparing the three resources in detail, this review assesses their differences,
some of which are not obvious. This includes the fact that coverage is
significantly different between the 587, 282, and 38 contributing sources,
respectively. This not only presents the "who-has-what" question, but also the
reason "why" any particular inclusion is considered valuable is rarely made
explicit. Also confusing is that sources nominally in common (i.e., having the
same submitter name) can have significantly different structure counts, not only
in each of the three but also from their standalone instantiations. Assessing a
series of examples indicates that differences in loading dates and structural
standardization are the main causes of this inter-portal discordance.