The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. The richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process delivering a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.

1. Using an Online Database of Chemical Compounds for the Purpose
of Structure Identification
Antony J. Williams, Valery Tkachenko and Alexey Pshenichnov
Royal Society of Chemistry
Introduction: Spectroscopy has a
primary role in identifying chemicals.
Verification is when a suggested
chemical structure is confirmed to be
consistent with the analytical data. This
work reports on how a public compound
database can be used for identification.
The ChemSpider Database:
ChemSpider (www.chemspider.com) is
an online database of >30 million
compounds from >500 different sources
including vendors, public resources and
publications. For each compound in the
database masses and molecular
formulae are generated.
The ability to search the database by
mass, and specifically monoisotopic
mass, can provide selected hits from
the database. The ability to search on
adducts and included/excluded
elements is also allowed. The search
interface is shown below.
Searching for “Known Unknowns”
ChemSpider has been used1 to identify
“known unknowns”, compounds that
may be unknown to the researcher but
known in the scientific literature/patents.
Using a monoisotopic mass search of
ChemSpider, and sorting search results
by the number of associated references
was shown useful in bringing the most
likely candidates to the top of the list.
Following a mass search hits can be
ordered by selecting the desired field. In
the example below, initial results were
sorted in descending order by the
number of references.
Little et al. showed this approach
applied to metabolites, pesticides,
drugs etc. as represented in Table 1.
ChemSpider Programming Interfaces
A number of MS instrument vendors
interrogate the ChemSpider database for
compounds. Companies including
Agilent, Bruker, Thermo, Waters and
others have tested the integration.
ChemSpider data sources are
segregated into types such as
metabolites, safety data, patents etc.
The programming interface allows a list
of data sources to be passed in the
query. If a biofluid sample is being
examined then only metabolite data
sources should be searched. A research
study utilizing ChemSpider identifying
pesticides in water2 has been reported.
References
1) Identifying “Known Unknowns” Using
ChemSpider, J. Little, A.J. Williams
and V. Tkachenko, ASMS
Conference, 2011
http://tinyurl.com/o3k69yn
2) The Detection, Identification, and
Structural Elucidation of Unknown
Contaminants During ToF Screening
for Pesticides in River Water E.
Riches, K. Worrall and H. Major,
http://tinyurl.com/pbgqzk2