ChemSpider is an online database of over 30 million chemical compounds sourced from over 500 different sources including government laboratories, chemical vendors, public resources and publications. Developed with the intention of building community for chemists ChemSpider allows its users to deposit data including structures, properties, links to external resources and various forms of spectral data. Over the past few years ChemSpider has aggregated almost 20000 high quality NMR and IR spectra and continues to expand as the community deposits additional types of data. The majority of spectral data is licensed as Open Data allowing it to be downloaded and reused in presentations, lesson plans and for teaching purposes. This poster will present our existing technology and our plans to host a million spectra in our developing online data repository.

1. ChemSpider – Building an Online Database of Open Spectra
Antony J. Williams1,Valery Tkachenko1,Alexey Pshenichnov1, Daniel Lowe2, Carlos Coba3,
Kevin Theisen4 and Rudy Potenzone4
1. Royal Society of Chemistry 2. NextMove Software 3. Mestrelab Research 4. iChemLabs LLC
Introduction: ChemSpider is an online
database of over 30 million chemical
compounds from >500 different sources
including chemical vendors, online
public resources and publications.
ChemSpider allows deposition of data
including structures, properties, and
various forms of spectral data. One
activity of the project is to host a
searchable database of 1D/2D NMR,
IR, Raman and Mass Spectral data.
ChemSpider has over 20000 spectra
and expands as the community
deposits additional data.
Sources of Spectral Data: The
majority of data are deposited by users
of ChemSpider. Submission of spectra
in the form of JCAMP-DX, or
images/PDF (for all spectra but
especially for 2D NMR) are supported.
Community-based curators will validate
and annotate the data to ensure that
only the highest quality data are
available on the database.
To create a large NMR database
we are using “text-mining” to extract
spectral data, together with their
associated chemical compounds, then
simulating visual forms of the spectra,.
We have text-mined a large patent
corpus to extract many hundreds of
thousands of NMR spectra to produce
visual depictions as shown in Figure 1.
Text mined spectra are of the form:
1H NMR (CDCl3, 400 MHz): δ = 2.57 (m, 4H, Me,
C(5a)H), 4.24 (d, 1H, J = 4.8 Hz, C(11b)H), 4.35
(t, 1H, Jb = 10.8 Hz, C(6)H), 4.47 (m, 2H, C(5)H),
4.57 (dd, 1H, J = 2.8 Hz, C(6)H), 6.95 (d, 1H, J =
8.4 Hz, ArH), 7.18–7.94 (m, 11H, ArH)
Figure 1: A spectral depiction from
converting the text-mined spectrum
above. This can be stored in JCAMP to
build a spectral database.
Spectral Visualization: Spectra are
viewed inside the JSpecView spectral
display widget1. Zooming, scrolling and
integration are possible. 2DNMR
spectra are viewed only as images.
Figure 2: The JSpecView spectral
viewing applet supports viewing JCAMP
spectra of 1D NMR, IR, UV-Vis and
Mass Spectrometry data.
Spectroscopic techniques produce
NMR and IR vibrational assignments,
and mass fragment peaks. We are now
working with iChemLabs HTML5
widgets2 for the display of assignments.
Figure 3: Assignments of spectral-
structure associations. Selecting the
peak at 7.5ppm highlights the protons
on the molecule. The assignments are
contained in the JCAMP spectral format.
Future Directions: We intend to
continue to grow the spectral database
by encouraging further depositions from
the community as well as investigating
the possibility of converting spectral
figures to spectral data to host in the
database.
References
1)JSpecView Project: an Open Source
Java viewer and converter for
JCAMP-DX, and XML spectral data
files,http://www.journal.chemistrycentr
al.com/content/1/1/31
2)iChemLabs Web Components
Spectrum Structure Correlations:
http://tinyurl.com/pkz26xf