ssJournal of Cheminformatics
Open AcceSoftware
The Spectral Game: leveraging Open Data and crowdsourcing for
education
Jean-Claude Bradley*1, Robert J Lancashire2, Andrew SID Lang3 and
Antony J Williams4
Address: 1Drexel University, Department of Chemistry, 32nd and Chestnut Streets, Philadelphia, Pennsylvania 19104, USA, 2Department of
Chemistry, The University of the West Indies, Mona Campus, Kingston 7, Jamaica, 3Oral Roberts University, Department of Computer Science and
Mathematics, 7777 S. Lewis Ave, Tulsa, Oklahoma 74171, USA and 4ChemZoo Inc, 904 Tamaras Circle, Wake Forest, North Carolina 27587, USA
Email: Jean-Claude Bradley* - bradlejc@drexel.edu; Robert J Lancashire - robert.lancashire@uwimona.edu.jm;
Andrew SID Lang - alang@oru.edu; Antony J Williams - antony.williams@chemspider.com
* Corresponding author
Abstract
We report on the implementation of the Spectral Game, a web-based game where players try to
match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry
and Infrared spectra. Each correct selection earns the player one point and play continues until the
player supplies an incorrect answer. The game is usually played using a web browser interface,
although a version has been developed in the virtual 3D environment of Second Life. Spectra
uploaded as Open Data to ChemSpider in JCAMP-DX format are used for the problem sets
together with structures extracted from the website. The spectra are displayed using JSpecView,
an Open Source spectrum viewing applet which affords zooming and integration. The application
of the game to the teaching of proton NMR spectroscopy in an undergraduate organic chemistry
class and a 2D Spectrum Viewer are also presented.
Background
Technology has made up to date information readily
available to students through open course materials,
recorded lectures, e-books, blogs, etc., and is offering
additional options to distributing information directly to
students other than through traditional lectures and text-
books[1]. As a consequence, an increasingly important
role for educators is one where they become guides to
knowledge and understanding; teaching skills and tech-
niques, which now include information literacy skills –
showing students how to locate, evaluate, and effectively
Traditional ways to reinforce skills, knowledge, and
understanding through practice include homework, quiz-
zes and labs. These traditional techniques can be
enhanced with the use of freely available technologies,
and in a world where the gaming market is beginning to
outperform both music and films[2], some instructors are
using technology and new freely available data to create
games that catalyze learning and aid in the teaching of
chemistry. Word puzzles have been devised to teach first
year general chemistry[3], named organic reactions[4]
and basic chemistry concepts[5]. Popular game shows
Published: 26 June 2009
Journal of Cheminformatics 2009, 1:9 doi:10.1186/1758-2946-1-9
Received: 27 April 2009
Accepted: 26 June 2009
This article is available from: http://www.jcheminf.com/content/1/1/9
© 2009 Bradley et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Page 1 of 10
(page number not for citation purposes)
use knowledge – and then to reinforce skills, knowledge
and understanding through practice.
such as Taboo[6], Jeopardy! [7,8] and Who Wants to be a
Millionaire?[9] have been adapted for general chemistry

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
review. Card games have been devised to teach carbohy-
drate chemistry[10], element symbols[11], functional
groups[12] and organic reactions[13]. An adaptation of
BINGO has been used to teach nomenclature[14]. A ver-
sion of the Name Game facilitates student interaction
while reviewing chemistry concepts[15]. There is even an
organic chemistry game that can be played on a cell
phone[16].
For spectroscopy, atomic absorption spectra can be prac-
ticed by moving virtual samples into a flame[17]. Infrared
spectra interpretation has been turned into a game by a
modification of checkers[18] or as a quiz[19]. Other
board games used to teach general chemistry include Con-
centration[20], CHeMoVEr to learn about balancing
chemical equations[21]. In addition to teaching applica-
tions, games can be used to solve chemistry problems. For
example, Foldit has been used to leverage crowdsourcing
to solve cases of protein folding[22]. Russell has exten-
sively reviewed older chemistry games[23]. In this report
we describe an additional game that can be played to help
learn organic chemistry – a game that was not possible
just a few years ago – The Spectral Game.
The spectral game
The interpretation of spectra has always been an essential
skill for mastering organic chemistry and many students
struggle to grasp the nuances of various spectroscopy tech-
niques. One of the problems is that traditional textbook
assignments are pre-selected to provide simple examples
that rarely deviate from what was learned in class. We
believe this can be a disservice to students in that it does
not prepare them for real-world structure elucidation
challenges. With these limitations in mind we took advan-
tage of the availability of the present perfect storm of
internet technologies, online databases of Open structure
and spectral data and flexible and intuitive tools for the
viewing of spectral data to design a spectral game to assist
in the teaching of spectroscopy in an entertaining yet edu-
cational manner.
Implementation: The spectral game website
The Spectral Game[24] was created by bringing together
Open Source spectral data, a spectrum viewing tool and
appropriate work flows for delivering these in a gaming
fashion. The Open Source spectral data identifiers and the
properties and identifiers of the chemical structures which
they represent are drawn from the ChemSpider data-
base[25] using freely available web services provided by
ChemSpider. These data are parsed and stored on the
Spectral Game server. The game uses these data to display
a series of spectra selected randomly one at a time,
together with a number of chemical structure images. The
and chemical structure images are pulled dynamically
from the ChemSpider database using an embed function-
ality described below.
The ChemSpider database is an online database of over 21
million chemical structures, related molecular properties,
links out to over 200 different data sources and, in rela-
tion to this game, is an environment where spectral data
can be uploaded and hosted for the benefit of the commu-
nity. At the time of writing there are more than 1400 Open
Data spectral data sets on ChemSpider. The majority of
these are proton and carbon-13 NMR spectra but there are
also infrared, near infrared, UV-Visible and mass spectra.
The community participates in the addition of spectral
data content by uploading data in JCAMP-DX format, to
the website[26]. Data have also been provided as collec-
tions by educational facilities (Pacific Lutheran[27]), soft-
ware providers (ACD/Labs[28]) and national laboratories
(NIST[29]). In order to facilitate the easy exchange of both
structure and spectral data ChemSpider has provided an
embed functionality[30] similar to that provided at many
other websites such as YouTube. These Open Data spectra
are imported into the game using this functionality
thereby allowing Open Data spectra to be called for dis-
play inside a webpage using a simple Javascript call as
shown below.
The javascript call of "<script type = "text/javascript" src="
http://www.chemspider.com/csjs
api.ashx?op=spec&tk=7283856c-a2d2-
4638a11ea873f84244&bid=1317&w=750&h=400"></
script>" calls the spectrum from ChemSpider and displays
it in a webpage as is shown below in Figure 1.
The applet used to display the spectra (JSpecView[31])
was developed at UWI[32] and is now the primary Open
Source spectrum viewing applet for displaying interactive
spectra on the internet. It allows zooming, highlighting of
regions within the spectrum, spectrum reversal and dis-
play of multiple spectra. Some changes were needed to the
viewer code to allow for the suppression of sample details
during the display so that users could not cheat by simply
looking up the details of the material under study via the
JCAMP-DX header. The first line of the header in a
JCAMP-DX file is ##TITLE = and often contains the name
of the sample. JSpecView has a menu option to display the
header values and this would obviously make it very easy
to answer the quiz. A new parameter was introduced
(OBSCURE) that activates a routine to replace the value of
the Title field with "unknown" so that any attempt to dis-
play the header lines would not give any advantage.
A brief introduction to the simplest JCAMP-DX protocolPage 2 of 10
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challenge for the player is to select the chemical structure
that matches the displayed spectrum. Both the spectrum
follows:

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
JCAMP-DX files consist of plain text that can be read and
edited by simple text viewers. The simplest type is divided
into two sections; the Header and the Data. The Header
defines the type of spectrum, the source of the data, the
instrument type and parameters as well as the dataset that
follows in terms of start and end positions of the X values
and deltaX. Many instruments make use of fixed separa-
tions of the X values and this is used in the method of
compression for JCAMP-DX files. As mentioned above,
the first line generally gives a description of the sample
and looks like ##TITLE=, the second line is generally
##JCAMP-DX = with a version number. IR spectra are
often found as version 4.14 while NMR need to be 5.01
since this corrected for problems of Shift References/Off-
sets not handled in earlier versions. JCAMP-DX version 6
that would cover 2D NMR was published as a draft for
comment, but has not yet been finalised.
The Data section generally begins with ##DATAXY =
(X++(Y..Y)) which is a shorthand notation for the idea
that with fixed changes in the X values it is possible to put
an X value at the start of the line and then provide a
number of Y values with the understanding that these cor-
respond to the next set of X values. The start of the next
made to ensure that no line is missing or duplicated. A
simple example from an IR file would be;
##XYDATA = (X++(Y..Y))
673 215867052 213571948 211374384 209305312
207332720 205205968 203152088
680 201167848 199108304 197021336 195063332
193056836 191013384 189185540
687 187358300 185164740 182889624 182557368
192119980 208444664 200564276
DeltaX was 1.0 and the Y values here have a ##YFACTOR
= defined in the Header of ##YFACTOR = 9.313225746e-
10 so that the actual values corresponding to X values of
673, 674, 675, 676 1/cm are calculated by multiplying by
the YFACTOR to give:
0.198904 0.196858 0.194931 0.193094
A range of compression types exist to cram more Y values
onto each line that make use of substituting the first digit
Interactive spectrum viewer JSpecViewFigure 1
Interactive spectrum viewer JSpecView.Page 3 of 10
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line begins again with an X value so that checks can be by a letter etc.

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
The end of the file is indentified by ##END=
Gameplay
At the beginning of the game two structures, one correct
and one incorrect are shown below the spectrum, see Fig-
ure 2, and the user is asked to click on that structure that
is the best match for the spectrum displayed.
The structures are extracted from ChemSpider using simi-
lar embedding functionality for chemical structures as
used for spectra. If the user selects the correct structure
then they proceed to the next set of spectrum and struc-
tures and the process is repeated. The player needs to
examine the spectrum to compare various features to con-
firm or reject each of the structures. These include chemi-
cal shifts, multiplicities, peak intensity, functional groups
and so on. In NMR users should be able to quickly distin-
guish aromatic protons from alkyl protons, aldehydic res-
onances from exchangeable carboxylic acid protons and
methoxy singlets from methylene groups within a chain.
In infrared spectra the user would be looking for specific
functional group vibrations such as carbonyl groups.
These simple filters can be enough to distinguish spectra-
structure associations early in the game but complexity
changes as the player progresses. The game becomes
increasingly difficult with the number of associated struc-
tures increasing, to a maximum of five per spectrum. As
the number of structures increase they also become more
structurally similar. When a player reaches a score of forty,
rounds also become timed, see Figure 3, and the player
must select an answer before the countdown expires. The
amount of time a player gets decreases as rounds progress
An Early Round of the Spectral GameFigure 2Page 4 of 10
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An Early Round of the Spectral Game.

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
to a minimum of ten seconds. So, even spectroscopy
experts will find the game challenging.
Complexity also increases dramatically for the C-13 spec-
tra where the number of carbon atoms in all of the struc-
tures is made equivalent to the number of carbon atoms
present in the correct structure. This can be confusing
until the player takes issues other than chemical shift into
account: symmetry, peak intensity related to nature of car-
bon nucleus and so on.
The game continues until the player gets a spectrum vali-
dation wrong. At that point the player is given their per-
which allows for direct score comparison amongst mem-
bers of the same group.
Crowdsourced curation
There may be a number of reasons that the player may get
the spectrum assignment wrong. The user may simply not
have the skills to perform the validation correctly and we
have provided a wiki[33] of spectroscopy resources for
players to brush up on their spectroscopy skills. Alterna-
tively, the spectrum uploaded to ChemSpider itself may
be wrong and incorrectly associated with a structure. One
of the side benefits of the Spectral Game is the examina-
tion of the data and reporting of potential issues to the
Later rounds become timed and have more structures to choose fromFigure 3
Later rounds become timed and have more structures to choose from.Page 5 of 10
(page number not for citation purposes)
formance relative to the list of both recent and top players.
The game also allows players to associate with groups
hosts of the game. As players progress through the game
they can flag spectra initially displayed in reverse and

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
leave comments associated with each of the spectra and
curators on ChemSpider can review the data and take the
appropriate actions. The percentage of time that a spec-
trum is matched correctly is also recorded giving a meas-
ure of how "difficult" the spectrum is to interpret. Website
analytics show that within the last two months 3,434
unique visitors from 68 countries have combined to
examine the spectra over 55,000 times as they played the
game. Such crowdsourced curation efforts have resulted in
the deletion or re-association of certain spectra from the
database, have allowed the curators to re-reference the
spectra or remove solvent peaks which were dominating
the spectra to the point that compound resonances were
not visible and have allowed the curators to add annota-
tions to the spectra regarding the presence of impurities.
An interface has been provided to ChemSpider curators to
quickly review comments on individual spectra and link-
through to ChemSpider to review, edit as appropriate and
then remove the flags from the Spectral Game, see Figure
4. As a result of the Spectral Game, the quality of spectral
data on ChemSpider has improved significantly with 3
spectra being removed from the database and over a
dozen being processed to re-reference and remove solvent
peaks. An additional side benefit is that the game has
encouraged additional deposition of spectral data to the
ChemSpider database thereby benefiting the chemistry
community as a whole, not just the players of the Spectral
Game.
The spectral game in second life
The Spectral Game was adapted to the multi-user virtual
environment of Second Life by bringing together three
tools[34]. First, we used the Orac molecule rezzer[35], a
Second Life molecule building tool that takes SMILES,
InChIs or InChiKeys and converts them to conformation-
ally reasonable 3D structures. Second, we scripted a
JCAMP spectrum viewer that allows interactive zooming
and integration of desired regions via chat in Second Life.
Finally, we used Open Data spectra from ChemSpider.
The game begins by clicking on the spectrum display
board. A spectrum then appears with several molecules in
the surrounding area, see Figure 5. The player can zoom
into any area of the spectrum by typing a command such
as "zoom 1.2–2.5", which specifies the desired ppm
range, in the chat box. By clicking on the correct molecule
the player scores 2 points and gets another spectrum to
analyze. Clicking on an incorrect molecule will cause the
player to lose one point. When all spectra have been proc-
Spectral curation interfaceFigure 4Page 6 of 10
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Spectral curation interface.

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
essed (a typical number is 5) the player is given their per-
formance status in a list of top players. The game can also
be terminated at any time by typing "quit."
In class assessment
The Spectral Game was evaluated in one of the author's
(JCB) undergraduate Organic Chemistry classes
(CHEM242 at Drexel University) during the winter 2009
term[36]. Both the web and Second Life versions were
used in different ways.
Workshops where the instructor led the class discussion
while projecting the web version of the game were useful
for a larger number of students, especially when students
had just started learning to analyze spectra. Some IR and
C NMR spectra were analyzed this way but the majority
were H NMR. A class discussion would evolve about the
key differences between the expected spectra of the mole-
cules on display and then the instructor could zoom into
relevant regions to explore those details. In this way, with-
out any planning, all of the key concepts in the course
relating to NMR were repeatedly reviewed. When the
opportunities arose, simple coupling patterns, peak shifts,
symmetry and diastereotopic groups were highlighted.
A main advantage of the Spectral Game compared to text-
book problems is that real-world spectra were made avail-
able. Large solvent peaks (such as HOD at 4.8 ppm), peak
distortions, overlapping peaks in complex coupling pat-
terns and impurities were pointed out and the students
were shown how to address this. Since the spectra are ran-
dom, the instructor does not know ahead of time which
spectra and molecules will be presented. This means that,
on occasion, the instructor may not be able to solve the
problems based on simple heuristics taught in class. This
a working chemist might use in practice. We believe that
such discussion is essential to help train students for real
world research.
The game was also used individually by students. During
class workshop time the instructor could circulate to assist
students sequentially. Students were also encouraged to
play the game from home by offering a prize for the top
score during competition periods lasting about a week
each. Two molecular model kits and a textbook were given
out over the course of the term. Players can specify a group
when logging in to play and this makes it easy to view the
high scores within the class or compared to all the people
from around the world playing. As noted by others, com-
petition can be highly motivating for some students[10].
Because it requires more time to set up and demonstrate,
the Second Life version was not used as much as the web
version during the course. The ability to view molecules in
3D in Second Life is an advantage, especially for bridged
cyclic structures. However, the main advantage of Second
Life is the ability of students to interact with others in ava-
tar form, whether it be other students in the class, the
instructor or people from around the world[37]. This type
of networking is not yet possible with the current web ver-
sion of the game.
2D spectral game
Obtaining high quality 2D NMR open data sets is not as
easy as finding 1D data. Fortunately, one of the authors
(AJW) had been involved previously in a study involving
automated versus human validation of 1D and 2D NMR
data sets[38]. The paper describes a method for structure
validation based on the simultaneous analysis of a 1D H
NMR and 2D 1H-13C single-bond correlation spectrum
such as HSQC or HMQC. When compared with the vali-
dation of a structure by a 1D HNMR spectrum alone, the
advantage of including a 2DHSQC spectrum in structure
validation is that it adds not only the information of 13C
shifts, but also which proton shifts they are directly cou-
pled to, and an indication of which methylene protons are
diastereotopic. Using multiple real-life data sets of chem-
ical structures and the corresponding 1D and 2D data, it
was possible to unambiguously identify at least 90% of
the correct structures in an automated fashion. ACD/Labs
provided us with the 30 sets of 1D and 2D spectra pre-
sented in the publication together with the pairs of correct
and incorrect structures. We used these data in a 2D NMR
Spectral Game for users to start to learn how to use the
combined information available from both 1D H1 and
2D HSQC data for identifying the correct structure. The
development of this game has required the development
of a new tool for visualizing 2D NMR spectra on the web
The Spectral Game in Second LifeFigure 5
The Spectral Game in Second Life.Page 7 of 10
(page number not for citation purposes)
tended to happen more with carbohydrate derivatives.
This was an opportunity to discuss other techniques that
(described below) and requires the player to use the H1
NMR spectrum in the standard JSpecView applet together

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
with the 2D data display to interrogate the data and
decide on the most appropriate match.
Interactive 2D spectrum viewer
Multi-dimensional spectral data files lack a standardized
format and are usually several megabytes in size. This
poses problems for displaying interactive 2D spectral data
on webpages. Lacking an Open Source viewer, websites
spectrum viewer. The viewer is based on the Open Source
flot[39] JavaScript library which allows for the interactiv-
ity – zooming of both the interior and side 1D spectra and
updates of ppm values, see Figure 6. All this is achieved
client side.
The data displayed in the 2D Spectrum Viewer is extracted
from images of 2D spectral data using GD[40], a php
Interactive 2D Spectrum ViewerFigure 6
Interactive 2D Spectrum Viewer.Page 8 of 10
(page number not for citation purposes)
usually display static images of spectral data. These issues
resulted in us developing an Open Source interactive 2D
graphics library. A php script downloads an image from a
web server, in our case from ChemSpider, extracts the data

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
pixel by pixel and exports the data in a format that can be
read by the 2D Spectrum Viewer. The php code can be
integrated with the viewer creating a dynamic 2D spec-
trum viewer that can be deployed in web pages, see Figure
7.
Conclusion
New technology has great potential to benefit education.
From this example, it should be clear how important
Open Data can be for stimulating rapid re-mixing for edu-
cational examples. As more data become available, the
usefulness of the Spectral Game and similar initiatives will
become even greater.
Availability and requirements
 Project name: Spectral Game
 Project home page: http://spectralgame.com
 Operating system: Web Based – Platform independ-
ent
 Programming languages: HTML, PHP, JavaScript,
JAVA (JSpecView)
 Other requirements: Java 1.5
 License: MIT License (HTML, JavaScript) – GNU
Lesser General Public License (JSpecView).
All files and related documentation are available from the
project website http://spectralgame.com.
 Project name: 2D Spectrum Viewer
 Project home page: http://spectralgame.com/2d/
2dviewer/
 Operating system: Web Based – Platform independ-
ent
 Programming languages: PHP, JavaScript
 Other requirements: GD, flot
 License: GNU Lesser General Public License.
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
The Spectral Game was conceived by JCB and ASIDL.
ASIDL wrote the code. AJW contributed spectra and struc-
The Same 2D Spectrum: Static PNG (left) and Interactive 2D Spectrum Viewer (right)Figure 7
The Same 2D Spectrum: Static PNG (left) and Interactive 2D Spectrum Viewer (right).Page 9 of 10
(page number not for citation purposes)
ture images from ChemSpider and curates content. RJL
modified JSpecView to remove title information from

Journal of Cheminformatics 2009, 1:9 http://www.jcheminf.com/content/1/1/9
Open access provides opportunities to our
colleagues in other parts of the globe, by allowing
anyone to view the content free of charge.
Publish with ChemistryCentral and every
scientist can read your work free of charge
W. Jeffery Hurst, The Hershey Company.
available free of charge to the entire scientific community
peer reviewed and published immediately upon acceptance
cited in PubMed and archived on PubMed Central
yours you keep the copyright
being viewable. JCB tested the game in an undergraduate
organic chemistry class and provided prizes for contests
involving gameplay. The 2D Spectral Game and 2D Spec-
trum Viewer was conceived by AJW and ASIDL. ASIDL
wrote the code. AJW contributed 1D and 2D spectral sets
and structure images from ChemSpider.
Acknowledgements
The spectral data on ChemSpider have been deposited by multiple users
and we acknowledge specific ChemSpider users for their depositions: Dr
Chris Singleton and Heinz Kolshorn. Data were also sourced from the web-
sites of Pacific Lutheran University, the NIST Webbook and software pro-
viders and provided by ACD/Labs.
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