ChemSpider: An Online Chemical Information Resource
ABSTRACT ChemSpider is a free, online chemical database offering access to physical and chemical properties, molecular structure, spectral data, synthetic methods, safety information, and nomenclature for almost 25 million unique chemical compounds sourced and linked to almost 400 separate data sources on the Web. ChemSpider is quickly becoming the primary chemistry Internet portal and it can be very useful for both chemical teaching and research.
- SourceAvailable from: Yuri TsentalovichExperimental Eye Research 01/2014; · 3.03 Impact Factor
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ABSTRACT: This work is the first comprehensive report on the quantitative metabolomic composition of the rat lens. Quantitative metabolomic profiles of lenses were acquired with the combined use of high-frequency nuclear magnetic resonance (NMR) and high-performance liquid chromatography with high-resolution mass-spectrometric detection (LC-MS) methods. More than forty low molecular weight compounds found in the lens have been reliably identified and quantified. The most abundant metabolites in the 3-month-old Wistar rat lens are taurine, hypotaurine, lactate, phosphocholine and reduced glutathione. The analysis of age-related changes in the lens metabolomic composition shows a gradual decrease of the content of most metabolites. This decrease is the most pronounced between 1 and 3 months, which probably corresponds to the completion of the lens maturation in one-month-old rats and to the high rate of the young lens growth. The enhanced levels of tryptophan, tyrosine, carnitine, glycerolphosphate, GSH and GSSG were found in lenses of senescence-accelerated OXYS rats; for some metabolites, this effect may probably be attributed to the compensatory response to oxidative stress.Experimental Eye Research 06/2014; · 3.03 Impact Factor
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ABSTRACT: The increase in the volume and heterogeneity of biomedical data sources has motivated researchers to embrace Linked Data (LD) technologies to solve the ensuing integration challenges and enhance in-formation discovery. As an integral part of the EU GRANATUM project, a Linked Biomedical Dataspace (LBDS) was developed to semantically interlink data from multiple sources and augment the design of in silico experiments for cancer chemoprevention drug discovery. The different components of the LBDS facilitate both the bioinformaticians and the biomedical researchers to publish, link, query and visually explore the heterogeneous datasets. We have extensively evaluated the usability of the entire platform. In this paper, we showcase three different workflows depicting real-world scenarios on the use of LBDS by the domain users to intuitively retrieve meaningful information from the integrated sources. We report the important lessons that we learned through the challenges encountered and our accumulated experience during the collaborative processes which would make it easier for LD practitioners to create such dataspaces in other domains. We also provide a concise set of generic recommendations to develop LD platforms useful for drug discovery.13th International Semantic Web Conference, Riva Del Garda, Italy; 10/2014
ChemSpider: A Hub for Online Chemical Information Resources
*ChemSpider, Royal Society of Chemistry, U.S. Office: Wake Forest, NC-27587
1. Internet-based chemistry
The World Wide Web continues to have an expanding and profound effect on providing access to
chemical information. A chemist may wish to know a variety of information about a given
chemical compound including physical and chemical properties, molecular structure, spectral
data, synthetic methods, known reactions, safety information, and systematic nomenclature and
chemical names. In the past, having access to this variety of information required a small library
of different reference works, since no one resource contained all this data. This was problematic
both in terms of cost and physical space for storage. Now there is a single web site that not only
provides all this information for millions of compounds but also is free. This website is the Royal
Society of Chemistry’s ChemSpider [1, 2].
As a cheminformatician interested in integrating together large amounts of data, specifically
structure-based data, spectral data and large quantities of physicochemical data, the author,
together with a number of software developers decided to pursue the challenge of integrating
together web-based chemistry data. Using a nominal infrastructure of just three computer servers
and developing bespoke software using Microsoft technologies (specifically a .NET architecture
using a SQL server database) ChemSpider was released to the community as a platform
containing >10.5 million unique chemical structures sourced from the PubChem database 
integrated to a small number of online resources. The original system included both structure and
rudimentary substructure searching. Within a few months of release the ability for users to
register and upload chemical compounds and annotate and curate data was introduced. The
amount of data online continued to grow with depositions from chemical vendors and other
online chemical databases and reached around 20 million chemicals. Within a period of three
years the ChemSpider platform had developed a significant level of popularity with the
community and was acquired by the Royal Society of Chemistry .
Today ChemSpider is a free, online chemical database offering access to physical and chemical
properties, molecular structures, spectral data, synthetic methods, safety information, and
nomenclature for over twenty six million unique chemical compounds, sourced and linked out to
almost four hundred separate data sources on the web. ChemSpider is fast becoming the primary
chemistry internet portal and it can be very useful for both chemical teaching and research.
ChemSpider is not just a search engine layered on terabytes of chemistry data but is also a
crowdsourcing community for chemists. Registered users can enter information and annotate and
curate the records. The requirement to register and login is to prevent anonymous acts of
vandalism. The chemical community has been forthcoming in adding information including new
chemical structures, associations between structures and publications, addition of analytical data
such as spectra and the curation of chemical identifiers and property data.
ChemSpider has been described as the Google for Chemistry and a Wikipedia for chemists. By
aggregating data and linking it together using a chemical structure as the primary record in the
database, ChemSpider has been able to link together Wikipedia , PubChem , ChEBI
(Chemical Entities of Biological Interest)  and KEGG (The Kyoto Encyclopedia of Genes and
Genomes) , chemical vendors, a patent database, and both open and closed access chemistry
journals. Where possible, each chemical record retains the links out to the original source of the
material thereby associating a microattribution. These links allow a ChemSpider user to source
information of particular interest, including where to purchase a chemical, as well as toxicity and
metabolism data and so on. Aggregating that level of connected information via a classical search
engine, like Google, would be very time consuming.
ChemSpider has a number of advantages over a simple Google search. The variety of information
about a compound provided at ChemSpider is hard to match on any other free web site. The data
continue to be validated, updated and expanded by practicing chemists. ChemSpider provides
links to many other online sources for further information. This plethora of links now includes
Google Books, Scholar and Patents, Microsoft Academic Search, RSC Databases, Books and
Publishing website and an ever-increasing number of government, commercial and academic
(http://www.chemspider.com/4445428) in ChemSpider. The entire record spans multiple pages
including links to patents and publications, pre-calculated and experimental properties and links
to many data external data sources and informational websites.
1: The header of the chemical record for Domoic Acid
ChemSpider aggregated over 25 million unique chemical entities in just over 3 years. New
additions to the database are made daily especially since it is now integrated to the RSC
publishing process whereby new compounds identified in prospected RSC articles are deposited
and released to the community as the article is published. Many of the compounds in the current
database have already been curated, and the process is ongoing. In comparison the Chemical
Abstracts Service (CAS), which has been in the business of aggregating chemistry-related data
for over a century in order to create the CAS registry, recorded its 50 millionth chemical structure
in 2009 .
Searching the web using classical search engines is less useful than ChemSpider since these
services do not provide structure-based searching of the internet nor do they systematically
organize data curation. The closest comparison in terms of validated and crowdsourced
contributions to the domain of chemistry are the chemical pages in Wikipedia; however,
Wikipedia has information on far fewer compounds and supports only text searching not structure
The ChemSpider “web services” provide programmatical access to ChemSpider and allows for
instrument vendors to utilize the data for the purpose of structure identification. This opportunity
in particular is being used for the purpose of compound identification by mass spectrometry .
The data are also available to the Open PHACTS project , a project funded by the Innovative
Medicines Initative , and ChemSpider is one of the key particpants in the project. As
ChemSpider continues to expand in scope, capabilities and data the site is likely to become the
dominant free online resource for chemists especially as it supports a number of additional
projects as discussed below.
3. Synthetic Reactions on ChemSpider
The recently added ChemSpider SyntheticPages  provides a source of online data regarding
chemical synthesis procedures. This database is created by the community, for the community.
Chemists populate the online database with one or more of their chemical reactions outlining how
to perform a reaction. ChemSpider SyntheticPages grows as the community continues to
contribute content. What type of reactions suit? The reactions could be for a new compound or a
known compound from the literature or from an authors’ own publications. Also, it does not
matter if a similar prep is already in the database. There is a benefit to submitting as early stage
researchers should realise that potential employers have free and direct access to examples of
their work, including the time-consuming "starting material" preps that perhaps did not make it
into the papers or thesis. It is fast to submit an article - certainly less than an hour from start to
finish, and probably a lot less if the author already has the text in electronic format for a report.
The kudos of being a part of a database hosted by the RSC should not be underestimated and the
issuance of a permanent digital object identifier (DOI) link provides curriculum vitae value. The
value of the database will grow exponentially with an increasing number of pages covering an
increasingly broad array of chemical syntheses.
Figure 2: A ChemSpider SyntheticPages article regarding a hydrogenation process
4. Making Chemistry Mobile
As there has been an unprecedented growth in new ways to access online information using
mobile devices [14, 15] (for example, iPhones and iPads using the iOS operating system and
Android devices) it made sense to deliver access to ChemSpider and its related projects on such
platforms. Initially the ChemMobi  application from Symyx (now part of Accelrys) was
developed using the ChemSpider web services. This was soon followed by mobile websites
versions of both ChemSpider and ChemSpider SyntheticPages. Numerous other iOS apps then
made use of the web services. The Royal Society of Chemistry contracted the development of a
ChemSpider Mobile app  and it has since been downloaded many thousands of times and
runs on both iPhone and iPad.
Figure 3: The ChemSpider website optimized for mobile devices. These screen captures obtained
from an iPhone.
5. Additional projects integrating ChemSpider
An increasing array of projects are now being supported by ChemSpider as they serve up content
via the programming interface. ChemSpider is already becoming an important resource for
teaching, learning, and research. Specifically, the spectroscopic data, over 3000 spectra in total,
are the basis for the Spectral Game, which has already been used by over 10000 students .
This game allows students to learn how to interpret NMR spectra by validating either H1 or C13
spectra against two or more structures. Increasing in complexity as the game progresses by
increasing from 2 to 5 structures to choose from to match with the spectrum, the game has been
played by thousands of students from almost a 100 different countries.
Other RSC resources have recently been unveiled utilizing integration to ChemSpider data. These
include the Learn Chemistry Wiki  and SpectraSchool  to help in the education of
secondary school children. Since ChemSpider offers unrivalled online access to chemistry data
via application programming interfaces such projects will continue to expand in scope and
Figure 4: The Learn Chemistry wiki: a wiki environment utilizing ChemSpider data on its
ChemSpider is presently one of the richest sources of chemistry data available online. It has been
recognized with a number of awards in 2010 including the Bio-IT Best Practices Award for
community service  and the ALPSP  and i-Expo  awards for innovation. The
ChemSpider database is the foundation platform for a series of related websites and applications
and presently serves many hundreds of thousands of requests every day. ChemSpider is likely to
increase in prominence and impact in the coming years as the quantity of data grows and the
diversity of integrated data sources increases.
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