Archive for August, 2012

Do you know about Natural Product Updates?

Natural Product Updates (NPU) gives you the molecules involved in key developments in natural product chemistry. Thanks to our work in interpreting what chemists mean, not just what chemists draw, ChemSpider now links to NPU’s data for 13800 natural products since 2005, of which 7800 are brand new to ChemSpider.

Where ChemSpider has information on a compound in NPU you will see the image above, as in, for example, calothrixin B. This is a link to NPU page on the RSC Publishing Platform.

Soon we’ll be integrating more of our graphical databases into ChemSpider. Watch this space!

For those of you who were interested by our previous blog post ‘Publish to ChemSpider’ ELN plugin generates elnItemManifest, and are at ACS Fall 2012 in Philadelphia, more details about this project will be described by Dr Simon Coles (Southampton University) in his oral presentation “Towards publishing semantic descriptions of Electronic Laboratory Notebook records” (paper ID: 17061 and final paper number: 90) in the “CINF: Division of Chemical Information division”, and “Herman Skolnik Award Symposium” session, on August 21, 2012 from 10:50 am to 11:05 am at Philadelphia Marriott Downtown, Room: 302/303.

If you are at ACS Fall 2012 don’t forget the other ChemSpider at ACS Fall 2012 in Philadelphia events.

You might not think so, but you’re very good at taking a two-dimensional drawing and converting it into a three-dimensional shape in your head. No, really, you are.

Fig. 1. Galactose in perspective.

Take the drawing of galatose in Fig. 1. Even if you’re not a chemist, you can tell which bits of the ring are at the front and at the back, which bonds point up and which bonds point down. If you actually are a chemist, you’ve been trained to apply this geometrical intuition to work out what’s going on at each of the five stereocentres.

However, if you ask the InChI algorithm about the stereochemistry of this molecule, it’ll say that there is no stereochemistry in there and you’re looking at a stereoless description of which atom is attached to which. Since we use the InChI algorithm to say whether two records describe the same molecule, this puts us in a quandary, and there are thousands of entries in ChemSpider that come from just such a drawing and hence lack stereochemistry.


As part of the Royal Society of Chemistry, the ChemSpider team likes to get involved with all of the other projects that are going on within the RSC, and we were really excited to be asked to provide our expertise to the SpectraSchool resource. This HE STEM funded program provides a range of resources to help in the understanding of the principles and practice of spectroscopy and spectroscopic methods.
SpectraSchool brings together Spectroscopy resources, an Introduction to Spectroscopy*, Interactive Spectra and the Spectroscopy in a Suitcase scheme which affords school children the chance to use modern spectroscopic equipment in their classroom.

The SpectraSchool resource was originally developed with the University of Leicester who collected and assigned many of the spectra that displayed within the site. Now that SpectraSchool is part of Learn Chemistry we have helped to integrate new features, including a new HTML 5 based spectrum viewer that provides interactive display of spectra. The fact that this is based on HTML 5 means that the spectrum can be viewed on just about any device that has a modern browser (eg, computers, tablets, phones or even touch screen tvs).

A student visiting the site has the ability to zoom in on peaks and to see which features of a chemical structure give rise to a particular peak in a spectrum; by selecting either a peak or a particular part of the structure (see the highlighting of the methyl group in the structure of caffeine below and the corresponding peak in the adjacent 1H NMR spectrum).

SpectraSchool and Chemistry in the Olympics are great examples of the RSC’s new microsites which bring together lots of great resources and tools in a fresh and exciting interface.

Take a look at SpectraSchool and LearnChemistry today we welome feedback through the in page feedback links or connect with us and other chemistry educators in the Talk Chemistry forums. Why not start exploring this great (free) educational resource today?



* The Introduction to Spectroscopy was developed in collaboration with the University of Cardiff

Once again the RSC will be attending the American Chemical Society’s Fall meeting which will be held in Philadelphia, Pennsylvania, August 19-23, 2012, where the RSC stand will be located at booth 701.

Several members of the ChemSpider team will be attending the conference; both to give presentations and also to chat/answer questions on the booth. If you are attending the conference please drop by and say Hello and ask any questions that you have (you might even be able to get a free coffee – available on a first-come first served basis from 11 am on both Monday and Tuesday). We will also be running an exciting ChemSpider competition to coincide with the conference. You can get details from our Booth #701, or by checking out the ChemSpider blog.

There will be two key ChemSpider events in Philadelphia:
A special On-Stand demo – Monday 20 August, 11 am, Booth 701
“ChemSpider and You: A workshop exploring how ChemSpider can help you find chemical information” – A 2 h workshop for both newcomers to ChemSpider and experienced searchers alike. 10am-12pm Tuesday 21 August, Exhibit Halls A-B, Workshop Room 2 (You can register for the workshop via the conference website – we will try and accommodate anyone who just turns up on the day.)

In addition members of the ChemSpider team are giving a number of talks, including some early glimpses of exciting new tools that we are working on. The presentations are listed below – for more details including the abstracts for each of the talks see the Technical program.

‘Mining public domain data as a basis for drug repurposing’, Philadelphia Marriott Downtown, Room 302/303, Sunday 19th August, 4.15PM – 4.40PM

‘Putting chemistry into the hands of students – chemistry made mobile using resources from the Royal Society of Chemistry’, Pennsylvania Convention Center, Room 109B, Sunday 19th August, 10.50AM – 11.10AM

‘Feeding and consuming data to support Open Notebook Science via the ChemSpider platform’, Philadelphia Marriott Downtown, Conference Room 307, Monday 20th August, 2.05PM – 2.30PM

‘Approaches for extraction and “digital chromatography” of chemical data – a perspective from the RSC’, Hilton Garden Inn Philadelphia, Salon D, Monday 20th August, 2.30PM – 2.55PM

‘Delivering an online service for validating and standardizing chemical structure files using the ChemSpider platform’, Philadelphia Marriott Downtown, Franklin Hall 6, Tuesday 21st August, 9.15AM – 9.35AM

‘ChemSpider compound database as one of the pillars of a semantic web for chemistry’, Philadelphia Marriott Downtown, Grand Ballroom Salon H, Tuesday 21st August, 4.55PM – 5.10PM

‘How can the International Chemical Identifier (InChI) be extended to non-trivial chemicals?’, Philadelphia Marriott Downtown, Franklin Hall 6, Thursday 23rd August, 9:35AM – 9.55AM

‘Serving up and consuming community content for chemists using wikis’, Philadelphia Marriott Downtown, Franklin Hall 6, Thursday 23rd August, 9.55AM – 10.15AM


We look forwards to seeing you at the conference!

ChemSpider has become one of the worlds primary online resources for finding data, information, links, images, spectra..and on and on…about “chemicals”. Building a database of over 28 million chemicals that grows in some way in content, functionality and richness on a daily basis is, to say the least, a lot of work. But our cheminformatics team here at the RSC is not scared of work. We like it! So when we decided that it was time to enhance our efforts around the management of chemical reactions to move from ChemSpider SyntheticPages to a database of chemical reactions containing 10s if not 100s of thousands of reactions the question was how. What software platform would we use? Where would we source reactions? What functionality would we need to roll out as an early display of capability to entice users to test it out, give feedback and, ultimately, get involved. We made those decisions and we will be showing off the results of our project “ChemSpider Reactions Database” (yes, we’re very creative with our project titles aren’t we!!!) at the Fall ACS in Philadelphia.

If you want to learn what we are up to in regards to chemical reactions come and visit with us at the ACS booth…we’ll show an early view of over a quarter of a million reactions in an online, free to access database. We’ll chat about some of our future plans and hopefully engage you in a discussion about whether or not you would be willing to contribute reactions to the database. Wouldn’t it be good if we can provide to synthetic chemists a platform for accessing and managing reactions as we have done for chemicals. Of course, seamlessly integrated and platform independent…served up by the latest web technologies and mobile-enabled. What the future could look like… exciting times!

ChemGoggles? What on earth is ChemGoggles? Is this a pair of safety specs for chemists? No…what would be the fun, and the cheminformatics (!!), in that? ChemGoggles will be shown at the ACS meeting in Philadelphia in a couple of weeks and will be a very early display of our venture into the development of an Android app for “photographing” an image of a chemical and searching the ChemSpider database. It will be a matter of finding an image of a chemical (paper, publication etc), taking a photo using an Android device, using structure recognition software to convert the image to a chemical and then searching ChemSpider. It will be imperfect, an early version, but nevertheless a tantalizing display of some of the new directions we are presently taking at the Cheminformatics group here at RSC.

Chemistry is complex. Anybody who has been involved with the creation of electronic datafiles containing thousands of chemical compounds and associated data (chemical names, properties etc) will tell you that errors creep in. ChemSpider has >28 million unique chemical entities and these have been sourced from many different places/groups/individuals. Some of these have been deprecated as we have determined, both manually and algorithmically, that the data are in error. Over the years we have learned a lot about data quality and ways in which algorithms can be applied to data prior to deposition on ChemSpider.

Some obvious structure-based errors that can be checked for would include: hypervalency (e.g. pentavalent carbons), charge imbalance (a compound has no neutralizing counterion for example), absence of stereochemistry (e.g. a compound with 12 possible stereocenters only has one assigned). There are many other such errors that can be detected algorithmically. It’s the old adage of why apply a human to what a computer can fix. With this in mind we have been working on a system called the ChemSpider Validation and Standardization Platform (CVSP for short). This system will serve multiple purposes. It will be one of the foundation blocks for checking structure-based data for our publications (i.e. catch bad chemistry before it is published!), it will be used for validating chemistry for our databases (Natural Product Updates, Methods in Organic Synthesis and Catalysts and Catalyzed Reactions), it will be used to check and validate depositions going into ChemSpider, it will serve data related to the Open PHACTS project  and it will serve the community by providing an online website where you can upload your own SDF files (and other file formats in future) to validate the structures.

I won’t go into detail here about all of the functionality and capability of the system as we will discuss this in further detail on this blog. However, we will be unveiling the system in its present form at the ACS meeting in Philadelphia. Come along and meet some of the team involved in building CVSP and give us your feedback!