ChemSpider Blog

The free ChemSpider mobile app developed in collaboration with Alex Clark (innovator of the Mobile Molecular DataSheet, Reaction101 and Yield101) is now available for download from the iTunes store! The full details of the app, and some associated screenshots, are outlined on the SciMobileApps wiki here. A brief overview is given below…

“ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page. Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the Royal Society of Chemistry.”

We will look at developing an Android app for ChemSpider, taking into account what we learn from the early use of the iOS Mobile app.

A screencast of the functionality of ChemSpider Mobile is available below.

Only two days until the start of this year’s Fall ACS meeting in Denver. The ChemSpider team is busy preparing for the meeting, packing bags, polishing talks and honing workshop skills.

Please drop by and say “Hi!”

We’d like to repeat our invitation to everyone at the conference to drop by the RSC booth (Booth 1100). Where, of course you can chat with the ChemSpider team, get a quick demo (and find out more about our latest features), pick up our hot-off-the-press User Guide or scoop some exclusive ChemSpider goodies!

To celebrate the release of the new iPhone/iPad app* we have a limited number of covers for 3G and 4G iPhones as well as iPads

*The app itself is free to download from the AppStore.

You can also find out about lots of other things that the RSC does: from publishing books and journals to the promotion of chemistry worldwide. We’ll also have lots of information on our new e-membership option, which is making its’ debut at this meeting. Also keep an eye out for members of our Editorial staff from journals including: OBC, MedChemComm, PCCP, Soft Matter and RSC Advances, who will be scouring the conference in search of lots of new and exciting research.

Natural Product & Synthetic Chemists

I’d like to make an extra special invitation to any Synthetic chemists and Natural products chemists – from PhD students to Professors (please pass this on to all your friends and colleagues who will be at the meeting). The ChemSpider team really wants to hear about your research. Tell us about your latest publication or the work that you are most proud of, and we can make sure that your key compounds from these publications are in ChemSpider, on a platform freely accessible to chemists everywhere. If you are more interested in methodology you shouldn’t feel left out – ask us about ChemSpider Synthetic Pages.

ChemSpider related talks and workshops

Antony Williams (most-definitely the hardest working man I know) is giving a number of talks and workshops (details below) which are sure to be entertaining as well as thought-provoking and will be well-worth squeezing into your schedule.

We look forward to meeting you.

“Aligning scientific expertise and passion through a career path in the chemical sciences”

Colorado Convention Center, Room: 110, Sunday 28^th August 2011, 1.40PM – 2PM

“Chemistry in the hand: The delivery of structure databases and spectroscopy gaming on mobile devices”

Colorado Convention Center, Room: 110, Monday 29^th August 2011, 9.05AM – 9.35AM

“ChemSpider: Does community engagement work to build a quality online resource for chemists?”

Colorado Convention Center, Room: 110, Tuesday 30^th August, 10.10AM – 10.50AM

“An Introduction to ChemSpider – A Combination Platform of Free Chemistry Database, Free Prediction Engines and Wiki Environment”

Colorado Convention Center, Room 503, Wednesday 31^th August 2011, 08.30AM – 11AM

“Structure representations in public chemistry databases: The challenges of validating the chemical structures for 200 top-selling drugs”

Colorado Convention Center, Room: 110, Wednesday 31^st August 2011, 10.45AM – 11.05AM

As I mentioned in my blog post a few weeks ago, over the last few months we have been hard at work trying to improve how we organise all of the information and features that can be found when you view a ChemSpider record. And now you can see the fruits of our labour.

We hope that you find the changes we’ve made give you a better and easier user experience. While we think that the changes will be clear and intuitive, I’d like to highlight a few key features in my next few posts.

Inline help

When you look at compound pages and other useful pages, you should now see a lot more Question mark symbols dotted throughout the pages. We’ve called this approach inline help: rather than giving you an in-depth help resource on a separate page or as a PDF, it is much more useful to have a little snippet of help right at the point in the page where you need it. Clicking on the question mark symbol should bring up a yellow text box with short guidance (where there is a need to provide more complete help, we’ll provide a link to a page which contains much more detailed information). Of course, do let us know if you have any suggestions for improvements to the help text.

Default infobox ordering*

Many users indicate they most often look for names (or name-structure associations), physical properties and spectral data, so we have put this information at the beginning of the record. Now when you come to a record, by default the Names infobox is the first box listed followed by the Properties, Spectra and the Articles infoboxes.

None of your favourite infoboxes have been removed (in fact we’ve created some new ones – see later). If you don’t like the default order, it is easy to change the ordering of the infoboxes by clicking on the titlebar and dragging them up or down the record. ChemSpider will remember your order and will use this for all future visits to the site from that PC (in the same browser/profile).

*If you have visited the site before ChemSpider will remember your previous settings. If you want to see the new default order you will need to clear your browser history or delete the ChemSpider cookies that are saved in your profile.

New infoboxes: Searches and Chemical Vendors

ChemSpider has always had great features, for instance:

The Similar Search – that allows you to find records for compounds that have the same skeleton, but have different stereochemistry or isotopic labels

The ability to load the structure from the current record into a structure search, so that you are able to modify it and construct a new search.

However, this hasn’t always been made very clear, in our redesigned compound page we have aimed to make these powerful search tools easier to discover and understand.

The Searches Infobox

Now you can find these all together in the Searches infobox – along with our Google Scholar custom queries which allow you to perform one search across publications using all of the validated synonyms (saving you from having to perform many separate searches for individual synonyms). We also help you to perform ‘structure searches’ of Google (in the form of an InChIkey search).

The Chemical Vendors Infobox

We’ve also created an infobox  just to display Chemical vendor information, so that it is much quicker to find if the compound in the record is commercially available.

In my next post I’ll finish off discussing the improvements that we’ve made to the site. But of course, if you have any comments or questions about the features I’ve discussed here, please leave a comment below, or send an email to the ChemSpider inbox.

There are multiple structure drawing editors on ChemSpider. And we could add more! For example, one we don’t have is JSDraw and we also don’t have the ChemDoodle components in place, yet, though I am VERY impressed with the spectral display components that are integrated into the SpectralGame that ChemSpider supports. Compared to just a few years ago there is now an abundance of structure drawing editors in the form of Applets and JavaScript Editors. So many in fact that it can be confusing to the user. The user in reality should not worry about the technology behind the editor. It should be quite simple, especially when it comes to something as simple as the editor being the interface to querying ChemSpider. It should display perfectly on the browser(s) and platform(s) used by the user, it should be intuitive and easy to use (preferably without having to resort to reading help files), and essentially, it should “do what I want it to do”. Not at all an unreasonable list of demands right? Not so easy to deliver on mind you!

On ChemSpider we have multiple structure drawing editors. If you visit this page and open up the selection window by using “Click to Edit” you will see the editor below and, underneath the editor shown, a series of editors that you can choose from.

There has to be an order of listing the editors…the listed order is NOT a preferred order from our point of view. Just a list. We have heard feedback from numerous people about their preferred editor. Some live and breath the Java Molecular Editor (JME). Some prefer Accelrys JDraw because they already use Accelrys Draw. Many think that Elemental is a great Javascript Editor.

We are left with a choice….leave all editors (which has a cost in time to support them, keep them updated, tested etc) or reduce the number of editors to just a couple (or three). So, we welcome your input, on this blog post as a comment, or via the survey on SurveyMonkey here. We’d like your input to help steer our decision. Thanks

Previously there was ChemMobi, then there was our implementation of ChemSpider for a mobile browser and then ChemSpider SyntheticPages for a mobile browser. At next weeks’ ACS meeting in Denver we hope that the ChemSpider mobile app developed in collaboration with Alex Clark (innovator of the Mobile Molecular DataSheet, Reaction101 and Yield101) will be available for download from the iTunes store! The full details of the app, and some associated screenshots, are outlined on the SciMobileApps wiki here. A brief overview is given below…

“ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page.

Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the Royal Society of Chemistry.”

An early view screencast of the functionality of ChemSpider Mobile is now available.  New movies showing the details of the app will follow in the near future but this is an early view for interested parties.

We’ve rejigged our data to make searching more reliable.

What have we done?

We’ve regenerated all of the InChIs in the database with version 1.03 of the InChI code.

What does that mean?

The InChI (international chemical identifier) is a short piece of text that describes the structure of a molecule. Each one is generated by a free and open-source computer program, which guarantees that it should be the same and there shouldn’t be conflicting InChIs for the same molecule. You can’t really write them by hand, because they look like this:

InChI=1S/C10H22ClN2O5PS/c1-3-10(9-18-20(2,15)16)12-19(14)13(7-5-11)6-4-8-17-19/h10,12H,3-9H2,1-2H3

ChemSpider is built on InChIs. If two molecules have the same InChI, then they’re the same record in ChemSpider, and if you can’t InChIfy it, you can’t put it in ChemSpider. That’s why we can’t do, for example, polymers yet.

We’re proud to be founder members of the InChI Trust, which supports this critical element in the sharing of chemical compound information.

What does all this mean for ChemSpider?

Because there is an active community supporting InChI who look out for these things, version 1.03 contained some bug fixes which mean that a very small number of the InChIs themselves, only a few dozen out of the whole database, have changed.

• P⁺–O^– bonds and P⁺–S^– are now treated slightly differently. This means that it will be easier to find the exact molecule you’re looking for, regardless of how it’s been drawn. (In principle this will also apply to analogous bonds containing arsenic, selenium, tellurium and antimony, but I can’t see any examples of this in the database.)
• There was a small bug where the InChI generated for a molecule with an azide group in it sometimes varied according to the input drawing. But that doesn’t happen now.

This regeneration has also allowed us to catch and clean up some errors in the data.

What happens next?

Version 1.04 of the InChI code will be released soon. With our new framework for processing large amounts of data we’ll be able to update our InChIs much quicker. The main changes in 1.04 that affect the InChI are to how it handles radical atoms in aromatic rings, nobelium, lawrencium and rutherfordium, so we anticipate that there shouldn’t be very many changed InChIs!

COPIED FROM THE CHEMCONNECTOR BLOG

Unless you have no interest in sports, or have your head under a stone, you will be aware of the fact that the next Olympics will be held in London in 2012. Peter Scott (one of the editors of ChemSpider SyntheticPages) and I were recently discussing how much of a role chemistry plays now in modern sports. I’m a runner, cyclist, swimmer and overall sporting type of guy and depend on wicking materials to keep me cool, nutritional support to get me through my 100-150 mile bike rides in a day, glide stick to “stop me chafing” (ow!) and graphite grease to silence the rattling chain on my bike. In fact it doesn’t matter what sport I am doing it is easy to notice the influence that chemistry has on my improved performance at my tender age of, ahem, just over 40 (and holding, for a while now).

I was reminiscing with Peter that Sir Graham Richards and I were chatting about pyrenes about a year ago and we lamented on how Benzo[CD]pyrene, shown here, looks just like the Olympic rings. There is another rather well known “Olympic molecule” of course, already captured on Wikipedia and named Olympiadane. It looks rather complex to synthesize and personally I think the benzopyrene looks a lot more like the Olympic rings so I attached the synonym Olympicene to it! In fact, if you search ChemSpider using the name Olympicene you will find it.

In a recent discussion about our online crowdsourced database of syntheses, ChemSpider SyntheticPages,(and not distracted at all by the conversation about the Olympics going to the UK next year!!!)  I mentioned again to Peter the molecule Olympicene and he searched ChemSpider to find it. We agreed that it would be fun to know how easy it would be too synthesize it and if it was done it would be a good synthesis to add to ChemSpider SyntheticPages. That was enough to trigger Peter into action and chat with one of his colleagues to see if he can make it.

And so it starts…the trials and tribulations of how to synthesize the chemical Olympicene will be captured on ChemSpider SyntheticPages step by step. We’re not sure how complex a synthesis it will be..time will tell. It will be great to add the analytical data to ChemSpider too as it gets generated..including all the intermediate reaction steps and associated data. ChemSpider and CSSP were designed to support projects like this so it will be a fun story to watch it work through.

If YOU have any thoughts about good synthetic approaches for what seems like a simple molecule post them on this blog. Actually, why not try synthesizing yourself and add your syntheses to SyntheticPages!? Every contribution is issued a DOI for your publication list!

It might be ideal to get a  number of synthetic approaches posted on ChemSpider SyntheticPages and see which one is the best! Watch this space. Also, I’ve set up a Twitter account to capture the progress at @Olympicene. Enjoy!

We will be hosting a training session for ChemSpider at the ACS meeting in Denver. Please register early.

An Introduction to ChemSpider – A Combination Platform of Free Chemistry Database, Free Prediction Engines and Wiki Environment

Where: Colorado Convention Center
Room: 503
When: Wednesday, August 31, 8:30 AM – 11:00 AM

>> Click here to register for this workshop
ChemSpider has become one of the premier free online chemistry resources used by many thousands of chemists around the world every day. Hosting over 26 million unique chemical entities, sourced from over 400 separate data sources, ChemSpider provides access to experimental and predicted data, links to patents and publications and uniquely offers the ability to deposit and share their own data online. With the intention of integrating and curating public chemistry resources for the community ChemSpider encourages participation from chemists around the world. Integrated to Wikipedia, Google Patents, Google Books, Google Scholar and PubMed, as well as to the RSC Publishing platform, ChemSpider provides access to chemistry contained in millions of articles. This training session will provide an overview of searching ChemSpider and will discuss how to deposit data and participate in curating the existing information. We will also provide an overview of ChemSpider SyntheticPages, our venture into providing a community-based resource of semantically enriched synthetic procedures and allowing community peer review. This will be an interactive session and you are encouraged to bring your laptops to work along and ask questions regarding present and future capabilities. ChemSpider is built for the community and we welcome your comments about how to make it better for your needs.

I’m sure that by now everyone has noticed that the ChemSpider homepage design changed just over a month ago. A few features moved around, the Molecules of Interest section was retired and perhaps most significantly the Search box was given a dose of CSID: 5791, becoming bigger and more prominent.

The reason for this wasn’t just to make the site more attractive (though I think it does look ‘prettier’). Our motivation for the change is to deliver a site that makes it easier for users to interact with and understand. And by doing so, hopefully make it quicker and simpler for you to get your tasks done using ChemSpider. The refresh of the homepage is hopefully illustrative of this: We think that as most users come to ChemSpider to search for information – it should be easy to get straight into a search, hence the greater emphasis on this feature.

In the next few days we will release another upgrade to the interface which is centered on making it easier to understand the data presented in the compound Record View pages. I’ll post a blog entry dealing with some of the key features in the next few days.

The development of ChemSpider is an ongoing process, and we are aware that even after this upgrade there will be aspects of the compound Record View pages that will need more work (and also other parts of the site that still need development). It’s not going to be easy: ChemSpider brings together a rich and varied set of data from a large number of sources – this poses many challenges. We also realise that there are many different tasks that each of you – as users – want to perform, and it is always going to be difficult to reconcile all of the different opinions/needs.

However, we are trying to make the site better for you. And therefore, we’d really like to know your opinions on the changes (please test new features for a few days first). We welcome your feedback on the redesign either in the form of blog comments or email feedback (chemspider-at-rsc.org).

Over the next week – keep your eyes peeled for the upgrade and my accompanying blog post which will endeavor to give you a good introduction to the new features.

We have text mined compound names from all RSC 2008-2010 journal articles and loaded these into ChemSpider – adding about 26,000 new-to-ChemSpider compounds with links back to the published articles. We’ve also simplified the view of compound name and chemical/biochemical term highlighting within the Publishing Platform HTML view, so readers can link out from compound names (direct to ChemSpider for related compound information) and from chemical and biochemical terms (to other linked articles). We’ll be extending this to cover our 2011-and-then-ongoing publications, then looking to go further back into our journal archive. Later this week we should also have the compounds visible from the article home page, also linking through to ChemSpider

We have also worked with the Utopia Documents team (getutopia.com) to apply these enhancements to our PDF – so with the free Utopia Documents PDF viewer (originally developed in conjunction with Portland Press for the Biochemical Journal), readers get any enhancements overlaid on top of the PDF as they’re reading and can link out just as they can from the HTML. As this is powered from an API from our Publishing Platform, any additional links we make in future will be reflected in real time without having to update the PDF. Anyone who’s seen Steve Pettifer’s Utopia demonstrations tends to say “wow” at the potential, so many thanks to the Utopia team in Manchester for adding support for RSC articles. As above, this will work on 2008-2010 articles just being loaded, and as we extend the coverage Utopia will pick up and display the additional links for these papers

The RSC’s free chemical database ChemSpider has added RDF functionality to its interface, in collaboration with the University of Southampton’s School of Chemistry. The availability of RDF allows the database records to be found and understood by semantic web tools, another step in ChemSpider’s mission to create a public chemical information infrastructure.

Richard Kidd, Informatics Manager at the RSC says “we are delighted to work with top academic teams pushing forward what’s possible with semantic chemistry, and we hope others will use the RDF representation of ChemSpider to support their own developments”

ChemSpider as a Linked Data source for oreChem

The machine-processable representation was specifically developed in order to leverage the core competencies of the ChemSpider database: resolvable identifiers; high-quality, curated metadata; and rich linking to the extensive RSC corpus. Furthermore, as part of the Microsoft Research-funded oreChem project, OAI-ORE technology is being used to facilitate the discovery and re-use of the chemical information in the correct context.

Prof Jeremy Frey and Dr Simon Coles commented “it is a pleasure for Southampton to work with the RSC’s ChemSpider as a culmination of our contribution to the Microsoft-funded oreChem project. As a member of the Southampton Chemistry eResearch team, this work forms the core of graduate student Mark Borkum’s PhD thesis. ”

“Enabling open, semantic chemistry in this way is a monumental step forward for the domain,” notes Lee Dirks, director of Education & Scholarly Communication for Microsoft Research, “We’re thrilled to have played a role in facilitating the creation of this resource and extremely pleased to see Southampton and the RSC innovating and leading the field.”

Another oreChem participant, Carl Lagoze, the Associate Professor, Cornell University Information Science, Co-Director Open Archives Initiative added “it’s wonderful to see the results of our work on OAI-ORE in this exciting application. It fulfils our goal of making the results of research easier to disseminate and reuse”

Read the rest of this entry »

ChemSpiderman, Antony Williams, will be giving ficve presentations at the #ACS Denver meeting in the fall. The times and dates will be listed when they become available. The list of titles is below.

Structure representations in public chemistry databases: The challenges of validating the chemical structures for 200 top-selling drugs

Chemistry in the hand: The delivery of structure databases and spectroscopy gaming on mobile devices

Aligning scientific expertise and passion through a career path in the chemical sciences

ChemSpider: Does community engagement work to build a quality online resource for chemists?

Identifying “known unknowns” using mass spectrometry data and ChemSpider

It’ll be a different type of talk than most I have given before on ChemSpider…should be fun!

I am happy to announce that ChemSpider is a part of the Open PHACTS project. It is detailed in the following PDF file but can be summarized with the extract from the Wikipedia article I recently posted.

“Open PHACTS is an Innovative Medicines Initiative project aiming to deploy a highly innovative open standards, open access, semantic web approach to address key bottlenecks in small molecule drug discovery – disparate information sources, lack of standards and information overload. It will become an open, integrated and sustainable chemistry, biology and pharmacology knowledge resource for drug discovery. It will provide tools for a comprehensive platform of chemical, biological and pharmacological information, confederated from vast, distributed and variable data and information sources. This semantically enriched and fully interoperable platform will deliver information on small molecules and their pharmacological profiles, including pharmacokinetics and ADMET data as well as on biological targets and pathways. The proposed platform will be a widely accessible, open innovation platform that will serve EFPIA partners as well as biotech and academic drug-discovery for one of their core business activities: knowledge discovery and verification. Practicing drug-discovery scientists in both the public and the private sector will turn to this service to: – integrate data on target expression, biological pathways and pharmacology to identify the most productive points for therapeutic intervention – investigate the in vitro pharmacology and mode-of-action of novel targets to help develop screening assays for drug discovery programs – compare molecular interaction profiles to assess potential off-target effects and safety pharmacology – analyse chemical motifs against biological effects to deconvolute high content biology assays.

The Open PHACTS consortium comprises 23 European core partners, with leading experts in the fields of data mining, annotation, small molecule data storage and manipulation, target related bioinformatics, pathway annotation, protein structure analysis, massive daily in silico reasoning, chemical biology, and computational chemistry. These are: Pfizer, Universität Wien>, Technical University of Denmark, University of Hamburg, BioSolveIT GmBH, Consorci Mar Parc de Salut de Barcelona, Leiden University Medical Centre, Netherlands Bioinformatics Centre, Royal Society of Chemistry, Vrije Universiteit, Spanish National Cancer Research Centre, University of Manchester, Maastricht University, ACKnowledge, University of Santiago de Compostela, >Rheinische Friedrich-Wilhelms-Universität Bonn, AstraZeneca, GlaxoSmithKline, Laboratorios del Dr. Esteve, Novartis, Merck KGaA, Lundbeck, and Eli Lilly.”

The Open PHACTS website can be found here. There will be a lot more details about Open PHACTS in the next few months. Follow the conversation on Twitter here: http://twitter.com/#!/Open_PHACTS

Dotmatics Limited is pleased to announce that it will provide its web-based structure drawing tool, Elemental, to the leading chemistry community website ChemSpider. Elemental provides a zero install drawing tool that lets users draw simple chemical structures or complex structure queries directly within a webpage.

Antony Williams, Vice President of Strategic Development for ChemSpider comments “Elemental offers ease of deployment and flexibility in structure drawing to our community of users and we are happy to embrace this web-based structure drawing platform as an entry point to the rich resources of ChemSpider.”

Dr Mike Hartshorn, Director and CSO of Dotmatics, said “We are delighted to be working with such a well-known chemistry resource as ChemSpider. The new tools will allow simple access to the wide range of structures and related information that is maintained by ChemSpider and the RSC”.

About Dotmatics
Dotmatics Limited (www.dotmatics.com) is a leading provider of web-based database integration and visualisation tools for use within the life sciences industry.

About the Royal Society of Chemistry
The Royal Society of Chemistry is the UK Professional Body for chemical scientists and an international Learned Society for the chemical sciences with more than 47,500 members worldwide. It is a major international publisher of chemical information, supports the teaching of chemical sciences at all levels and is a leader in bringing science to the public. www.rsc.org

About ChemSpider
ChemSpider offers a structure-centric community for chemists to resource data.  Offering access to over 25 million unique chemical entities from over 400 data sources and by providing a platform for crowd-sourced deposition, annotation, and curation, it is the richest source of free integrated chemistry information available online.  ChemSpider delivers data and services to enable the semantic web for chemistry.  www.chemspider.com

Contacts:
Mike Hartshorn
Dotmatics Limited, The Old Monastery
Windhill, Bishops Stortford
CM23 2ND, UK
Tel: +44 1279 654123
Email: info@dotmatics.com
www.dotmatics.com

Antony Williams
ChemSpider, Royal Society of Chemistry
904 Tamaras Circle
Wake Forest, NC 27587
Tel: 919-201-1516
Email: info@chemspider.com
www.chemspider.com

Last week Antony Williams gave three presentations about ChemSpider as a chemistry resource at the 241st ACS National Meeting  & Exposition in Anaheim.

For those of you who were not able to attend here are the presentations:

RSC ChemSpider as an environment for teaching and sharing chemistry