ChemSpider Blog

Since it was easy to do we will bring back ChemSpider online in Read Only mode for you to ccontinue using if you need it. This will mean that the web services will all be returned also. The only things that will not be enabled are deposition, annotation and curation. In order to block these we have disabled login. While it will be possible to add comments please note that these will be dealt with on the RSC system following rollover to their systems.

Over the past few months there have been a number of discussions in the blogosphere about the future importance and value of classical Impact factors but for now they remain the industries primary measure of, well Impact. With that in mind it was good to see this announcement from the RSC regarding recently published impact factors for Chemistry related journals. Nice…it’s good to know that we joined an organization that continues to focus on its core mission and strengths and be acknowledged by the readers and the industry for its efforts.

2008 Impact Factors – RSC leads the way for chemistry

25 June 2009
Publication of the 2008 impact factors, calculated by ISI, once again brought good news for authors and readers of RSC journals. 

ChemSpider will go offline today for the next 24 hours. We will switch the servers off at around 11am today (give or take some latitude). We will do a differential backup and restore to the RSC servers all changes to the database and switch over to their systems overnight. Testing performed over the weekend has proceeded rather well and we are hoping for a seamless transition, acknowledging that we will have this one day of downtime.

We apologize in advance for any disruptions. We know that there are a lot of people now using ChemSpider services to feed your own systems so our apologies in advance. We expect improved service for all when this transition is complete.

We’ll see you on the other side of this transition in just over 24 hours. Wish us luck…

The ChemBL blog is an excellent read and if you’re interested in “Open Access Drug Discovery And Medicinal Chemistry Data ” this is one for you. We are shamelessly, and WITH permission, taking some of the blogposts about New Drug Approvals and adding them into the descriptions on ChemSpider. Some examples are here and here. To date for all cases where we have added the description the compound itself was already on ChemSpider and with the correct name. That’s good news based on some of our subjective measures of coverage for the database.

The Spectral Game at www.spectralgame.com is powered by chemical structures and spectra from ChemSpider. A provisional form of our manuscript regarding this paper is now online at the Journal of Cheminformatics here:

The Spectral Game: leveraging Open Data and crowdsourcing for education

Jean-Claude Bradley , Robert J Lancashire , Andrew SID Lang and Antony J Williams

Journal of Cheminformatics 2009, 1:9doi:10.1186/1758-2946-1-9

Abstract (provisional)

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.

Since the RSC acquired ChemSpider we have been working hard with the IT team in Cambridge to transfer ChemSpider from our servers and onto the RSC servers. This has been quite a significant undertaking as now we will be dealing with development servers, staging servers and live servers. This is a significant departure from the environment we have been working in for the past couple of years where code was published to the live environment for testing. Some would say this was risky but with the limited resources we had available at the time it was what it was….oh, and it worked!

We have already started testing the system on the RSC servers that will go live sometime early next week. At present the intended schedule is that we will be switching over sometime between Monday and Wednesday. Of course, this is an intention at present and, based on testing, this may change. For right now we have stopped depositions onto ChemSpider. If curation activities continue we will sync these over to the live server next week so no issues there. ChemSpider will go offline next week sometime and, as the actual data becmes clearer, the announcements will be updated.

Watch this space…ChemSpider is moving to the RSC servers and their will be disruptions in the next few days.

When I present on ChemSpider and talk about community participation one of the common questions is “how many people curate? deposit? annotate? records on ChemSpider”. It’s a low number for each but, in my estimation, it is in-keeping with how we operate as individuals. If you compare the number of people reading Wikipedia articles to writing them I judge it has to be a pretty high ratio of likely >5000:1. Even if its 1000:1 you get the point. More people use than contribute. It is the same for most everything that we use…Amazon book reviews, Netflix DVD reviews, things like that. It’s only when it’s “about us” that the majority of us tend to contribute – to our blogs, our LinkedIn profiles, our Twitter account, our Friendfeed discussions, our Facebook pages etc. I judge this is because it makes us directly visible…we are showing what we are interested in and taking owenership for our comments, activities etc. This is of course human nature…the majority of us have that “look at me” mentality and “connect with like minds” and it is, in many cases, that need for incoming voyeurism and participation that has driven the incredible shift to social networking we are encountering.

There are then the “servants for the community”. In this case I mean servants with the most positive connotation. Those who slave away on Wikipedia articles and don’t immediately have their names up in lights. You actually have to dig under an article to find out who wrote/contributed to it. It’s not upfront and center. On Wikipedia chemistry there are a very small number of dedicated individuals who contribute large blocks of time to working on Wikipedia to improve its quality and content. There is a Long Tail of contribution of course but you might be quite surprised by the small number of “primary” contributors. If you check out their Wiki pages however these individuals are recognized and commended within their own community of participation yet may never be known by the readers of the articles.

On ChemSpider we have a similar situation. There are a very small number of primary curators (I will name them: Myself, Heinz Kolshorn and Barrie Walker – these people are enhancing ChemSpider literally daily). We have a smaller number of secondary contributors who add a spectrum once in a while, annotate a record occasionally or curate out bad data. I would say this is about 30 other people. We also have people who provide us data to deposit and they do it willingly but don’t want to have a hands on approach to depositing data onto the database.

When I was in the UK recently during my first week of employment with the RSC I gave a number of presentations. There was a lot of interest in what ChemSpider could bring to the organization and offer the community and a lot of discussions regardng “what if”. Of the audiences I would suggest that only a small portion actually laid their hands on the system to investigate its capability and an even smaller fraction chose to jump in, feet first, and use the system and participate fully. There was one spike in particular. During the evening after one of the presentations I noticed that one individual in particular was adding comments to individual records, questioning names, suggesting that structure layouts be changed and examining links to external resources. The first evening there were a few edits. The next night, even more, and since then this individual has continued, unabated, making edits and now enhancing the articles with new information, in this case YouTube videos.

David Sharpe is fairly new to the RSC and is one of those people who just cares. A silent contibutor in the background (until today!) who is cleaning and enhancing ChemSpider for the sake of the community. To be clear, his work on these activities has been done in the evenings and weekends and this past weekend he was exchanging emails with me about adding “Element Videos” to the elements on ChemSpider. David’s been moving across the elements on ChemSpider and using the YouTube embed functionality to put the Periodic Table videos from the University of Nottingham into the Description section of the appropriate records.

Check out for example the video for Sulphur here. As we move forward we will layer on a recognition system for individuals contributing to ChemSpider so that we can track the spectral depositions, curations and so on. We believe that such efforts warrant recognition and applause. Of course some will choose to be anonymous and remain in the background making their difference in a silent manner. We honor you all.

Scifoo is just a few weeks away and I was reviewing the list of attendees this evening to see who I would be sharing space with.

I am especially looking forward to spening time with Andrew Lang, one of the brains behind the Spectral Game. We’ve spoken on the phone, exchanged many emails and worked on a couple of projects together. But we get to meet at SciFoo!

Last time I was at SciFoo I spent time talking with Cameron Neylon and JC Bradley about Open Notebook Science. At that time I had lots of ideas about what we could do to support Open Notebook Science. We actually have done quite well but at that time we were severely resource constrained. Things are a little different now we have been acquired by the RSC and I am looking forward to talking about what’s necessary and possible now.

Nicko Goncharoff from SureChem will be there. Nicko and I have spent a lot of time together over the past few years, mostly by phone and over email as we worked to integrate SureChem into ChemSpider and use their software development kit under our ChemMantis semantic chemistry markup tool. It’s always good to see him.

Other people I hope to spend some time talking to: Peter Murray Rust from the university of Cambridge, Timo Hannay, Alf Eaton and Terry Sheppard from the Nature Publishing Group and Theodore Gray.

I have set up a LinkedIn Users and Advisors group today and welcome any LinkedIn users interested in ChemSpider to join the group and stay informed about our activities on ChemSpider. I hope that it also provides a useful environment for discussion and collaboration around ChemSpider.

The ChemSpider LinkedIn Group can be accessed here.

Oh boy do we have a lot of things to do with ChemSpider. Not only now, while shifting ChemSpider to the RSC infrastructure, but in the future as we do the work necessary to make ChemSpider the primary internet resource for structure-based chemistry. We don’t have small eyes in terms of what we want to deliver to the community. Far from it…we have big eyes and big ideas regarding what is possible and even, in most cases, how to get there. What is clear is that we need the appropriate skill sets to make it happen. At present all ChemSpider platform development work is done by our team over here in the US. We are looking to add a team member into the RSC Offices in Cambridge. We’re looking for someone with established Cheminformatics skills to work with us. They need to have an established track record in working in the field of Cheminformatics, have a deep knowledge of handling chemical structures, experience in working with web-based systems and, of course, have a big appetite for making a difference and wants to work with a fast-moving team. If you’re interested in talking with us about the opportunity ping me at antonyDOTwilliamsATchemspiderDOTcom.

There are a small number of primary chemical vendors serving the industry. These include companies such as Sigma Aldrich, Spectrum Chemical, Alfa Aesar, ThermoFisher and many others. There are also thousands of smaller companies serving the industry with their chemicals. These can very from a dozen to a few hundred chemicals but rarely number into the 10s of thousands offered by the larger companies. The large chemical companies offer excellent services in terms of delivery of catalogs to the door and circulation of updated CDs of information. I find the Aldrich catalog an excellent tool and have one on my desk, underneath my Merck Index.

Those smaller chemical companies are in the long tail of suppliers that the majority of chemists will never even hear of. Not unless there is some way for those suppliers to deliver their message regarding their list of products, availability and overall their existence, to interested parties. In China specifically there are many hundreds of small chemical companies popping up now. They cannot afford to market themselves via CD distribution and catalogs to their potential userbase and have to depend on their website to market their wares. They likely deposit their collections to the Available Chemical Directory from Symyx (a GREAT product and with a lot of quality work going into it in the background!), maybe into ChemACX from Cambridgesoft, onto ChemExper or onto the eMolecules site. Some of these offer up to date pricing and procurement systems while others offer simply “Get me a Quote” services whereby a chemist can request a quote directly from the vendor for the material of interest.

ChemSpider has been depositing chemical compound collections for chemical vendors, both large and small, for many months. The word seems to have got out that there is value to doing this. Despite the fact that we do not have, at present, the ability to list real time or availability pricing for compounds chemical vendors appear to be deriving value from the listings and chemists are finding chemicals for purchase via ChemSpider.

if there is a certain small molecule chemical vendor that you think we should list on ChemSPider let them know to contact us OR point us to their URL and we will contact them. One example of data added just today is the data set, small though it is, from Asiaron. They offer rich compound pages like this and are a good addition to the database.

I have ChemMobi running on my iPhone now and, I am happy to say, it looks just like it should. While visiting the RSC in Cambridge a couple of weeks ago I had a chance to hang out with James Jack, the Symyx consultant responsible for developing ChemMobi. That’s him on the left. No, that’s not him trying to hunt sharks with hand held harpoons, it’s him driving the “ChemSpider punt” in a race against the IT team from the RSC. Since we weren’t locals it seemed appropriate to challenge us to a speed punt down the river. This was of course preceded by the imbibing of adequate  amounts of flavored water and juices.

Strangely enough all of us in the ChemSpider punt did appear to have some undiscovered talents for punting. We very quickly lost the IT team back at the “juice house” and found them when we had finished our loop back from our destination. We realized that we had an unfair advantage since we had a dopted a strategy of punting from the surface of the vessel. They had not defined to us that they were doing the whole race in their own way…pushing with a pole while immersed. That’s our colleague Doug Spooner from the IT team showing us how to do it “IT style”.

ChemMobi will soon be posted to the App Store for you all to download and use. I’ll let you know when…hopefully within a week. All glory, love and adoration for the App should go to James jack and to Symyx for allowing him to do what he does best…get creative with software and structures!

I have given a number of talks regarding ChemSpider over the past few months and generally comment “ChemSPider hosts almost 21.5 Million unqiue chemical entities from over 200 data sources. As of today it is over 21. 5 million chemical entities. We have deposited data from a number of new contributors of late, many of these are smaller chemical vendors such as Bridge Organics and ExtraSynthese. However, we recently crossed the 21.5 million mark because we have started to take advantage of the eMolecules dataset made available as a downloadable set. There are over 5 million structures in the dataset.

Many, but not all of these, deduplicate onto the ChemSpider database. The 21.5 millionth structure links to this record on eMolecules as shown below.

When the data are added onto ChemSpider we automatically add SMILES, InChIs, MW, MF and a series of predicted physicochemical properties. This is for the new structures from eMolecules. In many cases however eMolecules is simply one more data source among many and information such as spectra, Wikipedia links, experimental data etc are all integrated. In this case though eMolecules can help you source a vendor for the material as is their strength.

ChemSpider has been around for about two and a half years. Based on the feedback we have received from the community regarding our humble offering to the chemistry community users like it. In most cases they “get it” too. They understand that we working to provide information to them that can assist their work. We are hoping to provide some glimpse of data, some snippet of information, some link of value which can enable their studies/research/inquiry. And, in some cases, people want more. Let’s be honest…WE want more. We want to deliver more value, provide more impact and integrate more data for you, the community.

Some of the things that we have been asked for over the past few months are more web services to tap into the experimental data available on ChemSpider (grabbing experimental properties for QSAR modeling for example), more reaction syntheses to peruse, improved speed for substructure searching, similarity searching, integration to more publishers literature and easier to navigate website. Good list!

We have  a set of priorities for the near term and will be doing our utmost to deliver them in time for the IUPAC congress in Glasgow in August and the ACS meeting in Washington later that month. But we want to hear from you. What do you, our users, want to see on ChemSpider. If you had your wishes, and resources were no object, there were no barriers to integration with any data source and you got to define the path forwar for ChemSpider what would it be?

Feel free to share it here on the blog or, if you’d prefer to be more anonymous with your comments, feel free to drop me an email at infoATchemspiderDOTcom. We want your input. Please don’t be shy…engage us and you might just get what you want (though some things might take a while!)

It’s been a long time since I blogged here on the ChemSpider blog. Now I am officially an employee of the Royal Society of Chemistry and have spent a week in Cambridge meeting my new colleagues, discussing the transfer of ChemSpider to their servers for hosting and working on plans for a relaunch of ChemSpider later in the year. More about that later. I’ll be back in action on this blog in the coming week.

I actually write on two blogs. This one will now be dedicated to ChemSpider activities specifically and focus on new functionality, plans and vision for ChemSpider as a service. My other blog, the ChemConnector blog (www.chemconnector.com/chemunicating) will be more of a personal blog. My views of cheminformatics, activities  in Chemistry and Science, Open Science, Open Access and Open Data and other things that interest me.

Glad to be back and looking forward to connecting with everyone again.