ChemSpider Blog

In the recent rollout of functionality we added to the home page statistics regarding the number of various types of spectra that have been added to ChemSpider as well as updates of new data associated with data sources. We will likely optimize these displayed further in the future but this is an initial display for the time being. It’s rather impressive how many different types of 2D NMR data are being uploaded to the database.

Part 4 in the exposure of new ChemSpider functionality from the recent update. We have been using the ACD/Labs Structure Drawing Applet on ChemSpider for the past three years. It’s been a great piece of technology and was one of the first applets, possibly the first structure drawing applet ever released. However, it’s old technology and we have been encouraged by our users to use a more modern applet. We are very fortunate to have been granted the right to use the Symyx JDraw applet and have had the pleasure of working with Keith Taylor and James Jack. For the time being we have left two applets online for the users to try out and provide feedback on. You can choose the ACD/applet or JDraw by selecting via the interface as shown below. Feedback welcomed.

Following on from other posts in this series from this week I’m going to continue to list new functionality over the holiday season. I’ll continue with the “Social Widget”. What IS the Social Widget? Well…it’s this thing to the left….it is an AddThis Button that is available for every compound page on ChemSpider now. If there is a particular chemical of interest on ChemSpider that you want to include into your social networking then you can do so by choosing the social networking site of interest and “adding” the link in there. For some it posts the link and for others it posts a thumbnail of the structure there that is linked back directly into ChemSpider.

So, if I posted to Friendfeed it will send the link directly into Friendfeed. I just did it..worked perfectly. For Facebook it actually carries the thumbnail as shown below on my Facebook page. SO, deposit some of your molecules onto ChemSpider and let the world know! Add some data, tell a story, post a reaction…and use AddThis to tell your network!

Following on from my previous post regarding new functionality on ChemSpider, the last one regarding improved integration to SureChem patents, I am happy to announce that we have improved the Pubmed integration. Previously we would stream way too many articles from Pubmed for some compounds. For example, retrieving articles about cholesterol would result in too long a page of Pubmed articles being displayed.We have now limited the number of articles retrieved and simply put a link at the top of the page for you to retrieve the rest of the links.

In this case when you click the link we initiate a full search using the Entrez Life Sciences API. The results for cholesterol are shown here. A small but user-friendly improvement…More to follow.

I’d never published in an RSC journal until recently when Sean Ekins and I published in Lab on a Chip. The process was good…fast and efficient. Now, I am an employee of the RSC now but these are objective comments and I’m looking forward to publishing more with the RSC. I do still publish with my co-authors with other publishers because of the nature of the work we do – cheminformatics fits well into ACS’ JCIM and the Journal of Cheminformatics and NMR papers still fit well into Wiley’s Magnetic Resonance in Chemistry. Our J Cheminf paper is still the most accessed article in that journal.

I was impressed to get a letter from the Editorial Director of the RSC in my inbox last week. It was directed to me as an author in an RSC journal. What was impressive was the fact that he took the time to issue this to all authors as well as the fact that the letter discussed the impact factors for RSC now matching those of the ACS. Very impressive and a nice touch from Jim Milne!

While some say “Silence is Golden” some of us find it deafening! One of my common statements regarding Press Releases and political commentaries is there is as much said in the “unsaid”. Why this lead in to this blog post? Well….the truth is we haven’t been very productive in the past few weeks with the delivery of new functionality onto ChemSpider and people have been asking me why we haven’t been so prolific with our updates. Well….in this case Silence is Golden based on the new functionality and data rolling out soon!

Historically we were introducing new functionality every few days and rolling it out with a “continuous beta” approach to delivery. We were also working on only three computers and were challenged with issues of uptime and handling. At the RSC we have access to development, test and live environments, we have a stable compute environment supporting the system that provides power support where previously we would have been at risk of outages. We have a support team who have “got our backs” and we are not dealing with all of the issues regarding keeping the environment healthy for the ChemSpider platform. With our new hosted environment and the drive to move away from our previous constant and ongoing updates to a more controlled process for rollout, specifically including internal testing prior to going Live, we have been working on procedures to ensure the best delivery. In parallel we have been working on a series of internal projects that are very exciting and you should see the results soon!

With our new processes in place, and our new systems now established we have been working on new functionality development and are happy to announce that we will now be moving towards regular updates, every few weeks. We’re starting this week with the roll out of a set of new capabilities for you to try out. I’ll highlight these in a series of blog posts over the coming days.Let’s start with this one…

We are happy to announce an improved integration to the patent web service provided to us via our collaboration with SureChem. We announced our initial integration to this service at the ACS meeting last fall in Washington and received a lot of positive feedback regarding the implementation. That rollout only provided integration to a subset of the entire collection, the USPTO. SureChem host data from a number of patent agencies and the collection includes USPTO Granted, USPTO Applications, European Granted, European Applications, WO/PCT and Japanese Abstracts. Thanks to their web service we now have the ability to retrieve information regarding those sources also. The image below shows the patents retrieved for Xanax. Check it out…give us your feedback and extend holiday cheer to SureChem also for their contribution to the community.

I hate the drive to Washington DC from Wake Forest North Carolina where I live. At the right time of day it’s kind of fun actually…some good music, my iPhone to talk to people on the drive and a chance to think, think, think without the interruptions from skype, email and even my own lovable children. BUT, at the wrong time of day a 4 hour drive becomes a 6 hour drive and I spend a lot of time parked up on the highways trying to move. It’s quite simply, hell. So, this week I decided to take an Amtrak train up from Raleigh to Washington to stay with my colleague Valery Tkachenko the night before my presentation at the FDA.

It didn’t start well. The train left the station 30 minutes late. The guy sitting next to me on the train clearly hadn’t bathed for a few days but the train was full so there was initially nowhere else to sit. He slept the entire way anyway so we didn’t exactly engage much until he lay his head on my arm and proceeded to salivate in my general direction at which point I, the one that was awake, suffered an intense myoclonic jerk and launched him to the other side of his seat to dribble into the central aisle. There was no wireless on the train. Food was expensive…a coke for $2. Stops were frequent and it took over 8.5 hours for me to get to Valery’s house. I did get a lot of work done on the ride but I’ll conclude it with NEVER AGAIN…I’d rather drive. Compared with the quality of train rides in Europe, of which I have had many of late, Amtrak leaves a lot to be desired. Enough whining…

I was in Washington to give a talk at the FDA in a symposium with a number of other online database teams. These included PubChem, ChemIDPlus, HSDB, DailyMed and one I hadn’t heard about yet… PillBox. I really enjoyed the talk about Pillbox…check out the site. Great design, simple and intuitive flow and a great vision. Loved it!

The presentation I gave was called “ChemSpider and How The Wisdom of the Crowds CAn Improve the Quality of Chemistry on the Internet.” The talk is on SlideShare with about 40 of my other talks here and is embedded below also.

Yesterday evening from 6pm until 8pm I participated in a remote presentation to about 30 students sitting in a room at Drexel University as a result of an invitation from JC Bradley. Two of us were speaking…Rajarshi Guha and myself. The entire session was conducted using shared Webex access and skype. The technology aspects worked very well. While the experience of sharing a room with my partner speaker was lacking there was definitely no lack of collaboration to make this work!

Rajarshi’s presentation was regarding “Molecular representation, similarity and search” and is posted online at Scivee here.

My presentation was entitled “Citizen Scientists and Their Contributions to Internet Based Chemistry” and covered the range of what is the status of chemistry on the internet, what databases are out there to look at, what is the status of quality on said databases, an overview of real time searching on ChemSpider, how to curate and deposit to the platform and some insight into what will be coming soon. The talk is shown below and directly on SciVee here