ChemSpider Blog

In January of this year we held a meeting in London with a group of interested parties who wanted to discuss with us how ChemSpider can be used to support metabolomics. From my point of view that was a very successful meeting in terms of providing an overview of what ChemSpider is capable of today as well as garnering feedback and input from a community of users applying mass spectrometry to perform metabolomics studies.

As a result we will be holding a round-table discussion here in the United States in Research Triangle Park, North Carolina, in April 2011, again for scientists interested in further refining how ChemSpider can be extended to serve the metabolomics community. An outline of the meeting is provided below. If you are interested in participating please respond to me directly at williams”AT”rsc”DOT”org by the deadline listed below. We will cap the attendance fairly quickly and are specifically looking for people who can be vocal about their needs and how we may be able to help with ChemSpider as a platform.

Metabolomics Round Table – Delivering Value to the Metabolomics Community via ChemSpider, a Public Domain Database

Hosts: John Shockcor, Waters and Antony Williams, Royal Society of Chemistry

When: April 21st, 2011

Venue: To Be Determined, Research Triangle Park, North Carolina

The metabolomics community presently utilizes public domain databases such as KEGG, LipidMap, DrugBank and a myriad of other online resources to assist in the analysis of data. However, rich as these resources are, they are limited in scope, are challenged by known data quality issues, and are not directly focused on serving the needs of the metabolomics community. ChemSpider is an online resource for the chemistry community hosted by the Royal Society of Chemistry with the intention of linking together online chemistry resources, cleaning and curating chemistry related data and collectively serving a number of communities. ChemSpider has been used by members of the mass spectrometry community, including instrument vendors, for the past 3 years. This roundtable meeting is to provide an overview of how ChemSpider is presently used by scientists working in the domain of metabolomics and garner feedback from the existing user base as well as new potential users to help define how ChemSpider can be enhanced to further support the needs of this community.

Antony Williams, VP of Strategic Development and host of ChemSpider at RSC, and John Shockcor, Director of Life Sciences Business Development at Waters Corp, invite you to attend thismeeting to provide input to steer development of ChemSpider to address the needs of the metabolomics community. An agenda will be defined in the near future based on interest.

If you are interested in attending please express your interest by sending an email to williamsa@rsc.org

The Royal Society of Chemistry will be heading to California for the Spring ACS Meeting where Antony Williams, the VP of Strategic Development for ChemSpider will be presenting several papers and hosting a ChemSpider Training Session.

The Training Session – “ChemSpider: A Community Resource for Chemical Data”  will be held on  Wednesday, March 30th from  8:30-11:00 AM in the Anaheim Convention Center,  Room 211 A.

This should be a lively and interactive session and is your opportunity to give feedback regarding present functionality and how you would like to see ChemSpider develop in the future. These sessions have proved popular in the past, so make sure to register early for your place here.

The titles and locations of the talks are:

RSC ChemSpider as an environment for teaching and sharing chemistry – Division of Chemical Education. March 28, 2011 from 9:45 am to 10:05 am. Disney’s Grand Californian Hotel , Room: Trillium B

Hosting a compound centric community resource for chemistry data – CINF: Division of Chemical Information. March 28, 2011 from 3:05 pm to 3:30 pm. Anaheim Convention Center , Room: 204 A

How the web has weaved a web of interlinked chemistry data – CINF: Division of Chemical Information. March 29, 2011 from 3:00 pm to 3:40 pm. Anaheim Convention Center , Room: 204 A

For a more pesonalized demonstration of ChemSpider you can also visit the RSC at Booth 903.

We look forward to meeting you in Anaheim.

I recently talked about ChemSpider and some of our recent and future developments at the STM Innovations Seminar 2010, in a flash session of 20-slide talks timed @ 15 secs a slide. Great fun to do, and a format which ensures much less suffering for the audience – or at least shorter but more concentrated suffering. Anyway, here’s ChemSpider in 5 minutes for an audience of non-chemists. The other slides and videos from the Seminar are also available. Thanks to STM for hosting the event and River Valley for filming it.

Bora Zivkovic is one of the most prolific scientific Bloggers online, is a passionate advocate of Openness in Science and one of the hosts for ScienceOnline. He recently interviewed me for his Blog Around the Clock blog. The blog is online here:

ScienceOnline2010 – interview with Antony Williams

Category: SO’10 • Scio10 Interviews
Posted on: May 20, 2010 11:18 AM, by Coturnix

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.

Today, I asked Antony Williams from ChemSpider to answer a few questions.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background? Tell us a little more about your career trajectory so far: interesting projects past and present?

Read the rest

Another article in an ongoing series of the application of Computer-Assisted Structure Elucidation (CASE) tools to the validation of elucidated structures. It is quite amazing how many chemical compounds are incorrectly elucidated but when you consider the complexity of the challenge again, then maybe not so surprising. This article published in RSC’s Natural Product Reviews examines ways in which CASE can be used to correct erroneous structures in the literature. I think it’s one of the best articles we’ve generated using the ACD/Structure Elucidator software package to elucidate and validate structures. The article is online here. I am fortunate to still be able to work with my friends Mikhail Elyashberg and Kirill Blinov from ACD/Labs after hours. They are brilliant scientists….

I gave a presentation at OpenSciNY 2010 last week. I already posted the talk here but the presentation was also captured and streamed. It was split into two pieces and there are available here and here and embedded below.

I recently had an interview with DeLene Beeland regarding ChemSpider and the ChemSpider Blog. I live in Wake Forest, North Carolina…just north of Raleigh and a few hours away from Charlotte. The interview was conducted on behalf of the Charlotte News and Observer and was entitled “an award-winning treasure trove of chemistry info“. Considering the amount of space she had to represent the conversation she did a great job.

As I sit here in JFK, delayed for yet another flight (and awake since 3:45am…ugh) I am happy to have flown here to participate in the OpenSciNY2010 gathering today. With Heather Joseph, JC Bradley and Beth Brown on the agenda, to name a few, it was a room of librarians and interested parties with their support out front and center regarding the support of Open Science. A great meeting but I need a couple of days good sleep at this point!

Our Article regarding “Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining” was published in Journal of Cheminformatics as an Open Access article a few weeks ago. The link is: http://www.jcheminf.com/content/2/1/3

Background: Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus. To achieve an acceptable recall and precision we used a number of automatic and semi-automatic processing steps together with disambiguation rules. However, it remained to be investigated which impact an extensive manual curation of a multi-source chemical dictionary would have on chemical term identification in text. ChemSpider is a chemical database that has undergone extensive manual curation aimed at establishing valid chemical name-to-structure relationships.

I gave a number of talks at the ACS Spring gathering and a couple of these were recorded and are now available online via the ACS Webplayer. if you didn’t make it to ACS and are interested in the talks the links are below.

Track : March 21, 2010

Life’s experiences mold us. One of the reasons I am in chemistry is the fact that my chemistry teacher said that I didn’t get chemistry. Mr Morris…I have to tell you that not only do I get it, I enjoy it, am challenged by it, am fascinated, stimulated and care about it. That said, I don’t deal well with praise. Challenges I love. Tough problems motivate me. More work is a good thing. Deadlines stimulate action. Praise shuts me up… I’m not sure what to do with it.

Last night at the Bio-IT Best Practices Awards Dinner in Boston RSC ChemSpider won an award for “Community Service”. My colleague Valery Tkachenko and I stepped on the stage and we willingly accepted the award. Each award winner was given the chance to speak and as I stepped up to the podium I felt a wave of emotion, my voice cracked and I murmured about how this was validation for what was at one a hobby project come to fruition, our contribution to the community and validation of our hard work.

At that moment last night I was finally immersed in a moment of “we have arrived”. We have been recognized not only by the users of the system but now voted by our peers in IT and Life Sciences as delivering value to the community and providing service. Last night was truly emotional and, whichever way I look at, was praise and recognition for our  humble offering to the community.

We are making a difference. We have big plans, great intentions and stand on a foundation of hard work, innovation and community engagement. The Royal Society of Chemistry is a good home for ChemSpider as the organization stands on the same foundations, and many more. Winning an award was a great feeling. We’re going to continue to work hard for the good of the scientific community, not for the awards but because it is needed and is the right thing to do. But hey, after last night, I’d like the chance to win another award and give thanks without a shaky voice and a wave of emotion flooding over me!

I am an NMR Jock by training (PhD NMR spectroscopist out of University of London, UK in 1988 with experience in gov’t labs, academia and Fortune 500 America over the years). As the Chief Science Officer for ACD/Labs for over a decade and running an NMR lab for a number of years I have been to the ENC over a dozen times but this week is the first time back at an ENC in 5 years. I am here to present at the ACD/Labs User Meeting about building an online spectroscopy database of spectral curves on ChemSpider and to present two posters on the database and the SpectralGame.com. The presentation and the posters went down very well…I am standing with the posters again tomorrow. I’ve had people shake my hand and tell me what a great system, they will contribute, they will use and congratulations and thanks for providing the system. There have been no detractors, no negativity at all but lots of smiles and kudos all around. I expect we will be receiving new spectral data in the next few days and weeks. Definitely worth being here. The only sad part is the number of people from Europe who failed to make it because of the volcano ash in the air over Europe.

The talk and posters are given below and are on SlideShare.

If any readers will be attending the ENC conference in Daytona Beach next month I hope you will stop by and visit the two posters I will be presenting. The poster details are given below.

The Spectral Game – Teaching NMR Spectroscopy Via a Web Browser
Antony Williams1; Jean-Claude Bradley2; Robert Lancashire3; Andrew Lang4

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. Each correct selection earns the player one point and play continues until the player supplies an incorrect answer. The game is played using a web browser interface using spectra from the ChemSpider database (www.chemspider.com) for the problem sets together with structures extracted from the website. Spectra are displayed using JSpecView, an Open Source spectrum viewing applet which affords zooming and integration of JCAMP spectra. Players of the game provide both active and passive feedback regarding the quality of the spectral data resulting in crowd sourced curation and validation of the data.

ChemSpider – Building an Online Database of Open Spectra
Antony Williams; Valery Tkachenko

ChemSpider is an online database of over 20 million chemical compounds sourced from over 300 different sources including government laboratories, chemical vendors, public resources and publications. Developed with the intention of building community for chemists ChemSpider allows its users to deposit data including structures, properties, links to external resources and various forms of spectral data. Over the past three years ChemSpider has aggregated almost 3000 high quality NMR spectra and continues to expand as the community deposits additional data. The majority of spectral data is licensed as Open Data allowing it to be downloaded and reused in presentations, lesson plans and for teaching purposes.

After a long week at the ACS meeting, four presentations, one poster and a two hour training…I headed over to the Lawrence Berkeley National Lab (LBNL) to give a talk. I was hosted by Jeffrey Loo. And I mean hosted. I give a lot of talks in a lot of places but it is rare to experience the level of coordination and organization that Jeffrey provided. After what was almost a 2 hour presentation and discussion I had the opportunity to share dinner with a number of people who attended the presentation and to continue our discussions. It was great…I am used to being shuttled out of the building after a presentation but being asked to have dinner and continue discussing is a much more pleasant transition…especially prior to a red eye flight home.

The presentation was recorded and will be available shortly. For now the actual presentation is given below.

I gave a talk at the ACS Meeting in the Future of Scholarly Communication Meeting yesterday. The abstract is below…and I DID talk about how Viagra keeps flower stems stiff. It was recorded and should go online soon and I will point to it again. For now I have linked the Slideshare presentation

Enhancing discoverability across Royal Society of Chemistry content by integrating to ChemSpider, an online database of chemical structures
The ability to query across a chemistry publishers content using chemical structure searching can dramatically enhance discoverability. RSC has been applying a number of procedures to integrate RSC’s ChemSpider community resource with our published content and databases. These include: 1) entity extraction procedures 2) chemical name conversion procedures using software algorithms and curated dictionaries 3) semantic markup and 4) a crowdsourced curation processes. This presentation will provide an overview of the processes we have utilized in order to provide structure-based integration to RSC content. We will discuss our ongoing efforts to extend the approaches to the mining of data from the rich supplementary information sections of many RSC publications. Our intention is to provide access to synthesis procedures and analytical data and further enrich the ChemSpider database for the benefit of the chemistry community.

I had the pleasure of giving a presentation at the Science Commons Symposium a couple of weeks ago. The meeting was held at Microsoft Research and, as is to be expected, Microsoft had all of the necessary technologies in place to capture the video and provide access to the presentations online. My presentation is available here and all talks are available from this page. It was a great gathering and it was a privilege to spend time with the participants and supporters of Science In The Open.

I had the privilege of presenting at a Science Commons Symposium this past weekend. (What wasn’t so pleasurable was the red eye home and the body ache I am suffering today!) I’m stealing the list of speakers directly off of the symposium page listing

Stephen Friend - Founder and President of Sage, a non-profit research organization that’s revolutionizing how researchers approach the treatment of disease

Peter Binfield – Publisher of PLoS ONE, an innovative online scientific journal and influencial leader of the open access movement

John Wilbanks – VP of Science Commons, an organization dedicated to making it easier to share scientific data and materials

Heather Joseph – Executive Director at SPARC and champion of Open Access

Antony Williams – VP of Strategic Development for the Royal Society of Chemist, Founder of Chemzoo and a leader in the domain of free access chemistry

Jean-Claude Bradley – Associate Professor of Chemistry at Drexel University and pioneer of the Open Notebook science effort

Cameron Neylon – Open Science evangelist, biophysicist and leading advocate of data availability

Peter Murray-Rust – Founder of Blue Obelisk, a group of chemists dedicated to Open Data, Open Source and Open Standards

I knew a number of the speakers personally but met Heather and Stephen for the first time. There was a clear commonality between the speakers and for the audience..that of having access to, and willingly sharing, data and knowledge. Clearly we are all serving the community in our own ways but there is a common frame of overlap in terms of the urgency with which this needs to be done and the big wins that can result from such efforts.  I had met John Wilbanks a number of times but this was the first time I heard him give his talk. For me personally he is a calming voice in regards to terms of licensing and access to data providing a guided tour of the path to the Creative Commons licenses. He introduced a particular statement that fits with ChemSpider  “..the goal is the sparking of generative science” and quoted Jonathan Zittrain who said “Generativity is a systems capacity to produce unanticipated change from unfiltered contributions from broad and varied audiences.”.

Boom-boom-pow. Did that ever hit. People have been asking me how is ChemSpider being used and how would I want it to be used. Here’s the answer…I want them to get value from it however they may use it. We cannot foresee all the ways that people might derive value from content on the database. We cannot define how scientists might choose to work together around the information available. There are a myriad of opportunities to discover something of interest on the database and we see a big part of our job to populate the database with data and links to additional information and to provide a searchable hub to access those data. We get emails emoting thanks for helping people to find “XXXX” and we’re happy to know that we helped. As I’ve said many times…there is method in our madness and despite the fact that we know SOME of the ways that our platform can be used it’s the “generativity” that is very exciting and we hope to hear about. That’s the web for you!

My talk from Slideshare is posted below

I am shamelessly lifting this post from the wonderful blog of Cameron Neylon by way of advertising a symposium that will happen at the end of this week. If you are on the West Coast and want to come and hear about the changes going on in the world.

“One of the great things about being invited to speak that people don’t often emphasise is that it gives you space and time to hear other people speak. And sometimes someone puts together a programme that means you just have to shift the rest of the world around to make sure you can get there. Lisa Green and Hope Leman have put together the biggest concentration of speakers in the Open Science space that I think I have ever seen for the Science Commons Symposium – Pacific Northwest to be held on the Microsoft Campus in Redmond on 20 February. If you are in the Seattle area and have an interest in the future of science, whether pro- or anti- the “open” movement, or just want to hear some great talks you should be there. If you can’t be there then watch out for the video stream.

Along with me you’ll get Jean-Claude Bradley, Antony Williams, Peter Murray-Rust, Heather Joseph, Stephen Friend, Peter Binfield, and John Wilbanks. Everything from policy to publication, software development to bench work, and from capturing the work of a single researcher to the challenges of placing several hundred millions dollars worth of drug discovery data into the public domain. All with a focus on how we make more science available and generate more and innovative. Not to be missed, in person or online – and if that sounds too much like self promotion then feel free to miss the first talk… ”

I will be speaking in a Science Commons symposium on the Microsoft Campus in Redmond in February. If you are interested in hearing John Wilbanks, Cameron Neylon, Heather Joseph, Jean-Claude Bradley, Stephen Friend and myself talking about accelerating scientific discoveries come and join us.

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

My friend and colleague Sean Ekins and I wrote a perspective for the RSC’s Lab on a Chip journal and it was released as an Advance Article, as Free Access, this evening.

The perspective is entitled “Precompetitive preclinical ADME/Tox data: set it free on the web to facilitate computational model building and assist drug development“ . The title is self-explanatory in terms of what we are trying to communicate. The paper is online now and available here.