ChemSpider Blog

I have been at the BCCE conference here in Dallas for two days. I gave two talks in a session hosted by Harry Pence and Bob Belford, participated in their workshop on Social Networking and spoke about how to set up a blog and my experiences of blogging and today led a workshop on Online Public Compound Databases. Today was 3 hours of discussions, an agenda that was strict enough to keep us on focus but free enough to allow lots of questions and real time web-based searching. I really enjoyed the challenge of the session in terms of discussing the challenges of teaching web-based literacy in searching for chemistry online. The Powerpoint aspect of the presentation is on Slideshare below

A few weeks ago we won an award from Bio-IT World for Community Service. Allison Proffitt from Bio-IT world interviewed me recently in connection with the award and some of the history behind ChemSpider and wrote it up for the magazine. The resulting article is also available online here.

We are in the process of a website redesign with the intention to deliver a new look and feel in time for the ACS meeting. We have some draft pages available online and we would like YOUR feedback please!

We have five drafts of the Home page that we would like your comments on. Let us know which one is your favorite by giving us the number of your favorite when you comment as well as any other comments.

Home Page 1

Home Page 2

Home Page 3

Home Page 4 (static image)

Home Page 5 (static image)

The draft of our Chemical Record page is here:

Chemical Record Page

Comments and feedback welcome!

We’re very proud that ChemSpider is one of the shortlisted finalists for the ALPSP 2010 Publishing Innovation award – the other finalists are Mastervision from DataSalon, Semantic Biochemical Journal from Portland Press, and UniPHY from the American Institute of Physics. The winners will be announced on 9 September at the ALPSP International Conference, so good luck to all, fingers crossed here and we’ll let you know the result.

First post for me on the ChemSpider blog, so a quick introduction. I’m Richard Kidd, and I manage the Informatics team at the RSC in Cambridge. We work on the technical enhancements of our publications (such as 2007 ALPSP Innovation award winner RSC Prospect) and we’re supporting the current and future ChemSpider developments alongside the original team – and this also includes support for ChemSpider users and depositors. We’re all here.

It is now a year since the Royal Society of Chemistry (RSC) acquired ChemSpider and much has happened in what is really  quite a short space of time.

ChemSpider has added more compounds and data sources, significant compound collections, there are now links to RSC Publishing and PubMed which are effectively making these resources structure-searchable, we have set-up a micro publishing platform with the development of ChemSpider SyntheticPages and we have facilitated mobile chemistry with the launch of  ChemSpider Mobile.

We are impressed with these developments and we hope you are too. We are always interested to hear your views.

Look out for even more new features which will be released shortly.

If you are attending the Fall ACS Meeting in Boston, August 22-26 you can learn more about all of these developments and more by attending an interactive workshop which is being held on Tuesday, August 24, 3:30 PM – 6:00 PM in the Boston Convention & Exhibition Center, Room 102B. Register now.

You could also attend one of the lectures being given by Antony Williams:

How community crowdsourcing and social networking is helping to build a quality online resource for chemists – August 22, 2010 10:25 am
LOCATION: Seaport Hotel, Room: Seaport Ballroom A

Chemistry in your hand. Using mobile devices to access public chemistry compound data – August 26, 2010 1:30 pm
LOCATION: Boston Convention & Exhibition Center, Room: Room 156A

 We look forward to seeing you there.

RSC Members got to hear all about ChemSpider SyntheticPages in a short article penned by Peter Scott and myself. We also ended up having the cover dedicated to the article. Meanwhile, over at ChemSpider SyntheticPages of late new depositions of syntheses are daily and the database is growing. Here’s hoping we have 500 syntheses online by the time we get to the ACS meeting in Boston!

In March of this year I attended the RSC Editors Symposium in Brussels and helped lead a couple of workshops with Richard Kidd about Enabling the Internet for Chemistry. The Editors Symposium is described here. The final report is very interesting in terms of what editors would like to see happen in the future and garnering feedback for our efforts today. The feedback on our sessions, shown below, was overwhelmingly positive. The sessions were fun, interactive and overwhelmingly positive.

D: Enabling the Internet for Chemistry:
ChemSpider and RSC journals

• I was very impressed by the ChemSpider search engine
• A valuable research AND teaching tool.
• The Chemspider workshop was the most interesting which looks to be very useful to the scientific community and I have been greatly encouraged to go away and try it for myself
• I was unaware of the content and use of this software and think it will be an extremely powerful resource
• I also enjoyed the session on ChemSpider and have had a long play on the tool. It has a lot of compounds but unfortunately at the moment not many references which limits its current use
• Although I was aware of ChemSpider, the workshop provided good information concerning the tremendous opportunities for exploitation in teaching and research
• I was also not aware of the power of ChemSpider and will certainly recommend its use to my institution
• The ChemSpider was very interesting as I believe it opens up huge possibilities for the RSC, for example, ChemSpider education, especially for pre-16 year olds which wasn’t addressed
• Very ambitious project; great service of RSC to the scientific community
• Learning about ChemSpider was a highlight as this new source has the potential to make a significant impact in how chemical structures are researched online

ChemAxon have introduced support for both PubChem and ChemSpider into their MarvinSketch canvas. This is in version 5.3.4. We also have fixed and updated the integration with ACD/ChemSketch and Symyx Draw integration is also in place. We are open to integrating to other structure drawing packages if you are interested.

ChemSpider wins ‘Most Innovative Software’ Award

18 June 2010

ChemSpider, the Royal Society of Chemistry’s online chemistry community and database, scooped the Innovative Software Award at the iExpo/KM Forum 2010.

The prize is organised by GFII (the Association for Professionals of the Information Industry) and recognises leading software providers in the information industry for their innovative capabilities and user interfaces.

The organisers, with the intention of promoting the industry of professional information and knowledge management, dedicated the prize for the 16th consecutive year to the most innovative organisations.

Presented by Didier Benard, from Sanofi Aventis R & D, the award recognises a non-commercial initiative in enhancing information online whether for the professional community or for the general public. The jury selected ChemSpider as an award winner for providing free access to data on chemical information (both text and structure-based), which is reliable and controlled by an international expert community.

ChemSpider links together compound information across the web, providing free text and structure search access of millions of chemical structures. With an abundance of additional property information, tools to curate and use the data, and integration to a multitude of other online services, ChemSpider is the richest single source of structure-based chemistry information available online.

Antony Williams, VP of Strategic Development, ChemSpider, said: “The recognition of our efforts to provide the internet’s premier online search engine for chemistry by such a distinguished panel of judges is very flattering. This award further encourages us to remain focused on the delivery of the world’s primary free chemistry portal.”

It’s nice to be acknowledged! An email in my inbox yesterday acknowledged the Mobilizing Chemistry presentation from the SLA.

“Mobilizing Chemistry – Chemistry in Our Hands” is being tweeted more than any other document on SlideShare right now. So we’ve put it on the homepage of SlideShare.net (in the “Hot on Twitter” section).

Well done, you!

- SlideShare Team

I have been in New Orleans for two days at the SLA conference and talking to librarians about ChemSpider and its direction, grand vision and progress. What a reception. There were two instances where I blushed…and that doesn’t happen often…in fact I’m done for this year now! We were showered with praise for our efforts …and of course given a long list of things to do! That’s always good. I gave two presentations…one as a general overview and the other on “Mobile Chemistry”, my views of what is going on in the domain and an overview of a series of Mobile applications etc. They are embedded below and on slideshare.

I use Twilert to track Twitter activity about ChemSpider. Looks like the announcement about Mobile ChemSpider caused quite a stir. One day’s Twilerts shown below…

If you are an iPhone user (as I am), have an iPad hanging around to check email 20/7 (I have to sleep sometime…), or use a phone with a browser, I suggest you point it to the new ChemSpider Mobile at  http://cs.m.chemspider.com. There you’ll see a simple interface, shown below, that allows you to search across our database of almost 25 million chemical entities based on chemical name (systematic, trivial or trade, registry number etc) and retrieve a list of intrinsic properties, a list of predicted properties, a list of associated identifiers, with links to Wikipedia if available, and a Google based search for the chemical based, for now, on the associated InChIKey. Check it out, give us feedback.

We are also working on providing access to ChemSpider SyntheticPages in the same way and the first screen shot is shown at the bottom. Things are always changing and, I believe, for the better.

Best-Practices_137

Originally uploaded by Bio-IT World

A couple of weeks ago Valery and I were in Boston at the Bio-IT meeting and received the Bio-IT Best Practices Award for Community Contribution. That’s us receiving the award (Valery on the left and me in the middle, with Kevin Davies, Bio-IT World Editor and Chief on the right) looking distinctly uncomfortable in shirts and ties! We don’t get to stand on an awards stage very often!

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 haven’t seen the movie yet about the bottled water industry. I can’t comment on the accuracy of what is represented. But, as a chemist, a father and as a water drinker I am definitely going to go see this movie. I encourage you to watch the trailer and decide for yourself whether its worth you seeing it too. When I have seen the movie I will make my comments about it…

In the past 48 hours I have read book reviews on Amazon, movie reviews on Netflix and articles on Wikipedia. I haven’t written any book reviews for Amazon, ever. I have not written any movie reviews for Netflix, ever. But, I have edited and curated articles on Wikipedia. Let’s bottom line it though…I am a taker from the resources more than a giver. I’m a busy guy and I believe that other people can review books and movies as well as I can (though of course we might differ on opinions). Where I feel an obligation to comment is in those places that I am really passionate…in the blogosphere when there is something being said that doesn’t sit squarely with me. I tend to challenge things I disagree with rather than applaud things I do agree with…except for my friends where I feel obliged to give them recognition for their efforts. Friends do that. I read a lot of blogs..a lot of web pages…a lot of resources. But I very rarely go out of my way to comment on the contribution the writer might have made to my day. I judge most of us operate in this mode. It is what it is….

As we work to produce a platform for the sharing of synthetic procedures/syntheses by developing ChemSpider SyntheticPages we run into the same challenge with this platform as we have with ChemSpider. It is related to the same human condition of us being users and takers over contributors. There is nothing inherently objectionable about this…we all do it. We contribute to something we care about, believe in, feel compelled to participate in. But, it does limit the rate of growth, the participation in and the success of a platform. In terms of a crowdsourcing platform it’s success can be measured by the number of visitors, the number of contributors, the quality of the content, the changes the platform can effect and a myriad of other factors. In terms of traffic ChemSpider continues to increase in terms of the number of visitors. The plot below shows the growth from mid July 2009 to the last week of April 2010. Overall we have seen a 3X growth. While the absolute numbers can be questioned, and differ from measurement system to system the trend is a self-consistent trend.The dip in December is called “Holiday Season”.

During this period have we seen a threefold increase in the number of curators? No. We have seen an increase of about 2X in the number of people who are adding data, links, publication links and spectra to ChemSpider though. But, let’s be clear about these numbers…this might max out at about 45 contributors max….for a peak of 45,000 visitors. That’s a very small percentage! It categorically shows that we take more than we give.

For ChemSpider SyntheticPages we are hoping for more contributions. More people to deposit their syntheses onto the system to share with the chemistry community. What can we offer to encourage such engagement?

1) Every record will have a DOI generated that you can list on your resume, should you choose. Basic development is done already. Testing is about the start.

2) You, the person who did the synthesis, get the recognition. You are the author. Each page can be attributed to a research group also so that the Group Leader would also be able to get aggregate recognition for contributions. it is why you see on pages “From the Research Lab of ****” for example

3) We will also host your analytical data and structures and perform mark-up of the article on your behalf until we have training materials in place for you to do your own markup. Your work will be “well-represented” in a free community resource for chemists that is destined to become one of the major contributors to the domain.

4) Your work will be repeated, peer-reviewed, critiqued and hopefully expanded upon…all good for your science and your reputation ultimately.

5) We will periodically offer recognition, rewards and acknowledgment for masterful synthetic procedures in a public forum. We intend to put in place a full recognition system, above and beyond that one in place at present.

So, what is standing in the way of adding your syntheses onto ChemSpider SyntheticPages. Other then some work, what is in the way? It’s a real question. Is it? 1) your boss won’t let you; 2) you don’t see the value or point in sharing your syntheses; 3) you are concerned about copyright transfer and think won’t be able to use the synthesis in  a future publication; 4) you don’t know how; 5) one of many other reasons. Let us know please….we need your feedback to position and develop CS|SP for you.

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