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…

twilert

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.

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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!

boraBora 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’10Scio10 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….

NPRblog

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.

blogimageI 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”.

activitybyweek

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.

A. J. Williams, V. Tkachenko: ChemSpider: How online resource of chemical compounds, reaction syntheses, property data can support green chemistry.

Track : March 21, 2010

Program Code: 920-3
Date: Sunday, March 21, 2010
A. J. Williams, V. Tkachenko, S. Shevelev, R. Kidd: Enhancing discoverability across Royal Society of Chemistry content by integrating to ChemSpider, an online database of chemical structures
Track : March 24, 2010

Program Code: 1020-8
Date: Wednesday, March 24, 2010

ecrystalsAs we expand the presence of analytical data on ChemSpider through the addition of various forms of spectral data it made sense to start work on expanding the collection of CIFS available on ChemSpider also. At present we have NMR spectra related to ChemSpider SyntheticPages waiting to go online and a large number of Raman spectra waiting to be processed and deposited. For now however our efforts are focused on the deposition of CIFS associated with the eCrystals platform at Southampton. This is manual work unfortunately as we need to confirm that the CIF itself matches the molfile that is online. When there are multiple components in a unit cell we need to ensure that we deposit against the correct structure etc. We should have a few hundred CIFs deposited in the next few weeks.

Since returning with early feedback from the American Chemical Society meeting in San Francisco a few weeks ago work has progressed on improving work flows and usability, specifically for depositors of new submissions to synthetic pages. Shortly an update to CS|SP will be made providing improved access to analytical data within a synthetic page, facile deposition of new pages (but we welcome your input to improve further!), a number of bug fixes and improved integration into the ChemSpider database. I am interested in talking to readers who might be interested in contributing to ChemSpider SyntheticPages but don’t know where to start. Please ping me at tonyATchemspiderDOTcom.

JC Bradley gave his own overview of CS|SP over at his blog recently….

The integration to NMRShiftDB has been switched off for the time being while some new bugs regarding the integration are resolved. We’ve been in discussions with Egon Willighagen regarding the nature of the integration challenges and it comes down to how the SMILES that are being passed to NMRShiftDB are being interpreted. Check out the comments section for more details. There is no time line associated with fixing this integration at present but we do want it resolved. We will be focusing our efforts on doing direct look ups into the database for the immediate future.

My article on Mobile Chemistry is now available online…

Mobile chemistry – chemistry in your hands and in your face

The technology we’ve got used to accessing through our desktops is moving at high speed to our mobile phones, says Antony Williams

It is amusing to watch movies from the 1980s and see the stars of the period holding a so-called ‘mobile phone’ to their ear. This mobile device used to be the size of a brick, with a pull-out antenna to boot. It served one function: to allow two people to talk to each other across a connection challenged by static and dropouts. How things have changed.

Comment

Read the rest of the article here

hirschhaeuser@gmail.com

I had previously announced the integration of NMRShiftDB as a beta integration. I have received feedback both on-blog and off-blog about the performance of the algorithms and the need for improved display of results. Wolfgang Robien, one of the major contributors to the domain of curated NMR databases and NMR prediction, gave feedback in the comments section regarding the performance of the initial integration. There was a significant bug highlighted in the integration that resulted in dropping double bonds when passing structures from ChemSpider to the API for NMRShiftDB. This was clearly a very significant issue but Stefan Kuhn has fixed the issue. NMRShiftDB was taken offline for a couple of days while the error persisted but is back online today with this issue resolved.

What we KNOW we need to do to enhance the integration is as follows:

1) Always display the chemical structure and associated numbering scheme

2) Display the spectrum type so it is clear what nucleus is being displayed

3) Indicate whether the spectrum displayed is a database hit or is a predicted spectrum

4) Display the details of the assignments including the number of SHELLS used in the HOSE code based prediction.

Our work on the integration to NMRShiftDB will continue and we will enhance it moving forward. Thanks to all for the ongoing feedback and testing.

opensciNY I will be presenting at the OpenSciNY 2010 conference on May 14th. OpenSciNY is a free, one-day conference on the impact of publicly accessible scientific tools & resources, open access publishing in the sciences, and open data/notebook efforts. I am looking forward to spending time with the attendees interested in these areas and being on the agenda with my fellow presenters, most of whom I know personally and have presented with on numerous occasions. In these gatherings, and with such a common mindset, the future of Open Science and its impact and contributions to society are clear. While there is much work to be done the momentum continues to gather. The future of OpenScience is exciting, stimulating and fun to envisage. Come along to OpenSciNY and engage with us!

Every year, Chemistry World and Education in Chemistry offer an internship over the summer for a would-be science writer to gain some experience working with two of the best chemistry magazines around.

The position is for 8 weeks (start/end dates negotiable) and comes with a bursary of £1750 sponsored by the Marriott bequest.

Activities undertaken would include researching and writing blog posts and news articles and recording podcasts for Chemistry World, writing a feature article for Education in Chemistry and pieces aimed at sixth-formers. They will also help lay out and proofread the print issue of Chemistry World.

For more details see : http://www.rsc.org/AboutUs/rscwork/Sciencewriterinternship.asp

Applicants should be members of the Royal Society of Chemistry. You can join up as affiliates at www.rsc.org/join.

bioitLife’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!

Andrea Wendel is a student at Potsdam University in upstate New York and is one of Martin Walker’s chemistry majors. Martin is on our advisory group for ChemSpider. Andrea was kind enough to answer the question “How do you use ChemSpider” and I felt it was of value to share the short report with the readers. We’d love to hear from other users about how you use ChemSpider and your feedback that could be shared with blog readers. Thanks

How I use ChemSpider

I use ChemSpider on a regular basis when I need additional or supplemental information about molecules or reactions. Homework or lab write-ups require the most need for this website. I use the main box in the center of the page to search for my information. I mainly use systematic names, trade names or formulas to search for my data. Most results appear in a very short time, which is very helpful. I rarely use the structure search option, although if my type of research was different I might find it more useful. For many of my lab write-ups and papers, the information I search for includes common physical properties such as boiling point, melting point, and density. The molecular weight and safety comments are also items I find extremely useful. The icon at the end of the information that leads you to the webpage it came from is another useful option, as the original source is very important to know. ChemSpider has many features that are useful to an undergraduate student.

By: Andrea Wendel

A couple of weeks ago I gave a talk at the Lawrence Berkeley National Laboratory at the end of the ACS meeting. It was great to meet the attendees and share some good conversations about Open Data, Open Science and our efforts with ChemSpider. The talk was turned into a screencast and is shown below.