ChemSpider Blog

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.

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.

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!

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.

As 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.

Read the rest of the article here

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.

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.

We’ve been depositing a lot of new data into ChemSpider over the past few weeks. We’ve been adding millions of new compounds from chemical vendors, from RSC databases and articles, from updated government databases, contributions from academia and from some of the online Open resources.

Recently I sat in on the presentation of Rich Apodaca who talked about ChemPedia. Rich shares a lot of the views that many of us do about the value of having open resources of chemical compounds online and has contributed ChemPedia to the domain. On Slide 20 of his presentation Rich gave an overview of a Missing Service that needed to provide a number of capabilities. These were an on-demand unique ID, expose a URL to link to the structure, support synonyms and integrate peer review. ChemSpider does all this with maybe one caveat…we expect the ID to include the URL….so  http://www.chemspider.com/Chemical-Structure.2034.html or http://www.chemspider.com/2034 is the link to the structure that we assert is the structure of Xanax. If you want to add additional synonyms  you can do so. If you want to curate, add comments etc you can (peer-review). If you want to add new compounds you can and you are issued a new ChemSpider ID. I would agree that our IDs are not as distinct as those that Rich and ChemPedia are generating..but they are of a similar format to PubChem IDs..i.e. “just numbers”. Check out ChemPedia and contribute! We are taking advantage of the fact that Rich makes the data Open for download and download the last iteration (664 compounds) and deposited them to ChemSpider here.

Tuesday morning at the ACS meeting here in San Francisco…two talks done, one 2 hour training session completed, one poster presented and two talks left to give before heading off to the Lawrence Berkeley National Laboratory to give my final talk before the dreaded red-eye home. I am so looking forward to sitting on a cramped plane overnight…

My presentations delivered so far are already on SlideShare and are linked below for display.

For the past few months we have been busily developing new functionality and capabilities for the ChemSpider platform with the intention of making navigation easier, enhancing integration to external resources, adding new rich data sources and providing access to brand new capabilities. This new functionality has been described in a series of recent blog posts today and is outlined below.

Improving the ChemSpider interface using tabbed infoboxes

Introducing NMR prediction capabilities to ChemSpider

Linking Google Patents searching to ChemSpider

Integrating RSC Databases into ChemSpider

Integrating RSC Publishing Beta into ChemSpider – includes integrations to Google Scholar, Google Books and Microsoft Academic Search

OVERVIEW

The LBNL Library is hosting a seminar for researchers interested in online collaboration, data storage and curation, data exchange, crowdsourcing, and open access.

This seminar will explore ChemSpider (http://www.chemspider.com/) – a free access service providing a structure centric community for chemists and the richest single source of structure-based chemistry information.

EVENT DETAILS

March 24, 2010 – Wednesday
3:00 p.m. – 4:30 p.m.
Building 50 Auditorium, Lawrence Berkeley National Laboratory

Bring your laptop for a hands-on demo session.”For non-Berkeley Lab personnel: Please contact Jeffery Loo (JLLoo@lbl.gov) by Monday, March 22, 12:00 p.m. for a visitor pass and shuttle bus directions.  A visitor pass is required for entry into the Berkeley Lab by guests.

ABSTRACT

The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).

ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.

This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.

We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.

Following the presentation and a question and answer session, a hands on session showing how to search for, curate and deposit data on ChemSpider will be given for interested parties.

SPEAKER

Antony Williams, PhD, is a leader in the domain of free access chemistry. He is the Vice President of Strategic Development at the Royal Society of Chemistry and is the host of ChemSpider, a free online structure centric community for chemists.

ChemSpider began as a hobby project in a basement and went on to become one of the most popular Chemistry websites with the highest quality of data available online. Antony spent over a decade in the commercial scientific software business as Chief Science Officer for ACD/Labs, one of the domain leaders in scientific software. He is an accomplished NMR spectroscopist with over 100 peer-reviewed publications. During his career he was the NMR Technology Leader for the Eastman-Kodak company and has worked in both academia and national government research institutions.

We are presently receiving sign ups for our training session on ChemSpider. The session will be on Monday afternoon between 4-6pm (details below) It is free to attend and we’d love to see you there if you are in San Francisco at that time. Sign up here…

Royal Society of Chemistry
How to get started with ChemSpider – Searching, Structure Deposition and Database Curation
Instructor(s): Antony Williams, VP Strategic Development ChemSpider
Where: Moscone Center
Room: 110
When: Monday, March 22, 4:00 PM – 6:00 PM
>> Click here to register for this workshop
This session will give the opportunity to learn more about how to search ChemSpider, how to deposit your structures and how you can participate in curation of the data.  Presenter: Antony Williams, VP Strategic Development ChemSpider

I was sitting down today to review what presentations are coming up in the next few weeks and how much writing and travel was ahead of me. Ugh. Painful. During the next few weeks of conference season there will be a lot of talks and, as usual, a lot of late nights before the presentations to write new talks or modify existing talks. I will be at the ACS meeting in San Francisco this spring and will be giving four presentations, a poster and leading a training session on ChemSpider. The presentations are outlined below. Looking forward to seeing you there and it would be great to hear from any of you who would like to get together and connect about community chemistry over a coffee.

Presentation: Utilizing ChemSpider as a platform for education and exposure of student data to the community.

Educators and students now have access to rich internet resources of information. RSC’s ChemSpider is a community resource of structure-based chemistry delivering data including chemical compound collections, reaction synthesis procedures, physicochemical property and various forms of spectral data. ChemSpider offers the opportunity for the community to participate in populating, annotating and curating the data on ChemSpider. We believe that ChemSpider offers an opportunity for educators and students to participate in the ongoing development of a rich resource for the chemistry community. This presentation will suggest some potential uses of the ChemSpider website in terms of integrating into lesson plans. We will also outline how students can expose their structure and reaction-based research work via the ChemSpider platform for the benefit of the community and their online scientific reputation.

Presentation: ChemSpider – How An Online Resource of Chemical Compounds, Reaction Syntheses, and Property Data Can Support Green Chemistry

ChemSpider is an online database containing in excess of 20 million chemical compounds and associated experimental and predicted physicochemical data, reaction synthesis details and analytical data. A significant amount of the data contained within the database has been harvested and collated from a number of inventory systems and integrated to provide a centralized resource for the community. The ChemSpider database has the added benefit of being available for community deposition, annotation and curation. As a result it offers the potential for researchers to share their latest research with the public and participate in the creation of a rich resource of chemistry related information for the Green Chemistry community. This presentation will provide an overview of present capabilities and discuss the future vision for the platform.

Presentation: ChemSpider, how a free community resource of data can support teaching NMR spectroscopy

ChemSpider is an online database of chemical compounds, reaction syntheses and analytical data. Provided by the Royal Society of Chemistry, our intention is to provide a free internet resource of chemistry related data for the community. ChemSpider is unique in its role of allowing user depositions of chemical structures, synthesis procedures and analytical data and, in so doing, provides an environment for crowdsourced gathering of information. To date over 2000 1D and 2D NMR spectra have been deposited online by the community and are available for reuse. The data have been used as the basis of a spectral game whereby students can learn NMR by interacting with the data. This presentation will provide an overview of the tools and capabilities presently available on ChemSpider to support teaching NMR in the undergraduate curriculum and will outline how the community can participate in enriching this resource for the benefit of all.

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.

Poster: Utilizing ChemSpider as a platform for education and exposure of student data to the community

Recently I announced the release of ChemSpider  SyntheticPages. We are honored to have an editorial board of chemists to assist in directing the project and they are introduced below:

A couple of days ago I came across a video on YouTube about “Water Marbles”. I’ve inserted it below…I recommend watching it…it’s excellent!

It’s excellent because by time I had finished watching this I was both excited and confused. Confused because how could I not of heard of this experiment. Even if it was to work why were those spheres so big and uniform? Excited because I’d been looking for some good kitchen chemistry to do with my kids and this would be a great example. I couldn’t really get my head around how the observations were working but on a rushed grocery expedition prior to going into ScienceOnline2010 #scio10 this part weekend I threw everything necessary into the grocery basket to repeat the experiment.

At ScienceOnline2010 I was involved in a number of discussions, as usual, regarding data quality, curation and assertions….this being based on my experience with curating the ChemSpider database. Today I sat in on a discussion entitled “Getting the Science Right: The importance of fact checking mainstream science publications — an underappreciated and essential art — and the role scientists can and should (but often don’t) play in it – Rebecca Skloot, Sheril Kirshenbaum, and David Dobbs.” it was an interesting exchange with comments such as “newspapers and magazines don’t check facts” and the urban myth that a one minute kiss burns 26 calories while the fact is that a Hershey’s Kiss contains 26 calories.

Post ScienceOnline2010 I got home this afternoon to find my kids desperately wanting to do kitchen chemistry so, with pessimism I started to work through the experiment with them. They mixed and stirred and cooled and heated. They got to see a lot fizzing and to see crystals grow which they thought was great. It of course failed dismally as it has for many other people, including this guy, but they had a great time. In parallel I was doing some fact-checking to see whether or not to prepare them for disappointment.

There have been a lot of exchanges online about this topic of water marbles with chemists exchanging concepts about the science behind it if it did work. See here for example. The video has gone viral across many sites. Very impressive for a hoax really…and it did get me interested in doing kitchen chemistry. The truth is a lot easier though…and still good chemistry! Watch Steve Spangler in action below…

The polymer beads can be bought here.

There’s more Kitchen Chemistry to come but I think I’ll stick to some of Theodore Gray’s guidance …maybe time for some Mad Science at home…

I’m off to ScienceOnline2010 in a few minutes. It’s the last day of the conference and the experience has been a highly positive one. I’ve finally met people face to face that I have been connected with for over 2 years….and congruency is always good…they are as interesting, passionate and generally nice people face to face as they are online. I also managed to catch up with a number of old friends. I got to meet some new people focused on changing the flow of communication for ScienceOnline and working hard to do so. #scio10 is different….there’s an energy in the air that I haven’t experienced at any other scientific gathering other than SciFoo. This is an audience that is introducing me to social networking tools that I’ve never heard of…that doesn’t happen often. It has to be that over half the attendees are twittering. iPhones are everywhere. Flips are out capturing video in the sessions and are uploaded online shortly thereafter. The conversations are open, opinionated, full of energy and motivating. This is MY type of conference and I’m fortunate to live less than half an hour away.

The dinner event was fun, giggly, five minute “Ignite” talks were given (I gave two …one on Curating Chemistry online and one with JC Bradley regarding the spectral game). The first of those is linked here and shown below.

Today I will be giving a live demo of ChemSpider to anyone interested and around at the end of the conference. It’s nasty weather so people might be leaving early.

I found myself a virtual running partner for my 1000 miles in a year challenge assuming my calf muscle tear heals. We’re going to try and figure out how to raise money for asthma. Anyone want to join us as to form a virtual team let me know…

Bora and Anton have done a tremendous job organizing the conference. Clearly there is a great team supporting them and the Sigma Xi facility is excellent. Terrific conference all around….glad I spent the weekend this way…