ChemSpider Blog

My presentation today at the Wolfram Data Summit in Washington DC gave me a chance to rant about the quality of data online and ask the question who really cares? Many of the database hosts don’t appear to care (most don’t respond to emails when I find errors, very few give anyway to annotate an error for example). The talk seemed to be well received and shocked a few people.

Recently I co-authored a publication with Harry Pence for the Journal of Chemical Education. And today the news that it is published online. Please follow the instructions below if you want to be one of the first 50 people to obtain a copy.

“Your article, ChemSpider: An Online Chemical Information Resource, is now available on the Journal of Chemical Education website.  To view your article, please click on the ACS Articles on Request link below:

http://pubs.acs.org/articlesonrequest/AOR-gUuatr3ABq9RiePFMyaK

As part of the ACS Articles on Request e-prints service,  ACS authors may choose to e-mail or post this link on their website to distribute up to 50 free e-prints of their final published article to interested colleagues during the first 12 months of publication. After that 12 month period any author’s article may be accessed without restriction via the same author-directed link that appears above.  The link directs readers to the Full Text version of the article on the ACS Publications website.

Please note: To access the Articles on Request link, please log in to the Publications website using your ACS ID.  If you do not have an ACS ID, you will need to Register for one for free by clicking on “Register” near the top right corner of the website.”

The first circular for the 16th RSC-SCI Medicinal Chemistry Symposium, 11-14 September 2011, Churchill College, Cambridge, UK is now available here.

When you’re viewing a compound page in ChemSpider e.g. hydrogen peroxide there are several ways to find more detailed RSC information (articles and books) about that compound:

1. In the “Articles” infobox, the results under the “Links & References” tab are links to various journals that have either been deposited or added by ChemSpider users. When the RSC enhances one of its articles, the most important compounds in the article are submitted to ChemSpider for deposition (see here for more details), and when this happens, the article details are also deposited so that a link will appear in this box. As such, there usually won’t be thousands of links in this box, but those that are there will for example pick up references to compounds which maybe aren’t named explicitly in the article (but for example are drawn out in a figure) and as such couldn’t be found by a simple text serach.
2. The results under the “RSC Journals” tab in the “Articles” infobox are the results of passing a search into the RSC publishing platform to retrieve all of the journal articles that contain any approved synonym for the compound (in the “Identifiers” infobox under the “Names and Synonyms” tab). Since these lookups first appeared in ChemSpider 6 months ago (see here for more details) this platform has progressed from bring a beta version, to now being the fully-fledged publishing platform for searching on and delivering RSC journals, books and databases. To investigate the functionality of this platform more and refine your search results list, click on the link above the list of results to “Click here to explore results” and this will allow you to sort the results by date, or apply filters e.g. to restrict the results set by author, date range,  journal etc.). This is useful since for common chemicals, the list of results returned can be long.
3.  The “RSC Books” tab under “Articles” performs a similar search on occurences of the approved synonyms but on RSC books rather than RSC journal articles.
4. Likewise, the “RSC Databases” infobox shows search results of the same approved synonyms but this time the results are from the various RSC abstract databases named in its various tabs. This means that they contain references to the compounds in non-RSC articles.

With one week to go before the American Chemical Society meeting we have unveiled the new ChemSpider website for feedback and comments.We believe that we have made the site easier to navigate, more visually appealing and faster to navigate. The new site map should be very helpful in navigating the site.

We are presently gathering feedback from users with different browsers, updating some of our documentation and generally optimizing performance and navigation across the site. All feedback is welcomed…we’d love to hear from you!

Have you ever had a niggling feeling that you’ve been missing some corner of ChemSpider which might have a tool that will make your life much easier?

http://www.chemspider.com/Sitemap.aspx is the new sitemap for ChemSpider which lists all of the different pages in it and will help you to get an overview of all the different things that you can see and do on ChemSpider.

There are also brief descriptions about each page which will, where necessary, suggest input examples if you just want to try something out but aren’t quite sure what to type into the boxes. If you are a ChemSpider depositor or curator and view the sitemap when logged in you will see additional pages relevant to your assigned roles.

There will be two presentations and a training session about ChemSpider at the ACS meeting in Boston. We hope to see you there if you are attending the meeting. In any case the presentations will be uploaded after the conference onto the SlideShare site.

The presentations are:

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

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

The training session is detailed below:

“An Overview and Update of RSC-ChemSpider Capabilities”

Tuesday, August 24, from 3:30-6pm,  Boston Convention and Exhibition Center, Room 102B

The Fall American Chemical Society meeting in Boston is just around the corner and we are finishing up the integration of some recent developments. As is usual we have way more things that we wanted to deliver than we have been able to implement. But we’ve always got more ideas so this is no surprise. The biggest change is the new website redesign that a number of readers of this blog voted on and influenced. In the next few days I will announce new features and integrations that we will be delivering, all being well!

Pillbox is defined on the website as “…enables rapid identification of unknown solid-dosage medications (tablets/capsules) based on physical characteristics and high-resolution images.” I first heard about PillBox when David Hale, “host” of Pillbox, and I were on the same speaking agenda at a meeting in Washington. David is a very engaging speaker and I really appreciated the visual nature of what they are working to deliver. Trying to identify the pharmaceutical ingredients in a pill from the color and pill imprint etc is tough…then comes PillBox.

Using the API provided to PillBox we have integrated ChemSpider directly to PillBox. So, in the future when you search on Viagra on ChemSpider and find Sildenafil Citrate you will see a new link to Pillbox (we are determining where on the page at present) and under there you will see the links to Pillbox.

A search on Viagra on Pillbox will show this:

but using the API we can show the information embedded into the ChemSpider page as show below.

Notice that all three Viagra dosages are shown and each can be opened to preview one at a time. 

This is simply one more example of integrating into the online resources becoming increasingly available and focusing on having ChemSpider being a structure-searchable hub connecting them together.

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!

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