ChemSpider Blog

A couple of days ago I asked whether readers could see any issues with the structure of Micrococcin P1 published in the C&E News article this week. A few people took a stab on blog and off blog but only Stuart Cantrill from the Nature Publishing Group got it right. One double bond in the wrong place. Subtle, but rather important. General structure drawing tools will help with things like this. For example, a human might not see the issue in the structure of Taxol to the left very easily. Software tools designed to flag valency issues will show the issue easily.

In the expanded image the pentavalent carbon is marked. The same type of tools would have shown a positive charge on the sulphur in the ring for the incorrect structure of Micrococcin.In the same way, software tools can recognize charge imbalances and incomplete stereochemistry.

I sent an email to the editor of C&E News when I noticed the structure issue but didn’t get a response. Nevertheless it is an advantage of online publications that images can be swapped out easily. This has been done for the online article here at this point and the change, while subtle, is there (shown below).

The structure is now on the ChemSpider database here.

Drawing accurate representations of chemical structures is difficult. Copying them from publications can be fraught with errors and it is common to see that structures in publications are incomplete in their definitions of stereochemistry and that groups are missing anyway. Such is the nature of the beast. I have blogged recently about an observation of a structure drawing error in C&E News and the editor was kind enough to comment. Here’s an image of a structure from a C&E News article about Micrococcin P1 from this weeks magazine. Check out the structure….can you see any issues?

Now that ChemSpider is part of the RSC we will be able to offer some of our experiences in identifying potential errors in structures before they are published. There are ways to do this so that both authors and editors alike get flagged to such issues. This is way down the road from migrating ChemSpider to RSC servers but would definitely bring value to helping to ensure quality of data in Chemistry.

Feel free to post your comments regarding any issues you see with the structure as drawn.

PhysChim62 (PC) is someone I meet with regularly on the Wikipedia Chemistry IRC chats. We’ve never met but I judge we have mutual respect, earned through many hours of working to improve the chemistry on Wikipedia. PC has been at it for a long time and has a broad reach in the WP community…I’m focused primarily on structure validation and delivering tools which can be of value to Wikipedians. If you have an interest in Chemistry on Wikipedia it’s one to add to your blogroll/reader as PC will likely touch on this quite regularly, as well as other things of interest. The blog is at http://phoscarb.blogspot.com/.

We’ve received a lot of kudos, congratulations and praise for our decision to become a part of the RSC. We thank everyone who has gone out of their way to acknowledge the shift in our circumstances. We did have some concern that some people would judge us on “selling out” rather than going it alone. Based on the feedback to date our worries were unfounded.

Tonight the comments of Warren DeLano, developer of the Open Source platform PyMOL (more details here), truly struck a chord with me. His comments are below.

“DeLano Scientific LLC congratulates Antony Williams et al. on the acquisition of ChemSpider by the Royal Society of Chemistry. This historic event provides a compelling example of how an independent open-minded project (open-access, open-data, open-source, etc.) can increase its resources and extend its longevity without compromising on its core mission, as is always necessary when a project “sells out” to a for-profit company beholden to narrow fiduciary objectives.

We hope that the ChemSpider / RSC example will both inspire more open-minded individuals to strike out on their own with similarly ambitious efforts and encourage various non-profit and government entities to actively recruit successful projects back into “the establishment” in ways which do not compromise project integrity and yet can enable even greater long-term positive societal impacts.”

Specifically the statement “without compromising on its core mission” hit me. It’s exactly why the fit with the RSC felt right. RSC are focused on Advancing the Chemical Sciences and look upon ChemSpider as a way to help the community to access information, data and knowledge and bring together chemists, publishers, vendors and other parties. It’s been our mission all along. So, we are not compromised as we have the same intentions. A great match.

Thanks to Warren for the recognition. Much appreciated.

I’m heading over to the UK shortly for a week-long meeting with the RSC. In case there is any confusion I WILL be an employee of the RSC working on ChemSpider and we are building our ChemSpider team at present. I’m really looking forward to the meeting as I have already met many of the people and they are skilled, focused and yet lighthearted and funny. Yes, funny. Maybe it comes with territory of working with a young, passionate team of people. One thing about the RSC that I enjoyed during my last visit was the ENERGY in the building. The place is buzzing. There is a lot of young passionate energy with mature skills in the building and it is focused on growing the reputation and impact of the society. Even the “older guys” of which I am now one (!) have this youthful spirit that they bring to RSC. It’s great.

BUT, enough is enough. Okay, I might still run 5km a few days a week, and I might still lift weights a few times a week but gravity is not my friend and I do not have the lithe, supple physique that I had as a 30 year old. Add to that twin boys tearing me apart and bilateral rotator cuff injuries from said boys and I have not been able to stay in shape to the level I had hoped this past year. So, imagine my surprise when I am told that for the inaugral ChemSpider presentation to RSC staff in June I will be expected to dress appropriately. Here’s me thinking that meant a shirt and tie (and best behavior) but no…here comes a package with a “party dress” for me. Sure…make fun of the ChemSpiderman moniker why don’t you! Look at that costume. I wouldn’t wear it when I was young and lithe. Not my thing that. Sorry guys, I have my limits..it’ll be shirt and tie and maybe best behavior but no Lycra Spandex Spidey suit for me for my presentation at RSC!

An article in the latest C&E News discusses the acquisition of ChemSpider by the Royal Society of Chemistry. I certainly appreciate the comments of Robert Massie, President of CAS who stated:  “CAS has worked with Williams in the past,” CAS President Robert J. Massie notes. “We join everyone who is interested in the advance of chemical information in recognizing his considerable contributions. We are delighted to see that his creativity and enthusiasm will continue to benefit the chemical enterprise.”

I worked a lot with CAS while I was at ACD/Labs (over 10.5 years and left there as their Chief Science officer). I was intitmately involved in the development and deployment of a number of software tools and visited Columbus many times. I have many fond memories of working with the CAS team and there are some great people working at the organization. I hope that in my new role at the Royal Society of Chemistry that I will have the opportunity to work with CAS again in a collaborative and cross-publisher manner to the benefit of the  Chemistry Community.

With the news about the RSC acquiring ChemSpider assets sterting to settle it is time to get back to work. One of the things we are noticing is that people are really starting to take advantage of the ability to integrate their articles to ChemSpider via the Add DOI function that is available to registered users. If you want to associate a paper with a single chemical structure then it is very easy and uses the CrossRef service to Fetch the Result from a DOI lookup and deposit directly to ChemSpider. The four images below outline the way in which this can be done. In this example I want to associate two particular articles with the record for  1,2-dioxetanedione shown below.

It’s easy. Navigate to the record of interest, Make sure that the structure is the correct structure of interest and Simply click the Add DOI button above the chemical structure to the left. Don’t forget you must be logged in! Now, Enter the DOI, click on LookUp and confirm that the title retrieved is the correct publication. Then click on OK. Now the publication will be submitted for a curator to confirm that it is appropriate and it will show up online under the supplementary information when approved.

There are also processes for depositing an SDF file with a single publication and the SAME process is applied to connecting via PubmedIDs (Add PMID). Try it out. Help the community discover publications by adding appropriate DOIs to particular records. Look at how many there are associated with cholesterol already.

The logo to the left says it all really. The Royal Society of Chemistry has acquired ChemSpider. Is that a good thing? ABSOLUTELY it’s a good thing. One of the most prestigious, forward-looking, high-quality and innovative societies in the world, who have already demonstrated their commitment to the Chemistry community, have chosen to bring ChemSpider under their wing and give it a home. This is good for us for a number of reasons. Specifically we will no longer have to deal with our very significant resource limitations but more than that it lends credence and validation to the work that we have been doing over the past 2 years. It seems so long ago now but ChemSpider was first unveiled to the world at the ACS Spring meeting 2007. What began then only as a hobby project is now being recognized by the community as one of the primary resources for internet chemistry.

ChemSpider has an interesting story really. It was started to release our creativity on the world of internet chemistry to see if we could deliver value and something more than was already available. It was clear that PubChem was becoming a valuable resource for the world of drug discovery, that Wikipedia was gaining traction for encyclopedic articles and that eMolecules/Chmoogle was out to help people purchase chemicals. It didn’t seem that anyone was going after the challenge of becoming a centralized resource for integrating these resources together (and others of course). The development of a structure-centric platform for the community allowing depositions, curation and annotation and expansion to allow linking to articles, blogposts, wikis and the hosting of analytical data, prediction engines and other software utilities for the community seemed appropriate. And so we began. We were applauded for our efforts by some and dismissed and ridiculed by others. Nevertheless we plodded forwards forming relationships, expanding our network, increasing our visibility and expanding our reach in terms of integrated resources. With a clear focus on serving the community, a passion for quality and an intention to stay in relationship with our users, contributors and supporters we worked hard. Very hard.

Building ChemSpider has not been easy. It has not only been a labor of love but it has been done under duress at times, under severe time and resource constraints and with lots of late night hours. This time was given willingly, not only by our own intimate team but with significant contributions from some of our Advisory Group and by members of the community at large. We thank you all. We had support through sponsorship and this allowed us to cover the costs associated with improving our hardware and purchasing software and covering travel costs as necessary. Members of the commercial chemistry software community provided tools to us to use, at no cost. We were made welcome at conferences and round tables discussing the future of Open Chemistry. We grew our reputation by word of mouth only and by doing what we said we would do. Some of our early critics are now some of our loudest advocates. It’s all been very humbling, incredibly enlightening and genuinely invigorating (while also being very tiring!)

Over the past 2 years we have been approached by a number of organizations to merge/acquire/consume. In all cases things didn’t feel quite right. The experiences and instincts covered a diverse range: we might be acquired and switched off, we might be engulfed by bureaucracy and process that would prevent us from producing at the speed to which we and our users have become accustomed, and we might be offered career paths that could be destructive in terms of life balance (I’ve had parts of my life where I have not seen my own home for almost 3 months because of travel schedules and will not do that to my family again).

When we were approached by the RSC, and engaged in discussions with them about their interest in what we were doing, it was clear that we are like-minded. Our want is to have a positive impact on the flow of data, knowledge and information in the domain of chemistry. We are honest in our relationships and focused in producing results. We are doers and not talkers. We want what we produce to enhance the ability for chemists to access chemistry-related resources and speed up their research. Bottom line we want to help advance the chemical sciences. Do a search on “advancing the chemical sciences” on Google and see what comes out on top. Or don’t..just look below

The_RSC is focused on advancing the chemical sciences and we want to help! In fact, we’ve been destined to do so since ChemSpider went online and when RSC approached us it felt as if this could be a marriage made in heaven. Over the past few months of discussions matching up our interests and ideas with those of the RSC, and then going through the entire due diligence process it became clear that we are indeed well-matched. No, I’ll say ideally matched.

Things will never be the same again. Not just for us but for internet chemistry. We can now TRULY get to work and not worry about bandwidth constraints and how to buy our next disk drive. The community can stop worrying that their investments in time into expanding and enhancing ChemSpider will be lost. There is no need to worry about ChemSpider “going away”.

Watch this space. We will announce the new and improved ChemSpider later in the year but the present version will remain active for everyone for the time-being. We will be migrating the present version to RSC servers for improved performance over the next few weeks. Our long term goal is simple: To deliver the primary online platform where chemists will resource information and collaborate across the worldwide community of chemistry.

Tell us what you think. Please do. If you read this blog and have remained quiet previously please give us feedback about this announcement. We hope you will celebrate this path forward the way we are. It’s going to be just great!