ChemSpider Blog

One blog I check out a few times per week is that of Derek Lowe who writes In the Pipeline. What makes Derek’s blog different, in my opinion, is that he has many years under his belt as a synthetic chemist in pharma companies. He watches what is going on in his industry and makes us aware of his opinions and those of others. He’s still active in the lab and makes us aware of the challenges of lab syntheses and, I find, with some historical perspectives regarding what is “was like” then versus now. Always well written with high feedback In the Pipeline is likely one of the most frequented blogs out there.

Today I read about Schering-Plough’s thrombin receptor antagonist compound, SCH 530348. I am an SP shareholder and was rather disappointed by the recent news about Vytorin. Let’s hope the retrials provide new results. However, SCH 530348 looks more exciting according to Derek’s comments and talking to other people in the industry.

I searched ChemSpider for the structure since it seemed of interest. SCH 530348 is based on a natural product called himbacine and Derek had linked to it from his blog but, I assumed, he couldn’t find the structure of interest on the database. Neither could I. So, about 5 minutes work and it was on the database, with the link to the ASAP article and tagged etc as shown below. The link is here.

Links & References

Any user of ChemSpider can do this now. ANYONE. If you are interested in how let me know! I have some documents already prepared tou guide you through the process and need to update others but the database can be expanded by everyone now…not quite Wikipedia but not bad at all! What do you think?

The past few days have been very interesting for ChemSpider and the discussions regarding the licensing of Open Data under Creative Commons. There have been a number of exchanges in the blogosphere commenting on what this means/should mean for Open Data.

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Does ChemSpider really violate Open Data with CC SA?

John Wilbanks replies to the ChemSpider/OpenData discussion

I am Still DELIGHTED with ChemSpider

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The unfortunate public disclosure of an internal document regarding ChemSpider has resulted in some excellent public dialog about Open Data and licensing and I am glad that the outcome, while potentially very messy, has been controlled and appropriate dialog. I will not reiterate the details of each of the blogs but have generally commented on them directly. I thank John Wilbanks specifically for the gracious manner with which he addressed a potentially explosive situation.

This situation didn’t make me angry..just frustrated. ChemSpider has become a focus for attention over the past few months. Maybe it’s because we are doing the right things? Maybe it’s because we are challenging the status quo? Maybe it’s because people know me personally after 10 years in the commercial sector?

We are doing the best things we can - with no funding, “spare time resources” (all work is night and weekends by volunteers!), to make a difference and build a community. We have taken a lot of hits over the months and it has been distracting, especially for me who has chosen to remain engaged in a public discourse on the blogosphere. It is no longer healthy. It has distracted us from our mission..it is way too time-consuming and delivers little value to our users. Our users I care about. Our self-professed non-users I don’t.

We will likely pull all Creative Commons licenses shortly and resolve our “Openness” with a declaration as originally advised by Peter Suber. It was good advice then and is more pertinent now.

I have also posted a statement to Peter Murray Rust’s blog thanking him for his apology and declaring my intent. This may be misinterpreted, and will likely garner a reaction, but I hope my intent is clear here. If you deposit data to ChemSpider then your data remains yours. We are not assuming copyright. We will do our utmost to navigate the complexities of licensing as appropriate. We might fail. Our role is to serve our users.

We are getting out of serving any agendas other than our own…we are Building a Community for Chemists.

This is what I posted to Peter’s blog

“Peter, I thank you for the applause regarding our implementation of licensing on ChemSpider. I also acknowledge and accept the apology you have issued publicly to John Wilbanks, ChemSpider and members of the advisory board.

I believe that some good has likely come out of the conversations over the weekend - maybe a little more confusion, maybe a little more clarification (especially around John’s “data in the public domain” comments) and maybe a few more relationships. This latter part is especially of interest to me as we work on creating a community for chemists.

Now to the outcome for ChemSpider. ChemSpider went live in March of last year with a “who knows where it will go” approach. From the moment we went live you have paid attention. However, rarely has this been with any sense of support but, rather, a framework of negativity. You have criticized our science and our intent. You have projected your judgments as truths. I have addressed these judgments many times but rarely with acknowledgment from your side. It has been a lot of work for both of us. To be clear, I have judged your efforts around Open Notebook Science for NMR similarly.

ChemSpider appears to have a center spotlight now in terms of licensing and Open Data. I acknowledge these are significant parts of YOUR agenda and a key part of what you have worked on for many years. I judge your other agendas to be Open Access, Semantic Web and associated technologies. I honor your work in these areas and feel you have contributed and will continue to contribute to the ongoing shifts of Open science prevailing at present. Thank you.

Our agenda for ChemSpider is different. We are building a community for chemists (Notice the recent shift from the original vision “Building a Structure Centric Community for Chemists” as we expand out of structures only.) At present, we are doing what we can to support the needs of chemists researching structure-based information. We are integrating information. We are more than a “linkbase”. We are actively supporting Open Notebook Science. We ARE listening to our users, the community, our collaborators and our advisory group.We have delivered a valuable solution in the past year with no cost to the users, to the tax-payers, with no grants and based on the hard work of a small dedicated team of volunteers only.

The past year has been very distracting for us, and me in particular, in terms of your comments and judgments about ChemSpider, and by association, about myself. I have tried to clean up a number of these on the ChemSpider blog (http://tinyurl.com/45acav) but acknowledge you might have different view points. These discussions have been draining and have distracted us from our core mission of serving our users.

At this point I need to withdraw from the dynamic we have co-created around our relative agenda(s). I honor and acknowledge what you are out to achieve. I wish for the same from you. I do not believe that our intentions are contrary or mutually exclusive to your own. I think that time will prove this to be true.

I believe that you judge our efforts to be in conflict with those of your WorldWide Molecular Matrix but I doubt that is true. I will respond shortly to some historical posts regarding your call for a structure collection for your eChemistry Project with Microsoft. We are willing to help and I am open to a discussion should you wish to collaborate. I am working with the Wikipedia:Chemistry team to build a validated SDF file for the public domain and we can make this available to you. “