There was a discussion on Friendfeed last weekthat resulted from my comments regarding this blog post : “Throwing down the gauntlet for my fellow geeks”. I always prefer that people read the original blog post rather than me take snippets out of context. That said, the last paragraph said

“My argument is this: there is so much useful information that needs to be organized in a format that is free, navigational and easy to access. One person cannot do it alone; we all need to contribute for the betterment of science, in general. I envision a hybrid of Doug Taber’s Organic Chemistry Portal, Wikipedia and a condensed version of SciFinder. I’ll gladly contribute! How do we get the ball rolling?”

What followed was a great exchange between many members from the blogosphere and I made a number of comments. One snippet from one of my many comments is here:

” J said ” I have two concerns about chemspider. First (and it’s minor), calculated/hypothesized data makes me a bit nervous. I’m jaded because my PI refers to calculated properties as “really expensive guessing.”

Without meaning to sound overly critical there is the purists world and there is the reality of industry. Calculated data have saved MANY a project in industry where the calculated data said “take another look at what you measured”. I was involved with the development and marketing of commercial software tools for PhysChem prediction, nomenclature generation and NMR prediction. Look at the story of hexacyclinol for an example of NMR prediction DISPROVING the experimental method. Look at the report by Gernot Eller about nomenclature and how well chemists can generate chemical names themselves ( downloads the PDF). I have seen directly how PhysChem prediction can RESCUE projects where measurement protocols fail. I am NOT saying that prediction outperforms experimental measurement but be very careful in judging it harshly as you WILL meet it and be grateful should you move to industry. Your PI should not be so judgmental and purist in nature. By the way…upload a molecule here:

J said… “The bigger concern is the lack of experimental conditions. My point is that it might be fine to know the molecular weight of thionyl chloride (for example), but an experimental procedure(s) that outlines its use would be most beneficial.”

Yes, I agree. But someone has to CREATE that information in order for others to use it. ChemSPider is run on no-funding, no grants, and no fees to use. We depend on the community, users like yourself, to help. We will provide an environment to deposit information but we need people to do it. CAS will charge for you to access information but they are aggregating OTHER peoples work and work hard to do it. In Wikipedia people BUILD the platform and users populate it. If you’d like to see info on ChemSPider tell me where it is or put it in there.

Take a look at the Description section for this molecule: The description was taken from Paul Docherty’s blog and is VERY useful and elegant in its description. ANYONE can post their info to ChemSPider…”

I continue to see a lot of discussions about what platforms should do, that data needs to be Open, that the community needs access to high quality tools (with of course the encouragement from many that they should be Open Source.” My comments are as follows at this stage…ChemSpider is here…it’s been here for two years now. it’s clear that we continue our momentum to deliver systems, services and data to the community. We must be doing something right as we retain our average of over 5000 unique visitors per day (the image below is for the first two weeks of this month.

That said, the MAJORITY of chemists in the world have not heard of ChemSpider, especially in the student community. At a presentation at UNC Chapel Hill last week only one person in the room had heard of and used ChemSpider. At most conferences people have not heard of ChemSpider. I believe this is reminiscent of Wikipedia in the early days. Only a small group of users adopted it and found value but for some reason it reached a Tipping Point and more and more people started using it, contributing to it as well, of course, criticizing it. We’ve actually gone the other way…there was a lot of criticism of ChemSPider in the very early days but now more and more people are using it. We have a group of curators and a small group of contributors/depositors. This latter group is the one I want to expand if possible.

It is possible, and has been for a long time, to deposit structures, spectra, images, descriptions, properties and so on onto ChemSpider. The majority of these are easy for users to do. The documentation exists to help you through this process. There seems to be some trepidation when it comes to depositing data with us. I CANNOT say that our data model is perfect as there are things we want to improve, but only if they are to be used and of value to the community. But, what we have now can be of value to the community.

Matthew Todd prompted me on a Friendfeed conversation to see whether or not we could support one of his synthetic procedures. He pointed me to his post on The Synaptic Leap. He also deposited his procedure on ChemSpider here. He didn’t create anything especially for ChemSpider..just deposited what he’d already created and made it accessible to the ChemSpider user group. I did later insert the image of the sample vial.

We have the same situation going on now for the Spectral Game where existing data available online is being downloaded, reprocessed and re-deposited. It’s all work but if such work could be distributed across the masses then ChemSpider as a resource can expand, everyone benefits and we can focus on improving the platform.

So, my request to you, the readers – please let your colleagues know about ChemSpider and encourage them to use the system and give us feedback. If there are resources you would like deposited on ChemSpider please let us know. If you have things already prepared, online and available, please consider ChemSpider as an additional way to deliver your message.

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10 Responses to “Supporting Synthetic Procedures from the Synaptic Leap”

  1. Doug Taber says:

    1. Can the Spectral Game be played on a Mac? I tried, but it said I needed a Java plug-in. When I followed the link to the Java plug-in, it said that it was not available for a Mac.

    2. Does the game have combined data sets, 1H, 13C, NMR, MS?



  2. Andrew Sun says:

    there is always so much useful information that needs to be organized in a format that is free but profitable, navigational and easy to access.

  3. Antony Williams says:

    Doug…the game should be supported on Mac OSX

    MAC OS is listed for the latest 6u12 of Java

  4. Cameron Neylon says:

    I get something similar when using Safari – but when using Firefox it works just fine. In Safari you get directed to an odd Sun site that seems to be out of date and certainly isn’t very helpful. I am wondering whether JSpecView is pointing at an old version of Java or similar?

  5. Reto Mueller says:

    [citation]organized in a format that is free but profitable[/citation]

    I can judge Doug Taber’s Organic Portal is not profitable and does not get tremendous financial support. They maybe do not have programming skills or do not rely on crowd sourcing… So they work hard to put all the content online.

    Comparing with other chemistry sites, which just display Text Data received from Elsevier and publish news that everyone publishes ( the chemical community must recognize the differences and the efforts, but nothing happens.

    Indeed, if the chemical industry sponsors the organic chemistry portal, they for sure can bring more content online. They for sure can program more tools even for own crowd sourcing experiments.

    Why? We absolutely need more diversity! Currently, thousands of Wikipedia copies are spread over the internet. The organic chemistry portal is slightly different – not only textually based, but I am sure they could organize their data better if the industry books more advertisement.

    Sorry. I am sure, there is enough money. But comparing with german-based
    They received after funding 1 000 000 Euro support by the german goverment.
    Now they have 20 co-workers just for marketing purposes…

    And do they produce more/better content?

    How can Doug and his coworker enter this market? It is NOT possible.

  6. ChemSpiderMan says:

    THis input from Bob Lancashire, developer of JSpecView

    “Maybe the JRE is not properly installed for Safari, since it would probably not automatically detect Safari on installation and the .DLL files would have to be manually copied to the correct folder????
    It would recognise Firefox and so that works OK…

    JSpecView does not point to anything, it is the Javascript on the web page that calls the applet and attempts to discover whether the user has a JRE installed, and if they do, is it at least 1.5+”

  7. ChemSpiderMan says:

    Doug….sorry I missed part 2 of your question first time around. At present the game does not support a combination of data but it is very early days. We are working on building the spectral collection initially then can start assembling collections of data for elucidation purposes.

  8. Antony Williams says:

    Reto..I can tell you that ChemSpider “does not get tremendous financial support.” We have no grants supporting the work. We are fortunate enough to be able to source some funds from doing some customer web service development for some companies. We, of course do WAY more than just displaying text data and news that everyone else has. If the chemical industry sponsors would support us, as well as the Organic Chemistry Portal then a lot more could of course be brought to the community. Maybe there is an opportunity for us to collaborate…I think what Doug et al produce is excellent.

    The German government is very supportive of chemistry…I’ve observed it directly and they are fortunate to get the support.

  9. Reto Mueller says:

    [citation]The German government is very supportive of chemistry[/quote]

    Yes, but CLEARLY spoken: supporting “” is just spending money for a commercial service. 1 Mio Euro made big and this is now not helpful if a competitor wants to enter the market.

    Another example: FIZ-Chemie was supported for the development of chemgapedia. Several millions of Euro. Now what happens? They just fill in Google Adsense into their pages and lower the income of all the web sites that HAVE NEVER BEEN SUPPORTED BY THE GERMAN GOVERNMENT. And in addition, they have enough money to translate all their content into French and English too.

    So please, be careful! I have nothing against financial support of scientific activities, BUT CHEMIE.DE AND FIZ-CHEMIE are more or less commercial suppliers in a field, where we have enough competitors – even better services…

    ACS against the public-supported NIH database. It is the same. Sorry. The principle is: governmental support of activities that compete with an already existing commercial supplier is NOT ALLOWED (even in the current EU law).

    If someone wants to sue German Authorities, please give me a hint.

    Best regards


  10. Chris Singleton says:

    So, with your reference to Gladwells ‘Tipping Point’ , how shall we start an epidemic of ChemSpider? I’ve been telling colleagues constantly, it just seems to take quite aq bit of time for this to build up.

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