Copyright©2009 Antony Williams
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 (http://tinyurl.com/ctofhj 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: http://www.chemspider.com/Services.aspx
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: http://www.chemspider.com/Chemical-Structure.8215220.html. 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.Stumble it!