We have made significant advances in the structure deposition system on ChemSpider. We’ve reported on our advances previously and working hard to polish it.In parallel we’ve done work to support deposition of batches of structures (100s to many thousands) as well as the deposition of CSV files to support Open Notebook Science. We are going to roll out deposition in phases – single deposition first, batch deposition next and then CSV file based batch deposition.

So…why are we encouraging the deposition of structures onto ChemSpider. We agree that we could accept RSS feeds (and we will). Our view is that people might to have “bragging rights” on their latest synthesis, might want to expose their latest paper on ChemSpider, might have a link to an article online that they might want to expose to people. While there are MILLIONS of structures online there is new chemistry reported everyday. What other system is there available as a structure-based community for chemists where people can deposit their structures, stories, links and comments to share with others? (And open up a conversation with others about synthesis, analysis etc.) Think of it a little like Flickr or YouTube for chemical structures. Anyone can post their structures for people to browse.

I’ve been doing some example depositions to show what’s feasible…these are simple to do…a few minutes work maximum.

1) I was a co-author of a publication and received a copy today. I wanted to put a link to the paper and associate it with the structure we analyzed. The structure already existed on the database so this was information to be added to the existing structure. Scroll down to the end of the page for this record to see this Supplemental information

Martin, G.E., Hilton, B.D, Blinov K.A. and Williams, A.J. “Using indirect covariance spectra to identify artifact responses in unsymmetrical indirect covariance calculated spectra “, Magnetic Resonance in Chemistry

[DOI: 10.1002/mrc.2141]

2) A new publication was released this week regarding a new compound Quesnoin. David Bradley blogged about it on Spinneret. In this case I wanted to add the structure, information about the structure as well as a link to the recently published article. Scroll to the bottom of this record.

There are many other examples online too here (1,2,3). Look at the Supplemental Information in each case.

There are some final tweaks being made at present but single deposition is now rolled out. We are looking for people NOW to start using the system so please ping me. An overview of the system is available here.

deposition_workflow1.png

 

 

The future will include users creating their own “catalogs” of structures, “social networking” and discussions around structures, team-based discussions, public and private structure collections and so on. It’s coming…in stages. We start here with the single deposition process.

Stumble it!

One Response to “The Progress of Structure Deposition on ChemSpider”

  1. Miklos Simonyi says:

    Your search results for structures of allo.Muscarine and epiallo-Muscarin are erroneus. The correct structures can be found in the paper by Michelot D and Melendez-Howell LM, Mycol. Res. 107(2): 131-146 (February 2003), at Fig 7, p 135.

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