Laying out intrinsically three-dimensional molecular structures in a readable way on a two-dimensional page is a hard problem for human beings, let alone for algorithms, which is why ChemSpider stores a 2D layout alongside the InChI, which only describes which atom is connected to which other atom.

This is a really valuable resource for enhancing our RSC journal articles, so we’ve been experimenting with adding galleries to compounds, with examples here and here. Is this what PDFs you download from the website should look like? Would a digest gallery of the latest articles published be more useful? Do let us know.

As this is my first posting on the ChemSpider blog I should introduce myself. I’m Colin Batchelor and I’m in the Informatics team at the RSC. Some of my work is on ChemSpider, but I also work on informatics for RSC Publishing, and I’m a member of the InChI subcommittee.

Stumble it!

3 Responses to “ChemSpider compound galleries”

  1. Egon Willighagen says:

    I think this is interesting progress… I assume the InChIKey or even InChIs are embedded in the metadata of the images in those tables? That would reconstruct quite some cow…

  2. Jean-Claude Bradley says:

    Colin – I love the concept. A very useful part of your galleries is that you provide a machine readable identifier (InChIKey). I have been going through articles recently to test out our solubility prediction algorithm, which requires me to represent the molecules in some format. It would be so helpful if chemistry publications provided some type of identifier that could be quickly copied and pasted for these types of applications. It is time consuming and error prone to draw the structures in ChemSketch to get the SMILES (most of the compounds I have come across are not in ChemSpider yet although they are after I process them). Here is an example: http://tinyurl.com/23kzxsv

  3. Antony Williams says:

    The problem I see with the InChIKey is that there are so many variants of it out there for what is supposed to be a particular compound (see http://tinyurl.com/28j482r). Of course the InChIKeys being listed in the compound galleries come directly from ChemSpider so we know they will get you back there…no guarantees it will get you onto the right pages on other DBs. Adding the ChemSpiderID in with a link is a natural extension as there is no variation in the ChemSpiderID of course…it is what is shown. The link will save you the copy and paste of the InChIKey.

Leave a Reply