As part of a collaborative project with Jean-Claude Bradley from Drexel University (and member of our Advisory Group) we are in the process of delivering new capabilities for the upload of “activity data” associated with one or more structures, the display of these data with the associated structures on ChemSpider and the download of these data to the desktop. Our efforts are part of JC’s overall workflow outlined here.

So far we have enabled the ability to upload CSV files containing SMILES strings and associated data, converting the CSV files on the fly to SDF files for deposition onto ChemSpider. We have also enabled a general capability for the download of collections of data using checkbox selection and download as an SDF file with associated properties. Rather than insert images into this blog posting please click here to see the PDF of the Powerpoint overview.

While we have the deposition process and downloading process essentially completed (except for testing) we now need to resolve the process for deduplicating the submitted data onto the database (or generating new structure records) as well as defining the format for display on the site. Watch this space.

Stumble it!

2 Responses to “Uploads, Downloads and Managing Activity Data on ChemSpider – Open Notebook Science Support for JC Bradley at Drexel University”

  1. Jeff says:

    Hi, I just recently heard about ChemSpider, and oh my gosh, I am completely overwhelmed by how cool this whole project is! Do any existing efforts come to mind to integrate these tools into a chemistry classroom? I’m thinking of inquiry-based activities for students, with a workflow something like

    1.) Ask a question about how structure and activity are related.
    2.) In an online interface, ask students to draw up some ideas they’d like to test
    3.) Students explore the data related to their structural queries, form some preliminary hypotheses, and test their ideas with more targeted searches.

    Anyway I just wanted to say thanks, I appreciate the spirit of open science and the tremendous resource you’re creating!

  2. Antony Williams says:

    Thanks for the compliments. It is nice to have our efforts appreciated. There are certainly many ways to use the site and I have asked whether anyone would like to help design a lesson plan around the system but can’t get any takers. Interested???

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