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Export to Excel, TEXT and SDF files

Once you have identified a set of search results, you may want to work with the data further in another application: to put into a lab notebook, insert into a power-point presentation, or to load into another analysis application. You will need to export the data from CDD in a format that is most appropriate for your next step. Data export is available to CDD Vault subscribers with any user-role above readonly.

"Export results" link appears in the tool-bar of the results table on the Explore Data/Search tab.

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Before you export, don't forget to customize your report to include any additional molecule or protocol related information in your export.

Once you start an export, you will see a yellow status bar at the top of the export page. A download link will appear in this bar, which will turn green when the file is ready. You may log-out of the database during an export; when you log back in, the green bar will appear throughout the application.

 

The 3 export types available for the search results.

 

Excel (.xls) file is the most versatile export that includes images of structure and plots.

  • Human-readable and understandable.
  • Data table similar to the results table in CDD: column will have headers with CDD field name and protocol/readout definition name.
  • Structures are exported by default as embedded picture (.png) files, linked to their cells. to include other structure formats, customize your report.
  • "Monochrome printer friendly" option to export structures in black and white, instead of color.
  • <span">Dose-response plots are exported as embedded picture (.png) files, linked to their cells.
  • <span">Export file size is capped at a maximum of 10,000,000 total cells, which means that if you export a protocol with 1 readout for each molecules, you can get up to about 3,300,000 molecules in a single file. We cannot guarantee that your computer or Excel version can handle this though, and strongly encourage you to export to computer-friendly .csv files.

 

Plain Text (.csv) file is a great format to export a large amount of chemical and biological data.

  • Can be easily converted to human-readable.
  • Comma-separated text file can be opened with Excel and any text editors.
  • Molecule structure is not included by default. Make sure to include CXSMILES under "customize your report" link to export structures (! Please do recall the standard limitations of SMILES for stereochemical information. To be on the "safe" side, use SDF format if you intend to import structures again !)
  • Images data can not be included.
  • No export size restriction. for large exports, you may log out of the database while an export is in progress, and return later to download the file.
  • CDD uses UTF-8 compliant .csv format for a maximum of compatibility.
  • Troubleshooting: Do you have issues with certain special characters in Excel, such as greek letters or other?
    The reason is that Microsoft Excel is unable to properly display UTF-8 compliant CSV files when they contain non-English characters. See this separate article on how to easily fix this.

 

SDF (.sdf) file is standard for chemical databases, and may be used directly for most other chemistry applications. 

  • Machine-readable, but not for most humans.
  • MOL structure representation is included by default.
  • Highly recommended for most accurate representation of stereochemical information.
  • Image data can not be included.
  • No export size restriction. For large exports, you may log out of the database while an export is in progress, and return later to download the file.
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