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Keemei: Validate tabular bioinformatics file formats in Google Sheets

Keemei (canonically pronounced key may) is an open source Google Sheets add-on for validating tabular bioinformatics file formats, including QIIME mapping files.

Keemei supports validating QIIME metadata mapping files, providing validation similar to QIIME’s validate_mapping_file.py command-line script. QIIME’s load_remote_mapping_file.py script can be used to load Google Sheets that have been validated by Keemei (see this tutorial for details).

Keemei also supports validating SRGD files (e.g., for use with geneGIS). For more information about SRGD files and geneGIS, visit http://genegis.org.

If you use Keemei for any published research, please include the following citation:

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets.
Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG.
GigaScience. 2016;5:27. http://dx.doi.org/10.1186/s13742-016-0133-6

Find the Keemei paper here.

Available in the Chrome Web Store
Fork me on GitHub
Videos

Getting started with Keemei

The following videos will help you get started with Keemei. There are also installation and usage instructions in the sections below if you’d prefer not to follow along with the videos.

These videos were created by Riley DeHority and are provided by North Carolina State University’s Biotechnology Program (NCSU BIT), find their Youtube channel here.



Install

How do I install it?

Before installing Keemei you will need to create a free Google Account and log in. To install Keemei, click the image below to be taken to the Chrome Web Store:

Available in the Chrome Web Store

Click the blue button with the plus sign (+) to install the add-on. You will be prompted to give Keemei permissions that are required to operate. Once authorized, you’re ready to start using Keemei!

Alternatively, you can install Keemei from within a Google Sheet by clicking Add-ons > Get add-ons... and searching for Keemei.

Warning: please read!

Keemei displays validation status by modifying cell background colors and notes. If you use Keemei, you will lose ALL existing cell background colors and notes in the active sheet. There are future plans to minimize Keemei’s impact on your Google Sheets, but for the time being this is a caveat of using Keemei.

Usage

How do I use Keemei?

In this section you’ll learn how to use Keemei to validate some example data. These data are derived from:

  1. QIIME’s Illumina Overview Tutorial mapping file
  2. “88 Soils” QIIME mapping file (Lauber et al., 2009)
  3. geneGIS example SRGD file

These data are for demonstration purposes only. Errors have been intentionally introduced to illustrate validation with Keemei. Do not use these data for analysis.


Getting started

  1. Log in to your Google Account and install Keemei if you haven’t already.
  2. Open this Google Sheet. This is a publicly-viewable spreadsheet with the example data described above.
  3. Click File > Make a copy... and name your copy of the spreadsheet.

You now have a copy of the example data to validate with Keemei.


Validating your data

First we’ll see how to validate a QIIME mapping file with Keemei.

  1. Make QIIME Illumina Overview Tutorial the active sheet if it isn’t already.
  2. Validate this sheet by clicking Add-ons > Keemei > Validate QIIME mapping file:

    Validate active sheet

  3. Cells with warnings are colored yellow and cells with errors are colored red. A sidebar summarizes the validation report and lists invalid cells:

    Validation results

  4. Click cell A3 in the sidebar to see why it is invalid. We see there are duplicate sample IDs in cells A3 and A5:

    Sidebar details

  5. In the spreadsheet (not the sidebar!), hover your mouse over cell A3. This is another way to find out why a cell is invalid.

    Cell hover

  6. Make fixes to any number of invalid cells and re-validate by clicking Add-ons > Keemei > Validate QIIME mapping file. Repeat this process until all cells are valid.

Resetting the status

  1. To clear the validation status on the active sheet, resetting cell background colors to white and clearing notes, click Add-ons > Keemei > Clear validation status:

    Clear status


Locating invalid cells

Keemei’s sidebar provides a way to focus on an invalid cell in order to fix it. This feature is especially useful if you’re working with large sheets that would require scrolling to find and fix invalid cells.

  1. Make QIIME 88 Soils the active sheet.
  2. Validate this sheet by clicking Add-ons > Keemei > Validate QIIME mapping file.
  3. The two invalid cells (O46 and O66) are not visible in the sheet. Click the magnifying glass next to cell O46…

    Cell focus 1

  4. …to scroll to that cell in the sheet and focus on it:

    Cell focus 2

  5. Hit “Enter” after gaining focus to begin typing in the cell.

Validating SRGD files

In the previous sections we validated QIIME mapping files. Keemei also supports validating SRGD files by clicking Add-ons > Keemei > Validate SRGD file. Validation results are displayed in a similar manner.

Make SRGD_example the active sheet and try validating it as an SRGD file. How many invalid cells are there?

Help

How do I get help with using Keemei?

To report an issue with Keemei or ask a question, click Add-ons > Keemei > Help and then click Report an issue:

Report an issue

Be sure to select the option to provide your name and email address if you would like a Keemei developer to follow up with you:

Include name and email address when reporting an issue

FAQs

How do I update to the latest version of Keemei?

Keemei will automatically update to the latest version available in the Chrome Web Store.

Does Keemei work in “old” Google Sheets?

Keemei is only officially supported in “new” Google Sheets. Keemei may work in “old” Google Sheets but this has not been tested. Support for “old” Google Sheets is not planned.

About

Credits

Keemei was developed by Jai Ram Rideout (@jairideout) in the Caporaso Lab. See the full list of Keemei’s contributors here. Keemei’s logo was created by John Chase (@johnchase).

Licensing

Keemei is available under the new BSD license. See here for Keemei’s license.

Keemei uses and distributes Moment.js, available under the MIT license. See here for Moment.js’ license.