RDP MIMARKS GoogleSheets

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What is the RDP MIMARKS GoogleSheet?

The RDP MIMARKS GoogleSheet helps to manage your metadata.

RDP supports the Genomic Standards Consortium's Minimum Information about a MARKer gene Sequence (MIMARKS) Project -- "a consensus on an ideal and minimum set of contextual data that should be reported for marker genes." [Yilmaz P., R. Kottman, D. Field, R. Knight, J. R. Cole, L. Amaral-Zettler et al. (2011). The “Minimum Information about a MARKer gene Sequence” (MIMARKS) checklist: Capturing contextual data about marker gene sequences and introducing MIxS, a unified standard for sequence checklist development including environmental data. Nat Biotechnol.; accepted 18 February 2011.]

More information can be found on the MIMARKS homepage where you can also find other projects promoting the MIMARKS standards like Terragenome (International Soil Metagenome Sequencing Consortium).

Why has RDP elected to use a Google spreadsheet?

  • It's preloaded with MIMARKS-compliant attributes
  • It's easy to use, no computer IT infrastructure required
  • You can access it from anywhere using any web device
  • You can manage data over time / monitor revision history
  • You can share with your collaborators
  • It works with submission tools (Sequin and WebIN)
MiMarks4.png

How can I give feedback on the MIMARKS GoogleSheet?
RDP welcomes any feedback on this project. Email rdpstaff@msu.edu with your comments or suggestions.

How do I use the MIMARKS GoogleSheet?

1. [Follow this link to load the RDP_MIMARKS Google spreadsheet]

You will need to "Sign in" to your Google account (upper right hand corner) in order to activate the menus. Use "File, Make a Copy" to get your own spreadsheet. DO NOT download or copy into an Excel spreadsheet as you will lose all embedded definition comments and validations. THIS COPY WILL NOW BE YOUR OWN Google Spreadsheet to edit and share/protect as you see fit.

2. Choose the environmental package for you samples from the tabs at the bottom of your COPIED Google spreadsheet.
Air Host-Associated Human-Associated
Sediment Plant-Associated Human-Gut
Soil Microbial Mat/Biofilm Human-Oral
Wastewater/Sludge         Built Environments (New Summer 2014)         Human-Skin
Water Miscellaneous Natural or Human-Vaginal
    Artificial Environments

All 15 preconfigured MIMARKS environmental packages are included as worksheets. Choose the environmental package relevant to your research. Copy the user input Columns (C and D) for each of your samples (embedded validation will also copy within the sheet). You can choose to delete any of the worksheets not relevant to your research with the drop down menu that appears when you click on the tab. (Be sure to examine the other menu options here also.)

3. Enter you metadata

There should be a User Input Template and Units Template column for each sample you would like to manage. Do not enter data into any cells other than those in the "User Input" or "Units" column. You may change the column heading of the copied User Input columns to contain your sample names. All rows containing mandatory attributes and cells requiring a unit entry are highlighted in orange. A new column for "Preferred Units" has been added in v. 4 (Summer 2014).

You can add rows for non-MIMARKS metadata you would like to collect (CAUTION: duplicate structured_comment_names and item names are not allowed in the submission packages).

4. Store and share with your collaborators

Share your Google spreadsheet with your research colleagues to view or view and edit according to your needs.

5. Export your MIMARKS-compliant data -- NOTE: You MUST have a PROJECT NAME IN CELL C2 to export data

After you collect your metadata, you can export your MIMARKS-compliant data by selecting the menu item "MIMARKS Export". Choose your desired output: WebIN or Sequin in RDP_MIMARKS v. 0.1. Use our added MIMARKS Export tab and select your desired format. You may need to give permission to run the script. A new window will open with your results as text to COPY and PASTE into a text file for your submisssion.

Mimarks2.png


Col. A = Structured Comment Name: name of a checklist item as it will appear in GenBank structured comments.

Col. B = Item (attribute): full name of item as it appears in the publication. Note: definitions (a description of the item, including links to ontologies and other resources that can be used to fill in values for the item) appear in the embedded comments of this column.

Col. C = User Input Template: Validated input column for user data. It is set up to help you by validating (verifying) your input according to MIMARKS requirements. Once copied for your samples, you can replace "User Input Template" with your sample name as the header.

Col. D = Units Template: Lists the MIMARKS standard units for each entry. (Required user input is designated by orange boxes.)

Col. E = Preferred Units (when designated). New with v.4 (Summer 2014).

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