GeOMe FIMS spreadsheet validation and upload

Validating and uploading the spreadsheet

If SIBN is performing the lab work for your project, please only work through the “validation” portion of this section and then email the spreadsheet to your project manager. We will take care of uploading everything for you.

Once we have a spreadsheet fully populated, our next step will be to validate and possibly upload the spreadsheet to the GeOMe FIMS database. (Again, if SIBN will be conducting your lab work, please only validate the spreadsheet, then forward it to your project manager.) The validation step checks every specimen record to make sure that they meet the set of rules established by the project.

Validation without loading

  1. Go to https://geome-db.org/ and click on Workbench.
  2. If you are already logged into GeOMe, you will click Load Data at the top left, and then tick the “Only validate data” box at the top of the Load Data screen.
  3. Or, if you are not logged in, click Validate Data at the top left.
  4. Where it says ‘Excel Workbook’, click the Browse button to select your spreadsheet.
  5. Select the pre-existing expedition called “_SIBN_Validation” and click the Validate button.
  6. If your spreadsheet passes validation, great! Forward it on to your SIBN program manager and skip the rest of this section. Otherwise, please resolve the errors you are given and try validating again.

Note: To pass validation, your data must be in a tab named Samples within the spreadsheet.

_images/fims_validation.png

Validation and loading

  1. Go to https://geome-db.org/, click on the user profile image with the down-pointing caret at the top, and then click on Sign in.

  2. Log in with your pre-assigned GeOMe username and password. (You do not need to log in to validate your spreadsheet, but you must be logged in to upload it to the database).

  3. After logging in, go to Workbench and then click Load Data at the top left.

  4. Where it says ‘Excel Workbook’, click the Browse button to select your spreadsheet.

    1. If this is the first time you have uploaded this plate to GeOMe, you will need to assign an “Expedition Name”. In the Expedition Name drop-down that appears, click the plus sign to the right of the box and enter your plate name. (The same plate name should go in Expedition Title and Expedition Code.) Remember to follow the FIMS naming conventions, and make sure not to repeat a previously created expedition code.

    Note: While the expedition title can be modified at any time, the expedition code is a unique identifier and cannot be changed.

    1. If you are adding to or updating data you have previously uploaded, simply select the associated project from the Expedition Name drop-down. Do not click “Replace expedition data” unless you want all of the previously uploaded data to be replaced with the new data.
  5. If you are ready to upload your spreadsheet, click the Load button. If there are no errors, the screen should return a “Successfully Validated!” message.

A few notes:
  1. To pass validation, your data must be in a tab named Samples within the spreadsheet.
  2. If you have already tried to upload data and validation failed, you may have to tick the box that says “Replace expedition data” when uploading it again.
_images/fims_validation_upload.png

Can I add a few records to an existing expedition by just uploading those new records?

YES! As long as you do not tick the “Reload Data” option, GeOMe will add new data to existing data. Just make sure you select the correct expedition to add the records to.

Check that the spreadsheet was successfully uploaded

Even though we received a “successfully validated” message, you should make sure your data made it into the database successfully. The following step will also show how to retrieve data from the FIMS if you ever want to make changes. Click on the Query button at the top of the screen.

On the Query page, you will be able to view the data from any expedition in any of the individual projects (e.g. SI Barcoding CBOL, GGI, SI Bioblitz, etc.) in the GeOMe FIMS. This is why it is so important not to include sensitive information (e.g. highly accurate GPS coordinates for protected species, fasta files, etc.) in spreadsheet uploads. To see the expedition that was just uploaded, first click on “Switch to Advanced Search” in the top right of the search screen. Then select SI Barcoding CBOL from the Individual Projects dropdown. Once the project is chosen, the list of expeditions will be populated. Scroll through the list of expeditions until you find the one you just created (or start typing it in, to bring up a shorter list). If you do not see it in this list, then your data was not successfully uploaded.

Select the expedition you just uploaded and click the Search button.

_images/fims_database_query.png

This will display an HTML table view of the specimen records in this expedition. It will be incredibly hard to read and scroll through, but be happy it made it in there.

You can click the Download button to download a fresh Excel spreadsheet of this expedition. However, be advised that the wells are out of order and that you will lose any styling (colors, bold/italics, etc.) from when you originally uploaded the spreadsheet. Also, the default spreadsheet name is “geome-fims-output.xlsx”, so be sure to rename it with your expedition name immediately.