Sample Managers

This section gives an overview of the COPO features that are delegated to sample managers [1] who are responsible for accepting or rejecting samples produced by sample submitters [2].

Note

• Make a request to the indicating the type of profile manifest group that you would like to be assigned to as a sample manager and the associated profile type.

  The permission will be granted after the request has been approved.

See also

• View images produced by sample submitters

• Download permits produced by sample submitters

• Sample managers’ Frequently Asked Questions

• Profile types and associated profile types brokered through COPO

Accessing the Accept or Reject Samples web page

Note

The button will only appear on the web page if you are granted permission to be a sample manager.

Once the button is clicked, the accept/reject samples web page will be displayed.

If you have been granted permission as a sample manager, you will receive an email notifying you that sample(s) has been submitted after a user uploads a manifest.

Similarly, you will receive an email when samples have been rejected.

Click the button to navigate to the web page to accept or reject samples.

Alternatively, navigate to Accept/Reject Samples’ web page.

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Guidelines for Searching Profiles and Samples on the Accept or Reject Web Page

Navigate to the Accept or Reject Samples web page.

See How to access Accept or Reject Samples web page section for guidance.

Querying using Profiles search box

In the search box on the left of the Accept or Reject Samples web page, query the desired profile by inputting the profile title or a substring of it. Then, press the ENTER key on the keyboard to perform the search for the desired profile.

Hint

The profile search box does more than just search for keywords within the profile title. It also looks for any samples associated with the profile that contain the search query.

If a match is found in any of the samples, the relevant profile will be displayed in the results table.

Other potential search queries include the value of any of the following fields:

• name of sample co-ordinator

• RACK_OR_PLATE_ID

• SPECIMEN_ID

• TUBE_OR_WELL_ID

• biosampleAccession

• public_name

• sraAccession

Accept or Reject Samples web page: Profiles table search box

Querying using Samples search box

In the search box on the right of the Accept or Reject Samples web page, query sample metadata then, press the ENTER key on the keyboard to perform the search.

If a match is found in any of the sample records, the relevant sample(s) will be displayed in the Samples table.

Accept or Reject Samples web page: Samples table search box

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Guidelines for Sample Managers Assigned to Multiple Manifest Groups

Note

The manifest dropdown menu will only be displayed on the Accept or Reject samples web page if you as a sample manager, belongs to more than one sample manager manifest group.

If you have been granted permission to be a sample manager for more than one manifest group, you can accept or reject samples for more than one manifest group by following the steps below:

1. Click the dropdown menu displayed beside the Choose to Accept or Reject web page title on the left side of the Accept or Reject Samples web page as shown below:

   

   Accept or Reject Samples web page: Manifest dropdown menu beside ‘Choose to Accept or Reject’ web page title

   
   

2. A list of all the manifest groups that you have been assigned to is then displayed.

   Choose the desired manifest group from the dropdown menu as shown below:

   

   Accept or Reject Samples web page: Manifest dropdown menu with options displayed

   
   

3. To accept samples, see the Accepting samples section

   OR

   To reject samples, see the Rejecting samples section

   
   

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Accepting or Rejecting Samples

Profiles are displayed according to the associated profile type group that you have been assigned to as a sample manager.

You can check which associated profile type a sample is associated with, by clicking the desired profile on the left of the web page in the Profiles tab on the Accept or Reject Samples web page then, checking the Associated TOL (Tree of Life) Project column for any sample record in the Samples table displayed (if the profile has submitted samples) as shown below:

Sample records associated with a single associated Tree of Life (ToL) project type

Sample records associated with multiple associated Tree of Life (ToL) project types

Note

A Samples table record will only be displayed if the desired profile that is clicked/highlighted on the left of the web page has submitted samples.

Hint

• See Accept or Reject Samples for more than one manifest group section for guidance if you are assigned to more than one manifest group and would like to accept or reject samples.

See also

• List of associated profile types (i.e. secondary projects) brokered through COPO

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Accepting samples

Note

If you have already accepted samples but the samples are still displayed in the Pending Samples tab, it is likely that the samples are associated with another profile type group and is pending action by another sample manager.

See Samples awaiting another review FAQ for additional information.

1. Choose a desired profile on the left of the Accept or Reject Samples web page from the Profiles tab

2. In the Pending Samples tab, select desired sample record(s) by clicking the checkbox(es) associated with the sample record(s) (if the selected profile has samples).

   Then, click the button as shown in the examples below.

   
   

   

   Accept or Reject Samples web page: Accepting samples within DTOL profiles

   
   

   

   Accept or Reject Samples web page: Accepting samples within ERGA profiles

   
   

   A confirmation popup dialog will be displayed as shown below after the button is clicked.

   Click the Okay button to accept the selected sample record(s) or click the Cancel button to cancel the action.

   

   Accept or Reject Samples web page: Accept samples confirmation dialog

   
   

3. If the Okay button is clicked, the accepted samples will proceed to the processing stage and will be displayed in the Processing Samples tab as shown in the examples below:

   

   Accept or Reject Samples web page: Accepted DTOL samples at the processing stage

   
   

   

   Accept or Reject Samples web page: Accepted ERGA samples at the processing stage

   
   

4. After the samples have been processed, the samples will proceed to the accepted stage and will be displayed in the Accepted Samples tab as shown the examples below:

   

   Accept or Reject Samples web page: Accepted DTOL samples at the accepted stage

   
   

   

   Accept or Reject Samples web page: Accepted ERGA samples at the accepted stage

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Rejecting samples

1. Choose desired profile on the left of the Accept or Reject Samples web page from the Profiles tab

2. In the Pending Samples tab, select desired sample record(s) by clicking the checkbox(es) associated with the sample record(s).

   Then, click the button as shown below:

   

   Accept or Reject Samples web page: Rejecting samples

   
   

3. The samples will proceed to the rejected stage and will be displayed in the Rejected Samples tab as shown below:

   

   Accept or Reject Samples web page: Rejected samples at the rejected stage

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Download Submitted Sample Manifests

As a sample manager, you can download submitted (filled) manifests by following the steps below:

1. Navigate to the Accept or Reject Samples web page.

   See How to access Accept or Reject Samples web page section for guidance.

2. On the left of the Accept or Reject Samples web page, click the icon in the Samples Link table column of the Profiles table row for the profile that you would like upload a manifest for or update a submitted manifest for as shown below:

   

   Accept or Reject Samples web page: Navigate to ‘Samples’ web page by clicking the link associated with a DTOL profile

   
   

   OR

   

   Accept or Reject Samples web page: Navigate to ‘Samples’ web page by clicking the link associated with an ERGA profile

   
   

3. The Samples web page will be displayed as shown below:

   

   Samples web page for a DTOL profile

   
   

   OR

   

   Samples web page for an ERGA profile

   
   

4. Download the submitted manifest by following the guidelines described in the How to Download Submitted Sample Manifest section

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Download Submitted Permits

If you have been assigned as a sample manager, you can view the permits submitted for submitted sample(s) on the Accept/Reject Samples’ web page by following the steps below:

Note

• Permits can only be downloaded for submitted samples that are pending action by a sample manager or have been accepted by a sample manager.

• Permits exist for ERGA [5] profiles only.

Hint

To download submitted permits for samples within the Accepted Samples tab, CTRL + Click the desired sample record(s) then, click the button to download permit(s) submitted for the selected record(s).

1. Navigate to the Accept or Reject Samples web page.

   See How to access Accept or Reject Samples web page section for guidance on how to access the Accept or Reject Samples web page.

2. Select the sample record(s) that you would like to download the permits for.

   Then, click the button to download permit(s) submitted for the selected sample record(s).

3. If any permit submission(s) exist for the selected sample record(s), the permits will be automatically downloaded for the selected sample record(s).

   Hint

   Permits are downloaded as a .zip file

   If no permits were submitted for the selected sample record(s), a message is displayed in the popup dialog indicating such as shown below:

   

   Accept or Reject Samples web page: Popup dialog displaying message, ‘No permits exist for selected sample record(s)’

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View Submitted Images

If you have been assigned as a sample manager, you can view the images submitted for submitted sample(s) on the Accept/Reject Samples’ web page by following the steps below:

Hint

To view submitted images for samples within the Accepted Samples tab, CTRL + Click the desired sample record(s) then, click the button to view image(s) submitted for the selected record(s).

1. Navigate to the Accept or Reject Samples web page.

   See How to access Accept or Reject Samples web page section for guidance on how to access the Accept or Reject Samples web page.

2. Select the sample record(s) that you would like to view images for.

   Then, click the button to view image(s) submitted for the selected sample record(s).

   

   Accept or Reject Samples web page: Pointer to ‘View images’ button

   
   

3. If any image submission(s) exist for the selected sample record(s), a popup dialog will be displayed with the image(s) submitted for the selected sample record(s) as shown below:

   Hint

   Click the image to view a larger version.

   

   Accept or Reject Samples web page: Popup dialog displaying submitted image(s) for selected sample record(s)

   
   

   OR

   If no images were submitted for the selected sample record(s), a message is displayed in the popup dialog indicating such as shown below:

   

   Accept or Reject Samples web page: Popup dialog displaying message, ‘No images exist for selected sample record(s)’

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Upload Manifest or Update Submitted Manifest on behalf of Manifest Submitters

Note

• The manifest dropdown menu will only be displayed on the Accept or Reject samples web page if you as a sample manager, belongs to more than one sample manager manifest group.

• The Samples table will only be displayed if the selected/highlighted profile has submitted samples.

Hint

• All sample field values can be updated by sample managers.

• Some sample field values can be updated by sample providers. See the Updating Samples section for information about which field values can be updated by sample providers.

• Samples can be updated by resubmitting the manifest with the updated metadata.

The following steps can be followed to upload a manifest or update a submitted manifest on behalf of a manifest submitter [2]:

1. Navigate to the Accept or Reject Samples web page.

   See How to access Accept or Reject Samples web page section for guidance.

2. Search for the profile that you would like to upload a manifest for or update a submitted manifest for.

   See Guidelines for Searching Profiles and Samples on the Accept or Reject Web Page section for guidance on how to query profiles and samples on the Accept or Reject Samples web page.

3. On the left of the Accept or Reject Samples web page, click the icon in the Samples Link table column of the Profiles table row for the profile that you would like upload a manifest for or update a submitted manifest for as shown in the examples below:

   

   Accept or Reject Samples web page: Navigate to ‘Samples’ web page by clicking the link associated with a DTOL profile

   
   

   

   Accept or Reject Samples web page: Navigate to ‘Samples’ web page by clicking the link associated with an ERGA profile

   
   

4. The Samples web page will be displayed as shown in the examples below:

   

   Samples web page for a DTOL profile

   
   

   

   Samples web page for an ERGA profile

   
   

5. If you do not have the submitted manifest for the profile, see the How to Download Submitted Sample Manifest section for guidance on how to download the submitted sample manifest. Then, refer to the Updating Samples section for guidance on how to submit the modified manifest.

   OR

   If you have the submitted manifest for the profile, see the Updating Samples section for guidance on how to update the submitted manifest.

   OR

   If you would like to upload a newer version of a manifest that has already been submitted on behalf of the manifest provider, please follow the steps below:

   1. Download the submitted manifest by following the guidelines described in the How to Download Submitted Sample Manifest section if you do not have the newer version of the manifest with the sample metadata information.

   2. Transfer the sample metadata from the submitted manifest into the newer version of the manifest.

   3. Send an email to the COPO team at , indicating the profile type as well as the profile title and requesting that the samples be removed from the profile.

      The samples has to be removed from the profile so that the sample metadata in the newer version of the manifest can be registered in the profile.

      Important

      Please request that the samples be removed from the profile only if you are certain and have the newer version of the manifest with the sample metadata information.

      The samples cannot be restored after they have been removed from the profile.

   4. Upload the newer version of the manifest by referring to the guidelines described in the desired link below to learn more about each type of manifest submission:

      • Aquatic Symbiosis Genomics (ASG) manifest submission

      • Darwin Tree of Life (DToL) manifest submission

      • Darwin Tree of Life Environmental (DToL_ENV) manifest submission

      • European Reference Genome Atlas (ERGA) manifest submission

   Hint

   See Downloading Manifest Templates section for information about downloading manifest templates.

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Footnotes

[1]

See term: Sample manager

[2] (1,2)

See term: Sample submitter. Sample submitter may also be referred to as a manifest provider or manifest submitter.

[3]

See term: ASG.

[4]

See term: DToL. DToL may sometimes be referred to as DTOL.

[5]

See term: ERGA.