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Table of Contents


Researchers reach biobanks when they need biospecimens with similar traits for their studies. For example, one might need blood samples

...

extracted from 'Caucasian' males

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50-60

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years

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old who have smoked for ten years or more.

The ability to seek out a specific collection of biospecimens is critical for any biobanking database. Using SpecimenCatalog, the researchers can request specimens. Based on the availability and screening of specimens, request managers can approve and distribute the requested specimens.

How to request specimens?

This section explains how researchers can directly request specimens from OpenSpecimen. You can skip this section if you do not plan to give access to researchers to request using OpenSpecimen. 

OpenSpecimen allows researchers to view the summary of available specimens , and search and request for desired specimens. There are two options to publish for publishing specimens to the researchers:

  • Catalog with login for specific investigator study.

  • Public catalog without login for general biobanking specimens.

This page describes the workflow for requesting specimens from the catalog with login.

Request specimens as a logged-in user

  • Log in as the researcher.

  • Navigate to "Collection

    protocols

    Protocols" → Click on the

    ‘View Catalog’ icon

    'View Catalog'.

  • The system displays a dashboard showing the summary of the specimens available.

  • Click on the

    ‘View Catalog’ button

    'View Catalog' to see the available specimens.

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  • Search the specimens of interest by applying any filters from the left side. You can use the search feature to find the specific filter.

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  • Select specimens of interest and click on the

    ‘Add to Cart’ button → 

    'Add to Cart → Click on the

    ‘Cart’ button

    'Cart' that shows the number of specimens added to the cart.

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  • Review the specimens in the cart and add aliquots details if needed. Click on the

    ‘Confirm Request’

    'Confirm Request' button.

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  • Complete the "

    Request’ form

    Request Form' and click on the

    ‘Submit Request’

    'Submit Request' button. If the IRB ID is submitted,

    then

    it is matched and linked with the corresponding Distribution Protocol. 

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  • On successful request submission, you get a popup like the one below.
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  • An email notification is sent to the Requestor and the Request Managers of the catalog along with the requested specimen csv.
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Roles

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Request manager Access: The request manager also needs 'Read' access on to the 'Catalog' resource.Image Removed

Requestor Access: To access the catalog, you will need to must read access to 'Catalog' and 'Collection Protocols' resources.

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You can view the collection protocol and participant data only if you have 'Read' access on either of 'ParticipantPhito the 'Participant Phi' or 'Participant' resources.

User Group: Using the user group feature, admins can assign catalogs to user groups. This configuration is available only for a private/logged-in catalog.

Navigate to the catalog and add the 'User group' to which you wish to give access to the catalog. Refer to the wiki page for user group details.

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  1. If a catalog is assigned to a specific user group, only those users group can access the catalog. Whether they can only read or create/update catalog is based on their role and permissions on catalog resources.

  2. If the catalog is not assigned to a specific user group, it is accessible to all users with access to the Catalog resource.

  3. If the user has access to the catalog but it's not added to a specific user group, then that user will not have access to configured private user group catalog.

Catalog Access

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Navigate to the catalog → click on the catalog card on the home screen.

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You will see all the available catalogs. You can click on the 'View Catalog' icon on the right-hand side to access the catalog.

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Request Access

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Clicking on the catalog

requestor

system will navigate the user to the catalog's requests list view.

You can navigate to the catalog result view screen using the 'View Catalog' option, as displayed in the below image.Image Removed

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Requestors can edit their requests as long as they are in 'Pending' status.

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The requestor can edit their request form but not add/edit the specimens tab details. After a request is submitted, the specimen add/edit will have to be done by the Request managers.

Request email notification:

The requestor sends the email notification

is sent to the requestor

after successfully placing the request for specimens. This email contains Specimen request CSV with the list of specimens and request form content.

This csv can be configured by request managers via 'Specimen Query' in the catalog.