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Introduction
Welcome to OpenSpecimen 101!
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By the end of this course, you should be able to understand not only the the basics of how OpenSpecimen can be configured, but also know how to choose your collection protocol, register participants, enter visit information and collect specimens, process specimen derivatives and aliquots, and manage specimen storage.
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Overview of OpenSpecimen Application
The basic design of most projects involve registering participants. Each participant has one or more visits at which one or more samples are collected and processed at each of the visit events. It should be noted that occasionally a lab / study records only specimen data and OpenSpecimen is able to accommodate this as well.
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Collection Protocols (CPs) represent the lab’s specific workflow, the expected visits and the specimens to be collected. CPs are unique to each study. For each of your studies, the BMIC staff will work you to configure a unique CP which allows the study team to set the number of events (Visits) along with the number of expected specimens to be collected at each visit, and document the processing associated with each sample. OpenSpecimen supports this one-to-many concept as shown in the diagram below where the participant has one registration event, then one or more subsequent visits where clinical data can be captured at each visit. Additionally, one or more samples are collected and processed at each of the visit events
Figure 1 represents the types of information that can be captured at each level of the data. This predesigned template provides a method to link each sample back to the person from whom it was obtained and the clinical data associated with that person. Samples can be collected at PLANNED or UNPLANNED visits. Continue reading to learn more! |
Overview of Sample lineage : the relationships of processed samples
Primary samples that are collected directly from a participant are typically processed into other sample types which are either stored or aliquoted and stored.(expand below for explanation)
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This is an example of a typical lifecycle of whole blood processed into serum or DNA and then aliquotted.  In OpenSpecimen, this hierarchical relationship is represented in a parent-child structure. Samples of any lineage can be parents of additional samples. So these relationships do not stop at the aliquot level.
 For instance, it’s possible to make a primary cultured cell line from a frozen aliquot of PBMCs. This relationship is captured by creating a derivative from an aliquot. OpenSpecimen uses colored dots as a visual indicator of status to show the status of a sample:
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Click on the topics below to get started!
Table of Contents
Access OpenSpecimen
Navigate a Collection Protocol
Register a Participant
Record Visit
Collect Samples
Collect Derivatives and Aliquots
Store or Transfer Specimens
Create Boxes
Using Queries