Once you have obtained your username and received an email with account information, you may access OpenSpecimen on the Training server.

Log in to OpenSpecimen using your uNID and password, choosing ‘utah.edu’ from the domain name dropdown. Use your uNID password to access the system.

When your request for an OpenSpecimen account is approved, we will create a Longitudinal CP for your use which will allow you to experiment with the OS system. This is a training server and no actual patient data should be entered into the fields. You are welcome to create your own CP too, but it is easier to learn your way around with an established template.

Abbreviations and general concepts:

OS: OpenSpecimen

CP: Collection Protocol: refers to the laboratory-specific study or project to which participants are registered.

Long title: Descriptive title of your project

Short title: This will be your CCTS ID

Code: This will be used to generate the PPID for your participants. It must be unique throughout the system. The acronym for your lab and PI initials are a good choice, adding an abbreviation for the subproject is applicable if there are subprojects that will need their own CP.

PPID: Participant Protocol Identifier: refers to the unique number associated with one participant in a specific CP.

UID: unique identifier in numerical order

Parent Specimens: any primary sample collected, such as blood, tissue, buccal swab, etc.

Child Specimens: any aliquots or derivatives of the parent specimen

Derivative: secondary sample type created from a parent sample (i.e. DNA is a sample type derived from whole blood or other tissue)

Aliquot: maintains the same sample type as the parent sample. Aliquots can be created from both parent samples and their derivatives.

Cards: From the Home Screen of OS each feature can be accessed from a ‘Card’

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General OS navigation:

1. From the Navigation bar on the upper left, navigate to ‘Collection Protocols’ (CP) by clicking on the 'Collection Protocols' card or choose 'Collection Protocols' from the dropdown list from the ‘Navigate To’ icon in the upper left corner.

    

    

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2. You will be shown a list of the CPs assigned to your Site.

3. Click on the Collection Protocol title. A demo CP has been assigned to you upon signing up. Otherwise, you can click on any other CP you see in the list in order to view its details.

4. This navigates to the Participant Overview page which displays a list of the current participants and a section entitled ‘Filters’. A new protocol will have no participants added yet.

5. By default, the Participant list displays the PPID, the participant name, Master Patient Index, Registration Date, and Age.

6. The ‘Filters’ section on the right is used for searching or filtering the participants by the fields shown.

7. Selecting Dates using the calendar icon:

   1. From any date field, select the calendar on the right-hand side of any date field.

   2. In order to proceed backward and forward, either click the left or right arrows, or click on the month/year in the top line to toggle to different years:

       

       

   3. This will display all the months in the current year. Select the month and day as prompted.

       

       

   4. To proceed further back by year, then click on the year field again.

       

       

   5. This will display years in 20-year increments. Then you can select the left arrow to go back as far as necessary. Then you can select the year. Select month and day as they are displayed. Click ‘Done’ and the date will appear in the date field.

       

Participant Level Overview

Subject-specific information entered during initial registration can be viewed at the Participant Level. Also displayed is the overview of all visits and a summary of the specimens that have been collected.

1.  Click on a PPID in the left-hand column.

2. On the left-hand side of the screen is a menu under which participant-specific data may be viewed:

    

    

3. Overview tab is displayed first which shows:

   1. All fields at the Participant level for the given participant. These fields are described in detail in the ‘Participant Data Entry’ section of the Data Entry knowledge article.

   2. Medical Identifiers table shows the MRN and the site at which it was obtained, if applicable. This section is blank and will not appear for samples obtained from sites for which no MRN is available.

   3. Occurred Visits: This table shows any visits that have been collected for the participant.

       

       

      1. Event Label: Code for the Visit, followed by the description. If your study does not have defined collection timepoints, all events will be recorded under the same Event Label.

      2. Name: Configurable for each individual CP

      3. Date: The date of the patient visit.

      4. Collection Stats: shows how many individual planned samples were collected from the patient during the visit (green bar), the darker green bar shows the number of unplanned specimens, missed specimens are shown in gray, and any pending collections and shown in orange.

      5. Utilization Stats: Shows the number of collected specimens that are stored (green bar), not stored (purple bar), or ‘closed’ (red bar).

      6. Hovering over the colored bar will display the stats for the specimens.

      7. Clicking the 3 vertical dots on the right brings up a menu to view or edit the Visit details, collect a new Visit with the same name and specimen criteria, collect pending or unplanned specimens, or print labels.

          

          

   4. Pending Visits:

       

       

      1. This table shows any expected visits, so no Event Label will be displayed. The name displayed under Visit is the name assigned to the planned visit under the configured CP. Because it has not been collected, the name is not participant-specific at this point.

      2. The expected date will be shown based upon the time table assigned for planned visits when configuring the original CP.

      3. Pending Specimens: the number of expected specimens per the specimen requirements configured in the original CP.

       

4. Consents tab will show the participant's answers to the consent statements as assigned to the given protocol.

   1. The consent statements based upon the study protocol’s specific consent documents. However, the BMIC is developing general consent statements for OS that are coded, from which you can choose. They are being added as needed and are in development.

   2. The top section contains fields for Signature Date, a consent witness (who must be an OS user), and Comments in which the consent version can be captured.

   3. The fields and the answers to the statements are editable with the ‘Edit’ button:

   4. A signed .pdf of the participant’s consent statement can be uploaded by clicking on the wrench:

   5. Choose the file from your computer and click on 'Upload'

5. Visits tab shows the overview of the Visits (this does not actually take you to the participant’s visit page, it only shows a summary)

   1. For unplanned studies, all specimens will be collected under one Visit

   2. The Specimen field is shown on the right and will list all specimens recorded for the participant including:

      1. Sample type submitted (whole blood, saliva, tissue, etc.)

      2. Derived specimen type (DNA, RNA, etc.)

      3. Any aliquots of the parent or derived specimen

      4. Specimen label

      5. storage location, if available

6. Specimens tab shows a detailed list of all parent specimens, any derived or aliquoted specimens, and their individual status (collected, pending, exhausted, closed, etc.), their label (specimen name), and storage location, if stored.

7. Forms tab shows any custom forms associated with the CP at the Participant level

8. Specimen Tree tab is accessible from any of the levels above and functions as an on-and-off switch to view the specimen table.

Visit (or Event) Level Overview

The ‘Visit’ level for each participant is where visit specific events are recorded, such as the site where the collection occurred, and any clinical diagnostic details associated with that collection event.

Each Visit can have multiple specimen collections. These specimen requirements can be assigned per visit or can be recorded as received for unplanned studies in which the exact specimen type or amount is not known ahead of time.

1. The Visit overview for any participant may be accessed by selecting the Visit Name from the Occurred or Pending Visits table on the Participant Overview page

    

    

2. The screen displayed will include the details collected during the visit, and the status (pending or complete)

    

3. Naming Convention

   1. Visit name: includes the Visit Code and the Description, such as ‘T0D: Pre-surgical' or 'T30D: 30 day follow-up’ (these are set during CP configuration and are unique to each CP)

   2. Event Label: Example: ‘T0D: Pre-surgical’

      1. T0D represents time point of zero days and is set by the system based upon the time points of the collections.

      2. ‘Pre-surgical’ is the Event Label and can be configured during CP setup.

4. You will know you are in Visits by the header at the top left of the screen.

   1. It will display: CP name / PPID / ‘Visits’

       

       

5. On the left, the navigation bar changes and shows 4 tabs:

    

    

   1. Overview: Displays all the participant specific data associated with a Visit and the table of specimens or pending specimens for that visit

   2. Path Report: Path reports may be uploaded here as .pdfs and will be displayed

   3. Forms: Visit level custom forms can be accessed from this tab

   4. Specimen Tree: As in the Participant overview, this tab is accessible from any of the levels above and functions as an on-and-off switch to view the specimen table.

   5. Additional unplanned specimens may be collected from the overview screen by clicking the ‘+ Add Specimen’ button.

       

Specimen Level Overview

1. Select ‘View Specimens’ from the level of the overall CP

2. This navigates to the complete list of all of the collected specimens, their derivatives, and any aliquots.

3. The left screen displays the complete specimen list, which by default includes: Specimen Label, Created On Date, Type, Anatomic Site, Pathology Status, Quantity, and Storage Location

    

    

4. Filters are displayed to the right. As most specimen lists are extensive, the list may be filtered by common properties, such as those displayed in the list. However, these filters may be configured to fit the needs of the lab.

5. Any sample may be selected from the list to view the details.

    

6. If there are custom forms attached at the Specimen level, those forms can be accessed from this page by clicking on the Forms tab.

7. The Events that can be associated with any sample are shown in the dropdown list accessed from the Events tab: