Visit-level data fields are designed to record clinical details that can change over time. Each visit has its own unique characteristics, such as date, site at which the visit occurred, clinical diagnoses and status (which can change over time).

Planned longitudinal studies are usually pre-programmed with the time points or visit descriptions expected for participants based upon study design. Each ‘Visit’ is programmed with the expected primary specimens to be collected by the study coordinator and, in some cases, the processed specimens derived from the primary samples. Therefore the visit descriptions and specimens will differ for every protocol.

Specimen and visit level data can be collected in a single step or in two steps. The single step process bypasses the visit page where detailed clinical data is recorded.

Single-step Specimen Collection process

Collect Visit and specimen information on a single page. This step bypasses the Visit Page and navigates directly to the Specimen collection page.

From the participant overview page, there will be one or two tables displayed: ‘Occurred Visits’ (if any previous visits exist) and ‘Pending Visits’. From the ‘Pending Visits’ table, select the down-arrow next to ‘Collect’ and select, ‘Specimens’.
The Specimen Collection page is displayed for the visit. There are two sections:
1. The upper section displays visit level fields (red)
2. The lower table displays the expected specimens at that visit (blue)
Default visit fields can be edited as needed, default settings are as follows:
1. Visit Date will default to the current date
2. Visit Site is usually set in the protocol
3. Collector and Receiver will default to current user
4. Quality defaults to acceptable, any other choice will apply to all specimens collected
Collection and Received dates need be specified, set time if necessary
Planned Specimen table: record any necessary data that differs from expected.
1. Quantity: editable if volume or other quantity unit is different than programmed value
2. Container: choose any manually selected containers to store primary samples
3. Label printing should be pre-programmed but can be manually selected
4. Status defaults to collected, but can be set as otherwise if a sample was not collected.
Example: Final Specimen Collection page following data entry and editing:
1. Entered collection & received dates,
2. Edit volume of total blood for plasma and PBMCs,
3. Selected container to store PAXgene tube,
4. Selected manual printing of label for PAXgene tube
Click ‘Submit’ to collect samples as described.
System navigates back to the Participant overview page and the summary of the visit collected will appear in the ‘Occurred Visits’ table and will disappear from the ‘Pending Visits’ table.

Two-Step Process

This process is recommended if collecting clinical data at the time of specimen collection. Note that any of the visit information can be edited at a later date.

This Visit page can be accessed during the collection process using the Collect Visit feature. Choose ‘Visit’ from the ‘Collect’ button in the Pending Visit table on the Participant overview page.
This navigates to the Visit page which displays additional fields not found during the Single step process.
1. Clinical Diagnoses can be entered in one of two ways. Multiple diagnoses may be chosen.
  1. Typing any part of the description of the clinical disease will display the matching choices in the dropdown.
  2. Typing the ICD 10 code (without ‘.’) will display the matching diagnosis. Note: OpenSpecimen uses ICD 10 diagnosis codes to record clinical disease descriptions which enables data querying and manipulation across studies.
  3. Example: typing ‘diabetes’ will display all subtypes of any ICD 10 containing ‘diabetes’.
2. Clinical Status can be used to record if a participant is a No Diagnosis / Control or to record their clinical status as related to the specific study. Each study will choose their own usage of these terms.
3. Cohort currently records only Case vs. Control. If your study has different designations for Cohort, these can be recorded with a custom field.
4. Surgical Pathology Number may be entered, if available.
5. Comments is a text field available for free typing.
Visit data are saved by selecting:
1. ‘Create’ directs the user to the Visit overview page where details can be viewed and reviewed and edited if necessary; OR
2. 'Proceed to Collection' directs the user to the Planned Specimen Collection page (see <description> above)
Create navigates to the Visit Overview Page which displays the Visit details and the specimen table.
If there are multiple visits, each visit will have its own Overview Page and its own forms attached if any are attached at the Visit Level.
1. For each visit, the menu bar on the left shows 4 tabs and defaults to ‘Overview’:
2. If a Path Report is available as a .pdf, it may be uploaded from the Path Report tab.
3. If form-specific data is to be entered, any attached forms can be accessed from the Forms tab.
4. The Specimen Tree tab functions as it does for Participants, by displaying the the specimen tree on the screen being viewed.

Editing Clinical data after using the single-step specimen collection

It is common that clinical diagnoses or pathology is not obtained until after specimen collection occurs. If this is the case, the Clinical information can be added or updated at any time using ‘Edit’ on the Visit page.

The Visit page can be accessed after collection by selecting the ‘Event Label’ in the ‘Occurred Visits’ table.
Choose ‘Edit’ for the Completed Visit.
Edit or update any fields as described above.

NEW PAGE:

Collecting Planned Derivatives and Aliquots

The previous section reviewed collection of planned primary specimens. Typically primary specimens are processed in the laboratory into different sample types, which are often stored as aliquots.

These derived sample types can be pre-programmed into each protocol for ease of recording. This step can occur during the initial collection or can occur at a later time point if processing is performed by a different lab tech or at a different time than the primary sample collection. Timing is set based upon the design and workflow of each protocol or laboratory.

In the Baseline visit of the Demo Study, two samples have planned derivatives and aliquots. These can be collected by navigating to the Specimen table on the visit page. The Collect button will appear once one or all of the pending samples are selected by clicking the box(es) to the left of the samples.

Clicking the ‘Collect’ button will navigate to a new ‘Specimen Collection’ page, where details about each derivative and aliquot can be recorded.

Clicking Submit collects all data as shown.

Quantities and number of aliquots are shown according to the Specimen Requirements set for each Event <link>, but any of these values can be edited. This figure shows that we expect 12mL of plasma, which should be split into six 2mL aliquots.

If less than 12 mL of plasma were obtained resulting in fewer aliquots, these values can be changed.

Change the number of total aliquots by clicking the vertical kebob icon.

Expand the aliquots to edit each one individually by clicking on the '+' icon.

After submitting, the specimen table can be expanded to show all primary specimens and their child samples.

Need a section on collecting unplanned specimens.

Need an unplanned specimen collection page, covered:

Next section should be on collecting pre-planned derivatives and aliquots. This will vary depending on protocol. Might be part of original collection. So it’s tough to cover. But I think it belongs in its own page. Collecting pre-planned processing events

Then creating unplanned deriv and aliqs.

That begs the question of if we need to have a separate page that describes Events and SRs.

In order to grasp this, we first have to cover what derivatives and aliquots are, which is on the derivative/aliquot page that occurs after this step.

Need to revisit the below section: I don’t think it’s necessary now.

Specimen Data Entry

CPs in which no Visit Level data is necessary, one can proceed directly to specimen collection from the Participant Registration page.
Each CP can be configured for multiple visits. Each visit can be configured to have specific specimens that are to be expected. The expected specimens will be displayed in the ‘Specimens' box on the Visit Overview Page for each visit.
1. For example, in the planned longitudinal study shown in this figure, there are 3 expected visits. T0D, T1D, and T30D.
2. At T0D (pre-surgical), there are 2 expected specimens:
  1. Whole Blood (in ACD Vacutainer)
  2. Buccal Swab
3. For unplanned studies for which specimen type cannot be predicted, no specimen type is shown.
From the Visit Overview Page, the expected specimens are shown in the Specimens table.
1. To collect one or more expected specimens, select the box next to the Description for the sample to be collected. Or select the top box (circled in red below) to select ‘all specimens’ and record all collections one one screen.
2. Once one or more samples are selected, additional options appear on the menu bar for the Specimens table.
3. Select the ‘+Collect’ from the bar to proceed to the Specimen collection page, where specimen-specific data will be recorded.
The Specimen Collection page will display all of specimens that were chosen in the previous step.
In this screen the Visit Site defaults to that entered for the Visit recorded in the previous step. If the Visit details were bypassed at the Participant Registration step, then you must enter the Visit Site here.
The Collector and Receiver will default to the current user. If these are other than the user, they may be chosen from the dropdown list, but the person must exist in the OS user list.
Collection Date and Received Date will default to the current date and time, but may be edited if different.
If necessary, edit the sample quantity if it differs from expected.
Details about sample Quality may be chosen, if desired. The dropdown list is on the right side of the screen.
If the sample is to be stored, then the Container location can be chosen by clicking on this icon:
This will open up the search for available containers. Click the search button to search for avialable locations.
You must have a container built and assigned to your Site in order to store specimens. This will be addressed in a separate Knowledge Article.
Selecting ‘Submit’ will navigate to the Visit Overview page and show the Specimen Table with the collected specimens indicated with a purple dot and the Specimen Label assigned according to the CP Label details set up at CP configuration.