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).
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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:
The upper section displays visit level fields (red)
The lower table displays the expected specimens at that visit (blue)
Default visit fields can be edited as needed, default settings are as follows:
Visit Date will default to the current date
Visit Site is usually set in the protocol
Collector and Receiver will default to current user
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.
Quantity: editable if volume or other quantity unit is different than programmed value
Container: choose any manually selected containers to store primary samples
Label printing should be pre-programmed but can be manually selected
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:
Entered collection & received dates,
Edit volume of total blood for plasma and PBMCs,
Selected container to store PAXgene tube,
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.
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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.
Clinical Diagnoses can be entered in one of two ways. Multiple diagnoses may be chosen.
Typing any part of the description of the clinical disease will display the matching choices in the dropdown.
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.
Example: typing ‘diabetes’ will display all subtypes of any ICD 10 containing ‘diabetes’.
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.
Cohort currently records only Case vs. Control. If your study has different designations for Cohort, these can be recorded with a custom field.
Surgical Pathology Number may be entered, if available.
Comments is a text field available for free typing.
Visit data are saved by selecting:
‘Create’ directs the user to the Visit overview page where details can be viewed and reviewed and edited if necessary; OR
'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.
For each visit, the menu bar on the left shows 4 tabs and defaults to ‘Overview’:
If a Path Report is available as a .pdf, it may be uploaded from the Path Report tab.
If form Form-specific data is to be entered, any attached forms can be accessed from the Forms tab.
The Specimen Tree tab functions as it does for Participants, by displaying the the specimen tree on the screen being viewed.
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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.
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Clicking the ‘Collect’ button will navigate to a new ‘Specimen Collection’ page, where details about each derivative and aliquot can be recorded.
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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.
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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.
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Expand the aliquots to edit each one individually by clicking on the '+' icon.
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After submitting, the specimen table can be expanded to show all primary specimens and their child samples.
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DELETE BELOW
Need a section on collecting unplanned specimens.
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