Single-step Specimen Collection process
As previously mentioned it is possible to collect visit and specimen information on a single page. This step bypasses the Visit Page and navigates directly to the Specimen collection page. This can be done either when adding a new participant to the CP or for an existing participant.
If you are adding a new participant, select the ‘Proceed to Collection’ button at the bottom of the page.
If the participant already exists in the CP, navigate to the participant’s overview page.
There may 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 settings are as follows but these can be edited as needed:
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’. Note that this value will apply to all specimens collected. If a single specimen has a quality issue, you will need to navigate to that sample and change the quality description.
Collection and Received dates typically 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 (detailed description is covered in ‘Containers’ section.
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.
On the screen shot below you can see the following collection tasks which were performed:
Entered collection & received dates,
Edited 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.
Two-Step Specimen Collection 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.
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 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 (as described above).
‘Create’ navigates to the Visit Overview Page which displays the Visit details and the specimen table. All specimens will appear as ‘Pending’ (noted by the yellow dot next to the description).
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-specific data is to be entered, any attached forms can be accessed from the Forms tab. (As as example, patient’s medications usually change over time and a different form can be completed at each visit for medications.)
The Specimen tree tab functions as it does for Participants, by displaying the the specimen tree on the left side of 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.
To collect planned specimens after entering the clinical data on the Visit Page
If no specimens are displayed in the Specimens table, select ‘Show Pending’ from the ‘More’ button on the Specimen Table displayed on the Visit Overview page.
Select all or some of the specimens to be collected. Once selected, the ‘Collect’ button will be displayed. Choosing ‘Collect’ will navigate to the Specimen Collection page as described previously. Enter or edit details as needed.
