This is the primer on LM data entry for the ClinOmics study.
Useful site addresses
Labmatrix Lab Loader
If you are importing clinical labs or cultures, you'll also be using the Labmatrix Lab Loader web application, which lives at https://lmlabs.cancer.gov/; your account information is again the same as your NIH username and password.
We have a centralized support system for NCI's Labmatrix installation. Emailing your request means that it is automatically entered into our work tracking system, and doesn't linger in a specific user's inbox; we can also track our responses to issues, and collaborate within our own group in solving problems as they come up. So please submit all requests for assistance via this email address! It's available as a link from Labmatrix's help page, on the login page of Labmatrix, and as a link at the bottom right of the Labmatrix home page.
Separation of the Person and the Subject
A critical distinction to understand in Labmatrix is the distinction between a Person and a Subject, a distinction that reflects the difference between a human being's properties (e.g., name, demographics) and the properties related to that human's participation in a study (e.g., the start date of the participation, their custom ID on the study). The distinction allows Labmatrix to enforce access limitations so that study data is only visible to that study's users, yet the general information about NIH patients is visible to the entire NIH community. Below is a simplified diagram showing the relationship of the two; the green area is the Person and associated data, and the yellow area is the Subject and associated data.
The notion of a Person (also known in Labmatrix as a Contact) reflects the information which specifically describes a human being's properties – things such as name, date of birth, gender, race, ethnicity, and medical record numbers. This is the part of the above diagram in the green box; you'll note the small "Race" and "Medical Record Number" boxes, which indicate that a single Person might have more than one of these (e.g., multi-racial, or different MRNs at different institutions).
The Person records for all NIH patients – e.g., those with NIH Clinical Center medical record numbers – must be placed into the "Patients" access group in Labmatrix! This is because they need to be accessible to all Labmatrix users. Don't worry – nearly 100% of the time, the wizard described below will handle this for you, but I document this just so that everyone knows why this is set up this way.
The notion of a Subject is what connects a Person to a study – e.g., the Person named "John Doe" is participating on a study named "Cancer Stem Cells", so that Person has a Subject record which links him to the Study. The easiest way to remember this distinction is by remembering that any one human being can participate in more than one study – for example, the person John Doe might be participating in a Derm Branch study, a Radiation Oncology Branch study, and a Surgery Branch study.
There is still only one human being, so there's only one Person record, but there are multiple Subject records linked to that Person which each represent the person enrolled on a specific study. The entire NCI can access that one Person record, but only those people with permissions to access each individual study can access each individual Subject record and the data that's linked to it. (So in the above diagram, each yellow box represents a separate access group, and the data within each is only accessible to those users with the proper permissions on that study.)
In Labmatrix, if you're viewing a Person record, there will be a "Subjects" tab on that record which will show you all the Subjects that you have permissions to see for that Person.
Entering new subjects into Labmatrix
Because of the above distinction, when it's time for you to enter a new subject into Labmatrix, that person might already be in Labmatrix (e.g., they're participating in another study), or a colleague might have already entered their subject info for this specific protocol into Labmatrix. As a result, there's a wizard which helps us avoid duplication that might result from not checking for existing records first, and this wizard is the primary mechanism by which you'll enter your subjects.
In order to enter a new subject, click on the "Subjects" module link in the top row, and then use the "New Subject" link at the top left below the modules bar; this will launch the wizard. The first step will ask you to enter an MRN and choose a study (you'd choose the ClinOmics study from the list of those available to you), and then you click "Search" to check to see if there's an existing record for that MRN on the study. The list will likely come up empty, meaning that nobody has entered this subject yet; there will then be a "Search Persons" button at the bottom of the wizard which will search to see if there is an existing Person record with that MRN (meaning that the person is already in Labmatrix).
If there is an existing Person record: it will come up in the list, and you just highlight the row and click "Create Subject From This Person", which will open a "New Subject" pane pre-populated with the link to the correct Person record.
If there is not an existing Person record: the list will be empty, and there will be a "Search CDR" button at the bottom which will then search the demographics registry for that MRN. So long as it's a valid and correct NIH Clinical Center MRN, clicking this button will bring up the demographics as they're recorded in CRIS for the person; you then just click "Use This Person" at the bottom, and a "New Person" pane will come up pre-populated with all the demographics from the registry. Look these over as a final validation, and then click the "Save" button; this will then bring up a New Subject pane which is pre-populated with the link to the correct (new) Person record.
Once you're entering the new Subject record, there are a few bits of info that you'll enter:
- In the "Enrolled Studies" field, choose the ClinOmics study, which will also populate the "Primary Study" field with this study;
- Enter the subject's ClinOmics ID in the "Custom ID" field (this is critical in order for Scribe to be able to sync the subject's GAUS data into Labmatrix).
Once you're done entering the subject info, click the "Save" button at the bottom of the record to save it.
The GAUS data form is accessible within a subject's record, in the "Custom Data" tab within that record.
Entering new GAUS data
In order to enter new information, you use the "My Workflows" menu that's part of a subject's record.
- Search for and retrieve the relevant subject record so that it's visible in the lower-right Workspace pane.
- Click the "My Workflows" menu at the top left of the subject's record pane.
- Within this menu, there's a "ClinOmics" entry, with "GAUS" as a subentry; click this.
- Enter the data, and click "Save" when complete.
- Once saved, the new record will appear in the "Custom Data" tab of the subject's record.
Viewing existing GAUS data
All existing data for subjects is visible within the "Custom Data" tab of the subject's record.