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 between Person and Subject records, when it's time for you to enter a new subject into Labmatrix, that subject might already have an existing Person record in our instance – they might be participating in another study, or have had tissue procured in the operating room, for example. As a result, there's a wizard which helps us avoid the duplication that results from not checking for the existing Person record first; this wizard is the primary mechanism by which new subjects are entered into the NCI instance of Labmatrix.
In order to enter a new subject, use the "New Subject" link at the top left of either the Subjects or Contacts module. This will launch the wizard.
Since your subjects are all NIH patients, you proceed with the first step of the wizard by entering the NIH Clinical Center MRN, choosing your study ("GI Cancer Tissue"), and then clicking "Search" to allow Labmatrix to search for an existing record for that MRN on the study. Since there isn't likely to be one, the list will come up empty; 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.
Please enter MRNs into Labmatrix without dashes; this consistency helps us make sure that when we do our regular QA checks for duplicate records, we don't miss any.
If there is an existing Person record: 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-referenced to the correct Person record.
If there is not an existing Person record: If there isn't an existing Person record, then 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 correct demographics 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 it over to make sure it's correct! Finally, click the "Save" button; this will then bring up a New Subject pane which is pre-referenced to the correct (new) Person record.
Finishing the New Subject record
In the New Subject record, you will want to choose the correct study (again, "GI Cancer Tissue") in the "Enrolled Studies" field. If you have a custom ID for the subject (e.g., an ID assigned by the enrollment group or your data management team), then enter it into the "Custom ID" field.
Entering protocol-related information
If you are going to record on-study and off-study dates for your subjects on the study, the relevant IRB Protocol record exists for you to associate with your Subject records. When you're in the New Subject pane, you'll notice that there's an IRB Protocols tab – this is where this information is recorded. First, you have to choose the correct study (as described above), and then clicking on the IRB Protocols tab will bring up a drop-down menu from which you can choose the 11-C-0112 protocol. This will add a row for the protocol, and you can enter the start and end dates here.
After entering this, click "Save" at the bottom of the record, and the subject will be fully entered into Labmatrix.
Entering the subject's visit information
For each visit, you are recording H&P information, as well as prior therapies, current medications, and lab data.
H&P, prior therapies, and current medications
All data but the lab test data is contained in a custom data form designed for your study; it is named "11C0112 Clinical Data", and you enter a new record for a subject by using the "My Workflows" menu on the Subject record.
- Open the Subject record so that it's visible in the lower-right Workspace pane.
- From the record, click the "My Workflows" menu in the top line.
- From this menu, choose "11C0112 Clinical Data".
- This will open a new "11C0112 Clinical Data" record in your Workspace pane; enter the data, and then click "Save".
Once saved, the new "11C0112 Clinical Data" record will now appear in the "Custom Data" tab of the Subject's record.
Lab data is imported from CRIS into Labmatrix via the Labmatrix Lab Loader.
Once you've chosen your subjects, you then enter a date range for which you'd like to look up results. There are shortcut buttons to allow you to choose just the last week of results, which allows you to do weekly loads easily. Once you enter the date range, you'll be presented with a list of your chosen subjects and all the results for those subjects in that date range.
If you've chosen multiple subjects, the list of results will be collapsed so as to make it easy to see how many were found – each subject will be listed in a line along with the number of results found for that subject, and you then click on the subject to expand the list of results beneath it.
In the list of results, you can check off any individual one, or use the checkbox in the header row of a lab panel to choose all the results in that panel. (Any results which have already been loaded will show a pre-checked and greyed-out checkbox.) Once you've chosen the results you wish to load, scroll to the bottom and click "Choose Labs", which will load them and display a confirmation page to you.
When results are loaded into Labmatrix, they will display in two different Custom Data Forms – labs will show up in the "Clinical Labs" form, and cultures will show up in the "Clinical Cultures" form.
Finally, there is a help page in the Labmatrix Lab Loader application which answers many of the common questions or issues; it's accessible via the links on the right of the web application itself. (Most importantly, it addresses the most common question, which relates to accidentally terminating your Labmatrix Lab Loader session by logging into the Labmatrix application itself and leaving "Terminate any active sessions for this account" checked!)
Editing your custom data
Editing the visit data is as easy as editing the records that were entered above. We include this section in the primer, though, because there is one minor bit of the interface that might prove confusing – choosing which "Edit" button to use to edit the visit data (vs. editing the entire subject record).
In Labmatrix, when a subject has a single record for a given custom data form (e.g., "11C0112 Clinical Data"), viewing that form in the "Custom Data" tab will display the single record in its full-view format. In this format, the way to edit the record is to click the "Edit 11C0112 Clinical Data Record" button at the bottom right of the record's display. This is as opposed to the "Edit" button that's at the top right of the Subject record display – this button edits the entire Subject record (e.g., the protocol enrollment date, etc.).
Once a subject gets more than one record for the custom data form, though, they will then be displayed in tabular format, and it's much easier to edit a single record – you just right-click on the record and choose the "Edit" option from the pop-up menu that's displayed.