This is the primer on data entry for the Natural History of Lung Cancer protocol (PI: Guha, protocol number: 14-C-0105). In Labmatrix, the study is generally named Thoracic Malignancy Tissue & NatHx.
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 "Thoracic Malignancy Tissue & NatHx"), 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 "Thoracic Malignancy Tissue & NatHx" study, which will also populate the "Primary Study" field with this study;
- If your subjects will have protocol-specific custom IDs, enter this subject's ID in the "Custom ID" field;
- Click on the "IRB Protocols" tab, and in the "Select IRB Protocol to Assign" pulldown, choose the "14-C-0105" protocol;
- Fill in the protocol-specific information for 14-C-0105 (protocol start date, consent sign date, etc.) as needed.
Once you're done entering the subject info, click the "Save" button at the bottom of the record to save it.
Natural history & tobacco use data
This protocol has two primary data recording forms, the Thoracic Malignancy Patient Info form (for most of the natural history data) and the Tobacco Use Hx form (for the tobacco use data). Both forms are accessible within a subject's record; existing data is present in the "Custom Data" tab within that record, and entry of new data takes place via the "My Workflows" menu at the top of the record.
Entry of new natural history or tobacco use 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 pane.
- Within this menu, choose either "Thoracic Malignancy Patient Info" or "Thoracic Malignancy Tobacco Use", whichever you are entering;
- 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 natural history or tobacco use data
All existing data for subjects is visible within the "Custom Data" tab of the subject's record.
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!)