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. 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.
You proceed with the first step of the wizard by entering either the patient's NIH Clinical Center MRN or the MD number (including the "MD" prefix, e.g., MD-11-123) choosing your study ("Molecular Diagnostics"), and then clicking "Search" to allow Labmatrix to search for an existing record on the study with that same identifier. If one doesn't exist, the list below the search fields 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 identifier (CC MRN or SoftPath ID).
NIH Clinical Center MRNs are entered without dashes, whereas SoftPath IDs are entered with dashes. If you make a mistake with this, the wizard should handle it appropriately, but the ideal is to respect these guidelines.
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; the next step will involve pulling the demographic information in from the CDR (our blanket term for the various clinical data registries that contain demographics, such as CRIS and SoftPath). In the "Sync With Registry" field, choose "SoftPath Patient Registry", and in the "Organization" field, choose "Lab of Pathology, NCI", and then click the "Search CDR" button at the bottom. This should 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.
Finally, in the New Subject record, you will want to choose the correct study (again, "Molecular Diagnostics") in the "Enrolled Studies" field. To complete the record, click the "Save" button at the bottom of the window.
Entering Biomaterials for Subjects
The last remaining step is to enter information about the biomaterial. This is done from the Subject record, using the "Create" menu (with the small green plus icon) at the top of the record.
Labmatrix has four biomaterial types, two of which – "Body Fluid" and "Tissue Sample" – are of relevance for the primary biomaterial entry. Pieces of tissue are should be entered with the type "Tissue Sample", whereas fluids should be entered with the type "Body Fluid". And note that bone marrow biopsies are considered tissue samples, and bone marrow aspirates are considered body fluids!
With the Subject window open, click on the "Create" menu, choose the "Biomaterial" option, and then choose either "Body Fluid" or "Tissue Sample" from the submenu. This will bring up a new Biomaterial window, with the source subject pre-entered as the subject from which you created the new specimen.
In the New Biomaterial window, fill in the following fields:
- Type: choose the type of tissue from the pulldown menu
- Current Status: choose "In inventory, stored"
- Current Status Date: choose the date that the tissue was received (you can double-click in the field in order to automatically enter the current date)
- Barcode: enter the DNA number here
Then click "Save" at the bottom of the window; this saves your primary data, and leaves you with a pane open showing you the new biomaterial. In this pane, again click the "Create" menu (with the small green plus icon), choose the "Custom Data Record(s)" option, and then choose "LMD Case Data" from the submenu – this brings up a new custom data entry window, and is where you enter your lab-specific data about the specimen. In this window, fill in all the relevant fields:
- Date in
- Date out
- SoftPath number (if any)
- MD number (the same MD number as was assigned to the subject above)
- Working Dx (free-text field)
- Assays (a table of data which reflects all the assays performed on the specimen – and note that the assay can be selected from the pulldown menu or typed in freetext)
- Final Dx
When finished, click "Save" and the data will be attached to the biomaterial record.
Editing the biomaterial's custom data
Editing the custom 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 custom data (vs. editing the entire biomaterial record).
In Labmatrix, when a biomaterial has a single record for a given custom data form (e.g., "LMD Case 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 LMD Case 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 Biomaterial record display – this button edits the entire Biomaterial record (e.g., the biomaterial type, etc.).
Once a biomaterial 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.