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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.

General Information

Useful site addresses

Labmatrix is a web-based application, and is accessible at the URL https://labmatrix.nci.nih.gov/labmatrix/. Your login credentials are your central NIH username and password.

Manuals for Labmatrix can be found at the bottom of the home page once you've logged in.

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.

Getting help

All assistance with Labmatrix and related tasks should be emailed to: ncilabmatrixhelp@mail.nih.gov.

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.

Person

The notion of a Person 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).

Subject

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 Subject record, there will be a gray box near the top of the record with the information about the Person, and then a link within the record that lets you bring up the Person record itself. If you're viewing a Person record, then there's a tab that will list all the Subjects for that one 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.

In order to enter a new subject, click on the "Data Entry" menu at the top of the home page, and then use the "NIH Subject" menu item underneath "Create New". The first step will ask you to enter an MRN, and then you should click "Search" to check to see if there's an existing record for that MRN.

If there is an existing Person record: the record will be opened, with an alert message at the top reading "A single Person record has been found." You should click on the "Subjects" tab to make sure that there isn't already a subject record for this study. If there isn't, just use the "Create New Subject" link a the top right of the record, enter the study name (Thoracic Malignancy Tissue & NatHx), and click "Create Subject".

If there is not an existing Person record: the NIH demographics database will be queried, and if the MRN matches a known patient, a new Person record will be created and opened (along with an alert that reads "A new Labmatrix Person record has been created from the NIH Registry"). Now, you can use the "Create New Subject" link at the top right of the record, enter the study name (Thoracic Malignancy Tissue & NatHx), and click "Create Subject".

Once you're entering the new Subject record, you need to:

  1. Enter the subject's custom study ID into the Code field.
  2. Click on the Forms tab, then the Subject Protocols form in the left-hand column, and then the "Add Subject Protocols..." link near the top of the record; add a new record with the 14-C-0105 protocol along with the protocol start date.

Once you're done entering the subject info, click the "Save" button at the top 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, in the "Forms" tab within that record, and entry of new data takes place in the same location.

Entry of new natural history or tobacco use data

In order to enter new information, you use the relevant form from the left-hand column of the "Forms" tab for the correct subject..

  1. Search for and retrieve the relevant subject record so that it's open.
  2. Click the "Forms" tab at the top of the record.
  3. From the left-hand column listing of all the relevant custom data forms, choose the correct form (Thoracic Malignancy Patient Info or Tobacco Use Hx).
  4. Click the "Add <form name>..." link at the top of the record (below the tab bar), and enter the data.
  5. Repeat steps 3 and 4 for any additional forms you need to enter.
  6. Click the "Save" button at the top of the record when data entry is complete.

Once saved, the new record will appear in the "Forms" tab of the subject's record.

Viewing existing natural history or tobacco use data

All existing data for subjects is visible within the "Forms" tab of the subject's record.

Loading labs

Labmatrix Lab Loader is a separate web application from Labmatrix, and is accessible at https://lmlabs.cancer.gov/. When you log into Labmatrix Lab Loader, you are presented with a home page and the relevant action links on the right side. Choosing the subject for whom you wish to load labs can be done either by study or by individual MRN; if you use the "lookup by study" option, you are presented with a list of studies on which you have permissions and then a list of subjects on your chosen study, and you can choose one or more subjects from this list.

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.

Multiple subjects

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!)

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