GNU LIMS: Laboratory Information Management System for the Healthcare and Biomedical sectors

GNU LIMS, also known as Occhiolino, is a modern Laboratory Information Management System for the healthcare and biomedical sectors, that has emerged as a GNU Health sub-project.

The Laboratory Modules manage the request, creation and evaluation of laboratory analyses. As far as the LIMS (Laboratory Information Management System) functionality, GNU Health is very flexible. You will be able to link it to the patient chart and to the financial management of the Health Center.

It is able to link to financial management, and create services and invoices / billing from the laboratory requests.

Occhiolino has been integrated to GNU Health since the very beginning. Starting 3.2, there is a dedicated repository to concentrate the development efforts and to better serve the GNU Health community.

Requesting a Laboratory Test

New lab order creation process. Among other information, it contains the lab test type, and the associated health service.

To create a new Lab Test Request record there are two possibilities:

1. Click on the Relate button in the patient form and choose the Request Lab Test command.
2. Click on the Request Lab Test command in the main navigation.

In either case a dialog will open that allows you to enter the following information:

• Date: The date and time of the request (default values are the current date and time)
• Urgent: A checkbox to indicate an urgent request
• Patient: The name of the patient (link to a patient record)
• Doctor: The name of the health professional requesting the laboratory test
• Tests: One or more tests to be performed

Test Types

GNU Health Laboratory Test Types

The laboratory module allows you to chose from a list of different lab tests and to create the specific one that you need, with their analytics, normal values, etc. etc.

Managing Laboratory Tests

List of lab orders and requests from GNU LIMS

To check for new laboratory test request and to create test reports, the members of the laboratory staff will open the Health → Laboratory → Lab Test Requests section in the main navigation. This brings up the list of Lab Test Requests, showing all information described above.

In addition there is a State column indicating whether a request is a Draft or Ordered. As soon as a laboratory staff member creates a laboratory test by clicking the Action button and selecting the Create Lab Test command, the state of the request will change from Draft to Ordered. In addition the font color of the request will change from blue to black, making it easier to distinguish between pending requests and requests being processed.

GNU LIMS barcode standards and QR for samples

Storing Laboratory Test Results

A laboratory test record allows to store the values of all test criteria contained in a specific test plus some extra information.

To access test results there are two possibilities:

1. Click on the Relate button in the patient form and choose the Lab Reports command.
2. Click on the Health → Laboratory → Lab Test Results command in the main navigation.

The Lab Tests Results form is structured as follows:

Laboratory Reports

GNU LIMS lab test results. Form view

The print layout of a laboratory test is called a laboratory report. You can preview and print laboratory reports from the Lab Test Results form by clicking the Report button and choosing the Lab Report command. Any anomalous value (i.e. a value below the lower limit or above the upper limit of a test criterion) is printed in red.

Lab orders and Health Services

[Needs to be documented]

Configuration

To configure the available laboratory tests, go to the Health → Configuration → Laboratory section in the main menu. There you have two options: You can create, edit, or delete test types (including their test criteria), and you can configure the units used in the tests.

Lab Test Units

GNU Health: Configuration of lab test units

By double clicking on Health → Configuration → Laboratory → Lab Test Units you will get the list of all units defined in the system. Configuring a unit is quite simple, since there are only two fields:

• Unit
• Code (in most cases identical to Unit)

Lab Test Types

By double clicking on Health → Configuration → Laboratory → Lab Test Types you will get the list of all test types defined in the system. A test type serves as a template for an individual test. It contains a list of test criteria, including information about standard values for each test criterion. It is also linked to a product which allows to properly charge the test's cost to the patient.

Main Info Tab

GNU Health: Configuration of lab test types

In the Main Info tab of the test types form you can manage the following information:

• Test: The full name of the test (typically in capital letters)
• Code

Below there is the list of Test Cases (or test criteria, as they are called elsewhere) of a test type. Each test case consists of the following information:

• Sequence: A number to create an order within the test cases of a test type
• Analyte: The substance or aspect to be analysed
• Lower Limit: The lower limit of the range where a value is considered to be normal or not critical (used for information purposes, but also used to print a test case in red if a value is outside the range)
• Upper Limit: The upper limit of the range where a value is considered to be normal or not critical (used for information purposes, but also used to print a test case in red if a value is outside the range)
• Reference: A text field to add more information about the expected values of a test case
• Units: The unit of the values in a test cases (used for Upper Limit, Lower Limit, and the test value itself)

Using the Service field at the bottom of the Main Info tab each test type is linked to a product. The product defines the price of a test to be charged to the patient. So for each test type record you will need a product record; this product record is typically named after the test type.

Extra Info Tab

The Extra Info tab contains a text field Description for additional information about a test type.

Interfaces with Laboratories and LIMS

GNU Health allows to enter the results of the analytes manually for any type of test. However, in many cases, it's not feasible to enter this information manually, since it will be a lot of work and prone to human error.

Generally, the health professional creates a lab test order, and this is sent to a laboratory. When the laboratory processes the order, the results are sent back in either paper or digital form. Moreover, in larger institutions, the center connects with their own laboratories and lab systems. The interface will allow to automatically retrieve the results from the lab and upload them to GNU Health.

In order to automate the task for processing the data, both the health institution and the laboratory need to agree in the way the data format and transferred. There are different formats and message exchange methods (csv, xml, web services, HL7, ... ), and they can fit different scenarios.

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