Basic EHR Setup For a Medical Practice

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Basic EHR Setup For a Medical Practice

This document detail all the initial steps an admin needs to set up a practice’s EHR. It focuses on the Administrative duties and will require Administrative access.

The initial setup of a LibreHealth EHR practice consists of five sections:

  • Setting up LibreHealth EHR using Global settings
  • Facility Settings
  • User Settings
  • Calendar Administration
  • Practice Settings

Ruba Awayes, LibreHealth EHR Documentation Intern, August 24, 2020

Setting up using Global settings

Global settings are the general settings applicable to different services offered by LibreHealth EHR. Most are Administrator-level system activities but some are more fundamental EHR settings such as data display format preferences. They should be configured first so the EHR will properly display the modules downstream in the setup process. Defaults in the Global settings are all for English-US standards.

The Administrator should survey all Globals settings before commencing system configuration to determine what specific information to have on hand. That information will include both Practice Management and clinical factors – such as whether more than one language will be used-, the functional roles and workflows performed by the clinical staff and desired report formats.

They can be found at Administration – Globals,


The following tabs will show as follows:


Some specific Global settings will need to be checked to setup your own clinic, these includes Locale, Calendar, Security and Miscellaneous.

For details of all the Global settings, please see Globals.


Locale allows you to choose the languages used, locale, and cultural factors such as money notation, date and time format, and what to translate.


  • Default Language: Select the chosen default language displayed on the system.
  • All Languages Allowed: Allow all the available languages to be displayed as choices on menu at login.
  • Allowed Languages: Select which languages to be chosen on the login page.
  • Allow Debugging Language: Display an option for the debugging language, 'dummy', on the Login page.
  • Translate settings for the labels of following features:
    • Layouts
    • Translate Lists
    • Translate Access Control Groups
    • Translate Patient Note Titles
    • Translate Document Categories
    • Translate Appointment Categories
  • Units for Visit Forms: Choose display of US and/or metric measurement units, primarily used for vital signs and growth charts.
  • Display Format for US Weights: Choose whether weights use decimal or ounces, used for vital signs.
  • Telephone Country Code: Enter the telephone country code.
  • Date Display Format: Choose date display format as MM/DD/YYYY, DD/MM/YYYY, or YYYY-MM-DD, where MM is the 2 digit month, DD is the 2 digit date, and YYYY is the 4 digit year.
  • Time Display Format: Choose whether to display in 12 hours or 24 hours time.
  • Currency Decimal Places: Select number of digits after decimal point for currency, usually 0 or 2.
  • Currency Decimal Point Symbol: Symbol used as the decimal point for currency.
  • Currency Thousands Separator: Select a symbol to separate thousands of currency.
  • Currency Designator: Select code or symbol to indicate currency.
  • Age Display Format: Format for age display.
  • Age in Years for Display Format Change: Select at what age to only show years for the age.


Calendar allows you to set some general properties of the calendar like the start and end time slots to be displayed, length of each calendar block and the display colors of appointments.


  • Disable Calendar: Do not show calendar in LibreHealth EHR.
  • Calendar Starting Hour: Set the time for first slot in calendar
  • Calendar Ending Hour: Set the time for last slot in calendar
  • Check Selected Appointment Time: Do not register appointment with time outside clinic hours.
  • Calendar Refresh Frequency: The period of wait to refresh changes.
  • Resource Title: Select which part of the provider's name to be displayed on the top of the calendar.
  • Calendar Interval: Length of time for each schedule slot.
  • Default Calendar View: Choose default calendar view (Day, Week, or Year), Default is 1 Day.
  • First day in the week: Choose the first day of week.
  • Your weekend days: Choose which days are the weekend days.
  • Appointment Display Style: Choose how appointments should be displayed on the calendar using combinations of first name-last name, title and its description.
  • Appointments - Number to Display: Choose number of appointments to display in the Patient Summary and Onsite Patient Portal.
  • Appointment Overbook Statuses: A particular slot can be overbooked in certain cases, for instance, when there is a cancellation (x) or when patient does not arrive. This field is used to specify the allowed statuses.
  • Appointment Display Sets - Ignore Display Limit (Last Set): Ignore the appointment display limit to allow all appointments to be displayed for the last set.
  • Appointment Display Sets - Colors: To assign different colors to multiple appointments in the same calendar slot for better visibility.
  • Past Appointment Display Widget: A positive number will show that many past appointments on a widget in the patient summary screen. A negative number will show that many past appointments on a widget in the patient summary screen and reverse the sort order.
  • Providers See Entire Calendar: Enable if you want the providers to see all appointments by default and not just their own.
  • Display Canceled Appointments in Calendar: To determine if canceled appointments be displayed on calendar.
  • Auto-Create New Encounters: Automatically create a new encounter when an appointment check in status is selected.
  • Patient Flow Board:

These settings control the behavior of patient flow board, which is a main menu item.

    • Disable: Don’t display the patient Flow Board
    • Show Visit Reason: if enabled, visit reason will show in patient Flow Board
    • Show Patient ID
    • Show Exam Room
    • Show Visit Type
    • Show Patient Encounter Number
    • Flag Double Booked Appt
      • If selected, double booked appointments will be flagged in orange in Patient Flow Board
    • Allow Date Range
      • If selected, this setting allows a date range to be selected in Patient Flow Board
    • Ending Date
      • Ending date for the date range if data range is enabled
    • Timer Interval
      • The period of wait to refresh changes on the Patient Flow Board
    • Default Status
    • Number of Minutes to display completed checkouts
    • Enable Random Drug Testing
      • This setting allows to select patients for drug testing
  • Percentage of Patients to Drug Test: This setting allows to specify percentage of patients for drug testing if random drug testing is enabled.
  • Maximum number of times a Patient can be tested in a year: Zero indicates that there is no limit.


Miscellaneous contains items normally don’t fit elsewhere. You will find a lot of the other menu items duplicated in this menu group.


  • State Data Type: Specify the state data type for use of employer or subscriber state in demographics.
  • State list: List used by the 'State Data Type' option.
  • State List Widget Custom Fields: This setting displays the custom state form for the add list widget. This form will ask for title and abbreviation.
  • Country Data Type: Specify the field type for use of employer or subscriber country in demographics. The field types allowed are same as state data types mentioned above.
  • Country list: List used by 'Country Data Type' option.
  • Medicare Referrer Is Renderer: If enabled, this setting forces the referring provider to be the same as the rendering provider. This is allowed only for Medicare.
  • Financial Close Date (yyyy-mm-dd): The payments posted cannot go below this date. This ensures that after taking the final report nobody can post for a previous date.
  • Patient Label Type: To specify the avery label type to display patient labels in popups on left navigation screen.
  • Barcode Label Type: To specify barcode type to display barcode labels in popups on left navigation screen.
  • Print Patient Address Label: Allow to display patient address labels in popups in left navigation screen.
  • Envelope properties:

The following are the display properties of the envelope in portrait layout.*

    • Envelope Width and Height in mm: Specify the width along x-axis and height along y-axis
    • Font Size in Pt: Sets the font size of the address text on the envelope
    • Envelope x-axis and y-axis starting pt: Specify the distance in mm from the top and right most edge of the envelope respectively to set the margins


Security allows you to set user passwords, security certificates, and system settings.


  • Idle Session Timeout Seconds: Maximum idle time in seconds, before logout. Default is 7200 (2 hours).
  • Require Strong Passwords: If enabled, you are required to enter a strong password with the following properties: At least 8 characters in length. Has at least three of: a number, a lowercase letter, an uppercase letter, a special character.
  • Require Unique Passwords: If enabled, this setting ensures that none of the last three passwords are allowed when changing a password.
  • Permit unsalted passwords: Storing passwords without adding a salt is an old mechanism. It is advisable to set this flag to false so that authentication is done only by using the new mechanism of salted passwords.
  • Default Password Expiration Days: Specify default number of days for password expiration. If it is set to 0, the feature is disabled.
  • Password Expiration Grace Period: Specify number of days allowed to login with an expired password.
  • Enable Client SSL: To enable client SSL certificate authentication. (Default is off)
  • Path to CA Certificate File: Full path to CA certificate file used for creating client SSL certificates for HTTPS.
  • Path to CA Key File: Full path to CA key file.
  • Client Certificate Expiration Days: Number of days that the client certificate is valid.
  • Emergency Login Email Address: This setting allows to specify an email address to receive user login activation messages in case of emergency.


Facilities contains some Practice Management settings; these are used to identify the facility in billing activities such as x12 claim files, through the interfaces with external services (such as an e-prescription service) and in other interactions with external agencies. Technically speaking, most of the information is optional if the practice is cash based but the information does appear on statements, referral forms, CCR/ CCD forms and reports- even if insurance is not used.

Facilities can be found under Administration Menu.


The following window will show the available facilities in the system, as follows:


Click ‘Add’ button to enter your facility's information, the following panel will show:


Enter the requested information in each area in the panel.

The required fields that you have to enter:

  • Name: The name of your facility
  • Legal Entity: Enter the type of the legal entity
  • Color: Click the color link beside the ‘Pick’ and choose a color for the display of the items for this clinic to distinguish each facilities information from the others

Note: If insurance billing is involved, the one facility that houses the provider’s practice office, must be designated as the ‘Primary Business Entity’.

The remaining information will be the Address, City, Phone, and Country. Make sure to include the correct address information, as it will be used for billing. Choose whether your facility is a billing and/or Service Location and enter your facility's CLIA number and Tax ID (it can either be the tax ID the practice receives with their business license, or if it is a small practice it is usually is the provider’s Social Security Number). If your clinic is a billing location you may check the 'Accepts Assignment'.

Remember to click the ‘Save’ button to save your clinic's information.


Users Settings are account settings for all staff authorized to use the EHR system including access permissions to various EHR functions, identifiers for external activities – especially Rx data – and the practice's calendar. It is also used to identify Providers in billing activities such as x12 claim files, through the interfaces with external services and in other interactions with external agencies.

Users can be found under Administration Menu


The following window will show, as follows:


This screen shows the controls to add a user account, view user accounts grouped by facility, and a checkbox to show or hide inactive users.

Click ‘Add User’ button to enter your user’s information, the following panel will show:


Enter the requested information in each area in the panel.

The required fields that you have to enter:

  • Username: The desired username to be displayed
  • Pass Phrase: The new user's password
  • Your Pass Phrase: The password of the person creating the user account, to confirm they are authorized to do so
  • First and Last Name: The user’s first and last name

The remaining information will be:

  • Default Facility: Choose your facility from the dropdown menu that lists all facilities in the system (if the provider must change the default facility, if they have multiple facilities and need to bill from them individually)
  • Provider and Calendar Checkboxes:

Provider: Select if the user is a Provider Calendar: Select if the user is allowed to use the calendar, making and changing the schedule

  • Federal Tax ID: If the user is a provider, provide their Tax ID to ensure proper billing for their services
  • DEA Number and NPI: If a provider, enter those provider's numbers
  • Provider Type: Choose the provider’s speciality from the dropdown menu
  • See Authorizations: which user authorizations this user may view: "None", "Only Mine", "All"
  • Taxonomy: An auto generated value provided by the LibreHealth EHR system
  • Calendar UI: Format of the calendar that will display when this user logs in: "Outlook", "Original", "Fancy"
  • NewCrop eRx Role: Role titles for NewCrop eRx activities (choose it if the practice enabled e-prescription module, otherwise it does not apply)
  • Default warehouse: Only applies if the practice has an inventory set up, then that dropdown will be populated from that configuration and you can pick the warehouse.
  • Access Control: Select the type of access to LibreHealth EHR this user will be authorized

Please note if the practice has multiple facilities, the provider will have to change ‘default facility’ dropdown in the user profile, every time they log in to the EHR, in order to keep the billing correct for the different facilities.

Remember to click the ‘Save’ button to save the new user.


The calendar displays the daily appointment schedule and provides data for real time facility monitoring, billing purposes and reports. It also allows for provider schedule creation including custom appointment categories and specific time-block categories that can be configured within a provider’s calendar to create an efficient and accurate scheduling process.

The following basic calendar configurations must be set in order to setup a new facility practice in LibreHealth EHR.

Set Calendar Globals

Calendar Globals allow to set some general properties of the calendar like the start and end time slots to be displayed, practice weekend days and length of each calendar block. Please refer to “Setting up LibreHealth EHR using Global settings” to check that these properties are properly set.

Set Date Format

Date Display Format in Globals – Locale allow to set the desired date display format. The dates appear as MM/DD/YYYY, DD/MM/YYYY, or YYYY-MM-DD, where MM is the 2 digit month, DD is the 2 digit date, and YYYY is the 4 digit year. These dates formats vary depending on the geographic location.

Calendar Administration

Calendar Administration settings allow to customize different categories of time slots (events) for providers, patients, and the clinic.

The events for providers that can be configured may include different types of appointments they want to have in specific time block or special purpose uses of their time. The custom events for patients may include different services they receive in the facility like health and behavioral assessment, ophthalmological services, and preventive care services. The events for the clinic include holidays and closing time.

Calendar administration settings can be found at Administration – Other – Calendar Administration


The following window will open, as follows:


Users can create new category or use existing ones. The existing time block categories are shown within the drop-down list under the Select Category field, as follows:


The following settings can be set for each category:* Category display name

  • Default duration in minutes
  • A display color which can be chosen from a color picker
  • All day can be selected to display the category for the entire calendar time
  • Category description
  • Type indicates whom the category is applicable to – Patient, Provider or Clinic

Customize the categories per your requirements and click the ‘Update’ button to save the changes, or click ‘Delete’ button to delete the selected category.

Setting up provider's schedule in the Calendar

Setting up the In Office, Lunch and Out Of Office time for each provider. This will highlight the working hours of the provider where the appointments can be scheduled within this period only.

Clicking the ‘Calendar’ option in the Main Menu, will open the following window including the names of all providers in the system:


Select the name of the provider whom you want to set the calendar for, and click on the time where the provider will check in to the office. This will open the following dialog:


Click the 'Provider' tab and choose “In Office” from the 'Category' drop-down list. The Facility and Provider name should be automatically filled in for you, as well as the time that you selected.

You can select the ‘Repeats’ checkbox if you want to make this a repeating event, which allows you to set up an event only once for a given period of time.


The same process is used to create an “Out Of Office” event.

Please note that the ‘In Office’ and ‘Out Of Office’ events have no End Time, only a start time.

You can also add a lunch break to your provider’s schedule. This is done the same way, with the exception of the duration, where it has a start and end date.


When you are finished click 'Save' to update the calendar.

You will see the provider’s full schedule on the Calendar with the available time slots. Continue setting up the Calendar for all the providers in your facility.



The Practice Settings is the place to register and administer any internal or external pharmacies the practice works with, insurance companies and clearinghouses. You can also configure the Document Storage Repository structure.

Practice can be found under Administration Menu.


The following window will show the different Practices in the system, as follows:


Clicking the links in the navigation menu will open the Practice Administration page, where you can edit or update the facility’s information.


Click the ‘Add a Pharmacy’ button to enter the contact information for your clinic's pharmacy


Enter the relevant contact information for your pharmacy. A drop down menu lets you select the preferred method for transferring prescription information (by Printed document, Email, or Fax). Once you've entered the correct information, click 'Save' to add your new pharmacy.

X12 Partners

Before setting up any insurance companies, X12 partners information must be filled in first. These are the clearinghouses whom you will send electronic billing.

Click on ‘X12 Partners’ and then click the ‘Add New Partner’ button.


Enter the following information that will be provided to you by the X12 partner.


Remember to click ‘Save’ button to save the information you've entered.

Insurance Companies

Click ‘Insurance Companies’ link from the Navigation Menu will open the following:


Click ‘Add a Company’ button to add the information for the new insurance company.


Please note that the length of the name must not be longer than 35 characters, and the ‘Default X12 Partner’ dropdown is populated from the list of X12 partners just entered in the previous step.

Once you have entered the correct information, click ‘Save’ to add the new company to the list, or to save any updates.

Insurance Numbers

Each insurance company has specific ID numbers assigned to the facility's providers.

Click on ‘Insurance Numbers’ to see a list of your clinic's providers and their default ID numbers.


Click on a provider's name to bring up a list of insurance companies and the corresponding ID numbers that have been entered for that provider.


Click ‘Add New’ and enter the relevant information for adding this provider's numbers for another insurance company. Click ‘Save’ button to add the new number.


Organizes in a hierarchy the categories of documents that may be uploaded and attached to a patient record.

Click on ‘Documents’ to see a list of patient documents that have been uploaded.


Clicking the ‘Edit Categories’ button displays a hierarchy of the different types of documents that you can attach to a patient.


To add more categories click on the name of the folder under which your new category will be placed. Fill in the name of the new document type, and click ‘Add Category’. To add a new top level category, click on the ‘Categories’ folder.


HL7 Viewer

Copy and paste the HL7 file contents into the ‘Paste HL7 Data’ window -as shown below- Click ‘Parse HL7’ button, the parsed file will be shown below text area, but it is inoperative at present.



In this document, we reviewed the initial steps needed to be done to set up a new practice in LibreHealth EHR.

We have explored the five steps within the ‘Admin’ module with step-by-step instructions on how to set up each one of them.

If you have any questions, we recommend you ask our community support in the LibreHealth Forums (