Primary Sense


Quick Guide

Primary Sense - clinical decision support, population health management and data extraction tool

About Primary Sense

Deliver the right care to patients at the right time.

Primary Sense is an easy to use clinical decision support, population health management and data extraction tool that helps GPs deliver the right care to patients at the right time.

Designed by GPs, data experts and researchers, Primary Sense extracts de-identified general practice data and uses evidence-based algorithms to provide GPs with real-time medication alerts, reports and patient-care prompts. It also provides general practices and Primary Health Networks (PHNs) with on-demand reporting to help with population health management.

For a quick snapshot of how Primary Sense works in general practices, view the short introductory video.

As WAPHA’s data extraction tool of choice, the cost of Primary Sense will be fully subsidised for general practices in Western Australia that share their de-identified, full population health data set.

What are the benefits of using Primary Sense?

Primary Sense has been tried and tested in general practices since 2018 and it is already being used by more than 700 Gold Coast GPs.

Developed to offer a range of benefits for general practices, Primary Sense:

  • includes the Johns Hopkins ACG® System – the world’s leading population health analytics software – that identifies high risk groups and predicts future health needs to improve a patient’s care plan 
  • is easy to use with most GPs and practice staff requiring little or no training to get started 
  • provides real-time medication safety alerts, patient-care prompts and near real-time data extractions
  • provides on-demand reports to proactively plan care that can be used by GPs, practice managers and nurses
  • is compatible with major practice clinical software systems, such as Best Practice and Medical Director (Genie and Zedmed are in the development pipeline)
  • is hosted in Primary Health Insights (PHI) with all extracted, de-identified data privacy protected, securely stored and managed in Australia.
To find out more, view the Making the most of Primary Sense webinar with Dr Lisa Beecham, a Gold Coast PHN board member, discussing the benefits for GPs and the practice team.

If you would like to share the benefits of using Primary Sense with your practice team, download the benefits infographic.

Getting started with Primary Sense

To express your interest to use Primary Sense, email or call 1800 2 ASSIST (1800 2 277 478).

Primary Sense Overview

Eligibility criteria

Primary Sense is compatible with:
  • Best Practice
  • Medical Director

Genie and Zedmed are currently in the development pipeline.

Current incentives

Refer to the Practice Assist Practice Incentives Program webpage.

Primary Sense Frequently Asked Questions (FAQs)

General information

What is Primary Sense?

Primary Sense is a clinical decision support, population health management and data extraction tool for extracting, analysing and managing general practice data in a confidential and safe way.

Who developed Primary Sense?

The original version of Primary Sense was developed by Gold Coast Primary Health Network (PHN) in 2018 which has been used by various Gold Coast GPs since. Supported by Gold Coast PHN, WAPHA has led the development of Primary Sense, which is being made available to GPs in some PHNs during 2022.

How is Primary Sense different to other extraction tools?

Primary Sense:
  • provides ‘one click’ reports about issues that matter to GPs
  • stratifies patients into different ‘bands’ or ‘levels’ of complexity using the Johns Hopkins University ACG® System
  • uses real-time data in reports and alerts because it extracts new information every three minutes
  • requires little to no training
  • is owned and managed by PHNs and the team can quickly respond to the feedback and requests from practices
  • data is de-identified and encrypted before it leaves the practice.
Which PHNs use Primary Sense?

The PHNs currently involved in rolling out Primary Sense include:
  • WAPHA (Perth North, Perth South and Country WA PHNs)
  • Gold Coast
  • Brisbane North
  • Brisbane South
  • Nepean Blue Mountains
  • Northern Sydney
  • Primary Health Tasmania
  • Northern Territory
Can my practice use Primary Sense?

Primary Sense is compatible with Best Practice and Medical Director (Genie and Zedmed are in the development pipeline). There are a small number of minimum hardware requirements that are described in the Primary Sense IT Checklist and it is important the checklist is completed prior to installation. To find out more, contact WAPHA’s Primary Sense team by emailing

What about practices using Zedmed, Genie, Helix or Medtech​?

For those practices using non-compatible software, we anticipate Primary Sense will be available in early 2023 for both Zedmed and Genie.

Practices currently using Medtech and Helix will be contacted by WAPHA to ensure they will be supported to continue participating in the Practice Incentives Program Quality Improvement (PIP QI) Incentive.

Can my practice use CAT Plus as well?

Absolutely. There are no software conflicts between Primary Sense and CAT Plus. Both software packages have unique strengths and limitations. Ultimately, what practices do with their data is more important than the software package they use. 

Given that Primary Sense is WAPHA’s data extraction tool of choice, should practices wish to use the CAT Plus suite beyond June 2023, they will need to purchase a licence from PenCS.

How much does Primary Sense cost?

Primary Sense is fully subsidised by WAPHA for general practices in Western Australia that share their de-identified, full population health data set. Practices are responsible for any costs incurred from their IT provider relating to Primary Sense installation and maintenance.

For most practices with a standard set up to manage their own IT, there is unlikely to be IT costs in relation to the installation. However, if a practice is currently using a third-party IT installer to complete upgrades on any software, then they may incur an hourly cost for the IT provider to support the installation of Primary Sense.

What are the components of Primary Sense?

Four components work together to provide real-time reports and medication alerts. These include:
  • a data extractor tool – the extractor is installed on the server of the practice
  • a desktop app for generating reports and managing alerts
  • a database – located in the Azure cloud
  • the Johns Hopkins University ACG® System – located in the Azure cloud.
Refer to the Primary Sense Components infographic.
Will Primary Sense slow down our practice system?

Primary Sense has been designed to work in harmony with your IT systems without slowing down performance. We have extensively tested Primary Sense with practices and found no evidence that it affects practice systems. However, in the unlikely event that your system appears to be slower, our technical team can adjust your Primary Sense settings further.

How is Primary Sense funded?

As not-for-profit organisations, participating PHNs fund the operation of Primary Sense on a cost recovery basis and invest in further development of the tool. You can learn more about the role of PHNs by visiting the Department of Health website.

What is patient complexity and what are the levels?

There are six complexity levels, ranging from 0-5. Level 0 indicates a very low level of complexity with no known risks for poor health outcomes, while level 5 is the highest complexity. Patients with level 5 complexity typically have significant multi-morbidity and polypharmacy and are at greatest risk of poor health outcomes.

Is complexity different to hospitalisation risk?

Complexity levels reflect the current care needs of patients, while hospitalisation risk identifies estimated future care needs. While patients with higher levels of complexity are more likely to be hospitalised than those with lower levels, complexity is not directly associated with hospitalisation risk. Many Primary Sense reports, therefore, include both results.

How is complexity and hospitalisation risk calculated?

The same input data is used for both calculations. The complexity levels of patients in Primary Sense reports were calculated with Johns Hopkins University ACG® System. The Johns Hopkins University ACG® System is underpinned by a robust evidence base of >30 years of practical application. The tool is used in 20 countries and has been validated in different healthcare settings, including general practice.

How does stratifying hospitalisation risk and patient complexity benefit a practice?

Stratification identifies patients who are most likely to have poor health outcomes or benefit from assessments and other medical care. Stratification supports planned co-ordinated care for patients. Primary Sense also identifies patients who are eligible for reviews or occasions of service. Practices can use Primary Sense reports to prioritise patients and reassure themselves that no one is slipping through the proverbial gap.

Where is the information in the “existing appt” and other columns extracted from?

Primary Sense extracts information from the “appointment book” for each patient and displays this information on relevant reports. For Medical Director, it is limited to the next four weeks (due to limitations of data available in Medical Director to update changes in appointments, e.g., change of date/cancellations). Best Practice will search for any future appointment, which is not time limited.

Who will receive medication alerts? Are these the same as Medical Director/Best Practice alerts?

Medication alerts are generated at the point of prescribing, i.e., when a clinician is entering the prescription into the clinical software. Alerts are only sent to doctors who selected this function. Primary Sense medication alerts are different to Medical Director and Best Practice alerts. They are more specific, relate only to high-risk medications and take individual patient factors into account. For example, an alert for prescribing metformin will only be generated when a GP prescribes it for a patient with a recent eGFR <30ml/min.

Data sharing and governance

Primary Sense Data Sharing Agreement (DSA) and DSA Explanatory Note

With Primary Sense as WAPHA’s data extraction tool of choice, amendments to the Data Sharing Agreement (DSA) have been made which still align with the Commonwealth’s own DSA template for the extraction and use of clinical practice data.

The Explanatory Note below provides a summary of the key terms of the Data Sharing Agreement (Primary Sense) and to address potential queries that may be raised in your use of the Primary Sense Software (Software).

What will happen to my current DSA?

It is expected that practices will have two (2) DSAs active until you have been successfully transitioned to your new data sharing solution - Primary Sense. Once WAPHA has received a successful data extraction using Primary Sense you will then move over to the single Primary Sense DSA. 

I am a new practice wanting to share data, what DSA do I need?

For practices who are new to sharing data with WAPHA, you will be asked to sign a Primary Sense DSA.

You will need to complete the Expression of Interest (EOI) to transition to Primary Sense which will result in a Primary Sense DSA being raised. This DSA requires your authorised person to sign the agreement on behalf of the practice. This would be the Practice Owner or other nominated person within the practice.

What standards of data security are used?

Primary Sense uses the highest standards of data security to extract, analyse and manage general practice data. All data transmission is encrypted and sent over secure channels. It is stored or contained in reports that are locked down under multiple layers of access control.

Data Sharing Agreements between each general practice and its PHN specify what data is being extracted and what purposes it can be used for. Data is governed responsibly, privacy protected and securely stored and managed in Australia by the PHN-owned Primary Health Insights (PHI) hosting platform. PHI has been developed using the following guiding principles:

  • Patient privacy, data and cyber security are critical and a fundamental part of the platform.
  • Data governance processes are best practice and fit for purpose.
  • PHNs maintain full control of the data held on the platform.
The platform features multiple layers of security and a comprehensive governance framework. It complies with the Australian Privacy Principles and legislation.

Where is the extracted data stored?

Data is de-identified and encrypted when it is extracted before it is forwarded to the database. Extracted de-identified data is stored in the Primary Sense Database, which is located in the cloud-based Microsoft Azure, in Australia.

What does de-identified data mean?

PHNs are unable to accept identifiable data from practices. Identifiable patient information such as names and Medicare numbers are removed from data before it is sent to PHNs. Only practices can see patient identifiable data while using their computers and servers. No identifiable data leaves the practice.

How secure is the extracted data and the cloud?

Microsoft Azure provides industry standard security and adheres to Australian Privacy Principles.

Can someone hack the data between the practice, cloud and the PHN?

Extracted data is de-identified, encrypted and compressed before it leaves the practice. Even if the data could be hacked, it would be unintelligible. Primary Sense and the Azure cloud are monitored for inappropriate access.

Why does WAPHA receive extracted data from practices?

WAPHA is the operator of Western Australia’s three PHNs (Perth North, Perth South and Country WA) and uses extracted data for population health management and to understand the needs of practices and patients in their region. PHNs are responsible for commissioning services for their communities and data informs what services may need to be commissioned. It is also now a PIP QI requirement that practices share data with their PHN.

Does anyone other than WAPHA have access to the extracted data?

Only authorised WAPHA staff have access to the extracted de-identified data.

Do patients know that data is extracted and shared with WAPHA and can they opt out?

General practices are required to adhere to privacy principles when sharing de-identified data. Generally, this is included in the patient registration form and patients can opt out at any time. Primary Sense has a quick and easy patient opt out function for this purpose.

Important documents


How to proceed

WAPHA is offering Primary Sense to general practices in Western Australia. 

For further information, contact WAPHA's Primary Sense team by email at or call Practice Assist on 1800 2 ASSIST (1800 2 277 478).

Does Primary Sense need to be installed on every computer in the practice?
The extractor only needs to be installed once on your server. The desktop app can be installed on as few or as many computers and workstations as you like, but is designed to be installed on any computer with Best Practice or Medical Director.



We have various levels of support available tailored to meet your needs. The Practice Assist service is available to manage your enquiry and navigate you to the right support. Contact Practice Assist from 8am to 5pm, Monday to Friday (excluding public holidays). For questions related to access or use of Primary Sense please email or call 1800 2 ASSIST (1800 2 277 478).

Primary Sense Resources

Primary Sense - Getting started

The following resources have been developed to guide practices through the initial onboarding of Primary Sense.

Primary Sense - Inform your patients

The following resources have been developed to assist practices to provide information to patients on secondary use of data.

Primary Sense - Use in practice

The following resources have been developed to assist in the everyday use of Primary Sense.

Practice Management: Clinical: 

Primary Sense and Practice Data

The following resources are available to assist in the understanding of how practice data is managed by Primary Sense.  For resources in relation to reporting please go to the Primary Sense - Use in practice section above.

Primary Sense - Quality Improvement PDSA template topics

The Quality Improvement team has developed a range of PDSA templates that have a focus on the initial onboarding process for Primary Sense. 
  • Primary Sense – Desktop Installation
  • Primary Sense – Onboarding Staff
  • Primary Sense – Producing & Actioning Reports Process
  • Primary Sense – Practice Communication plan
  • Primary Sense – Practice Champion

To access these PDSA templates please reach out to your local QI Coach via Practice Assist or call 1800 2 ASSIST (1800 2 277 478)

Primary Sense Reports

Primary Sense Reports - Maximising use

The following resources have been designed to maximise your use of Primary Sense reports within your practice. 
Primary Sense Reports - Specific topics (user guides)
Alcohol Status Allergy Recorded 
Bowel and Breast Cancer Screening Cervical Cancer Screening 
Diabetes Management Ethnicity Recorded 
GPMP and TCA Health Assessments
Heart Health Check Influenza Vaccination 
Smoking Status   


Primary Sense Reports - How to videos

Primary Sense Reports - SMS Functionality

Primary Sense has a new SMS list feature

The SMS list feature is available in all Primary Sense reports and allows practice staff to identify specific patients to communicate with via SMS. 
To assist with learning more about the new SMS list feature and how it can be used, the following resources are available: 

Primary Sense Reports - Quick Reference Guides

Primary Sense has developed quick reference guides for reports now available. 

The quick reference guides have been designed to assist with the use of the below reports in relation to voluntary patient registration in My Medicare and also Hypertension management of patients.  
To assist with learning more about the new reports available, the following resources are available: 

Data Linkage Frequently Asked Questions (FAQs)

Frequently Asked Questions (FAQs)

Health data linkage is an established method of securely linking different de-identified data sets to better understand your patient’s journey across primary and hospital care. Data linkage can help WA Primary Health Alliance (WAPHA) to better understand the patient journey throughout the health system and support general practices and their patients through delivering the right services where they are needed most.

For further information, refer to the Data Linkage FAQs document
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