EMIS IM1 Patient Data Extract Service

EMIS is a general practice electronic medical record system in the UK. You can set up an automatic data transfer for a GP practice's patient data from EMIS into PKB using the EMIS Patient Data Extract Service (PDES). The transfer can only begin with the permission of a GP who is a data controller of the GP practice. The data controller must formally sign the contract authorising the data transfer and they can stop authorisation at any time in the future. 

Once this data transfer has been activated the GP practice's EMIS patients will be created in the GP practice's PKB team and the patient's demographics, allergies, diagnoses, medications, measurements & tests will be populated from the data in the EMIS extract. Note that only a subset of measurements and tests are currently processed. PKB plans to increase the amount of measurements and tests that can be processed into the patients' record the future. After the initial addition of all historical data, the record will be updated in PKB on a daily basis from the daily EMIS extract. 

How do I set up the extract service for my GP surgery?

To set up your GP practice for automatic transfer of your patients' data please contact the PKB team.

The PKB team will help your GP practice to set up their PKB site, and activate the extract service. Once the service has been activated the GP practice professionals will be able to work with their patients in PKB and view the EMIS data there.

Working with sharing agreements in EMIS Web

Information Sharing Agreements (ISAs) enable your organisation to share your data with patients and view data from other organisations in PKB. 

Once your GP surgery has signed a PKB ISA, PKB will request that your practice be configured for the EMIS patient data extract service. After 10 working days, the data sharing agreement can be activated within EMIS Web to share and view data in PKB.

To access sharing agreements in EMIS Web, you must have the appropriate Role Based Access Control (RBAC) activities in your role profile: 

• B0264 Access CSA (Perform Patient Trace), to perform cross-organisation searches using Patient Find and match patients across organisations in Registration.

• B0109 Local Restricted System Administration, to activate and deactivate sharing agreements.

• B0020 Control Consent Status, to change the value of the national flags indicating a patient’s preferences for restricting viewing of their Summary Care Record and detailed records.

Note: This activity must only be granted to users who can explain to patients the consequences of these choices. This activity controls access to sensitive personal data, which includes clinical and administrative information, i.e. it does not apply to demographic data.

Changes to the configuration for the EMIS patient facing API do not affect the patient data extract service. The configuration details for the patient data extract service are listed in the sharing agreement itself. 

How can I access the Data Sharing Manager in EMIS?

1. Click the EMIS icon in the toolbar

2. Point to Configuration

3. Click Data Sharing Manager.

Note: The Data Sharing Manager option is not available if you do not have any agreements in place.

How do I activate a sharing agreement?

1. Access Data Sharing Manager.

2. If required, on the Data Sharing Manager ribbon, click My Agreements.

3. At the bottom of the navigation pane, check the tabs to locate the agreement (Care record, Data distribution or Reporting). Existing agreements of the selected type are listed in the navigation pane, with a green tick beside active agreements and a red cross beside agreements that have been created, but not yet activated:

4.In the appropriate section in the navigation pane, click the agreement you want to activate. Details of the agreement are displayed in the right-hand pane.

5.On the Data Sharing Manager ribbon, click Activate Agreement.The agreement is activated for your organisation (i.e. other organisations can view your data). However, you cannot view information from other organisations until they also activate the agreement.

The following page shows examples of agreements that have previously been set up for GPs in Hillingdon: with Greenbrook Healthcare Ltd for the Urgent Care Centre located at Hillingdon Hospital (note that Greenbrook also operates the UCC at Northwick Park Hospital and clinical staff there will also have access to your patients’ records) and with Care UK for the NHS 111 and Out of Hours services. 

How do I deactivate a sharing agreement?

1. Access Data Sharing Manager.

2. If required, on the Data Sharing Manager ribbon, click My Agreements.

3. At the bottom of the navigation pane, click the tab for the appropriate agreement type (Care Record, Data distribution or Reporting). Existing agreements of the selected type are listed in the navigation pane.

4.In the appropriate section in the navigation pane, click the agreement you want to deactivate.

5.On the Data Sharing Manager ribbon, click Deactivate Agreement.

The agreement is deactivated for your organisation (i.e. your data will no longer be sent to PKB).

How can I view a sharing agreement?

1. Access Data Sharing Manager.

2. On the Data Sharing Manager ribbon, click My Agreements or click Enterprise Agreements. (The Enterprise Agreements options is only available for top level organisations with sharing agreements that are associated with child organisations.)

3.At the bottom of the navigation pane, click the tab for the appropriate agreement type (Care Record or Reporting). Existing agreements of the selected type are listed in the navigation pane.

4.In the navigation pane, click the required agreement. The agreement details are displayed on the main pane, along with current activation status, and tabs showing potential organisations sharing and viewing data. 

How can I view EMIS data in PKB?

To view EMIS data in PKB, our team will assist you in setting up your PKB site. 

Once set-up you can access EMIS data in PKB:

1. Log in as a professional to PKB.

2. Click on Go to view the patient list and choose a patient's record to enter

3. Click on Edit to view the patient demographics

Click on Sharing>Professionals to view the teams the patient is sharing with and the level of access.

Note: if the patient is sharing with teams or has manually entered data this will also be available in PKB. A GP team will only see data with the PKB privacy label that they have access to, or that they have entered themselves manually.  

Testing with early customers

PKB conducted service tests with our early adopter customers. The process involved: 

1. Activating the sharing agreement for that GP practice within EMIS.

2. Operational checks by PKB to ensure that the extract processing was passing all tests to allow extract processing. This occurred before the GP practice started their testing process.

3. Setting up test patients on the local EMIS web instance. 

4. Processing of the extract was enabled for these the test patients only.

5. The test patients were created on an EMIS specific test environment within the n3 network.

6. Following a test plan to review the appearance of these patients' data within PKB's user interface and comparing with the same patients within EMIS. Checks included:

   • New patient records created in PKB where required. All data have been transferred correctly for a patient. No incorrect data is in PKB and no extra data is in PKB incorrectly attributed with EMIS / the practice as the source. (There should still be non-EMIS data of course from other providers looking after the patient as well as the patient and carers.)

   • Additions of data subsequent to initial data sent are reflected correctly in PKB.

   • Updates or deletions of previously sent data result in an update on deletion in PKB.

   • No sensitive data in EMIS (as per the SCR sensitive exclusion list or other exclusion list) is included in PKB.  

7. Initially this focus was on patient creation and processing allergies, diagnoses and medications.

The testing plan signed off with these customers is available at this link and the accompanying screenshots can be reviewed in this document. The test number on the test plan corresponds to the test number in the screenshots document.  

Data transfer from EMIS to PKB

The data transfer from EMIS is in the form of a csv file which represents an export of EMIS database tables. One file is received per table on a daily basis. When a practice initiates the extract service bulk data is received for all regular patients with NHS numbers. From that point on a daily delta is sent which contains any modifications to the data since the previous extract and new patients with NHS numbers. 

PKB processes a subset of files to transfer data which includes:

First Stage

Second Stage

Future Stage

Not Available

• Care Plans - (collaborate in PKB)

• Alerts

• Consent (controlled by PKB)

• Document (no free text)

• Investigation - CareRecord_Observation (GUI Dev)

• Family - CareRecord_Observation (GUI Dev)

• Risks and Warnings

EMIS extract provides clinical codes for each data point and mapping tables (also received daily as part of the feed) which allows these codes to be mapped to DM+D for medications and Read v2/SNOMED CT for other types. In addition, there is a textual description for EMIS code which PKB displays on the front end to the patient and professional. Deletions and amendments are also transferred to PKB to update existing data. PKB tracks the source and time stamp for each data point from the GP for display along with all other data from all other sources about the patient.

Data processing by PKB

PKB currently processes the extract to create and update demographics, allergies, diagnoses, medications, and NHS Health Check measurements and lab test results.

Record creation

Records are created in the GP practices PKB team from the EMIS extract using the NHS number. If the patient has no NHS number in EMIS Web, a record can be created using the EMIS Patient Number.

The patient is added to the GP practice's PKB team allowing the team professionals the team's default level of access to that patient's data in PKB.

Email addresses from EMIS are not added to the created patient records. To allow a patient to register and access their record, their email address can be added in PKB. Once an email has been added, the patient will then receive an email to register.

If a patient was created in PKB already by another organisation but is not registered, it's possible to update their records from your GP practice extract but they will not be added to your team until the creating organisation facilitates this. If you have questions about this process please contact the PKB team

Diagnoses, allergies and medications

PKB creates and updates diagnoses, allergies and medications using the clinical codes received from EMIS. For diagnoses PKB will look-up the received SNOMED CT code in order to determine the privacy label, and data type to apply. For allergies PKB will apply a 'general health' privacy label, and will look-up the received SNOMED CT code in order to determine the data type to apply.

PKB has published the coding tables online in our developer wiki. Please contact us if you have feedback or suggestions. 

For medications PKB will display the code received but as this is sent as a separate table from EMIS the datatype will be medications. The privacy label will default to general but this will be editable by patients.

Measurements 

For measurements, PKB will look up the received Snomed CT code to determine the privacy label, and data type to apply. 

For a full list of measurements that are added to records,  please see this spreadsheet.

Tests 

For lab tests, PKB will look up the received Snomed CT code to determine the privacy label, and data type to apply.  

Snomed CT codes for lab tests are mapped to LOINC codes. This means the tests will appear in patient records on the same graph as other tests that have been mapped to LOINC codes and it is possible to include them in care plans. 

For a full list of lab tests that are added to records and their mapped LOINC codes, please see this spreadsheet.

EMIS extract service data exclusions

Patient opt-out codes

All 'regular type' patients will be extracted unless they have a specific opt-out code. If a patient later decides to opt in, this will be triggered by the addition of opt-in codes.

Patients whose records contain one of the following Read codes will have their data excluded from the EMIS extract entirely and thus no record will be created for patients with these codes.

This is implemented on the EMIS side; the codes to be excluded are specified as part of the EMIS extract set-up configuration.

If a patient has had an opt-out code in their record and you would like to opt them back in, in order to populate their PKB record, one of the following opt-in codes should be added to the patient's record in EMIS Web.

To add an opt-out code to a patient's record, or to opt the patient in (only needed if they previously had an opt-out code in record): 

1. In the patients EMIS Web record, click on 'Add' > 'Code'

Sensitive codes

In addition certain sensitive SNOMED CT codes, Read V2 codes and EMIS proprietary codes, as agreed with our partners, are excluded from the patient record. This means data points with these codes will not appear in the patient's record.

There are several sensitive code lists: 

1. 4 x SNOMED ref sets excluded by EMIS and not sent to PKB:

   • Gender related issues (SCTID: 999004351000000109)

   • Termination of pregnancy (SCTID: 999004361000000107)

   • Assisted fertilisation (SCTID: 999004371000000100)

   • Sexually transmitted disease (SCTID: 999004381000000103)

   • These lists also apply to codes sent in HL7 messages. PKB filters the data received and skips these

2. Additional sensitive code set. This is list of Read V2 and EMIS proprietary codes our customers favoured excluding. This list will apply to codes sent from the EMIS extract service, or sent in HL7 messages. PKB filters the data received and skips these. This list is also available on the coded data page.

3. Additional SNOMED ref set exclusions by PKB:

   • Safeguarding (SCTID: 999004351000000109)

   • Sexual Health Procedures (SCTID: 999003101000000109)

   • These lists also apply to codes sent from the EMIS extract service, or sent in HL7 messages. PKB filters the data received and skips these.

Patients and data marked as confidential

Some patients and individual items may have a confidentiality policy applied in EMIS Web. 

Confidential patients (i.e. patients that have a confidentiality policy applied to their entire record within that organisation) are not sent to PKB. 

Items which are marked as confidential in EMIS are not sent to PKB. Confidential items are defined by EMIS as items that have a confidentiality policy applied to them and cannot be seen by certain users within an organisation. This may be because the item is deemed sensitive, such as the record of a patient’s HIV status or a termination of pregnancy. 

EMIS extract schedule

EMIS sends a daily extract to PKB containing update for patients and new patients added in the last 24 hours. This extract is processed as soon as received.

Diagram of data flow