The OpenPathology Data Specification
This project will accept data in CSV format over SSH or SFTP to a secure area within the University of Oxford (how to get involved).
Participating organisations must provide the required fields (marked with an asterisk) on a monthly basis.
All other fields are optional. However, the more fields that are provided, the better potential there is for us to provide more powerful analyses.
You should also provide reference range data, preferably in a machine-readable format (e.g. a spreadsheet), and any mapping tables you have between your lab codes, analyte names, and READ codes.
On completion of any data sharing agreements, we will provide you with a login to upload data to your own area in our secure file server.
| Field | Description | Example value |
|---|---|---|
|
analyte_lab_code
|
The lab’s code for the test
|
WBC, H1BAc |
|
analyte_lab_name
|
The lab’s full name for the text
|
Serum total protein level
|
|
analyte_read_code
|
The READ code for the test
|
44D1.00 |
|
analyte_snomed_code
|
The SNOMED code for the test
|
200197461 |
|
analyte_result_measurement
|
Numerical value of a measurement result
|
14.4 |
|
analyte_result_units
|
The units that the test is measured in
|
mmol/L |
|
analyte_result_date
|
The date the measurement was made
|
2018-01-31 |
|
analyte_is_abnormal
|
A flag to show if results are considered within or outside
reference range
|
true, false |
|
analyte_is_abnormal_direction
|
For results outside the reference range, is it abnormally
high or abnormally low?
|
high,low |
|
analyte_result_comments
|
Free text field for additional comments about the
measurement
|
calculated using the CKD-EPI creatinine equation
|
|
analyte_lab_lims
|
The LIMS used to record the test (software and version)
|
WinPath 1.2 |
| specimen_code |
An identifier for the specimen
|
AB12K551W |
|
specimen_taken_date
|
Date the specimen was taken
|
2018-01-30 |
|
specimen_received_date
|
Date the specimen was received by the lab
|
2018-01-30 |
| specimen_type |
The type of the sample
|
blood |
|
requestor_organisation_name
|
Name of the location where the request originated
|
Beech Street Practice
|
|
requestor_organisation_code
|
ODS code of the location where the request originated
|
Y74004 |
|
requestor_name
|
Name of the requestor
|
Dr B Anderson |
|
requestor_registration_code
|
Registration code for the requestor
|
1032213B |
|
requestor_comments
|
Free text field for additional information from the
requestor, e.g. clinical observation
|
Investigation for suspected anaemia
|
|
requestor_order_set
|
The tests as requested by the requestor. This may be an
analyte (e.g. haemoglobin), a battery (e.g. FBC), or a
syndrome-specific test group (e.g. TATT)
|
|
|
requestor_used_ordercomms
|
A flag to show if the request came via an ordercomms system,
or manually
|
true, false |
|
internal_patient_identifier
|
Unique identifier for the patient. This will ideally be a
pseudonymised identifier which is consistent over time,
typically the hospital unit number, but never the NHS number
as this is not sufficiently pseudonomised
|
10922132 |
|
patient_department_code
|
Code for department where patient was seen, e.g. GP surgery,
A&E
|
GP,AE |
| patient_sex |
Administrative sex of patient
|
M,F |
| patient_age | Age of patient | 35 |