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.

It would also be useful if you are able to provide data about the reference ranges you use for each test.

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