Laboratory

ORU R01: Send test results and measurements to PKB

Overview

This message can be used to send unsolicited laboratory results and measurements to PKB.

Laboratory results

Laboratory results will appear in the "Tests" tab in the PKB web interface. A single laboratory report (a.k.a. order) can contain multiple profiles (a.k.a. panels), each of which is reported in its own OBR group.

Measurements

The ORU R01 can also be used to send measurements into PKB, such that they appear in the "Measurements" tab in the PKB web interface.

Please speak to us if you would like to do this, as you'll need to send pre-agreed SNOMED code values in OBX-3.1.

Any OBX-3.3 that specifies SNOMED CT (see table for exact values we match on) will be treated as a measurement, not a lab result, providing that one of our predefined measurement types matches on both:

the ID in OBX-3.1
the unit in OBX-6.2 (or else OBX-6.1 if OBX-6.2 was not provided)

A "content pattern" indicates how PKB will interpret the contents of your message. This provides additional guidance over and above the syntactic requirements of individual segments.

PKB supports two different content patterns for OBR groups. When a (non-radiology) report is received, we will inspect each OBR group to determine which content pattern has been provided.

Single textual laboratory report

PKB uses the following criteria to determine if the OBR group contains a single textual laboratory report:

There are 1 or more OBX segments, which together contain at least 2 lines of text
Each OBX segment declares a textual data type (TX, FT, ST)
All the OBX segments have matching test IDs (OBX-3.1 and OBX-3.3, case sensitive)

The test code information for a textual laboratory report is taken from the OBR segment (OBR-4).

The OBX segments are treated as lines within the report, and do not maintain their own identity. The contents of the OBR group will be kept together, and displayed as originally provided.

NTE segments will be treated as lines of the report, just like OBX segments; their contents will appear in the same location as provided.

Note: when sending a single textual laboratory report, some metadata fields will only be taken from the first OBX segment. Importantly, if you wish to apply a patient delay this must be provided in the first OBX segment.

Collection of individual test results and measurements

If an OBR group does not contain a single textual laboratory report, then it is assumed to contain a collection of individual test results and measurements, each of which is provided in its own OBX segment (with the exception of multi-valued measurements, such as blood pressure).

The test code information for an individual result or measurement is taken from the OBX segment (OBX-3). Test results and measurements are considered to be meaningful even outside the context of the report in which they were provided.

The comments for each test result will be the union of the comments (NTE segments) provided for the OBR group and the comments (NTE segments) provided for the test result specifically.

Comments are not saved for measurements.

PKB processes content of this form in an OBX-centric manner. That is, PKB extracts the test results and measurements from the report and does not guarantee to display them alongside the other test results and measurements with which they were originally provided.

Sometimes, the same test result might be reported as part of more than one profile. This is valid, providing that each OBX segment appears no more than once in any given OBR group. However, since PKB does not include the profile as part of the result identity then all except the first instance of the OBX segment will be silently ignored. It is not valid to provide different results for the same test ID in different profiles within a given laboratory order.

It is valid to provide more than one measurement for the same measurement type (as identified by OBX-3) within any given OBR group. All such measurements will be processed.

Each test result is associated with a test type. Test results of the same type are shown on the same graph.

PKB maintains a curated list of supported [[LOINC Test Type]] entries, each of which is identified by the combination of a LOINC code and a unit value. These are the same types that a user can select from when entering a test result in the web interface. As such, a manually entered test result is associated directly with a [[LOINC Test Type]].

When a lab result is provided via HL7 it is always associated with a [[Local Test Type]] (lab results received before July 2021 worked differently and were sometimes linked directly to a [[LOINC Test Type]] where a supported LOINC code was detected).

The term "local" indicates that this information captures a test type which might be unique to the source organisation; customers often have their own codes for various test types, which may or may not be LOINC codes. As such, the types captured by the [[Local Test Type]] entity are scoped to the source organisation.

Test results from two different sources will never share the same [[Local Test Type]] since these are scoped to the source organisation. By default, this means they have different test types and as such will not appear on the same graph. In order to appear on the same graph the [[Local Test Type]] entries must be mapped to the same supported LOINC test type. This is a process known as LOINC mapping.

When LOINC mapping occurs

When adding a lab result to a medical record, PKB will check to see if the [[Local Test Type]] can be matched to a supported [[LOINC Test Type]]. There are two situations in which a matching type might be found:

LOINC code provided in message. An explicit LOINC code match will happen if the following conditions are true:
- The code system matches (case-insensitively) the string "LOINC"
- The code value and unit value both match (case-sensitively) one of the LOINC test types supported by PKB.
Local code provided in message, LOINC-mapping pre-agreed with customer. If the customer and PKB have agreed mappings from local lab result test types to LOINC test types supported by PKB, then a match will be made if the following conditions are true:
- The code system, code and units all match (case-sensitively) one of the entries in the mappings for the source organisation

Impact of LOINC mapping

The key impact of this process is that different result types, from different sources, can be mapped to the same LOINC test type. This allows PKB to treat all results of all types which map to a particular LOINC test type as being safe to group together. As such, we are able to graph them together in the web interface, and return them all from an API call which accepts a LOINC code as a search parameter. We are also able to make more intelligent display decisions, such as showing a translated version of the test name. See our deployment guidance for more information on the benefits of LOINC mapping.

Relevant entities

Test result information is used to populate [[Lab Report]] / [[Lab Result]] / [[Local Test Type]] entities
Measurement information is used to populate [[Measurement]] entities

Please click through to the Data Model to explore the presentation of these entities in the web interface.

[[Lab Report]]

Matched on: [[Lab Report.External ID]] as derived from ORC-3.1 or OBR-3.1

When matched: Associated [[Lab Result]] entries are individually matched. Note: if a [[Lab Result]] that was previously provided with the [[Lab Report]] is omitted from this [[Lab Report]], the [[Lab Result]] will be left unmodified. It will not be deleted.

Particular care should be given to panels: if a panel is provided with a status of R then all [[Lab Result]] entries previously stored for the corresponding [[Lab Report]] will be marked as deleted, regardless of whether they were previously included in the panel being redacted or whether they are provided in the current message. If the message contains multiple panels where some but not all have a status of R, then PKB will first delete all results associated with the report ID before following the usual create or update workflow for lab results provided in panels that do not have a status of R.

When not matched: New [[Lab Report]] created.

[[Lab Result]]

Matched on: Results are matched on the test ID (OBX-3, or OBR-4 for textual reports). The test ID is matched only on the first and third components (code and code system), and matching is case sensitive.

When matched: If PKB detects a meaningful difference between the provided and existing lab result content, then the existing [[Lab Result]] is replaced in its entirety with the values provided in this message. A partial update is not performed.

Note: that the existence of more than one version of a given lab result is what determines whether PKB displays a correction indicator in the web interface. The correction indicator is not driven by the status value declared by the sender (e.g. OBX-11), and sending more than one message for a given lab order is not guaranteed to trigger the correction indicator since PKB dedupes updates that do not meaningfully change the content of the lab result.

When not matched: New [[Lab Result]] created.

[[Local Test Type]]

Matched on: The test type is identified by the Source Organisation (to ensure no namespace clashes) along with test code, test coding system and units (all matched case sensitively).

When matched: If an existing [[Local Test Type]] is found, it will be updated with the latest Test Name if it differs from what is currently stored. In this way, callers are able to update the display name for their local test types.

When not matched: A new [[Local Test Type]] is created.

[[Measurement Report]]

Matched on: [[Measurement Report.External ID]] as derived from ORC-3.1 or OBR-3.1

When matched: Unlike lab results, measurements in a report are not individually matched for corrections. However, similar to lab reports, if a panel has status R, then any measurements with a matching report ID will be deleted.

When not matched: New [[Measurement Report]] created.

[[Measurement]]

Matched on: There is no unique identifier on a [[Measurement]] submitted via HL7, so they cannot be updated individually.

When matched: N/A

When not matched: New [[Measurement]] created.

Definition

Segment	Field	Opt	RP/#	Component	Description	Example	Data Model (Lab Reports)	Data Model (Measurements)

Segment	Field	Opt	Component	Description	Example	Data Model (Lab Reports)	Data Model (Measurements)
MSH				Message header. This conforms to PKB's standard definition.
PID				Patient identification. This conforms to PKB's standard definition.
[ PV1 ]				This is used to include the Hospital Service Code of the observations
	PV1-10	O		Hospital service. See our notes on code sets for more information on our handling of coded data.		PV1-10 contributes to privacy label assignment.
			PV1-10.1	Hospital service code		[[Lab Report->Lab Result.Specialty]]	[[Measurement Report->Measurement.Specialty]]
{ [ ORC ]				Common order
	ORC-3	C		Filler order number. At least one of either ORC-3.1 or OBR-3.1 must be provided. It is an error for these values to differ.
			ORC-3.1	Filler order number	MYORDER0001	[[Lab Report.External ID]] if OBR-3 was not provided	[[Measurement Report.External ID]] if OBR-3 was not provided
	ORC-13	O		Enterer's Location
			ORC-13.9	Description	Laboratory 1	[[Lab Report.Enterer Location]]
OBR				Observation request
	OBR-3	C		Filler order number. At least one of either ORC-3.1 or OBR-3.1 must be provided. It is an error for these values to differ.
			OBR-3.1	Filler order number	MYORDER0001	[[Lab Report.External ID]]	[[Measurement Report.External ID]]
	OBR-4	C		Universal service identifier. See our notes on code sets for more information on our handling of coded data. For textual reports, these values override the ones in OBX-3, and as such OBR-4.1 is mandatory.		If a textual report content pattern The test type processing uses OBR-4 instead of OBX-3. Components 1-6 of OBR-4 will be saved into [[Lab Report->Lab Result.Code]]. Note that this will mean the service name and the test name might be the same for some textual reports.
			OBR-4.1	Service ID	LAB100	The privacy label lookup based on service code is performed regardless of which content pattern was provided. Then additionally: If a textual report Stored in [[Lab Report->Lab Result->Local Test Type.Test Code]] Else Ignored.	OBR-4.1 contributes to privacy label assignment.
			OBR-4.2	Service name	FBC	[[Lab Report->Lab Result.Service]] and [[Lab Report->Lab Result->Local Test Type.Service Name]] Note: the Local Test Type only stores the most recently provided service name.
			OBR-4.3	Service coding system	WinPath	If a textual report Stored in [[Lab Report->Lab Result->Local Test Type.Test Coding System]] Else Ignored.
			OBR-4.5	Alternative service name	Full Blood Count	Used instead of OBR-4.2 if OBR-4.2 was not provided.
	OBR-7	C		Observation timestamp. This will be used only if there is no timestamp in OBX-14. It is an error for neither to be provided.
			OBR-7.1	Observation timestamp	201505191657	[[Lab Report->Lab Result.Timestamp]] if OBX-14 was not provided	[[Measurement.Timestamp]] if OBX-14 was not provided
	OBR-14	O		Received timestamp.
			OBR-14.1	Received timestamp	201505191521	[[Lab Report->Received Timestamp]]
	OBR-16	O		Ordered by. If present, at least the family name must be given.		[[Lab Report->Lab Result->Source.Source Text]]	[[Measurement->Source.Source Text]]
			OBR-16.2	Family name	Foster
			OBR-16.3	Given name	John
			OBR-16.4	Middle names	Harry
			OBR-16.6	Title	Dr
	OBR-24	O		Laboratory discipline.
			OBR-24.1	Laboratory discipline.	ICU	[[Lab Report->Discipline]]
	OBR-25	O		Result status. If a value of R is provided: any lab results received previously for this report ID will be marked as deleted. OBX segments are not required and will be ignored. Otherwise: the report is processed as documented. Note: if the report contains multiple panels where some but not all have a status of R, then PKB will first delete all results associated with the report ID before following the usual create or update workflow for lab results provided in panels that do not have a status of R.
			OBR-25.1	Result status	F
{ [ NTE ] }				NTE segments can be used to include comments. NTE segments immediately following the OBR segment will be considered to apply to all results in this message.
	NTE-3	O	NTE-3.1	Comment
				Comment	This is a comment.	These OBR-level comments will be written to [[Lab Report->Lab Result.Comments]] Any OBX-level comments will be appended to the OBR-level comments.
{ OBX				Observation or result
	OBX-2	R		Value type. OBX segments with these value types are silently ignored: AD, CP, DT, DTM, ED, MO, PN, RP, TM, TN, XAD, XCN, XON, XPN, XTN For SN, a numeric value must be provided in OBX-5.2. For all other value types, note that: [[Lab Report->Lab Result.Value]] will be set if the supplied value can be parsed as a number, regardless of the declared value type [[Lab Report->Lab Result.Value Text]] will be set if the result is non-numeric [[Lab Report->Lab Result.Comments]] will be set if this is a textual report
			OBX-2.1	Value type	NM
	OBX-3	R		Observation identifier. See our notes on code sets for more information on our handling of coded data.		If an individual result content pattern The test type processing uses OBX-3 instead of OBR-4. Components 1-6 of OBX-3 will be saved into [[Lab Report->Lab Result.Code]].
			OBX-3.1	Test ID. If this is a textual report, this value will be overridden by OBR-4.1. Otherwise this value must be provided. If a measurement is being provided, this ID must match one of the predefined values which PKB can accept.	777-3	Stored in [[Lab Report->Lab Result->Local Test Type.Test Code]]
			OBX-3.2	Test name	Platelets	Stored in [[Lab Report->Lab Result->Local Test Type.Test Name]] Note: the Local Test Type only stores the most recently provided test name.
			OBX-3.3	Test coding system If this is a textual report, this value will be overridden by OBR-4.3 Note: PKB will only accept a measurement if this value is one of the following: ( sct, snomed-ct, snomed ct, http://snomed.info/sct, 2.16.840.1.113883.6.96 )	LOINC	Stored in [[Lab Report->Lab Result->Local Test Type.Test Coding System]]
			OBX-3.5	Alternative test name	Platelet count	Used instead of OBX-3.2 if OBX-3.2 was not provided.
	OBX-5	R		Observation value. If providing a structured numeric value (OBX-2 set to SN): OBX-5.1 must be one of: >, <, >=, <=, = (<> is also valid, but not supported. Results with this comparator will be silently ignored.) OBX-5.2 must be a number OBX-5.3 and OBX-5.4 are not supported. Results containing a non-empty value for either of these will be silently ignored.
			OBX-5.1	Value or comparator.	200	If numerical data, then value set in [[Lab Report->Lab Result.Value]] else if textual then value set in [[Lab Report->Lab Result.Value Text]] else if a multi-line report then values set in [[Lab Report->Lab Result.Comments]] else if SN then map to [[Lab Report->Lab Result.Comparator]]	[[Measurement.Value]] If a multi-valued measurement is being supplied, then the next OBX segment will contain the value for [[Measurement.Value2]]
			OBX-5.2	Value	200	If SN, then set in [[Lab Report->Lab Result.Value]]
	OBX-6	O		Units. See our notes on code sets for more information on our handling of coded data.
			OBX-6.1	Unit ID	X10TO9L	Used instead of OBX-6.2 if OBX-6.2 was not provided.
			OBX-6.2	Unit name.	10 to 9 per L	Stored in [[Lab Report->Lab Result->Local Test Type.Units]]	This must match the corresponding PKB permitted value.
	OBX-7	O		Reference range. Numeric ranges in the format x-y, <x, <=x, >x, >=x are all supported. If the range does not successfully parse as one of these formats then the contents of this field will be stored as a textual range. Special cases: An input of "-" will be treated as if no range had been provided An input of "0" will be treated as if "0-0" had been provided
			OBX-7.1	Reference range	100-300	If a numeric range provided, then the following values will be set appropriately [[Lab Report->Lab Result.Range Low]] [[Lab Report->Lab Result.Range Low Inclusive]] [[Lab Report->Lab Result.Range High]] [[Lab Report->Lab Result.Range High Inclusive]] else value set in [[Lab Report->Lab Result.Textual Range]]
	OBX-11	R		Result status. Only values of F and C will be processed. Values of I, O, P or X (which indicate pending or no results) are silently ignored, whilst any other values will cause an error.
			OBX-11.1	Result status	F
	OBX-13	O		Custom access rules for lab results. Currently supported: "{patientDelay:NUMBERdays}" with any whole number in place of "NUMBER" (no spaces). The patient will see that a lab result has arrived, but the result value will not be revealed until the set number of days past the date/time of observation have passed. If this field is not specified the patient will be able to see their results immediately. Note: if this OBR group is a textual report spanning multiple OBX segments, the delay must be provided in the first.
			OBX-13.1	Custom access rules	{patientDelay:3days}
	OBX-14	C		Observation timestamp. If this is not present, OBR-7 is used instead. It is an error for neither to be provided.
			OBX-14.1	Observation timestamp	201505191657	[[Lab Report->Lab Result.Timestamp]]	[[Measurement.Timestamp]]
{ [ NTE ] } } }				NTE segments can be used to include comments. NTE segments immediately following an OBX segment will be considered to apply only to the immediately preceding result.
	NTE-3	O		Comment
			NTE-3.1	Comment	This is a comment.	These OBX-level comments will be appended to [[Lab Report->Lab Result.Comments]] after any OBR-level comments.

Examples

An example of a lab result message.

MSH|^~\&|Corepoint|TDL|HL7API|PKB|201303080949||ORU^R01|ABC0000000001|P|2.4
PID|||9999999999^^^NHS^NH||Smith^John^Joe^^Mr||19700101|M|||Flat name^1, The Road^London^London^SW1A 1AA^GBR||01234567890^PRN~07123456789^PRS|^NET^^john.smith@company.com~01234098765^WPN||||||||||||||||N|
PV1|1|||||||||SPEC_01|
OBR|1|12F000005|12F000005|LFT^LIVER PROFILE^WinPath||201303080948|201303080000||||||||SST|E85109||||||201303080949||CHE|F
OBX|1|NM|BILI^Bilirubin^Winpath||5|umol/L|0-20||||F
OBX|2|NM|ALP^Alkaline Phosphatase^Winpath||120|IU/L|40-130||||F|||201303080000
OBX|3|NM|ALT^Alanine Transaminase^Winpath||20|IU/L|10-50||||F||patientDelay:3days|201303080000

An example of a measurement message.

MSH|^~\&|Corepoint|TDL|HL7API|PKB|201303080949||ORU^R01|ABC0000000001|P|2.4
PID|||9999999999^^^NHS^NH||Smith^John^Joe^^Mr||19700101|M|||Flat name^1, The Road^London^London^SW1A 1AA^GBR||01234567890^PRN~07123456789^PRS|^NET^^john.smith@company.com~01234098765^WPN||||||||||||||||N|
OBR|1||||||||||||||||||||||||F
OBX|1|NM|107647005^^sct||75|^kg^|||||F|||20200625103943+0100

Response

PKB will respond with a standard HL7 acknowledgement.

Supported single measurements

Snomed code	Label	Units
366162006	Central venous pressure (CVP)	cmH20
107647005	Weight	kg
162755006	Height	cm
276361009	Waist size	cm
301338002	Head circumference	cm
301898006	Body surface area	square metres
301331008	Body mass index (BMI)	kg/m^2
170804003	Ideal body weight	kg
162986007	Pulse	bpm
162913005	Respiration	rpm
105723007	Temperature	degrees Celsius
1036631000000109	Musculoskeletal Health Questionnaire (MSK-HQ) score
431314004	Oxygen saturation (SPO2)	%
257733005	Activity (Rating Scale: 0-10)
415882003	Axillary (under arm) temperature	degrees Celsius
15527001	Capillary filling	Seconds
251843005	Fluid output from drain	ml
366156001	Peak expiratory flow (PEF)	l/min
313222007	Forced expiratory volume in one second/Forced vital capacity percent (FEV1/FVC)
59328004	Forced expiratory volume in 1 second (FEV1)	Litres
366151006	Forced vital capacity (FVC)	Litres
873921000000106	Forced expired volume in 6 seconds (FEV6)	Litres
251932003	Forced expiratory flow rate between 25 and 75% of vital capacity (FEF 25-75)	l/min
273648008	Nine hole peg test	Seconds
414059009	Number of missed medications today
786441000000107	Grip strength - left hand	kg
786451000000105	Grip strength - right hand	kg
78564009	Heart rate measured at systemic artery	beat/min
1091811000000102	Diastolic arterial pressure	mmHg
72313002	Systolic arterial pressure	mmHg
810931000000108	QRISK2 calculated heart age	year
718087004	QRISK2 cardiovascular disease 10 year risk score	%
1325531000000102	QRISK3 healthy heart age	years
1085871000000105	QRISK3 10 year cardiovascular disease risk score	%
1082641000000106	Alcohol units consumed per week	u/week
230085005	Beer intake	u/week
230086006	Wine intake	u/week
230088007	Spirits intake	u/week
442547005	Alcohol units heaviest day	/day
230056004	Cigarette consumption	/day
230057008	Cigar consumption	/day
230058003	Pipe tobacco consumption	g/week
413173009	Minutes from waking to first tobacco consumption	min
836001000000109	Waterpipe tobacco consumption	times/week
401070008	Number portions fruit/veg daily	/day
129006008	Steps
1155968006	Mood

Examples

An example of a single measurement message.

MSH|^~\&|Corepoint|TDL|HL7API|PKB|201303080949||ORU^R01|ABC0000000001|P|2.4
PID|||9999999999^^^NHS^NH||Smith^John^Joe^^Mr||19700101|M|||Flat name^1, The Road^London^London^SW1A 1AA^GBR||01234567890^PRN~07123456789^PRS|^NET^^john.smith@company.com~01234098765^WPN||||||||||||||||N|
OBR||||||||||||||||^Ward^Olivia^Elsie^^Ms|||||||||F
OBX||NM|162986007^^sct||7|^bpm|||||F|||20200401140103+0100

Supported multi measurements

When providing a blood pressure reading you must provide an OBX segment containing the SNOMED code of the overall reading type, followed immediately by an OBX segment for each component reading you wish to provide.

Note that it is permitted to provide either a systolic or diastolic reading by itself, but the first OBX containing the overall code of the reading must still be supplied.

SNOMED code	Label	Units
75367002	Blood pressure
163035008	Blood pressure sitting
163034007	Blood pressure standing
163033001	Blood pressure supine
163030003		mmHg (systolic)
163031004		mmHg (diastolic)

Examples

An example of a multi measurement message.

MSH|^~\&|Corepoint|TDL|HL7API|PKB|201303080949||ORU^R01|ABC0000000001|P|2.4
PID|||9999999999^^^NHS^NH||Smith^John^Joe^^Mr||19700101|M|||Flat name^1, The Road^London^London^SW1A 1AA^GBR||01234567890^PRN~07123456789^PRS|^NET^^john.smith@company.com~01234098765^WPN||||||||||||||||N|
OBR|||MYORDER0001|||||||||||||^Ward^Olivia^Elsie^^Ms|||||||||F
OBX||NM|75367002^^sct|||-|||||F|||20191106091410+0000
OBX||NM|163030003^^sct||190|^mmHg (systolic)|||||F|||20191106091410+0000
OBX||NM|163031004^^sct||59|^mmHg (diastolic)|||||F|||20191106091410+0000