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Pathology Information Standards
Information Sharing and Feedback
February/March 2020
What we will cover today• Highlights/key achievements since the
2018/19 events• The proposed Roadmap of Change• SNOMED & Information Models working
together• Potential Requesting Model • UTL as a successor to PBCL• UTL Release Schedule
https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=14357424
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What are we trying to create?
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Message
UoM
Value
Code
Transfer clinical statement Sodium substance concentration in plasma 142 mmol/L
mmol/L
142
11078610000Sodium substance concentration in plasma
Qualitative values:High/LowAbsent/PresentOrdinals
Inter-related Pathology Workstreams
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A set of HL7 FHIR profiles to support
the electronic exchange of
pathology test results.
A national set of standardised units of measure for test results, aligned with the Unified Test List.
A logical, business-level representation
of the information relating to
pathology test results.
A national set of SNOMED CT codes that defines a standardised list of pathology test names.
Unified Test List
Information Model
Message Specification
Units of Measure
Stakeholder Engagement
Andy will now…..
Provide a brief update of the highlights/key achievements since the 2018/19 events
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Information Modelhttps://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=13047120
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Message Specificationhttps://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=13046960
Information Model & Message Specification – Done
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Business Process Definition
• Develop user stories / use cases
• Develop process / information flow diagrams
• Develop clinical scenarios
• Identify example test reports
Information Model Development
• Develop high level entity diagram
• Develop detailed entity diagram
• Develop data set definition
• Identify SNOMED CT patterns
Standards Specification Development
• Map Information Model to FHIR resources
• Identify SNOMED CT bindings
• Develop FHIR profiles
• Undertake FHIR curation
• Develop Implementation guidance
Existing Standards e.g. PMIP EDIFACT Existing FHIR Profiles
Information Model & Message Specification – To Do
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• Curate HL7 FHIR, R4 Core Profile incorporating the 4 FHIR, STU3 Pathology Profiles
• Undertake First of Type testing of pathology FHIR message specification
• Assess and evidence suitability for EDIFACT replacement
• Explore pathology test requesting processes, Test Groups (a.k.a. Profile, Panel, Battery) & others in more detail
• Extend to support Microbiology use cases
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Units of Measurehttps://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=13046992
Units of Measure – Done
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• Sample-based review of current units in use
• Reviewed and re-formatted Laboratory Standardised Representation (LSR) as an Interim Units Guide (IUG)
• Outlined provisional requirements for delivering Computable results & assessed LSR and UCUM against those
• Proposed next steps on aligning commonly used units with UCUM and SNOMED CT
• Incorporated the units in the Information Model, Message Specification and UTL work
Units of Measure – To Do
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• Identify the overlaps and gaps of commonly used units in SNOMED CT & UCUM
• Establish a pattern for combining unambiguous (human & machine readable) units
• Demonstrate and gather feedback on the pattern
• Evidence and Propose a Units of Measure Information Standard
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Unified Test List
https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=13047024
Unified Test List – Done
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• Used your, real world pathology test lists as inputs – Thank you!
• Naming convention and Editorial principles are based on ‘patterns’, applied to the SNOMED ‘observable entity’ type for results
• Publish in human-readable (HTML) format and as a separate Pathology SNOMED moduleto improve stakeholder review & enable more frequent releases
• Latest release (end of October 2019) contains approximately 1600 new concepts
• Core pattern is the triad of Property-OF-Thing-IN-Specimen. An extension to this pattern includes Method.
Test Name SNOMED Attribute Model (‘observable entity’ type)
Message Model (FHIR) (relative to SNOMED model)
SNOMED Term
COMPONENT
substance etc. being measured
PROPERTY
constrainsUoMField
DIRECT SITE
specimen
TECHNIQUE
method
RELATIVE TO
second component
of ratio, % etc.
UoM Time Patient/ Specimen
Precondition
Reference Range
REPORTED RESULT VALUE FROM TEST: n
Creatinine substance concentration in serum by enzymatic method
SNOMED Model + Message Model (FHIR)
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Unified Test List – To Do
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• Undertake First of Type testing of the UTL
• Formalise Designs, Editorial Principles & Release schedules
• Identify & apply further design patterns e.g. Microbiology, Antibodies
• Scale up and improve the Agile development & review process
• Explore Test requests, assess and evidence suitability for PBCL replacement
• Promote UK Content to SNOMED International
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Stakeholder Engagement
https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectID=14357424
Stakeholder Engagement - Done
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• Engaged with stakeholders involved and impacted across the Pathology eco-system
• Established consensus on standards being defined and ways to roll them into the ecosystem in discussions with NHSX, NHSI, NHSE and PHE
• Commissioned a Cross-organisational Governance Board for the proposed Pathology information standards being created
• International interest in adopting or aligning with our work
Stakeholder Engagement – To Do
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• Agree Clinical Leadership
• Agree with PHE, Reportable Diseases & Antimicrobial Resistance Stewardship
• International Agreements
• Continue Multi-organisational engagement to prepare for Implementation & use
• Create and engage closer via focussed reference groups
Andy will now…..
Share a proposed forward view/Roadmap for your feedback to identify any gaps and inform prioritisation
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Preparation for Implementation - Done
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• The Current Pathology Information Exchange Domain & Lessons Learned
• Implementation Principles
• Proposed Pathology Standards Implementation Roadmap
Preparation for Implementation – To Do
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• First of Type/Proof of Concept Testing
Haematology/Clinical Chemistry
ModelsUnits of MeasureFHIR specificationsUTL/SNOMED
MicrobiologyExtend/New:ModelsUnits incl. UCUMUTL/SNOMED CT
Histopathology?
Extend/New: ModelsUnits incl. UCUMUTL/SNOMED CT
Phil and Karim will now….
• Outline what the Pathology Information Model is and how it can support microbiology test reporting
• Talk about the relationship between the information model and the UTL
• Discuss a set of proposed test name patterns for microbiology
• Briefly describe how a microbiology report structure could be represented in FHIR
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Pathology Information Model – Overview
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• The model provides a logical, business-level representation of the information relating to pathology test results.
• It includes business entities (e.g. Patient, Test Result, Specimen), relationships between business entities and entity level data items. For example, the data items in the Test Result business entity include:
• Status• Category• Test Performed Date and Time• Test Result Issued Date and Time• Test Name and Code• Test Result Value
• The model consists of:• a diagram illustrating the business entities, relationships and data items (as per the
fragment shown above)• a tabular definition of the business entities and data items, together with associated
properties such as data types, value sets and cardinalities
Pathology Information Model – High Level
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• High level model depicts the key business entities and relationships between them but does not include data items or cardinalities.
• A Test Result may optionally form part of a Test Group (a.k.a. Profile, Panel, Battery).
• Note: to aid clarity, Individual level and Organisation level type entities (e.g. Performer / Performing Organisation) have been combined in this version of the diagram.
Pathology Information Model – Detailed
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• Detailed model includes entity data items and relationship cardinalities.
• Further detail is provided in a data set definition spreadsheet
Pathology Information Model – Data Set Definition
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Data Item Name Description Cardinality M/R/O Data Type Values
Identifier A business level identifier for the test result. 1..1 Mandatory Identifier
Status The status of the test result. 1..1 Mandatory Code registered | preliminary | final | amended | corrected | cancelled | entered-in-error | unknown
Category The general type of test result. 0..1 Required Code social-history | vital-signs | imaging | laboratory | procedure | survey | exam | therapy
Test Performed Date and Time The date and time that the test was performed.
0..1 Required DateTime
Test Result Issued Date and Time The date and time that the test result was issued to the requesting organisation.
0..1 Required DateTime
Test Name The name and code of the test that was performed.
1..1 Mandatory CodeableConcept SNOMED CT concept (observable entity)
Test Result Value The test result value. 0..1 Required Multiple
etc.
• Provides a detailed tabular definition of business entity and data item properties.• Extract below is taken from the ‘Test Result’ entity.
Microbiology Reports
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• Lab reports for microbiology investigations are often complex, containing a variety of individual test results (these may be quantitative, semi-quantitative and/or qualitative), coded interpretations and narrative.
• Report structure varies depending on microbiology sub-discipline (e.g. bacteriology), investigation/specimen type and test method.
• The following diagram illustrates a typical structure for a bacteriology report:
Microscopy
Specimen/Sample Observations
Culturing
Antimicrobial Susceptibility
Testing
e.g. for Cerebrospinal fluid investigations - the specimen turbidity (cloudiness), colour and the presence of clots are reported
Content varies depending on investigation - may include descriptions of detected micro-organisms (e.g. gram-positive cocci seen), WBCs, RBCs and other relevant characteristics
List of the micro-organisms that have grown; depending on the type of investigation the level of bacterial growth may also be included
For each identified micro-organism, a list of antimicrobials that may be used as potential treatment, with an indication of susceptibility or resistance
Example Microbiology Report – Urine Culture
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REPORTUrine CultureSPECIMENDate Collected: 2019-11-05 08:30:00Date Received: 2019-11-05 15:20:00Specimen Type: UrineMICROSCOPYWhite cells = >35 x10^6/LRed cells = 10-35 x10^6/LEpithelial cells +Casts = None seenCULTURE1) Staph. saprophyticus >10^8 cfu/L
SENSITIVITIESTrimethoprim SCefalexin SNitrofurantoin SFlucloxacillin SCOMMENTLikely to be clinically significant.
Example Microbiology Report – Mapping to Information Model
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REPORTUrine CultureSPECIMENDate Collected: 2019-11-05 08:30:00Date Received: 2019-11-05 15:20:00Specimen Type: UrineMICROSCOPYWhite cells = >35 x10^6/LRed cells = 10-35 x10^6/LEpithelial cells +Casts = None seenCULTURE1) Staph. saprophyticus >10^8 cfu/L
SENSITIVITIESTrimethoprim SCefalexin SNitrofurantoin SFlucloxacillin SCOMMENTLikely to be clinically significant.
Information Model vs SNOMED CT Semantics
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• Test Names defined as part of the UTL (i.e. the SNOMED CT Fully Specified Names) follow a naming convention of:
• Property-of-Thing-in-Specimen, for example:• Presence of Staphylococcus aureus antibody in serum
• Test Name and Specimen Type are defined as separate data items in the Information Model.
• Other contextual information such as Test Method (Technique) could be defined in the UTL Test Name or carried in the Information Model (or both).
• The Information Model and the SNOMED CT coded terms it contains can be used in various ways:
• Option 1 – use the Information Model as the primary method of conveying the clinical meaning of test results; SNOMED CT terms are used as simple value sets with no or minimum pre-coordination
• Option 2 – use highly pre-coordinated SNOMED CT terms to convey clinical meaning; reduced clinical context is provided in the Information Model
• Option 3 – use a combination of pre-coordinated SNOMED CT terms and the Information Model to convey clinical meaning
Proposed Approach (Option 3)
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Option 1
Information Model Context + SNOMED CT Value Sets
(SNOMED components)
Option 2
SNOMED CT Context and Logical Concept Model
(SNOMED clinical statements)
Information Model vs SNOMED CT Semantics (continued)
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SNOMED CT Concept Model
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Proposed Approach (Option 3)
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Proposed SNOMED CT Test Name Patterns for Microbiology
Presence of Staphylococcus aureus antibody in serum (observable entity)Presence of Aspergillus fumigatus immunoglobulin G antibody in serum (observable entity)
Property-of-Thing-in-Specimen
Arbitrary concentration of Rubella immunoglobulin G antibody in serum (observable entity)
Arbitrary concentration of Rubella immunoglobulin G antibody in oral fluid (observable entity)
Presence of Hepatitis C virus ribonucleic acid by nucleic acid amplification (observable entity)
Arbitrary concentration of Hepatitis C virus ribonucleic acid by nucleic acid amplification (observable entity)
Presence of Acanthamoeba species pluralis (observable entity)
Presence of Acinetobacter species pluralis (observable entity)
Variations
Organism SusceptibilitySusceptibility of organism to ampicillin (observable entity)
Susceptibility of organism to azidocillin (observable entity)Susceptibility of organism to azithromycin (observable entity)
Others under considerationAppearance of specimen – colour/turbidityPresence of gram pos/neg bacteria (microscopy) – seen/not seenNumber concentration/presence of organism in specimen - isolated/not isolated 36
Simplified FHIR Example
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<Observation><id value="culture-group"/><code>
<coding><system value="http://snomed.info/sct"/><code value="SCT-ID"/><display value="Culture"/>
</coding></code><hasMember>
<reference value="Observation/culture-res-1"/> </hasMember>
</Observation>
<Observation><id value="culture-res-1"/><code>
<coding><system value="http://snomed.info/sct"/><code value="SCT-ID"/><display value="Number concentration of Staphylococcus saprophyticus in mid-stream urine"/>
</coding></code><valueQuantity>
<value value="10^8"/><comparator value=">"/><unit value="cfu/L"/>
</valueQuantity><interpretation>
<coding> <system value="http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"/> <code value="DET"
</coding> </interpretation><hasMember>
<reference value="Observation/susceptibility-group"/> </hasMember>
</Observation>
Test Group
- Name: SCT ID | Culture
Simplified FHIR Example (continued)
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<Observation><id value="susceptibility-group"/><code>
<coding><system value="http://snomed.info/sct"/><code value="SCT-ID"/><display value="Antimicrobial susceptibility"
</coding></code><hasMember>
<reference value="Observation/susceptibility-res-1"/> </hasMember>…<hasMember>
<reference value="Observation/susceptibility-res-4> </hasMember>
</Observation>
<Observation><id value=susceptibility-res-1"/><code>
<coding><system value="http://snomed.info/sct"/><code value="SCT-ID"/><display value="Organism susceptibility to trimethoprim"/>
</coding></code><interpretation>
<coding> <system value="http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"/> <code value="S"/>
</coding> </interpretation>
</Observation>
Test Group
- Name: SCT ID | Antimicrobial susceptibility
Test Result
- Test Name: SCT ID | Organism susceptibility to trimethoprim (observable entity) |- Test Method: SCT ID | Minimum inhibitory concentration susceptibility test technique (qualifier value) |- Interpretation Code: S (http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation)
Break time before….
• Potential Requesting Model • UTL as a successor to PBCL
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Colin will now….
Share a first iteration of a requesting model following our Microbiology discovery phase, for your initial feedback and identification of interested parties to work with us
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Requesting and Panels
Target / Goals• Information Model
• FHIR Message
• Panels (/Profiles/Batteries/Test Sets/Care Sets)
• Content Structure (Patterns)
Approach• Build on / align with-
• FHIR (v4) Resources• Reporting Information Model
• Limit scope where possible (Minimum Viable Product, MVP)
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Reduce Improve Enable
• Unnecessary variation• Duplicate testing• Reporting burden
• Information sharing• Patient safety• Flexibility, efficiency, costs
• Machine Learning + AI• Patient access to records• New models of care
Out of CurrentScope
RequestingReporting
Building on + Extending the Approach
??
??
??
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Unified Test List
•Blood Sciences•Microbiology
Information Model
•Results•Blood Sciences•Microbiology•Request Summary
Message Specification
•FHIR DiagnosticReport
Units of Measure
•Current state•IUG•Future Requirements•Strategy/ Approach
Full Request• Blood Sciences• Microbiology
Draft SpecificationFHIR ServiceRequest
• Blood Sciences• MicrobiologyCompound Tests (Panels)• Information Model• Content Patterns
A lot!
Progress to Date
1. Initial Discovery2. “Straw Man” High Level
Information Model3. Potential FHIR mappings
(multiple!)4. A large and growing list of
questions…
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Sample / Specimen
This Photo by Unknown Author is licensed under CC BY-SA
Next Steps (1): Information Gathering
Data + Information1. Test (Requestable) lists, focused on Blood
Sciences and Microbiology. Metadata: code(s), name(s), discipline, source or authority…
2. Example (synthetic or de-identified) patient-level RequestsMandatory and optional data items e.g:i. Known / suspected condition(s), reasons for testingii. Sample / specimen informationiii. Preconditionsiv. Patient state
3. Requesting / Ordering system screenshots4. Lists of Requestable Panels/Profiles/…
i. Constituent testsii. Required metadata to make usableiii. Sources / References
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• Requestables withrequest count over time(high/low volume tests)
• Request size data (number of tests per request submitted)
• Example Requests matched 1:1 with the corresponding Report
• Panel naming models / conventions
Next Steps (2): Engagement
Project Reference Group• Data• Processes• Priorities + Preferences- “must
haves” and “could live withouts”• Current vs. Future needs• Technical options
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Examples- Current Questions• Request grouping
• A requirement?• What level of capability?• Impact(s) of change?
• Request vs. Report structure• Significant (important to maintain?)
• Sample + Specimen• Minimum viable capability?
• Panels- MVP?• Name, Code, components only?• Core national set?
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Requesting and PanelsTo get involved-
• Please talk to me during / after the session today
• Email- [email protected] (or use the team email below)
• Join the Project Reference Group!
Dedicated Requesting and Panels area coming soon-
Link: https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/view?objectId=18603856
Pathology Team collaboration area-
Web: https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/grouphome
eMail: [email protected]
Sarah will now….
Update you on completing the UTL as a successor to the PBCL by domain and volume across blood sciences, immunology and microbiology for your feedback
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So far…
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…and projected…
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PBCL Migration Path… …Current State
PBCL3923 rows
571 ‘D’ deleted (3350)
?2600 potential ‘value taking’ rows
?700 batteries/groupers
SNOMED Procedures
SNOMED Observable
Entities
SNOMED
UK PaLMExtension
SNOMED
UK Clinical Extension
SNOMED
International Core
Read V3 Codes
Read V2 Codes
UTLReportables
1630 > 1750 > > 2750
?Requestables
?900+ >
Everything in PBCL is in SNOMED but shouldeverything in PBCL be in UTL?
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What would that migration path look like for results?
PBCL Concept: 4Q80. | Glucose levelMapped to UK Clinical Extension concept: • 1018851000000108 | Glucose level (observable entity)
UTL Concepts – a mix of UK Clinical and UK PaLM extension concepts:
• Glucose molar concentration in plasma• Glucose molar concentration in serum• Glucose molar concentration in urine• Glucose molar concentration in faeces• Glucose molar concentration in CSF• Glucose molar concentration in peritoneal dialysis fluid• Glucose molar concentration in fluid
Possible new non-UTL hierarchy header concept in PaLM Extension:• Glucose molar concentration [in system] (observable entity)? 51
Liver function test panel (procedure)
Protein, totalAlbuminGlobulinAlbumin/globulin ratioBilirubin, totalBilrubin, conjugatedBilirubin, unconjugated
What would that look like for requests?Request Report/Result
Single test
Group code
Single testSingle test
A <Group> is always a SNOMED <Procedure> code? (Procedure codes cannot take result values. They may be the same codes in request and result or different and there may one or more than one.)
Example
Single test
Group code
Single testSingle test
Single test
Group code
Single testSingle test
Prothrombin time/INR panel (procedure)
PTINR
Liver enzymes panel (procedure)
ALT ASTAlk PhosGGT
Comprehensive liver function test panel (procedure)
All results combined?
Liver function test panel (procedure)
Single test
Group code
Single testSingle test
(based on British Society of Gastroenterology recommendations on liver blood tests)
SNOMED Procedure code
What we need from you:
A view on… • Re-mapping batteries/panels and other groupers to
procedure codes and creating two UTL sub-artefacts. • Enforcing SNOMED procedure types in coding message
‘test group’.• Risks/benefits of moving content to PaLM extension or
managing a mixed economy between Clinical and PaLMextensions.
Example panel/group sets in blood sciences please.Reviewers and testers of content for UTL additions please.
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Jay will now….
Update you on the proposed release schedule for the Unified Test List and discuss current and potential release formats.
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UTL Release Schedule – Considerations
• Enable incremental updates to UTL (2 monthly) to support feedback, governance and testing
• Decoupled from SNOMED CT UK Edition releases• Tied to SNOMED CT Releases in April and October to align with established
release timelines.• Tied to SNOMED CT UK Edition releases
• Minimise burden on adopters• Single Refset – with `reportables` and `requestables`?• Single extension/module – for those familiar with SNOMED CT Releases• Human readable version for feedback
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Proposed Release Schedule
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Aligned with SNOMED CT UK Edition
Aligned with SNOMED CT UK Edition
Aligned with SNOMED CT UK Edition
Beta release
Beta release
UTL Release Formats
• Please note, UTL itself is `Product in Development`.• Will be going through DCB process for approval as standard in 2020-21.
• Current Status:• UTL is published in SNOMED CT RF2 format in April and October• UTL Beta Releases are published current in HTML file format
• Human readable, with links for providing feedback• Other options:
• Spreadsheet format – for filtering, browsing, etc?• Online browser based – for browsing and feedback?
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Survey
https://forms.office.com/Pages/ResponsePage.aspx?id=Hwf2UP67GkCIA2c3SOYp4krun3leOSRPr5MglvwCL9RUOFM4Vk5NQkNWNUlNNzJEUDdXQUk4M0pIRy4u
Further Information or to Get Involved
https://hscic.kahootz.com/connect.ti/PathologyandDiagnostics/grouphome
Connect with us
@nhsdigitalcompany/nhs-digitalwww.digital.nhs.uk
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