SNOMED CT in Pathology - IHE Wiki

SNOMED CT in PathologyMarcial García RojoHospital General Universitario de Ciudad Real. SpainIHE AP. Paris, June 2 nd , 2012

BackgroundSNOMED CT useful in:• Reference terminology: Information Systems (IS)integration (semantic interoperability)◦ EHR – Pathology IS• Electronic request Pathology Study (specimens, anatomy)• Pathology report available in EHR (diagnosis, clinical problems,episode coding-billing)◦ Pathology IS and telepathology portal (specimens anddiagnosis)◦ Pathology IS and DICOM image manager (specimens anddiagnosis)◦ Pathology IS and hospital tumor registry, biobank IS,…• Interphase terminology◦ Searches made easier, Concept navigation, Qualifiers can beadded, synonyms are available

Pathology reports•Free text reports◦Coding specimens (procedures?), anatomy anddiagnosis•Structured reports◦Coding both the question and the answer•Question: Observable entity (Histological grade?)•Answer: Diagnosis and qualifiers

procedurespecimenprocedurespecimenprocedurespecimenclinical findingspecimen

Coding specimens• Spanish Society of Anatomic Pathology (SEAP):Consensus from 8 institutions from all over Spain.• Criteria for classifying specimens (withoutconsideration of workload or diagnosis)1. General topography (skin)2. Obtaining procedure or intention: In biopsies• Superficial biopsy (punch, tru-cut or needle)• Incisional biopsy• Enucleation• Complete excision (generally with adjacent tissue)• Partial resection of an organ• Complete removal of an organ• Removal of organ and adjacent structures (e.g. lymphadenectomy)• Special resection (Whipple, abdominoperineal,…) o method(stereotactic, endoscopy)

Coding specimens•Cytology◦Exfoliative cytology, brushings or scrapings◦Fluid sample◦Touch preparation◦Fine Needle Aspiration (FNA)•Autopsy◦Coded as procedures

Results of coding specimens andprocedures with SNOMED CT•Biopsies: 345 specimens and procedures◦112 specimens (32%) post-coordinated◦47 procedures (14%) post-coordinated•Cytologies: 206 specimens and procedures◦73 specimens (35%) post-coordinated◦92 procedures (46%) post-coordinated•Autopsies: 21 different procedures (3 postcoordinated)

Guidelines for coding withSNOMED CT• What to do when 2 similar codes are found(choose the most specific one).◦ 128157004 |tissue specimen from brain (specimen)|better than119398007 |specimen from brain (specimen)|◦ 438351003 | tissue specimen obtained by esophagogastrectomy(specimen) |includes:122631007 | specimen from esophagus obtained byesophagogastrectomy (specimen) |• “esophageal biopsy sample” or “tissuespecimen from esophagus”? “tissuespecimen” was preferred

Guidelines for coding specimenswith SNOMED CT• specimen from __(topography)__ obtained by __(procedure)__Where procedure “biopsy”. Procedure can be general (“excision”)or very specific (“Whipple resection | subtotal adrenalectomy”). (229concepts)• specimen from __(topography)__ obtained by __( |core|excisional |image guided core |incisional |open |…)__ biopsyVery specific procedures, from “incisional biopsy” to “stereotacticallyguided core needle biopsy” or “CT guided needle biopsy”. (55concepts).• specimen from __(topography)__ obtained by biopsy(specimen)Biopsy type is not stated. (46 concepts)• (topography)__ biopsy sample(75 concepts).• tissue specimen from__(topography)__(62 concepts)

Postcoodination rulesRefinement (C:A=V) (C:A 1 =V 1 ,A 2 =(V 2 ),…,A n =V n )• Specimens:◦ specimen : specimen procedure (attribute) = procedure◦ specimen : specimen source topography (attribute) = bodystructure◦ specimen :specimen source topography (attribute) = body structure ,specimen procedure (attribute) = procedure• Procedures:◦ procedure : procedure site - Direct (attribute) = body structure

Very specific anatomic regions•Very few precoordinated terms are veryspecific (post-coordinated needed)◦122683000 | specimen from left kidney, inferiorpole obtained by partial nephrectomy(specimen) |•A specific topographic code may be foundas precoordinated:◦12212007 | structure of superior segment of leftlower lobe of lung (body structure) |

Laterality118169006 | specimen source topography (attribute) |272741003 | laterality (attribute) |Values admitted by this attribute are descendants from theconcept: 182353008 | side (qualifier value) |:◦ 7771000 | left |• 51440002 | right and left |• 419161000 | unilateral left |◦ 24028007 | right |• 51440002 | right and left |• 419465000 | unilateral right |

Implementation of specific sitesand laterality•It may be easier implementing a databasefield “topography” coded with SNOMEDCT than post-coordinating specimens orprocedures with this attribute.

A possible error in SNOMED CT•“122622007 | specimen from pleuraobtained by lymph node biopsy |”•(included as a descendant of “pleurabiopsy sample”)

Adding new conceptsMS Access file(BatchRequestGeneral_MSSSI_Spain_06032012.mdb)• Submit Date• Submitter ID• Proposed FSN• Parent ConceptID• Parent FSN• Submitter Comment• Editor Action• "Reject": Reason• "Added": UUID• "Added with NameChange": FSN• Name ChangeReason• "Found": ConceptID• "Found": FSN• Editor Comment

Coding Pathology diagnosis•Pathologists should become aware of thestructure and contents of SNOMED CT•A shift from T, P, M schema to apolihierarchy and relationship schema•Pathologist’ diagnosis should be coded asmorphology (abnormal body structure) oras clinical diagnosis?

CAP Anatomic Pathology SubsetHierarchyApproximate CountBody structure 3,805Clinical Finding 2,024Procedure 780Observable entity 386Specimen 264Pharmaceutical / Biologic product 83Record artifact 67Organism 61Staging and scales 33Substance 24Qualifier value 21Special concept 12Events 9Situation with explicit context 9Physical object 4TOTAL CONCEPTS (Jan 2010) 7,582In daily practice, this subset was not considered useful by pathologists, mainlydue to the mixture of different hierarchies (clinical findings, body structure,observations,..), and due to the fact that many basic pathology diagnosis werenot included in the CAP AP Subset.

Implementation of SNOMED CT inHospital General de Ciudad Real•IHE: Structured Reports Value Sets (1,840possible values for observations)•HGUCR: 2,320 pathology diagnosis codesmapped to SNOMED CT• Search for descriptions that match the locallegacy codes was performed using CliniClueXplorer version 2010 1.243, using SNOMED CT2011-01-31 International Release and 2010-04-30 Spanish Edition.

Results. Implementation of SNOMEDCT. Hierarchies of precoordinated terms•Postcoordination needed in 19% (3conceptID needed only rarely) (81%precoordinated)•Morphology – Abnormal body structure◦Only 44% of the codes! (1076)•Clinical findings◦48% of the codes•Qualifiers, normal anatomic structures,procedures, physical object, substance,organism◦10% of the codes

Results•48% of the total terms could be codedusing the disorder hierarchy, using:◦In 1104 terms, using “disorder” hierarchy, e.g.Rosacea◦In 71 terms, using “finding” hierarchy, e.g.World Health Organization (WHO) grade I(central nervous system tumor)

Results• There were a 6% of the local morphologicaldiagnosis that were not well represented usingeither morphological abnormality ordisorder/finding hierarchies, and the followingSNOMED CT were found useful (generallycombined with other hierarchies):◦In 95 local terms, the use of a SNOMED CT qualifiers(generally combined with clinical or morphologicalcodes) was found useful, e.g. Granulomatous◦In 68 local terms, the use of SNOMED CT bodystructures was found useful, e.g. Undescended testis◦…

Postcoordination in practice•Initially, in case a combination of termswas needed, the initial combination ofterms was made without consideringSNOMED CT rules for post-coordination,but considering the best combination ofterms that define the concept according topathologists’ idea.

AttributesBody StructureLateralityClinical FindingAssociated With• After• Causative Agent• Due ToAssociatedMorphologyClinical CourseEpisodicityFinding InformerFinding MethodFinding SiteHas DefinitionalManifestationHas InterpretationInterpretsOccurrencePathological ProcessSeverityEventsAssociated With• After• Causative Agent• Due ToOccurrenceEvaluation ProcedureComponentHas SpecimenMeasurement MethodPropertyScale TypeTime AspectPharmaceutical/Biologic ProductHas Active IngredientHas Dose FormPhysical ObjectHas Active IngredientProcedureAccessDirect SubstanceHas FocusHas IntentMethodPriorityProcedure Device• Direct Device• Indirect Device• Using AccessDevice• Using DeviceProcedureMorphology• DirectMorphology• IndirectMorphologyProcedure Site• Procedure Site –Direct• Procedure Site –IndirectRecipient CategoryRevision StatusRoute of AdministrationSurgical ApproachUsing EnergyUsing SubstanceSituation with ExplicitContextAssociated FindingAssociated ProcedureFinding ContextProcedure ContextSubject RelationshipContextTemporal ContextSpecimenSpecimen ProcedureSpecimen SourceIdentitySpecimen SourceMorphologySpecimen SourceTopographySpecimen Substance

Postcoordination• Morphological concepts (morphologicallyabnormal structure) are primitive terms (not“sufficiently” defined) and CANNOT bepostcoordinated• CILLIATED CELL ADENOCARCINOMA• 35917007 + 125550007◦35917007 | Adenocarcinoma, no subtype (morphologicabnormality)◦125550007 | Tubal metaplasia (morphologicabnormality)

An example of lack of coherence inSNOMED CT• The concept “well differentiatedadenocarcinoma” is not available as precoordinatedterm in SNOMED CT in either bodystructure or in clinical finding hierarchies.However, there are available some morespecific similar codes like “follicularadenocarcinoma, well differentiated(morphologic abnormality)” or “well differentiatedadenocarcinoma, gastric foveolar type(morphologic abnormality)”.

Spanish Subset for Diagnosis•Specimen and Procedure subset ispublished in http://www.seap.es/•The Spanish Society of AnatomicPathology is currently working in apathology diagnosis subset that will bepublished next October.

Pathology IS and SNOMED CT

Structured pathology reports• The general approach to coding items on theCAP and IHE checklist that ask questions hasbeen to use concepts from the SNOMED CTObservable Entity hierarchy.• The answers to these questions can be chosenfrom concepts in any of several hierarchies.Primarily, they are found in the Finding,Disorder, or Morphologic Abnormalityhierarchies (van Berkum, 2003).

Why we like morphological codes• As pathologists, we feel the need to have ourpathology reports encoded using not onlyobservables (questions) and qualifiers (valuesets), but mainly using morphological codes thatsummarize all observations described in thereport.• Therefore, the section of the pathologydedicated to coding should contain a list ofmorphological codes associated with thecorresponding specimen.

Clinical findings preferred by EHR•In electronic health record studies, theclinical findings should generally bepreferred over the morphologicabnormality concept. In case there is onlya morphologic abnormality concept, itshould be post-coordinated with a focusconcept of "64572001|Disease (disorder)|"and linked with the concept model attribute"116676008|Associated morphology(attribute)|" (Lee, 2010).

Precoordinated primitive terms•Whenever a pre-coordinated concept isavailable, that should be the first choice. Ifthe pre-coordinated concept is a primitiveconcept, an alternative is to create a postcoordinatedexpression to ensure thenecessary semantics are recorded. Thereason is that terms encoded with primitiveconcepts are more difficult to query andtest for equivalency (Lee, 2010).

Linkage concepts in Pathology• The concept “histological grade (attribute)” is a linkageconcept.• There are some special concepts, like attributes (e.g.246229000 | histological grade (attribute)), that can beused as “linkage concepts”:• Question: 371469007 | histologic grade (observableentity),246229000 | histological grade (attribute)• Answer (values):370114008 | histological grades (qualifier value):384812005 | moderately differentiated263843001 | poorly differentiated263918006 | undifferentiated263933003 | well differentiated

Linkage concepts•Associated morphology is one of thelinkage concepts (attributes) used todefine clinical findings concepts.Associated morphology attributes specifythe morphologic changes seen at thetissue or cellular level that arecharacteristic features of a disease.

Morphology attributes• SNOMED CT concept model provides constraints forattributes that are used as defining relationships, both indistributed SNOMED CT content (so-called precoordinateddefinitions) and in post-coordinatedexpressions. This model describes that the domain ofthe attribute Associated Morphology is the ClinicalFinding hierarchy.• Procedure hierarchy concepts can have a ProcedureMorphology attribute.• Specimen concepts can have a Specimen SourceMorphology attribute.• All other hierarchies (body structure, events, physicalobjects,..) cannot have morphology related attributes.

Morphology attributes•Permissible values for AssociatedMorphology, Procedure Morphology, andSpecimen Source Morphology attributesare codes belonging to theMorphologically abnormal structure(SCTID 49755003) and its descendants inthe Body structure hierarchy.

Pathological process linkage concept•When the underlying pathological processfor a disorder are not structural and cannotbe represented by the associatedmorphology attribute (e.g. Autoimmune),the pathological process linkage conceptcan be used. Since July 2009, two newvalues Infectious process (qualifier value)and Parasitic process (qualifier value)have been added to the range forpathological process.

SNOMED CT and digital images:DICOM•Specimen Obtained (types, anatomiclocation, collection procedure)•Specimen processing (samplingprocedure, preparation procedure, stains,fixatives, embedding)•Diagnosis…

Open questions• Should pathology diagnosis be coded using the morphologicalabnormality sub-hierarchy (part of the Body Structurehierarchy) or should they be coded using Clinical Findinghierarchy?• Should we try to use mainly morphological codes, and whenthey are not available, could some diagnoses in pathologyreports be coded using clinical (disorder or findinghierarchies)?• Does using a mixture of hierarchies (Body Structure andClinical Finding) in pathology diagnosis coding make sensewhen implementing data exploitation of information systems?• Should we ask IHTSDO to complete the list of morphologicalcodes to add all those codes missing in the morphologicalabnormality sub-hierarchy?

Licensing SNOMED CTThe use of SNOMED CT in production systems requires a license.• IHTSDO: Most IHTSDO Member countries providesSNOMED CT free of charge to users, although somemay charge a small fee for cost recovery. The specificinformation is provided by your National ReleaseCentre.• Qualifying Research Project. If you are in a countrythat is not yet a Member of IHTSDO, you can obtain alicense to use SNOMED CT through IHTSDO. Qualifyingresearch projects may qualify for a free license.• Healthcare providers and others wanting to useSNOMED CT in the countries categorized as low incomeeconomies by the World Bank can obtain SNOMED CTAffiliate Licenses free of charge.

Conclusions•SNOMED CT needs to be improved inmorphology hierarchy•Pathologists need to understand better theSNOMED CT works. SEAP has publisheda guideline for specimens and procedures•Pathology IS allow both local terms andmapping to SNOMED CT•Digital slides management can beimproved with SNOMED CT