giorgi jgarkava - srp presentation - final

Gia JgarkavaMaster, Medical Informatics

July 10th, 2013

Master thesis

Revision of SNOMED CT post-coordination rules: from practice to theory

Future workIntroductionSNOMED CT

Post-coordination

Materials and Methods

Results

Identified issues

Proper concept

Post-coordination guide

Sample post-coordination

Overview

Giorgi Jgarkava 2July 10th, 2013

Components: Concept, description, relationship

19 top-level hierarchies (clinical finding, procedure, etc.)

300,000+ concepts

Underlying formal logic

Concept model (domains and ranges)

SNOMED CT


Three methods*

Refinement

Qualification

Combination

Problem: Only rules, no guideline

Post-coordination - Methods


* SNOMED CT Technical Implementation Guide - 8.2.1.2. Post-coordination



|Colectomy|

|Procedure|:

{|Method|=|Excision|,

|Procedure site|=|Colon structure|}

|Sigmoid colectomy|

|Procedure|:


|Procedure site|=|Structure of sigmoid colon|}

Three methods

Refinement

Qualification

Combination



|Gastrectomy|

|Procedure|:


|Procedure site|=|Stomach structure|}

|Duodenectomy|

|Procedure|:


|Procedure site|=|Duodenum structure|}

Three methods

Refinement

Qualification

Combination



|Gastroduodenectomy|

|Procedure|:


|Procedure site|=|Stomach structure|}


|Procedure site|=|Duodenal structure|}

Three methods

Refinement

Qualification

Combination

Requirements for post-coordinated expressions:*

Post-coordination - Requirements


* S. Schulz, D. Schober, M. Boeker and D. Raufie, "Pre- and post-coordination in biomedical ontologies," in OBML 2010 Workshop, Mannheim, 2010.

Validity

Expressivity

Reliability




Validity

Expressivity

Reliability


Grammatical

Sensible

Liver drainage

|Procedure|:{|Method|=|Drainage||Procedure site|=|Liver structure||Direct Substance|=|Substance|}

Post-coordinated concept

|Procedure|:{|Method|=|Drainage||Procedure site|=|Liver structure||Direct Substance|=|Chewing tobacco|}




Validity

Expressivity

ReliabilitySNOMED CT Editorial Guide

3. Scope and Boundaries

5. Attributes used in SNOMED CT

6. Individual Hierarchies




Validity

Expressivity

Reliability Variation between different users/browsers

What kinds of problems may prevent proper post-coordination?

What solutions may solve the problems?

How to organize the process?

Secondary Questions

What characteristics should post-coordinated procedure concepts have to be considered as proper?

Research Question

Research Questions


DIO (Data Integration for Research) procedures listAMC, 2009-2012 period

2,866 types of procedures

144,8011 procedures performed

CBV procedures terminology system

200 procedures analyzed (50 procedures from each quartile)

Materials


Methods – Mapping process


MappingCBV to SNOMED CT

Exploration

Experimentation

Methods – Snow Owl 2.0


Terminology browser

Authoring tool

Reasoner support

Extended search

Integrated concept model

Analyzed concepts 200

Directly mapped 102 (51%)

Post-coordinated 76 (38%)

Not mapped 22 (11%)

Results – Mapping


Results – Identified issues


Results – Issues 1 – SNOMED CT content


|Selective transsphenoidal pituitary adenomectomy|

|Procedure|:

{| Method | = | Excision - action |,

| Procedure site – direct | = |Pituitary structure|,

|Surgical approach|=|Transsphenoidal approach|}

Underspecified Concepts



|Selective transsphenoidal pituitary adenomectomy|

|Procedure|:

{| Method | = | Excision - action |,

| Procedure site – direct | = |Pituitary part|,

|Procedure morphology|=|Adenoma|,

|Surgical approach|=|Transsphenoidal approach|}

Underspecified Concepts



Inconsistent Hierarchies

Results – Issues 2 – Logic


Negation

DUODENUM - RESECTIE - EXCL. WHIPPLEResection of duodenum – excluding Whipple procedure

Numerical

MOND - PERMUCOSAAL 2E FASE - 1E IMPLANTAATIntramucosal dental implantation - 2nd phase - 1st implant

“Other”

HERSENEN - EXCISIE BRUGHOEKTUMOR-OVERIGE BENADERINGENExcision of acoustic neuroma - other approaches

Results – Issues 3 – Concept model 1


Diagnosis in procedure

ZYGOMA - REPOS.FRACTUUR ARCUS ZYGOMAT. - OSTEOSYNTH Repositioned zygomatic arc fracture – Osteosynthesis

Person involvement

ANALGESIE - EPIDURAAL DOOR ANESTHESISTEpidural anesthesia by anesthesiologist

ANAESTHESIE OPVANG TRAUMA PATIENT Administration of anesthesia for a trauma patient

Results – Issues 3 – Concept model 2


Laterality

SPEEKS.KLIER- EXTIRPATIE GLAND.SUBLINGUALIS – ENKELZIJDIGExcision of sublingual gland – single side

Complex procedures

ULNA - PLAATOSTEOSYNTHESE INCL.MONTEGGIAOsteosynthesis of ulna with plate - including Monteggia fracture

ANESTHESIE - BIJ VERVOER BEADEMDE PATIENT – INTERNAdministration of anesthesia for internal transfer of ventilated patient

Results – Proper concept criteria


Proper concept description (FSN, synonyms)

The concept should be fully defined

Proper position in the hierarchy

Usage of relationship groups when needed


Results – Post-coordination guideline



Step 2: Candidate parent concept

|Open reduction of fracture of ulna with internal fixation|

|Procedure|:

{|Method| = |Open reduction – action|, |Procedure site – direct|=|Bone

structure of ulna|, |Direct morphology| = |Fracture|},

{|Method| = |Fixation – action|, |Procedure site – direct|=|Bone structure

of ulna|, |Direct morphology| = |Fracture|,

|Using device| = |Orthopaedic internal fixation system|}





Step 3: Candidate parent concept definition

|Procedure|:

{|Method| = |Open reduction – action|, |Procedure site –

direct|=|Bone structure of ulna|, |Direct morphology| = |Fracture|},

{|Method| = |Fixation – action|, |Procedure site – direct|=|Bone

structure of ulna|, |Direct morphology| = |Fracture|,

|Using device| = |Bone plate|}





Step 5: Create target concept

FSN: Open reduction of fracture of ulna with internal

fixation by plate

Synonym: Osteosynthesis of ulna using plate

Step 4: Ancillary parent concept(s), if needed





Step 9: Qualification / refinement

|Procedure|:





|Using device| = |Bone plate|}

Step 8: Ancillary concept(s), if needed





Step 9: Ancillary sub-concept|Monteggia fracture management|

|Procedure|:





|Using device| = |Bone plate|},

{|Method| = |Reduction – action|,

|Procedure site – direct|=|Structure of head of radius|,

|Procedure morphology|=|Dislocation|}





Step 13: Equivalent concept

Step 14: Intra-axiom redundancy

Step 15: Report for IHTSDO



Guideline evaluation with larger sample size

Testing the method for mapping other terminology systems to SNOMED CT

Modification of the guide for other hierarchies

Development of golden standard for the concepts

Guideline evaluation in various settings with different users

Automation of post-coordination

Directions for future work


“Theory is necessary, but one gram of practice is more than tons of theory”

Paramhans Swami Maheshvarananda

Questions & Discussion


giorgi jgarkava - srp presentation - final

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