i2b2/NCBO Ontology Tools Lori Phillips, MS AUG meeting July 24-25, 2012

Ontology migration example A hospital has migrated from ICD-9 to ICD-10 Observation fact data is now a mix of legacy ICD-9 data and new ICD-10 data. How can the i2b2 ontology adapt to handle this situation? ICD-10 ontology needs to be created in an i2b2 format Legacy ICD-9 terms need to be integrated into ICD-10 hierarchy  When two or more coding systems are mixed together, one will assume the master position of establishing the hierarchy, and the others are mapped into it at various levels. Single integrated ontology can query for both ICD-9 and ICD-10 terms

Integrating ICD-9 terms into ICD-10 hierarchy

Why are hierarchies so important for i2b2? Hierarchies form the basis of both the visualization of the terms and the query mechanism itself. select * from metadata where c_fullname like ‘\Diagnoses\Respiratory system\Chronic obstructive diseases\Emphysema\%’ and c_hlevel = 5

Hierarchies in queries select patient_num from observation_fact where concept_cd IN (select concept_cd from concept_dimension where concept_path LIKE '\Diagnoses\Respiratory system ( )\Chronic obstructive diseases ( )\(492) Emphysema\%')

NCBO BioPortal ICD-10

Building an ICD-10 Ontology with NCBO services Pull data from NCBO via REST services. Reorganize information into i2b2 Metadata format METADATA COLUMN DATA TYPE (ORACLE) DATA TYPE (SQL) C_HLEVELINT C_FULLNAMEVARCHAR2(700)VARCHAR(700) C_NAMEVARCHAR2(2000)VARCHAR(2000) C_SYNONYM_CDCHAR(1) C_VISUALATTRIBUTESCHAR(3) C_BASECODEVARCHAR2(50)VARCHAR(50) C_METADATAXMLCLOBTEXT C_FACTTABLECOLUMNVARCHAR2(50)VARCHAR(50) C_TABLENAMEVARCHAR2(50)VARCHAR(50) C_COLUMNNAMEVARCHAR2(50)VARCHAR(50) C_COLUMNDATATYPEVARCHAR2(50)VARCHAR(50) C_OPERATORVARCHAR2(10)VARCHAR(10) C_DIMCODEVARCHAR2(700)VARCHAR(700) C_TOOLTIPVARCHAR2(900)VARCHAR(900) UPDATE_DATEDATEDATETIME DOWNLOAD_DATEDATEDATETIME IMPORT_DATEDATEDATETIME SOURCESYSTEM_CDVARCHAR2(50)VARCHAR(50) VALUETYPE_CDVARCHAR2(50)VARCHAR(50) bioportal/concepts/46302/all ICD10CM ontology/ICD10CM/0-ICD10CM ICD-10-CM TABULAR LIST of DISEASES and INJURIES class ChildCount 0 ……

NCBO Extraction workflow NCBO REST XML NCBO REST XML Request to extract ontology i2b2 Metadata Extraction Workflow ICD-10 Extracted Data Process

Extracted ICD-10 terms

What about my legacy ICD-9 data? Ideally we would like an i2b2 ontology that integrates ICD-9 into ICD- 10.

Mapping Tool Tool to verify/(re)assign ontology mappings.

Navigating the Mapping Tool Tree Displays terms mapped from one ontology within hierarchy of another Mapped terms are displayed adjacent to terms they are mapped to and appear in bold

Adding a new mapping ICD9:269.3, Mineral deficiency should appear for ICD10:E63 Other nutritional deficiencies Copy term ICD9:269.3

Adding a new mapping Paste onto ICD10:E63 Other nutritional deficiencies

Move or Unmap a mapping ICD9:416.8 Other chronic pulmonary heart diseases appears in two places: the one attached to ICD10:I27.2 appears incorrect and can be unmapped. Or it may be moved (drag and drop) up one level to ICD10:I27

The Unmapped Terms List Free form list of terms to be mapped Locate term you wish to map to in the hierarchy tree. Drag from table to term in the tree. If you make a mistake you can either reassign the mapped term within the tree or unmap it from tree. Unmap will cause it to reappear in the unmapped terms list if the term has no other mappings.

Finding the term to map to

Finding the term …

Assigning an unmapped term Drag from unmapped terms list Drop onto term we are mapping to

Unmapping a term Drag term from tree Drop onto unmapped terms list

Search Unmapped Terms By Name

Search Unmapped Terms by Code

Mapped Terms Viewer

Search Mapped Terms By Code

Search Mapped Terms By Name

Merging Ontologies Mapping tool provides a visualization of what the merged ontologies would look like What if we could extract a single integrated metadata table from this?

Integration tool Request to integrate Integration Workflow ICD9 into ICD-10 ICD-10 merged with ICD9 terms Mapper Cell For each mapped ICD-9 term, compute ICD-10 hierarchy Mapped ICD-9 terms

Integration of ICD-9 into ICD-10

i2b2 wiki: Community projects

Acknowlegements NCBO/bioportal Nigam Shah, Stanford University Ray Fergerson, Stanford University Paul Alexander, Stanford University i2b2 Janice Donahoe, Partners Alyssa Porter, Partners Nich Wattanasin, Partners