# Presentation: 305880

**Margaret Haber**
**Office of Communications**
**National Cancer Institute**

**Use of Mapping for caBIG Standard Vocabularies: Issues to Consider**

## Overview

-  Mapping: Why
-  Mapping: How
-  NCI Metathesaurus example methods
-  caBIG Mapping Issues and Questions

## One Answer is Mapping:Relating Terminologies for Effective Data Exchange

- A holistic view of information exchange requires broader interoperability, but...where do we place the fences?
- Clinical data, regulatory submissions, discovery research?
- Industry agreements, nationally accredited, global standardization?

## The Pillars of InteroperabilityNecessary but not sufficient

- Common information models across all domains of interest
- A foundation of rigorously defined data types (metadata)
- A methodology for interfacing with controlled vocabularies

## Interoperability Keys for Terminology

- Use of Industry Standards, where feasible
- Must allow for extensions to core standards
- Specialty terminology remains common
- Mapping is therefore essential
- Conformance with Data Models
- For process (logical models)
- For data flow (messages)
- For data at rest (database design)

## Mapping has been named as an essential part of enabling effective interchange between core, standard terminologies. Complete mapping includes:

- An initial high level map performed using algorithmic insertion formulas, such as lexical matching, followed by human review for accuracy
- Rule-based mapping of non-overlap areas using consistent, explicit coding principles
- Actual testing and implementation in systems that demonstrate accuracy and effectiveness for data capture, transfer, collection and interpretation

## High Level Map

- Identifies content/concept overlap and gaps
- Reveals issues of semantic equivalence or synonymy, differences in definition of terms
- Allows comparative analysis of classification systems and structural models
- Provides comparison of content coverage in required domains
- Allows system query to quantify comparisons for further analysis

## COSTART vs MedDRA vs SNOMED

| COSTART | MedDRA | SNOMED CT |
| --- | --- | --- |
| Saliva Increase | Salivary Hypersecretion | Excessive Salivation |
| Salpingitis | Salpingitis NOS | Salpingitis |
| Sarcoidosis | Sarcoidosis NOS | Sarcoidosis |
| Sarcoma | Sarcoma NOS | Sarcoma |
| Sarcoma Bone | Bone Sarcoma NOS | Sarcoma of bone and connective tissue |
| Schizophrenic Reaction | Schizophreniform Disorder | Schizophrenic Reaction |
| Scleritis | Scleritis NOS | Scleritis |
| Scleroderma | Scleroderma | Scleroderma |
| Sclerosis Multiple | Multiple Sclerosis | Multiple Sclerosis |
| Screaming Syndrome | Screaming | Screaming |

## Rule Based Map

- Often application and system dependent
- Requires domain knowledge and consensus to judge appropriate methodology for “concept-walking” between terminologies
- Must grapple with issues of pre- vs. post-coordination (full specification vs. composition) of terms and concepts
- Terminology assessment and gap analysis identifies new concept needs, driving both structural requirements for the terminologies and the mapping “rules” between them

## As an example of some issues that can be involved . . . .

## SNOMED CT

- Merger of the College of American Pathologists’ Systematized Nomenclature of Medicine (SNOMED) Reference Terminology (RT) and UK Clinical Terms Version 3 (CTV3 or “Read Codes”)
- Broad based “clinical terms” (CT) with 350,000+ concepts, >1.37 Million semantic relationships
-  Terms of License: Five year free distribution in US through NLM’s UMLS for English and Spanish versions including concepts, descriptions, relationships, and history. If terminated, the last version of SNOMED remains distributable with no further updates provided

## MedDRA (v7.1)

**Description**
**   **International dictionary of medical terms including some 65,000 diagnoses, signs & symptoms, adverse drug reactions, therapeutic indications, names/results of laboratory, radiological, and other investigations, surgical/medical procedures, social circumstances
**Developer**
**   **Under the auspices of the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) as agreed-upon terminology for regulatory reporting
**Terms of Licensing**
**   **Maintenance and Support Services Organization (MSSO) supplies MedDRA in various formats, multiple levels of subscription

## MedDRA vs SNOMED: Content

-  MedDRA content coverage, granularity (level of detail) and fully specified (pre-coordinated) terms suited to the capture of data relevant to adverse event reporting for drugs
-  SNOMED has broader/more granular content coverage for the representation of information in many domains of patient records, potential for enabling post-coordination (composition) of concepts

## MedDRA vs SNOMED: Structure

- MedDRA hierarchy not “is_a” but rather groups of related terms in a structure designed to maximize capture and retrieval of relevant related terms; these terms may fall into more than one higher level grouping
- SNOMED is concept based, with terms and true synonyms classified in an “is_a” poly-hierarchical structure; it is more reliant on composition to fully express granular concepts

## Example of MedDRA Terminology Links for Toxic Epidermal Necrolysis

- Skin and Subcutaneous
- Tissue Disorders

- Infections
- and Infestations

- Injury, Poisoning and
- Procedural Complications

- Immune
- System Disorders

- Epidermal and
- Dermal Conditions

- Ancillary
- Infectious Topics

- Chemical Injury, Overdose,
- and Poisoning

- Allergic Conditions

- Bullous Conditions

- Inflammatory Disorders
- Following Infection

- Poisoning and Toxicity

- Allergies to Foods,
- Food Additives,
- Drugs and Other Chemicals

**SOC**

**HLGT**

**HLT**

**LLT**

**PT**

**Toxic Epidermal Necrolysis – PT**

- Drug Eruption Lyell
- Syndrome Type

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Drug Eruption Lyell
- Syndrome Type

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

- Necrolysis Epidermal Toxic
- (Lyell Type)

## Example of SNOMED Terminology Links for Toxic Epidermal Necrolysis

- Chemical categorized structurally

**Toxic epidermal necrolysis ****Synonyms: Lell’s toxic epidermal necrolysis, supdpidermal type ****TEN – Toxic epidermal necrolysis ****Lyell’s syndrome**

- Chemical-induced dermatotogical disorder

- Disease of skin and/or subcutaneous tissue

- Chemical compound

- Chemical product

- Pyrazole derivative

- Chemical suspension

- Antipyrine

- Barbitone chemical

***Is a***

***Has finding site***

***Has causative***

- Non-infectious, vesicular and/or bullous disease

***Is a***

- Dermis

## Issues to consider when looking at potential standard terminologies before undertaking maps:

- Terminologies in use for health communications reporting must have clear policies and procedures for both national and international use (scope/extent of license, fees, maintenance)
- Reliable mechanisms for user feedback must be in place to ensure requirements for updates can be incorporated into the terminology and published on a regular basis
- The above requirement  (#2) becomes more challenging with terminologies that have very broad coverage or a wide user base

## Issues to Consider . . .

- Concept capture is only one part of the story – structure such as hierarchy is critical for aggregation and retrieval, and very important particularly for reporting applications
-  Hierarchies are also important in mapping, to indicate the intended meaning of a concept if ambiguous, and to provide appropriate terms for mapping (up-coding) from more granular terms/terminologies. Cross-maps thus require comparative structural analysis
- Size of the terminology and depth of hierarchies can be a significant issue for applications

## NCI EVS Goal – Integration by Meaning

-  **Clinical, translational, and basic research terminology have overlapping but specialized needs, therefore EVS assists to:**
- Integrate different conceptual frameworks
- Create terminological and taxonomic conventions across systems
-  **Provide terminology for:**
- Tagging: store/transfer/archive data for future analysis
- Reasoning: limited inferencing about data

## NCI Metathesaurus:

**Filtered UMLS Metathesaurus extended with additional required vocabularies**
**930,000+ concepts, 2,200,000 terms and phrases with definitions**
**Mappings among over 50 vocabularies**
**Extensive synonymy: Over 40,000 terms for neoplasms mapped to 7,000 concepts**
**Used as online dictionary and thesaurus, for mapping and document indexing**

**Notes:**
The current numbers are a little lower than this, 1.6 M, but they will be somewhat higher after our next build (will include CT)

1,691,850  783,158	NCI Metathesaurus	

## NCI Metathesaurus (2)

- Minor releases monthly, Major releases twice a year
-  Provides a mapped overlap and partial inter-relation of current versions of NCI required vocabularies, ex. The ICD’s, MedDRA, SNOMED, MeSH (NLM Medical Subject Headings), HCPCS (procedures), LOINC (lab values), drug terminologies (VA NDF, AOD, RxNORM, Multum, NCI Thesaurus drugs, etc.)

## NCI Metathesaurus Data Profile:

-  Multiple sources per “concept” or unit of semantic meaning
-  Hierarchically organized to reference NCI Thesaurus structures when possible – alternate source hierarchies may also be viewed
- 109 “Term Types” within concepts such as preferred term (PT), synonyms (SY), abbreviations (AB), obsolete (OB), brand name (BR) [drugs], etc.

## NCI Metathesaurus Profile (2)

- 135 “Semantic Types” divide groups of concepts into general domains of meaning such as “Neoplasms,” “Genes,” “Pharmacologic Substance,” etc.
- >5,600,000 asserted relationships between concepts ex.:
-  “Carcinoma” Clinically_associated_with “Lytic Bone Lesion,”
- “TP53” Gene_associated_with_Disease “Breast Carcinoma”

## Slide 24

## 
For Mapping caBIG Standard Vocabularies:
Is it advisable to offer a caBIG standard terminology set based on concept mappings to an existing standard terminology? 

**For Mapping caBIG Standard Vocabularies:**
**Is it advisable to offer a caBIG standard terminology set based on concept mappings ****to an existing standard terminology?**

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**Notes:**
OC using EVS and working to integrate EVS terminology into PDQ and cancer.gov. 

## Maybe...

**The answer is a qualified yes – but it’s not easy, and risks are present.**
**Maps are difficult to construct. **
**Even carefully constructed maps can convey some degree of false synonymy**
**Like terminologies, maps need maintenance.**

## Imprecise or False Synonymy 

-  It may not be possible to find an exact match between concepts in two terminologies.
-  Often the best one can do is to come “close.”
-  How is the degree of closeness indicated to a  user?
-  For certain applications, e.g., clinical, “close” may not be acceptable.

## Like Terminologies, Maps Require Maintenance 

- A map exists between a pair of terminologies, both of which are at specified revision levels or versions
- A change to either terminology requires that the map be re-verified and possibly redone

## This Raises Questions... 

- Who will consistently verify an update maps?
-  How committed is the mapping organization to this activity?
-  How much time is needed to update the map after either vocabulary changes?
-  What is the status of a mapped terminology extension in the interim?

## One Size Doesn’t Fit All 

-  There’s no single definitive map between a pair of terminologies
-  Maps must be based on a well-defined use cases
-  Different use cases may require different maps
-  	Example:  NLM makes multiple maps between CPT and ICD to meet varying use cases from providers and payers.

## Vocabularies for Reporting are Especially Demanding 

-  It’s extremely challenging to substitute an alternative terminology for one designed for specific purposes.
- FDA requires MedDRA for reporting adverse events
- It would be difficult to code adverse events using another terminology and map precisely to MedDRA for reporting.
-  There is significant potential to undermine the integrity of the reports submitted.

## The Bottom Line 

- Mapping is expensive, inherently limited, highly particularized, and represents an ongoing burden
- The payoff for a mapping effort must be justified by clear operational benefits
- If a mapped terminology becomes a caBIG standard, its ongoing maintenance and integrity becomes a significant concern for all users of that terminology
- The analysis that supports the decision to create such a map must consider all the costs and risks of doing so.

## EVS Team & Acknowledgments

**NCI Office of Communications**
**Margaret Haber**
**Larry Wright**
**NCI Center for Bioinformatics**
**Frank Hartel**
**Sherri de Coronado**
**Gilberto Fragoso**
**Contractors**
**Apelon, Inc.****	****	****Northrop Grumman, Inc.**
**Aspen, Inc.****	****	****Kevric / IMC**
**MSD****	****	****	****J. Oberthaler Consulting**
**SAIC ****	****	****	****Protégé/SMI**
**Collaborations & External Reviews**
**NCI: caBIG, CTEP, DTP, DCP, DCCPS, MMHCC, etc.**
**NIH: NLM, NHLBI**
**Govt: FDA, VHA, CDC, DoD, NASA**
**Other: CAP/SNOMED, AFIP, HL7, CDISC, MGED, W3C**