The NeighborhoodAuditing Tool

James GellerMichael HalperYehoshua PerlC. Paul Morrey

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Research PaperC.P. Morrey, J. Geller, M. Halper, Y. Perl.

The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS. J Biomed Inform, 42(3):468-89, 2009.

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Overview

Goals of an Auditor’s Tool for the UMLS Principles of Auditing with Neighborhoods The Idea of a Hybrid Display Current State of the NAT: Serving the Auditor Presentation of NAT Features Live Audit Session Planned State of the NAT: Guiding the Auditor Conclusions Future Work

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Auditing the UMLS

About 150 source vocabularies It is natural that inconsistencies will appear Over 2.1 million concepts and nearly 9.7

million terms* Two level structure consisting of the

Semantic Network and the Metathesaurus

*UMLS Metathesaurus version 2009AA

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Previous Work on Auditing H. Gu, Y. Perl, J. Geller, M. Halper, L. Liu, and J.J. Cimino. Representing

the UMLS as an Object-oriented Database: Modeling Issues and Advantages. J Am Med Inform Assoc, 7(1):66-80, 2000.

J. Geller, H. Gu, Y. Perl, and M. Halper. Semantic refinement and error correction in large terminological knowledge bases. Data & Knowledge Engineering, 45(1):1-32, 2003.

J.J. Cimino, H. Min, and Y. Perl. Consistency across the hierarchies of the UMLS Semantic Network and Metathesaurus. J Biomed Inform, 36(6):450-461, 2003.

H. Gu, Y. Perl, G. Elhanan, H. Min, L. Zhang, Y. Peng. Auditing concept categorizations in the UMLS. Artif Intell Med, 31(1):29-44, 2004.

Y. Chen, Y. Perl, J. Geller, and J.J. Cimino. Analysis of a study of the users, uses, and future agenda of the UMLS. J Am Med Inform Assoc, 14(2):221-231, 2007.

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Previous Work on Auditing (cont’d)

H. Gu, G. Hripcsak, Y. Chen, C.P. Morrey, G. Elhanan, J.J. Cimino, J. Geller, and Y. Perl. Evaluation of a UMLS auditing process of semantic type assignments. In J.M. Teich, J. Suermondt, and G. Hripcsak, editors, Proc AMIA Symp, pages 294-298, Chicago IL, Nov. 2007.

Y. Chen, H. Gu, Y. Perl, J. Geller, M. Halper. Structural group auditing of a UMLS semantic type's extent. J Biomed Inform. 2009 Feb;42(1):41-52.

L. Chen, C.P. Morrey, H. Gu, M. Halper, Y. Perl. Modeling multi-typed structurally viewed chemicals with the UMLS Refined Semantic Network. J Am Med Inform Assoc, 16(1):116-31, 2009.

Y. Chen, H. Gu, Y. Perl, J. Geller. Structural group-based auditing of missing hierarchical relationships in UMLS. J Biomed Inform. 2009 Jun;42(3):452-67.

Y. Chen, H. Gu, Y. Perl, M. Halper, and J. Xu, Expanding the extent of a UMLS Semantic Type via Group Neighborhood Auditing. J Am Med Inform Assoc, Accepted for publication.

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How we did it before the NAT: Provide Info as Paper Form

CPT: C1081844 Antonospora locustaeSRC: NCBISTY: T004T009 Fungus + InvertebrateDEF:SYN: Antonospora locustae | Nosema locustaePAR: Antonospora{STY: Invertebrate}CHD:

Data shown for this concept is from the UMLS Metathesaurus version 2006AC

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Auditing Results also Paper Form(C1081844) Antonospora locustaeSTY: Fungus + Invertebrate

No errors Semantic Type Error: Fungus Semantic Type Error: Invertebrate Add Semantic Type______________________ Ambiguity Other error_____________________________ Comments _____________________________

______________________________________

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Goals of an Auditor’s Tool for the UMLS

Display relevant information to the auditor. Do not overwhelm the auditor with too

much information. Help the auditor focus on areas most likely

to contain errors.Algorithms suggest likely erroneous conceptsConcepts are reviewed in a neighborhood

display

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Principles of Auditing with Neighborhoods

Several years of experience: Auditing is to a large degree a “local” activity.

Concepts have two kinds of knowledge elements:Textual Knowledge Elements: Preferred term,

CUI, synonyms, LUI, definition, sources, semantic types

Contextual Knowledge Elements: Neighbors

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Neighborhoods

Focus concept: The concept presently under review

Immediate Neighborhood: The set of concepts reachable from the focus concept by stepping one relationship (up, down, lateral, etc.)

Extended neighborhood: Includes parents of parents (grandparents), children of children (grandchildren) and siblings. No lateral chains.

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References about Neighborhood M.S. Tuttle, D.D. Sherertz, N.E. Olson, M.S. Erlbaum,

W.D. Sperzel, and L.F. Fuller, et al. Using META-1, the first version of the UMLS Metathesaurus. In Proc 14th Annu Symp Comput Appl Med Care, pages 131-135, Washington, D.C., 1990.

S.J. Nelson, M.S. Tuttle, W.G. Cole, D.D. Sherertz, W. D. Sperzel, M.S. Erlbaum, L.L. Fuller, N.E. Olson, From meaning to term: semantic locality in the UMLS Metathesaurus. In Proc Annu Symp Comput Appl Med Care, pages 209-213, Washington, D.C., 1991.

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Immediate Neighborhood

Microsporidia, Unclassified

Microsporidia <protozoa>

Dictyocoela Edhazardia

FibrillanosemaMicrosporidium

Kabatana

Oligosporidium

Cellular aspects of

Microbiological

Pathogenicity Aspects

virologic

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Extended Neighborhood

RELATIONSHIPS

SIBLINGS

GRANDCHILDREN

CHILDREN

FOCUS CONCEPT

PARENTS

GRANDPARENTS

Microsporidia, Unclassified

Microsporidia <protozoa>

Erroneous concept

fungus

PHYLUM MICROSPORA

Protozoa

Sporozeoa

Dictyocoela Edhazardia

FibrillanosemaMicrosporidium

Dictyocoela berillonum

Dictyocoela cavimanum

Edhazardia aedis

Fibrillanosema crangonycis

Microsporidium 57864

Dictyocoela dehayesum

Dictyocoela duebenum

Dictyocoela grammarellum

Dictyocoela muelleri

Dictyocoela sp.L11

Kabatana

Kabatana takedai

Microsporidium africanum

Microsporidium ceylonensis

Microsporidium cypselurus

Microsporidium prosopium

Microsporidium seriolae

Oligosporidium

Oligosporidium occidentalis

Microsporea

Cellular aspects of

Microbiological

Pathogenicity Aspects

virologic

SIB

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Up-Extended and Down-Extended Neighborhood

An up-extended neighborhood includes grandparents and the immediate neighborhood.

A down-extended neighborhood includes grandchildren and the immediate neighborhood.

Give auditor all s/he needs but not more.

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Semantic Type Neighborhood

If we provide the semantic types for every concept, those also form a neighborhood.

It is important to keep the information of which semantic types are assigned to which concepts.

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The Idea of a Hybrid Display

Diagrams are wonderful – as long as they fit on one screen.

Indented text is wonderful – as long as there are no or very few multiple parents.

But the UMLS does not fit onto one screen and there are many cases of multiple parents.

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What makes a diagram wonderful?

You can follow parent/child paths with your eyes.

You can get a feeling for everything a concept is connected to with one look.

You can see multiple parents and multiple paths with one look.

You can see global features (short and bushy versus tall and sparse, or (gasp!) tall and bushy).

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What makes indented text wonderful?

Indentation expresses parenthood compactly and elegantly.

There are no lines crossing. You don’t need a layout algorithm. There is a linear order in which to study

text.

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The Idea of a Hybrid Display (cont.)

Keep the best features of text and the best features of diagrams.

Maintain relative positions between the focus concept and its children, parents, etc.

Eliminate clutter of arrows.

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A Hybrid Diagram/Form Display of a Neighborhood

Children

Focus ConceptSynonyms Relationships

Parents

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Desirable Information Beyond Neighborhoods

Concept definition for Focus Concept Sources for concepts and relationships Assigned Semantic Types of concepts Definitions of relevant Semantic Types Global view of the Semantic Network

Indented (better for wide branches)Graphical (better for almost everything else)

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Current State of the NAT: Serving the Auditor

The Neighborhood Auditing Tool has been implemented to fully support display of neighborhoods.

Navigation to adjacent neighboring concepts is an easy click.

Additional features listed before have been implemented.

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Demonstration of NAT Features

Neighborhood Grandparents and

grandchildren Synonyms Relationships: Concept,

Sibling, Term Focus concept definition Sources: Concepts,

Relationships Display CUIs Semantic Type display

Semantic Type definition Semantic Network

(indented) Semantic Network

(diagram) Navigation Search (full, partial) Viewing History Choice of release Choice of sources

offline version

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Audit Example: A Cycle of Three Concepts An SQL query found three concepts

that participate in a PAR/CHD cycle. We follow an auditor’s review of this

cycle. O. Bodenreider, Circular hierarchical

relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. Proc AMIA Symp. 2001:57-61

offline version

The Cycle of Three Concepts

Mood Disorders

Affective Disorders, Psychotic

Bipolar Disorder

Relationship Sources: Medical Subject Headings National Drug File Reference Terminology SNOMED-2 Alcohol and Other Drug Thesaurus

Relationship Sources: Medical Subject Headings National Drug File Reference Terminology

Relationship Source: DSM-IV

Relationship Sources: DSM-IV and many others

Recommended Modeling

Mood Disorders

Affective Disorders, PsychoticBipolar Disorder

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Audit Example: Semantic Types

An algorithm determined that the concept Antonospora locustae was likely assigned incorrect semantic types.

We follow an auditor’s review of this concept.

offline version

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Preliminary Evaluation Study with NAT

Compare paper-based auditing and NAT-based auditing.

Counterbalanced groups. Recall improves with NAT use. Auditors

seem willing to investigate more concepts. Precision stays the same. Auditors’ mental

process does not improve.

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Conclusions

Preliminary study showed that people are more successful finding errors with NAT than with paper sources.

Recall improved with the NAT, precision did not.

NAT seems to nicely complement use of the UMLSKS.

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Future Work

Integration of algorithms for developing “audit sets” with NAT.

Recording and reporting auditor recommendations.

Facilitate team auditing where several auditors review the same sample.

Managing and reporting work flow of auditor teams.

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The Neighborhood Auditing Tool is available online at:

http://nat.njit.edu

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Auditor

Errors Recall Precision F

with NAT

w/o NAT

with NAT

w/o NAT

with NAT

w/o NAT

with NAT

w/o NAT

1 57 45 0.97 0.82 0.53 0.51 0.86 0.63

2 22 20 0.43 0.35 0.55 0.55 0.48 0.43

3 39 34 0.64 0.58 0.46 0.53 0.54 0.55

4 56 44 0.55 0.54 0.30 0.34 0.39 0.42

Avg. 44 36 0.65 0.57 0.46 0.48 0.57 0.51

Preliminary Evaluation Study

Improved Recall

The auditor finds it easy to search for more errors in the neighborhood of the suspicious concept.

With better recall and the same precision you still find more errors.

Semantic Types Example

The concept Antonospora locustae was selected for audit by an algorithm that found it was the only concept assigned to the intersection Fungus + Invertebrate in the UMLS 2007AA.

NAT Features Demonstration

Neighborhood

Cycle Example

An SQL query provided us with a list of concepts in the Metathesaurus that participate in cycles of length three.

One of these cycles exists among the concepts Bipolar Disorder, Mood Disorders, and Affective Disorders, Psychotic.