# Presentation: 035773

## Consistency between Metathesaurus

- and Semantic Network

- Workshop on*The Future of the UMLS Semantic Network * NLM, April 8, 2005

## Overview

- Defining consistency
- What does inconsistency mean?
- Testing consistency
- Comparing Metathesaurus relations to SN relations
- Aligning Metathesaurus concepts and semantic types
- Semantic type distribution of sets of descendants of Metathesaurus concepts
- Suggestions
- Enforcement mechanism
- Ontology of relationships
- CVF

- Two levels in the UMLS

## The UMLS: a two-level structure

## Slide 5

## Relationships can inherit semantics

- Semantic Network

- Metathesaurus

- Defining consistency

## The consistency “square”

## The categorization link

- Semantic Network

- Professional Society

- Metathesaurus

- Organism

- Bacterium

*isa*

*isa*

*is a**n instance of*

## Semantic Network relations

- 54 types of relationships
- 558 asserted relations (SRSTR)
- 6703 fully expanded relations (SRSTRE*)

- Semantic Network

- Disease or Syndrome

- Body Part, Organ,
- or Organ Component

## Metathesaurus relations

- REL vs. RELA
- Not always labeled

- 106 additional types of relationships
- ~7 M symbolic relations

## Metathesaurus relations

- Recorded
- at the term level: from source vocabularies
- at the concept level: from Metathesaurus editors
- Aggregated at the concept level

- Oat cell carcinoma of lung
- Carcinoma, Small Cell
- SCLC

- Lung structure
- Lung
- Pulmonary

## Not all relationships in hierarchies are isa (1)

- Autoimmune Diseases

- Addison’s disease

- Addison’s disease
- due to autoimmunity

- Tuberculous
- Addison’s disease

*is **generally** a*

**Notes:**
The economy principle may have even more unpredictable consequences, that we are going to illustrate here.

## Not all relationships in hierarchies are isa (2)

- Environment and Public Health [G03]
- 	Public Health [G03.850]
- 	Accidents [G03.850.110]
- 		Accident Prevention [G03.850.110.060]  +
- 		Accidental Falls [G03.850.110.085]
- 		Accidents, Aviation [G03.850.110.185]
- 		[...]
- 		Drowning [G03.850.110.500]  +

## Defining consistency

- SN rel. and Meta rel. must have the same direction
- SN rel. and Meta rel. must be of the same type (both hierarchical or associative)
- Meta rel. must be the same as SN rel. or one of its descendants

## Examples of consistent relations

- Body Part, Organ,or Organ Component

- Disease orSyndrome

*has_location*

*has_location*

## Examples of consistent relations

*affects*

*treats*

- What does inconsistency mean?

## The consistency “square” revisited

- ?

- ?

- ?

- ?

## What does inconsistency mean?

- Inaccurate/missing Semantic Network relation
- Inaccurate (/missing?) categorization
- Inaccurate Metathesaurus relation

- Testing consistency

## (A)  Consistency of associative relations

- [McCray& Bodenreider, 2002]

## Results

- 6894 pairs of related concepts
- 4496 (65%): a SN relation can be inferred unambiguously
- Validity confirmed  in 1981 cases
- 2515 not labeled in the Metathesaurus
- 1491 (22%): multiple possible SN relationships
- multiple possible Metathesaurus relationships
- 907 (13%): inconsistency SN/Meta relationships
- 372: no SN relationship between the STs
- 415: inconsistent SN/Meta relationship type (REL)
- 120: inconsistent SN/Meta relationship attribute (RELA)

## (B)  Consistency of hierarchical relations

- Relations used
- SN: isa
- Categorization: isa
- Metathesaurus: PAR/CHD + RB/RN
- Hypothesis
- For a pair of (ST, C), the concepts categorized by ST (and its descendants) correspond to the descendants of the concept C
- In the set of descendants of C, expected STs are the ST of C (and its descendants)

- ➊

- ➋

## ST-based classes vs. descendants

- Semantic type
- List of all conceptshaving this semantic type
- Concept
- List of all descendants
- Comparing the 2 sets
- Intersection of the 2 sets

- ➊

- [Bodenreider& Burgun, 2004]

## Analyzing inconsistencies

*Amphibian*

*Amphibia*

- 1126descendants

- 1135concepts

- 1124in common

- Miscategor-ization (?)

- Wronghierarchicalrelation

- Missinghierarchicalrelation

- Miscategor-ization

## Semantic types of descendants

- Concept
- Set of all descendants
- Distribution of semantic types in the set
- Allowable STs: ST of C and its descendants (strict) or ST from the same semantic group (loose)

- [Mougin& Bodenreider, 2005]

- ➋

## Analyzing inconsistencies

- 26,584 concepts studied
- 59% of their descendants have a semantic type incompatible with that of the original concept

## Analyzing inconsistencies

- # C0597249 Neoplasm of placenta (disorder) (neop)
- # * B: 190
- C0597249|ST|acab|    5.50|incp
- C0597249|ST|anab|    1.50|incp
- C0597249|ST|cgab|   76.50|incp
- C0597249|ST|dsyn|   27.50|incp
- C0597249|ST|inpo|    1.00|incp
- C0597249|ST|neop|   76.50|comp
- C0597249|ST|patf|    1.50|incp
- C0597249|SG|DISO|  190.00|comp
- # ------------------------------------------------------------

- Suggestions

## Aligning SN and Meta relationships

- 54 types of SN relationships
- 106 additional types of Metathesaurus relationships
- Some are simply synonymous(*caused_by* / *due_to*; *follows* / *temporally_follows*)
- Some are specialized relationships(*manifestation_of* / *definitional_manifestation_of*)
- Many types of mapping relationships, not in SN

## Add classification information to SN

- Explicit classificatory principles (in addition to textual definition and examples)
- Abandon economy principle and return to JEPD (jointly exhaustive/pairwise disjoint) approach

## Metathesaurus editing environment

- Use SN/Meta relation consistency as a constraint for assigning semantic types
- Use SN relations to suggest labels for unspecified Meta relations
- Use SN/Meta relation consistency to guide the review by the Metathesaurus editors
- Inaccurate categorization?
- Inaccurate Metathesaurus relation?

- Conclusions

## Conclusions

- Simultaneously
- Improve SN
- Improve categorization
- ST assignment can be automated in part

## Some references

- McCray AT, Bodenreider O.A conceptual framework for the biomedical domain.In: Green R, Bean CA, Myaeng SH, editors. The semantics of relationships: an interdisciplinary perspective. Boston: Kluwer Academic Publishers; 2002. p. 181-198.
- Bodenreider O, Burgun A.Aligning knowledge sources in the UMLS: Methods, quantitative results, and applications.Medinfo 2004:327-331.

## Some references

- Burgun A, Bodenreider O.Aspects of the taxonomic relation in the biomedical domain.In: Welty C, Smith B, editors. Collected papers from the Second International Conference "Formal Ontology in Information Systems": ACM Press; 2001. p. 222-233.
- Mougin F, Bodenreider O.Approaches to eliminating cycles in the UMLS Metathesaurus: Naive vs. formal.Proceedings of AMIA Annual Symposium 2005:(submitted).

## Slide 38

**Notes:**
My presentation is entitled: “Beyond synonymy: Exploiting the UMLS semantics in mapping vocabularies”.

First, I would like to acknowledge my co-authors from the National Library of Medicine: Stuart Nelson, Bill Hole and Florence Chang.

This research has been conducted at NLM in 1997 and early this year, as part of the Indexing Initiative.