# Presentation: 732827

## The Refined Semantic Network

- James Geller
- Yehoshua Perl
- New Jersey Institute of Technology

## Sources

- This presentation is based:
- on a pending proposal on Auditing and Extending the UMLS;
- [Gu et al., JAMIA 2000] and [MEDINFO YEARBOOK 2001]

## Fundamental Observation

- The UMLS requires that there is an assignment of one *or several *Semantic Types to each concept.
- This assignment provides semantics for concepts.
- We call the set of all concepts to which a Semantic Type S has been assigned the *Extent of S. *

## Problems (1)

- Assigning Semantic Types to *new* concepts is a complex manual task due to complexity, ambiguity and homonymy of medical concepts.
- Categorization is highly dependent on an editor’s specialty, background and priorities and thus not fully predictable.

## Problems (2)

- The extents of most Semantic Types are not uniform. If we look at the extent of a Semantic Type it may contain concepts with “second” assignments that are different from each other.
- A desire was expressed to make the SN deeper [McCray and Nelson 1995].

## Example (concrete)

- We are looking at all the 61 concepts to which the Semantic Type **Environmental Effect of Humans** (henceforth **EEH**) has been assigned (I.e., the extent of **EEH**).

## Are these concepts similar?

- Are *Classroom environment, Sanitation problem, Acid rain, *and *Industrial waste* really similar to each other?
- ONLY **EEH** is assigned to 54 of these 61 concepts.
- To 7 other concepts combinations of 3 additional Semantic Types are assigned. That’s why we say that the extent of **EEH** is not uniform.

## EEH & Finding: 2 concepts: Poor Sanitation, Sanitation Problem
EEH & Hazardous or Poisonous Substance: 4 concepts: Acid rain, Radioactive fallout, Radioactive waste, Smoke
EEH & Manufactured Object & Hazardous or Poisonous Substance: 1 concept: Industrial waste

**EEH** & **Hazardous or Poisonous Substance**: 4 concepts: *Acid rain, Radioactive fallout, Radioactive waste, Smoke*
**EEH** & **Manufactured Object** & **Hazardous or Poisonous Substance**: 1 concept: *Industrial waste*

- Concepts of non-uniform semantics

## Abstract Example with 4 Semantic Types. Boxes show extents.

- a, b, d, e, f, g

- b, g

- c, d, e, g

- W

- X

- Y

- Z

## Problem even in simple case

- One has to look into all boxes to see if a concept occurs in them or not.
- Definition: *Intersection of two extents*: The intersection of two extents contains all and only the concepts that occur in BOTH extents. We will use the symbol & for it.
- Example: Intersection of                            [a, b, c] & [b, c, d] --> [b, c]

## Example of Venn Diagram for X, Y, Z, W

- g

- b

- d e

- h

- c

- X

- Y

- W

- Z

## Our Solution to all 3 Problems

- Identify all existing intersections.
- Display every concept exactly once, in its pure “original box” or in a new “box” that corresponds to a unique intersection.

## h

- a, f

- c

- W

- X

- Y

- Z

- W & X & Y & Z

- g

- X & Y

- b

- X & Z

- d, e

- PURE Semantic Types (simple semantics)

- Intersection Types
- (Compound Semantics)

- g, h

- a, b, d, e, f, g

- b, g

- c, d, e, g

- W

- X

- Y

- Z

- Original Semantic Types (non uniform Semantics)

## Intersection Types

*Intersection Types* are “new” Semantic Types that are constructed by intersection of the extents of their component Semantic Types.
- The “names” of Intersection Types are constructed by chaining the names of their component Semantic Types together with &-signs.

## Semantic Refinement

- We call the process of constructing all necessary Pure Semantic Types and Intersection Types *Semantic Refinement. *
- Concepts are reassigned, so that every concept occurs only in one extent.
- After Semantic Refinement, every Semantic Type has a uniform extent.

## Pure Semantic Types have extents of simple concepts. (They are uniform.)
Intersection Types have extents of compound concepts. (They are also uniform!)

- Intersection Types have extents of *compound concepts*. (They are also uniform!)

## Advantages

- Extents of pure and intersection types now have a uniform semantics. That means, every extent contains concepts that are highly similar.
- Small sets of concepts are easy to review and also more suspicious.
- It is easier to see a concept that “does not belong” to a small set or even that a concept is “missing.”

## What does this have to do with the Semantic Network?

- Every intersection type S of types X, Y, Z,... should be added to the Semantic Network as follows.
- S is made a child of several appropriate Semantic Types. We allow multiple parents.
- This is the Refined Semantic Network: RSN

## The Refined Semantic Network of the Semantic Types W, X, Y, Z

- X

- Y

- Z

- X & Y

- X & Z

- W & X & Y & Z

## Subnetwork of SN with EEH Intersections and all their ancestors

- Event

- Entity

- Phenomenon or Process

- Conceptual Entity

- Physical Object

- Finding

- Manufactured Object

- Substance

- Human-Caused
- Phenomenon or Process

- EEH

- Chemical

- Chemical Viewed Functionally

- Hazardous or Poisonous Substance

- EEH & Haz. or Poi.. Sub.

- EEH & Finding

- Manu. Obj. & Haz. or Poi.. Sub.

- EEH & Manu. Obj. & Haz. or Poi.. Sub.

**Subnetwork of SN with EEH Intersections and all their ancestors**

- The RSN supports auditing.
- Auditing has helped us find mistakes in the UMLS.
- Removal of mistakes typically leads to simplifications of the UMLS and of the RSN itself, by removing wrong intersections.

## EEH Auditing Example

- The intersection of the extents of three Semantic Types **EEH** and **Manufactured Object** and **Hazardous or Poisonous Substance** contained only one concept: *Industrial Waste*
*Industrial smog* and *Factory smoke* are not* *considered **Manufactured Objects**, and our audit suggested that *Industrial Waste* should not be one either.

## More strange intersections

- We found concepts belonging to both **Human-caused phenomenon or process** and **Manufactured object**.
- It is out of the question that something is at the same time a process and an object.
- By creating the RSN we found this.
- It was caused by homonyms. E.g. *Video recording* as the process and as its result.

## Wrong Categorizations

- By reviewing the pure semantic types and intersection types we found various errors.
*Drinking water problem *and *PBC Airborne level *are missing a **Finding **assignment.
*Smoke *is assigned **Hazardous or Poisonous Substance, **but its subconcepts *Factory smoke *and *Second hand smoke *are missing such an assignment.

*Classroom Environment *and *College Environment *should not be assigned **EEH **at all.
- These and other errors were exposed by review of the extents, which should be semantically uniform.
- After correcting these errors, the concepts of **EEH** look very different.

## Venn Diagrams before/after audit

- 2

- 3

- 1

- 4

- 54

- EEH

- Finding

- Hazardous or Poisonous Substance

- Manufac-tured Object

- 40

- 10

- 5

- 3

- 4

- EEH

- Manufactured Object

- Hazardous or Poisonous Substance

- Finding

- Substance

## Revised Subnetwork of SN with EEH Intersections and all their ancestors

- Event

- Entity

- Phenomenon or Process

- Conceptual Entity

- Physical Object

- Finding

- Manufactured Object

- Substance

- Human-Caused
- Phenomenon or Process

- EEH

- Chemical

- Chemical Viewed Functionally

- Hazardous or Poisonous Substance

- EEH & Substance

- EEH & Finding

- Manu. Obj. & Haz. or Poi.. Sub.

- EEH  & Haz. or Poi.. Sub.

**Revised Subnetwork of SN with EEH Intersections and all their ancestors**

## Exclusive Semantic Types

- We found 143 concepts that are classified as both *Organic Chemical *and *Inorganic Chemical!!*
- Of those, 82 are assigned to *additional semantic types.*

## Redundant Categorizations

- Many concepts are assigned to a Semantic Type S and the parent or ancestor T of S. This is a redundant categorization, a no-no. [McCray and Nelson, 1995][Peng et al., AMIA 2002]
- Sample in* *1998:* Desertification *was assigned **EEH **and also **PHENOMENON OR PROCESS, **a redundant categorization. It was removed after our report.* *

## Auditing simplifies the RSN

- After correcting the assignments of those 143 (“organic”) concepts, 13 invalid Intersection Types disappeared.
- The RSN becomes simpler, as it has fewer Intersection Types.
- In a sample of 100 intersections with only one concept, only 15 were deemed legal. [Gu, JAMIA 2000]

## Renaming Intersection Types

- Instead of **Environmental Effect of Humans*** ****&**** ***Hazardous and Poisonous Substance*** *we rather have a designer rename it into: **Environmentally Hazardous or Poisonous Substance***.*
- An intersection of **Body Part*** ***&** **Manufactured Object** is a **Prosthesis***.*

## Subnetwork with simplified names

- Event

- Entity

- Phenomenon or Process

- Conceptual Entity

- Physical Object

- Finding

- Manufactured Object

- Substance

- Human-Caused
- Phenomenon or Process

- EEH

- Chemical

- Chemical Viewed Functionally

- Hazardous or Poisonous Substance

- Human- produced Environmental  Substance

- Environmental Finding

- Manufactured Hazardous or Poisonous Substance

- Environmentally Hazardous or Poisonous Substance

**Subnetwork with simplified names**

## Overall Results for UMLS 1998

- Level	Number of Pure Semantic Types at Level	Number of Intersection Types
- 1			1				0
- 2			2				0
- 3			4				0
- 4			20				0
- 5			41				56
- 6			23				203
- 7			23				163
- 8			17				187
- 9			2				234
- 10			0				212
- 11			0				89
- 12			0				16
- 13			0				3
- 14			0				1

## Concept Distribution UMLS 98

- Number of concepts/intersection type   How many intersection types with so many concepts
- 1						421           }  Many of these will
- 2						147           }  disappear
- 3						102           }  [GU, AIM 2004]
- 4						65
- 5						35
- 6						41
- 7						32
- 8						15
- 9						13
- ....
- 3947					1
- 4582					1
- 6705					1
- 19349					1
- 41564					1

## Streamlining Categorizations

- Currently several UMLS EDITORs may assign to new concepts any combination of semantic types.  Even combinations that don’t make sense.
- We propose that concepts may be assigned only existing pure and intersection types.
- If a new intersection type is desired it has to be “approved” by the NLM.

## Summary (1)

- We propose to change the SN as follows:
- Allow a DAG structure, to enable intersections (with multiple parents)
- Create the “lower half” of the RSN by our method of Semantic Refinement.  That takes care of deepening!
- Use various auditing techniques to eliminate all wrong intersections.

## Summary (2)

- Rename legitimate intersection types.
- The RSN limits the choices of a UMLS editor to reasonable intersections.
- This will prevent future UMLS mistakes.
- The RSN streamlines categorization, making it more accurate and easier.