=Paper=
{{Paper
|id=Vol-1747/IT704_ICBO2016
|storemode=property
|title=Representation of Parts within the Foundational Model of Anatomy Ontology
|pdfUrl=https://ceur-ws.org/Vol-1747/IT704_ICBO2016.pdf
|volume=Vol-1747
|authors=Melissa Clarkson
|dblpUrl=https://dblp.org/rec/conf/icbo/Clarkson16
}}
==Representation of Parts within the Foundational Model of Anatomy Ontology ==
https://ceur-ws.org/Vol-1747/IT704_ICBO2016.pdf
Representation of parts within the Foundational
Model of Anatomy ontology
A critique and proposal for enhanced structure and consistency of regional parts
Melissa Clarkson
Structural Informatics Group
University of Washington
Seattle, USA
mclarkso@uw.edu
Abstract— As biomedical ontologies grow in size and This paper examines part and class relationships within the
complexity it is crucial to develop methods for detecting Foundational Model of Anatomy (FMA) ontology—both
inconsistencies within ontologies. The Foundational Model of those explicitly declared and those implied by the lexical
Anatomy (FMA) ontology represents knowledge of human constructs of class names. The purpose of this work is to
anatomy, with structural organization provided by class and identify types of inconsistencies and to propose methods of
part relationships. Using a manual audit, I identify types of structural organization and lexical consistency that will make
inconsistencies arising from class and regional part the FMA more compatible with computational auditing and
relationships for regions of the body and the parts of organs. increase its usability.
Inconsistencies arise from both explicitly declared relationships
and relationships that are implied by the lexical constructs of II. BACKGROUND
class names. The purpose of this work is to propose methods of
structural organization and lexical consistency that will make The FMA represents knowledge of human anatomy using
the FMA more compatible with computational auditing and a series of organizing units at different levels of granularity.
increase its usability. These units include “Cardinal body part”, “Organ system”,
and “Organ” (Fig. 1) [1]. The FMA is one of the largest
Keywords—ontology; partonomy; anatomy biomedical ontologies, with over 104,000 classes and 140
types of relations. In addition to the subClass_of relation
I. INTRODUCTION defining the class hierachy, the main organizational structure
As biomedical ontologies grow in size, specificity and is provided by the regional_part relation (for spatial divisions
complexity, maintaining internal consistency of the of the body) and the constitutional_part relation (describing
representation becomes increasingly difficult. Because divisions for which the parts are simpler in composition than
ontologies can contain tens of thousands of classes, the whole) [2].
computational methods for detecting inconsistencies are
necessary for quality assurance efforts. One step toward III. METHODS
designing computational auditing methods is to identify This work is based on version 4.3 of the FMA, released in
patterns within the content that are useful for identifying February 2016. The OWL file was manually inspected in
inconsistencies in modeling or possible errors. Protégé (version 4.3.0).
Fig. 1. Overview of part relationships using high-level classes within the FMA. Classes representing organizing units are in the blue bar. Typical regional_part
and constitutional_part relationships among the subclasses are indicated with solid black arrows. SubClass_of relationships are indicated with gray dashed arrows.
IV. SUBDIVISIONS OF CARDINAL BODY PARTS For example, classes such as “Right side of head” and “Left
Each of the cardinal body parts (“Head”, “Body proper”, side of head” do not currently have any relationships to other
left and right “Upper limb”, and left and right “Lower limb”) classes. But because they are subclasses of “Subdivision of
are divided into a hierarchy of smaller regions using the head”, users can locate these terms to use in annotation.
regional_part relation. These divisions of the body are crucial B. Lexical consistency within class names
in helping users understand and navigate the FMA and to As shown in Fig. 3, some class names consist of a modifier
provide classes that can be lexically modified to create other
(such as “Surface of…”) and a body region or high-level class
classes.
for types of body regions. Consistency in referring to body
A. Alignment to the class hierarchy regions would aid auditing and ontology users. In cases where
As demonstrated in Fig. 2, there is an opportunity to tightly another anatomical term is traditionally used, the term
align the regional part hierarchy for cardinal body parts to the reflecting a consistent construct could be added as a synonym.
class hierarchy. Much of the structure for coordinating the two C. Consistency within the class hierarchy
hierarchies is already in place, but some regions of the body
Another source of inconsistency arises from the lexical
are classified as types of anatomical clusters instead of
implications of class names and their positions within the class
subdivisions of the body. This obscures the relationship of
hierarchy. As shown in Fig. 4, “Integument of chin” is a
those classes to other regions of the body.
subclass of “Integument of subdivision of mouth.” From this
There are two benefits to formalizing this organizational a user would infer that “Chin” is a “Subdivision of mouth”,
structure. First, it provides a place to classify all divisions of a which is confirmed by the subclass relationship for “Chin”
particular region—even if a class represents an alternative found in the FMA. However, as detailed in Fig. 4,
partition which is not reflected in the regional_part hierarchy. contradictions can easily arise. For example, “Set of jaws” is
This is important for classes such as “Trunk”, which have a subclass of “Set of subdivisons of head”, but “Jaw” is a
more then one partition scheme. Second, users could more subclass of “Organ cluster.” Correcting these inconsistencies
easily answer the question of what partitions are provided by depends upon first establishing a comprehensive
the FMA for a particular region of the body by navigating the regional_part hierarchy for subdivisions of cardinal body
class hierarchy beneath “Subdivision of cardinal body part”. parts.
Fig. 2. Matches and mismatches in classification of parts in the regional part hierarchy and the class hierarchy. Top left: The motif for modeling regional parts
is reflected in much of the class hierarchy beginning at “Subdivision of cardinal body part” (often using the phrase “Subdivision of…”). Top right: Example of
class hierarchy, showing subclasses of “Subdivision of head”. Two of the classes, “Face” and “Head proper”, have corresponding classes beginning with the
phrase “Subdivision of…”. Bottom: Examples of matches (green) and mismatches (gray) between classification in the regional part and class hierarchies.
Fig. 3. Phrases in class names relevant to body regions. Left: Examples of modifiers paired with terms for regions of the body. Right: Variation in wording of
terms which refer to high-level classes “Cardinal body part” and “Subdivision of cardinal body part”.
Fig. 4. Implications of class names referring to subdivisions of cardinal body parts. Top: Example of consistency in classification between “Integument of chin”
and “Chin”, with “Chin” a “Subdivision of mouth” in both statements. Bottom: Examples of inconsistencies between the implied and actual placement of a class
within the class hierarchy.
Fig. 5. Implications of class names referring to parts of organs. Top: Example of consistency in classification between “Segment of eyeball” and “Eyeball”, with
“Eyeball” an “Organ” in both statements. Bottom: Examples of inconsistencies between the implied and actual placement of a class within the class hierarchy.
V. ORGAN PARTS “subdivision”, “region”, “segment”, and “subsegment” it is
unclear whether these are synonyms or they carry specific
The FMA has a complex representation of organ parts. meaning when used in class names.
Parts are classified as either an “Organ component” (bounded
predominately by bona fide boundaries) or an “Organ region” The term “portion” should be reserved for subclasses of
(defined by fiat boundaries). Each organ region is further “Portion of tissue” and “Portion of body substance”, but has
classified as an “Organ segment” (with anchored fiat been applied to several regions of organs (such as
boundaries) or an “Organ zone” (with floating fiat “Intrapulmonary portion of pulmonary artery”).
boundaries).
VIII. CONCLUSION
As shown in Fig. 5, inconsistencies arise when the lexical
implications of class names do not match the class hierarchy. I have documented a variety of ways that inconsistencies
in the representation of regional parts occur within the FMA.
For example, “Region of crown of tooth” is a subclass of
“Region of organ component”. However, “Crown of tooth” is The first step to addressing these inconsistencies is to establish
a robust regional part representation of the cardinal body parts.
classified as an “Organ segment”.
It is unclear if the complexity of representation for organ Previous work to audit the FMA has used symmetric terms
(for example, “left” and “right”, “superior” and “inferior”) [3].
parts adds value to the FMA. But if retained, then auditing
methods should be developed to ensure consistency. This work identifies additional lexical modifiers that can be
used to detect inconsistencies in the class hierarchy, regional
VI. BRANCHES AND TRIBUTARIES part hierarchy, and class names.
Several types of organs have a tree structure, including ACKNOWLEDGMENT
arterial tree organs and venous tree organs. The regional parts I thank José L. V. Mejino Jr. for helpful discussions. This
of these trees can be described as a trunk plus either branches work was supported in part by funding from the International
or tributaries. The FMA has two specific types of Health Terminology Standards Development Organization
regional_part relations (branch and tributary) to relate branch (IHTSDO) to the Structural Informatics Group.
and tributary parts to the tree. However these relations are
applied inconsistently—duplicating the regional_part REFERENCES
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