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Structural Analysis of Biomedical Ontologies Center

Introduction

The Structural Analysis of Biomedical Ontologies Center (SABOC) is devoted to research exploring structural issues in medical terminologies and ontologies such as the Unified Medical Language System (UMLS), SNOMED CT, and the biomedical ontologies located in the NCBO BioPortal. Most of the research attention in these communities has concentrated on issues such as content creation and retrieval. However, our interests focus on "structural issues." For example, many medical terminologies are organized around a backbone of concepts connected by IS-A or parent/child links. Structurally speaking, such a hierarchy forms a directed acyclic graph (DAG). In a DAG, no cycles should exist. This is a structural constraint. In other words, starting out at one concept and following parent/child links upwards, it should be impossible to ever return to the starting concept. However, it has shown that the UMLS contains such prohibited cycles. Such cycles may be discovered by purely structural methods, without an understanding of the contents of the UMLS.

Another example relates to redundant assignments of semantic types of the UMLS Semantic Network to concepts of the UMLS Metathesaurus. According to the principles of the UMLS, if two semantic types are assigned to the same concept, they may never stand in a parent/child or ancestor/descendant relationship to each other. Yet, in our research we have discovered many cases where such assignments existed. We have reported these cases to the National Library of Medicine which has corrected many of them. In this case, again, the problems may be found algorithmically, without any human decision-making, as they are based on structure not meaning.

In other cases, our structural methods can propose to a human auditor likely problem areas, however, the final decision whether, indeed, a problem exists, must be made by a human domain expert. This Web site contains references to publications using such structural methods in a variety of areas, including besides auditing the topics of partitioning, abstraction, integration, etc.