OQAFMA Querying Agent for the Foundational Model of Anatomy: a Prototype for Providing Flexible and Efficient Access to Large Semantic Networks

Abstract

The development of large semantic networks, such as the UMLS, which are intended to support a variety of applications, requires a exible and e cient query interface for the extraction of information. Using one of the source vocabularies of UMLS as a test bed, we have developed such a prototype query interface. We rst identify common classes of queries needed by applications that access these semantic networks. Next, we survey STRUQL, an existing query language that we adopted, which supports all of these classes of queries. We then describe the OQAFMA Querying Agent for the Foundational Model of Anatomy (OQAFMA), which provides an e cient implementation of a subset of STRUQL by pre-computing a variety of indices. We describe how OQAFMA leverages database optimization by converting STRUQL queries to SQL. We evaluate the exibility and e ciency of our implementation using English queries written by anatomists. This evaluation veri es that OQAFMA provides exible, e cient access to one such large semantic network, the Foundational Model of Anatomy, and suggests that OQAFMA could be an e cient query interface to other large biomedical knowledge bases, such as the Uni ed Medical Language System