Resolution of redundant semantic type assignments for organic chemicals in the UMLS

Abstract

Objective The Unified Medical Language System (UMLS) integrates terms from different sources into concepts and supplements these with the assignment of one or more high-level semantic types (STs) from its Semantic Network (SN). For a composite organic chemical concept, multiple assignments of organic chemical STs often serve to enumerate the types of the composite’s underlying chemical constituents. This practice sometimes leads to the introduction of a forbidden redundant ST assignment, where both an ST and one of its descendants are assigned to the same concept. A methodology for resolving redundant ST assignments for organic chemicals, better capturing the essence of such composite chemicals than the typical omission of the more general ST, is presented. Methods and Material The typical SN resolution of a redundant ST assignment is to retain only the more specific ST assignment and omit the more general one. However, with organic chemicals, that is not always the correct strategy. A methodology for properly dealing with the redundancy based on the relative sizes of the chemical components is presented. It is more accurate to use the ST of the larger chemical component for capturing the category of the concept, even if that means using the more general ST. Results A sample of 254 chemical concepts having redundant ST assignments in older UMLS releases was audited to analyze the accuracy of current ST assignments. For 81 (32%) of them, our chemical analysis-based approach yielded a different recommendation from the UMLS (2009AA). New UMLS usage notes capturing rules of this methodology are proffered. Conclusions Redundant ST assignments have typically arisen for organic composite chemical concepts. A methodology for dealing with this kind of erroneous configuration, capturing the proper category for a composite chemical, is presented and demonstrated.

Auditing the assignments of top-level semantic types in the UMLS semantic network to UMLS concepts

“…It is a challenge to automate such a process, except for cases when well-defined rules are violated. As examples of such errors and their QA see studies of “an algorithm for detecting redundant ST assignment for UMLS concepts” [36] and “redundant ST assignments for organic chemicals” [32]. The error of Semantic Inversion [34] in this paper, also falls into this category.…”

“…These cases are common in the UMLS, especially for chemicals. Our previous research on combinations of STs is embodied in the Refined Semantic Network [23–32]. Further, for a study of disjunctive and conjunctive concepts in terminologies see work by Mendonca et al [33].…”

A review of auditing techniques for the Unified Medical Language System

“…Chen et al 47 modified RSN to model chemical concepts with multiple “Chemical Viewed Structurally” STs, identifying concepts with an invalid combination of STs and with incorrect ST assignments. Morrey et al 75 resolved redundant ST assignments for chemical composites with multiple STs based on the relative sizes of components in the molecular structure of a composite. A Chemical Specialty Semantic Network 76 was developed to provide a better categorization of chemical concepts in the UMLS.…”

“…In Gu et al, 45 , 71 2 refinements were presented. In Chen et al 47 and Morrey et al, 75 , 76 special modeling was required for chemical concepts and ISTs in which intersections are frequent. Then, in He et al, 21 a longitudinal study showed that, while NLM corrected reported errors, eliminating nonsensical or forbidden ISTs (by SN use notes), those ISTs pop up again after a year or 2.…”

Ontology alignment in the biomedical domain using entity definitions and context

“…Significant time and effort has gone into cross-referencing semantically equivalent entities across the ontologies, and new terms and alignments continue to be added as the field develops. These manual alignments are high quality, but considered to be incomplete (Morrey et al, 2011;Mougin and Grabar, 2014).…”