UVA Resources for the Biomedical Vocabulary Alignment at Scale in the UMLS Metathesaurus
This work addresses a domain-specific problem for biomedical informatics researchers by offering tools to improve vocabulary alignment, but it is incremental as it builds on existing methods.
The paper tackles the time-consuming and error-prone process of constructing the UMLS Metathesaurus by defining a new task called UVA and providing reusable resources, including a dataset generator, three generated datasets, and three baseline approaches, with all code and data publicly available.
The construction and maintenance process of the UMLS (Unified Medical Language System) Metathesaurus is time-consuming, costly, and error-prone as it relies on (1) the lexical and semantic processing for suggesting synonymous terms, and (2) the expertise of UMLS editors for curating the suggestions. For improving the UMLS Metathesaurus construction process, our research group has defined a new task called UVA (UMLS Vocabulary Alignment) and generated a dataset for evaluating the task. Our group has also developed different baselines for this task using logical rules (RBA), and neural networks (LexLM and ConLM). In this paper, we present a set of reusable and reproducible resources including (1) a dataset generator, (2) three datasets generated by using the generator, and (3) three baseline approaches. We describe the UVA dataset generator and its implementation generalized for any given UMLS release. We demonstrate the use of the dataset generator by generating datasets corresponding to three UMLS releases, 2020AA, 2021AA, and 2021AB. We provide three UVA baselines using the three existing approaches (LexLM, ConLM, and RBA). The code, the datasets, and the experiments are publicly available, reusable, and reproducible with any UMLS release (a no-cost license agreement is required for downloading the UMLS).