Dataset Information

AnnoDash, a clinical terminology annotation dashboard.

ABSTRACT:

Background

Standard ontologies are critical for interoperability and multisite analyses of health data. Nevertheless, mapping concepts to ontologies is often done with generic tools and is labor-intensive. Contextualizing candidate concepts within source data is also done in an ad hoc manner.

Methods and results

We present AnnoDash, a flexible dashboard to support annotation of concepts with terms from a given ontology. Text-based similarity is used to identify likely matches, and large language models are used to improve ontology ranking. A convenient interface is provided to visualize observations associated with a concept, supporting the disambiguation of vague concept descriptions. Time-series plots contrast the concept with known clinical measurements. We evaluated the dashboard qualitatively against several ontologies (SNOMED CT, LOINC, etc.) by using MIMIC-IV measurements. The dashboard is web-based and step-by-step instructions for deployment are provided, simplifying usage for nontechnical audiences. The modular code structure enables users to extend upon components, including improving similarity scoring, constructing new plots, or configuring new ontologies.

Conclusion

AnnoDash, an improved clinical terminology annotation tool, can facilitate data harmonizing by promoting mapping of clinical data. AnnoDash is freely available at https://github.com/justin13601/AnnoDash (https://doi.org/10.5281/zenodo.8043943).

SUBMITTER: Xu J

PROVIDER: S-EPMC10329488 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Publications

AnnoDash, a clinical terminology annotation dashboard.

Xu Justin J Mazwi Mjaye M Johnson Alistair E W AEW

JAMIA open 20230708 3

<h4>Background</h4>Standard ontologies are critical for interoperability and multisite analyses of health data. Nevertheless, mapping concepts to ontologies is often done with generic tools and is labor-intensive. Contextualizing candidate concepts within source data is also done in an ad hoc manner.<h4>Methods and results</h4>We present AnnoDash, a flexible dashboard to support annotation of concepts with terms from a given ontology. Text-based similarity is used to identify likely matches, and ...[more]

PMID: 37425489

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Dataset Information

AnnoDash, a clinical terminology annotation dashboard.

Background

Methods and results

Conclusion

Publications

AnnoDash, a clinical terminology annotation dashboard.

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