ArticleJournal of the American Medical Informatics Association : JAMIA2025
CDEMapper: enhancing National Institutes of Health common data element use with large language models.
Article in Journal of the American Medical Informatics Association : JAMIA, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- Implementing a Resource-Light and Low-Code Large Language Model System for Information Extraction from Mammography Reports: A Pilot Study.Journal of imaging informatics in medicine · 2026Article
- A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases.bioRxiv : the preprint server for biology · 2026Article
- Exploring common data model coverage of nursing flowsheet data: a pilot study using SNOMED CT and LOINC mapping.JAMIA open · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
objectiveCommon Data Elements (CDEs) standardize data collection and sharing across studies, enhancing data interoperability and improving research reproducibility. However, implementing CDEs presents challenges due to the broad range and variety of data elements. This study aims to develop a CDE mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs.
methodsWe propose CDEMapper, a large language model (LLM)-powered mapping tool designed to assist in mapping local data elements to NIH CDEs. CDEMapper has 3 core modules: (1) CDE indexing and embeddings. NIH CDEs were indexed and embedded to support semantic search; (2) CDE recommendations. The tool combines Elasticsearch (BM25 methods) with GPT services to recommend candidate CDEs and their permissible values; and (3) Human review. Users review and select the best match for their data elements and value sets. We evaluate the tool's recommendation accuracy and usability against manual annotations and testing.
resultsCDEMapper offers a publicly available, LLM-powered, and intuitive user interface that consolidates essential and advanced mapping services into a streamlined pipeline. The evaluation results demonstrated that the augmented BM25 with GPT embeddings and a GPT ranker achieved the overall best performance. The usability test also highlighted the effectiveness and efficiency of our tool. DISCUSSIONS AND
conclusionsThis work opens up the potential of using LLMs to assist with CDE mapping when aligning local data elements with NIH CDEs. Additionally, this effort helps researchers better understand the gaps between their data elements and NIH CDEs while promoting CDE reusability.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.