# FAIR-SMART expands access to supplementary materials for research transparency

**Authors:** Chih-Hsuan Wei, Robert Leaman, Po-Ting Lai, Don Comeau, Shubo Tian, Zhiyong Lu

PMC · DOI: 10.1371/journal.pbio.3003428 · PLOS Biology · 2025-10-09

## TL;DR

FAIR-SMART is a new system that improves access to supplementary materials in scientific research, making them more transparent and reusable.

## Contribution

FAIR-SMART introduces a novel system for standardizing and providing computational access to supplementary materials in biomedical research.

## Key findings

- FAIR-SMART aggregates and standardizes supplementary materials into a structured, machine-readable format.
- The system uses large language models to categorize tabular data, enabling efficient retrieval of over 90% of textual content.
- FAIR-SMART enhances FAIR principles by improving findability, interoperability, and reuse of supplementary data.

## Abstract

Supplementary materials accompanying scientific articles are critical components of biomedical research, offering detailed datasets, experimental protocols, and extended analyses that complement the main text. These materials play an important role in enhancing transparency, reproducibility, and scientific impact by providing in depth analyses and the details necessary for reproducing experiments. However, the lack of consistent and standard formats has limited the access to supplementary materials in scientific investigations. In response, we propose a novel system aimed to enhance FAIR access to Supplementary MAterials for Research Transparency (FAIR-SMART). Specifically, we first aggregate supplementary files in a single location, standardize them into structured and machine-readable format, and make them accessible via web APIs. Next, we employ advanced large language models to automatically categorize the tabular data, which represents over 90% of the textual content in supplementary materials, enabling precise and efficient data retrieval. By bridging the gap between diverse file types and automated workflows, this work not only advances biomedical research but also highlights the transformative potential of accessible supplementary materials in shaping the behaviors and decision-making processes of the scientific community. FAIR-SMART is freely available for supplementary materials data retrieval via its APIs: https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/FAIR-SMART/.

Supplementary materials that accompany scientific articles enhance transparency, reproducibility and scientific impact. This study presents FAIR-SMART, a tool that enables computational access to these materials, improving findability, interoperability, and reuse, thereby improving FAIR access to supplementary data at scale.

## Full-text entities

- **Diseases:** ovarian cancer (MESH:D010051), PMC (MESH:D020210), cancer (MESH:D009369), SM (MESH:D017034)
- **Chemicals:** CSV (-)
- **Species:** Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12637962/full.md

## References

33 references — full list in the complete paper: https://tomesphere.com/paper/PMC12637962/full.md

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Source: https://tomesphere.com/paper/PMC12637962