ArticleScientific reports2025
A computational framework for extracting biological insights from SRA cancer data.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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
1 citing paper in PubMed.
- Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research.Bioinformatics (Oxford, England) · 2026Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The integration of sequenced samples and clinical data from independent yet related studies from public domain databases, such as The Sequence Read Archive (SRA), has the potential to increase sample sizes and enhance the statistical power needed for more precise bioinformatic analysis. Data mining and sample grouping are the starting points in this process and still present several challenges, including the presence of structured and unstructured data, missing deposited data, and varying experimental conditions and techniques applied across the studies. Designed to address the main challenges of data mining and sample grouping for biomarkers research, the proposed methodology employs a computational approach integrating relational database construction, text and data mining, natural language processing, network analysis, search by Pubmed publications, and combining MeSH, TTD and WordNet database to identify groups of samples with the same characteristics. As a result, it identifies and illustrates relationships among sample collections, aiming to discover potential cancer biomarkers. In colorectal cancer (CRC) and acute lymphoblastic leukemia (ALL) case studies, this methodology effectively navigates SRA metadata, retrieving, extracting, and integrating data. It highlights significant connections between samples and patient clinical data, revealing important biological insights. The study grouped 2,737 (CRC) and 3,655 (ALL) samples into potential comparison groups, demonstrating the method's power in identifying relationships and aiding biomarker discovery.
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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.