ArticleBioinformatics advances2026
HERMES: an open-source mining tool for open-access literature.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The exponential growth of open-access scientific literature presents researchers with unprecedented opportunities but also poses a significant challenge: how to efficiently identify and prioritize relevant publications in a transparent and customizable manner. Existing search engines index large volumes of biomedical literature but rarely provide user-defined ranking options, reproducibility, or integration of domain-specific criteria. This gap is particularly limiting for specialized fields, where nuanced keyword combinations, literature recency, and contextual interpretation are critical. Results: We present HERMES, an open-source literature mining tool for targeted retrieval and ranking of full-text open-access publications from PubMed Central (PMC). HERMES employs a composite scoring algorithm that integrates keyword frequency, citation counts, and publication age to prioritize publications. It further supports summarization, biomedical entity recognition, and PDF report generation. An intuitive graphical user interface (GUI) allows researchers without programming expertise to perform complex literature mining tasks, while multithreaded processing ensures efficiency for large-scale queries. HERMES provides a reproducible and adaptable framework for literature discovery, empowering researchers to rapidly identify relevant literature and promoting transparency and community-driven extension. Availability and implementation: HERMES (version 1.2) is implemented in Python (3.11). The source code is freely available on GitHub at https://github.com/julien-charest/hermes and is distributed under the GPL-3 license.
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.