ArticleInternational journal of molecular sciences2022
The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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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.
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Who cites it
8 citing papers in PubMed.
- Faster, better?: Testing artificial intelligence accuracy for neurosurgical literature analysis.Medicine · 2025Article
- An Accurate and Efficient Approach to Knowledge Extraction from Scientific Publications Using Structured Ontology Models, Graph Neural Networks, and Large Language Models.International journal of molecular sciences · 2024Article
- Integrating omics databases for enhanced crop breeding.Journal of integrative bioinformatics · 2023Review
- Biophysics education section and computational training discussion at VII Congress of Russian Biophysicists.Biophysical reviews · 2023Article
- BGRS: bioinformatics of genome regulation and data integration.Journal of integrative bioinformatics · 2023Article
- Medical Genetics, Genomics and Bioinformatics-2022.International journal of molecular sciences · 2023Article
- Research Topics of the Bioinformatics of Gene Regulation.International journal of molecular sciences · 2023Article
- BioGraph: Data Model for Linking and Querying Diverse Biological Metadata.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%.
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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.