ArticlePLoS computational biology2015
miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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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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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Text-mining clinically relevant cancer biomarkers for curation into the CIViC database.Genome medicine · 2019Pooled it
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- Integrating text mining and knowledge graph to enhance biopharmaceutical process optimization.PloS one · 2026Article
- A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease.NPJ Parkinson's disease · 2024Article
- Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks.Database : the journal of biological databases and curation · 2024Article
- Large Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression.Biomedicines · 2024Article
- DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles.Database : the journal of biological databases and curation · 2024Article
- Literature Mining of Disease Associated Noncoding RNA in the Omics Era.Molecules (Basel, Switzerland) · 2022Review
- Identification of human gene research articles with wrongly identified nucleotide sequences.Life science alliance · 2022Article
- miRetrieve-an R package and web application for miRNA text mining.NAR genomics and bioinformatics · 2021Article
- Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types.Journal of translational medicine · 2021Article
- emiRIT: a text-mining-based resource for microRNA information.Database : the journal of biological databases and curation · 2021Article
- Two miRNA prognostic signatures of head and neck squamous cell carcinoma: A bioinformatic analysis based on the TCGA dataset.Cancer medicine · 2020Article
- Constructing knowledge graphs and their biomedical applications.Computational and structural biotechnology journal · 2020Review
- Named Entity Recognition and Relation Detection for Biomedical Information Extraction.Frontiers in cell and developmental biology · 2020Review
- Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.Database : the journal of biological databases and curation · 2019Article
- A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning.Database : the journal of biological databases and curation · 2019Article
- Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.Computers in biology and medicine · 2018Article
- Transfer learning for biomedical named entity recognition with neural networks.Bioinformatics (Oxford, England) · 2018Article
- Murine Oviductosomes (OVS) microRNA profiling during the estrous cycle: Delivery of OVS-borne microRNAs to sperm where miR-34c-5p localizes at the centrosome.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations. We conducted full-scale text mining using miRTex to process all the Medline abstracts and all the full-length articles in the PubMed Central Open Access Subset. The results for all the Medline abstracts are stored in a database for interactive query and file download via the website at http://proteininformationresource.org/mirtex. Using miRTex, we identified genes potentially regulated by miRNAs in Triple Negative Breast Cancer, as well as miRNA-gene relations that, in conjunction with kinase-substrate relations, regulate the response to abiotic stress in Arabidopsis thaliana. These two use cases demonstrate the usefulness of miRTex text mining in the analysis of miRNA-regulated biological processes.
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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.