ArticleBioinformatics (Oxford, England)2022
tmVar 3.0: an improved variant concept recognition and normalization tool.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- PubMind: literature-based genetic variant extraction and functional annotation using large language models.Nature communications · 2026Article
- A graph-based approach to variant description extraction from sequences.NAR genomics and bioinformatics · 2025Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools.Bioinformatics (Oxford, England) · 2024Article
- Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach.Database : the journal of biological databases and curation · 2024Article
- The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop.Database : the journal of biological databases and curation · 2024Article
- Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes.Database : the journal of biological databases and curation · 2024Article
- Towards discovery: an end-to-end system for uncovering novel biomedical relations.Database : the journal of biological databases and curation · 2024Article
- PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge.Nucleic acids research · 2024Article
- Comparison of literature mining tools for variant classification: Through the lens of 50 RYR1 variants.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Cancer-Alterome: a literature-mined resource for regulatory events caused by genetic alterations in cancer.Scientific data · 2024Article
- BELB: a biomedical entity linking benchmark.Bioinformatics (Oxford, England) · 2023Review
- From function to translation: Decoding genetic susceptibility to human diseases via artificial intelligence.Cell genomics · 2023Review
- Tracking genetic variants in the biomedical literature using LitVar 2.0.Nature genetics · 2023Article
- AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning.Bioinformatics (Oxford, England) · 2023Article
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5 authors.
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Abstract
motivationPrevious studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision.
resultWe propose tmVar 3.0: an improved variant recognition and normalization system. Compared to its predecessors, tmVar 3.0 recognizes a wider spectrum of variant-related entities (e.g. allele and copy number variants), and groups together different variant mentions belonging to the same genomic sequence position in an article for improved accuracy. Moreover, tmVar 3.0 provides advanced variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar 3.0 exhibits state-of-the-art performance with over 90% in F-measure for variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar 3.0 as well as annotations for the entire PubMed and PMC datasets are freely available for download. AVAILABILITY AND IMPLEMENTATION: https://github.com/ncbi/tmVar3.
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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.