ArticleBioinformatics (Oxford, England)2023
GNorm2: an improved gene name recognition and normalization system.
Article in Bioinformatics (Oxford, England), 2023. 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
- Literature-informed gene extraction and ranking for multimodal data fusion.Briefings in bioinformatics · 2026Article
- CellExLink: End-to-end cell-type recognition and normalization in biomedical text.PLoS computational biology · 2026Article
- GeneReL: a large language model-powered platform for gene regulatory relationship extraction with community curation.Database : the journal of biological databases and curation · 2026Article
- Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation.Bioinformatics advances · 2026Review
- Do LLMs Surpass Encoders for Biomedical NER?Proceedings. IEEE International Conference on Healthcare Informatics · 2025Article
- Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine).JAMIA open · 2025Article
- ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature.PLoS computational biology · 2025Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- EnzChemRED, a rich enzyme chemistry relation extraction dataset.Scientific data · 2024Article
- Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach.Database : the journal of biological databases and curation · 2024Article
- BELHD: improving biomedical entity linking with homonym disambiguation.Bioinformatics (Oxford, England) · 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
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Authors and funding
5 authors.
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Abstract
motivationGene name normalization is an important yet highly complex task in biomedical text mining research, as gene names can be highly ambiguous and may refer to different genes in different species or share similar names with other bioconcepts. This poses a challenge for accurately identifying and linking gene mentions to their corresponding entries in databases such as NCBI Gene or UniProt. While there has been a body of literature on the gene normalization task, few have addressed all of these challenges or make their solutions publicly available to the scientific community.
resultsBuilding on the success of GNormPlus, we have created GNorm2: a more advanced tool with optimized functions and improved performance. GNorm2 integrates a range of advanced deep learning-based methods, resulting in the highest levels of accuracy and efficiency for gene recognition and normalization to date. Our tool is freely available for download. AVAILABILITY AND IMPLEMENTATION: https://github.com/ncbi/GNorm2.
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