ArticleBioMed research international2015
GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.
Article in BioMed research international, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Trial
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- Taiyi: a bilingual fine-tuned large language model for diverse biomedical tasks.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- Ensemble pretrained language models to extract biomedical knowledge from literature.Journal of the American Medical Informatics Association : JAMIA · 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
- MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species.Bioinformatics (Oxford, England) · 2024Article
- A Combined Manual Annotation and Deep-Learning Natural Language Processing Study on Accurate Entity Extraction in Hereditary Disease Related Biomedical Literature.Interdisciplinary sciences, computational life sciences · 2024Article
- GPDminer: a tool for extracting named entities and analyzing relations in biological literature.BMC bioinformatics · 2024Article
- Semantics-enabled biomedical literature analytics.Journal of biomedical informatics · 2024Article
- Mining drug-target interactions from biomedical literature using chemical and gene descriptions-based ensemble transformer model.Bioinformatics advances · 2024Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The automatic recognition of gene names and their associated database identifiers from biomedical text has been widely studied in recent years, as these tasks play an important role in many downstream text-mining applications. Despite significant previous research, only a small number of tools are publicly available and these tools are typically restricted to detecting only mention level gene names or only document level gene identifiers. In this work, we report GNormPlus: an end-to-end and open source system that handles both gene mention and identifier detection. We created a new corpus of 694 PubMed articles to support our development of GNormPlus, containing manual annotations for not only gene names and their identifiers, but also closely related concepts useful for gene name disambiguation, such as gene families and protein domains. GNormPlus integrates several advanced text-mining techniques, including SimConcept for resolving composite gene names. As a result, GNormPlus compares favorably to other state-of-the-art methods when evaluated on two widely used public benchmarking datasets, achieving 86.7% F1-score on the BioCreative II Gene Normalization task dataset and 50.1% F1-score on the BioCreative III Gene Normalization task dataset. The GNormPlus source code and its annotated corpus are freely available, and the results of applying GNormPlus to the entire PubMed are freely accessible through our web-based tool PubTator.
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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.