ArticleBioinformatics (Oxford, England)2011
GeneTUKit: a software for document-level gene normalization.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
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- Biomedical literature mining: graph kernel-based learning for gene-gene interaction extraction.European journal of medical research · 2024Article
- GNorm2: an improved gene name recognition and normalization system.Bioinformatics (Oxford, England) · 2023Article
- PlagueKD: a knowledge graph-based plague knowledge database.Database : the journal of biological databases and curation · 2022Article
- Assigning species information to corresponding genes by a sequence labeling framework.Database : the journal of biological databases and curation · 2022Article
- NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.Journal of biomedical informatics · 2021Article
- PGxCorpus, a manually annotated corpus for pharmacogenomics.Scientific data · 2020Article
- Early Detection of Adverse Drug Reactions in Social Health Networks: A Natural Language Processing Pipeline for Signal Detection.JMIR public health and surveillance · 2019Article
- DES-Mutation: System for Exploring Links of Mutations and Diseases.Scientific reports · 2018Article
- Capturing the Patient's Perspective: a Review of Advances in Natural Language Processing of Health-Related Text.Yearbook of medical informatics · 2017Review
- Hybrid Semantic Analysis for Mapping Adverse Drug Reaction Mentions in Tweets to Medical Terminology.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2017Article
- PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.PloS one · 2016Article
- Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion.Database : the journal of biological databases and curation · 2016Article
- Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.BMC bioinformatics · 2015Article
- PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool.Scientific reports · 2015Article
- Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features.Journal of the American Medical Informatics Association : JAMIA · 2015Article
- GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.BioMed research international · 2015Article
- pGenN, a gene normalization tool for plant genes and proteins in scientific literature.PloS one · 2015Article
- Quantifying the impact and extent of undocumented biomedical synonymy.PLoS computational biology · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLinking gene mentions in an article to entries of biological databases can facilitate indexing and querying biological literature greatly. Due to the high ambiguity of gene names, this task is particularly challenging. Manual annotation for this task is cost expensive, time consuming and labor intensive. Therefore, providing assistive tools to facilitate the task is of high value.
resultsWe developed GeneTUKit, a document-level gene normalization software for full-text articles. This software employs both local context surrounding gene mentions and global context from the whole full-text document. It can normalize genes of different species simultaneously. When participating in BioCreAtIvE III, the system obtained good results among 37 runs: the system was ranked first, fourth and seventh in terms of TAP-20, TAP-10 and TAP-5, respectively on the 507 full-text test articles. AVAILABILITY AND IMPLEMENTATION: The software is available at http://www.qanswers.net/GeneTUKit/.
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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.