ArticleDatabase : the journal of biological databases and curation2012
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.
Article in Database : the journal of biological databases and curation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
What it found
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Who cites it
55 citing papers in PubMed.
- Integrating curation into scientific publishing to train AI models.Bioinformatics (Oxford, England) · 2026Article
- Towards discovery: an end-to-end system for uncovering novel biomedical relations.Database : the journal of biological databases and curation · 2024Article
- Cancer-Alterome: a literature-mined resource for regulatory events caused by genetic alterations in cancer.Scientific data · 2024Article
- Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision.Patterns (New York, N.Y.) · 2023Article
- Fine-tuning large neural language models for biomedical natural language processing.Patterns (New York, N.Y.) · 2023Article
- Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.Database : the journal of biological databases and curation · 2022Article
- Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning.Journal of the American Medical Informatics Association : JAMIA · 2021Article
- Evaluation of literature searching tools for curation of mismatch repair gene variants in hereditary colon cancer.Advanced genetics (Hoboken, N.J.) · 2021Article
- COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics.Nucleic acids research · 2021Article
- Acronyms and Opportunities for Improving Deep Nets.Frontiers in artificial intelligence · 2021Article
- ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed.Frontiers in molecular biosciences · 2021Review
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- RCorp: a resource for chemical disease semantic extraction in Chinese.BMC medical informatics and decision making · 2019Article
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- An effective biomedical document classification scheme in support of biocuration: addressing class imbalance.Database : the journal of biological databases and curation · 2019Article
- BLASSO: integration of biological knowledge into a regularized linear model.BMC systems biology · 2018Article
- Global trends in infectious diseases of swine.Proceedings of the National Academy of Sciences of the United States of America · 2018Review
- Development and validation of the PEPPER framework (Prenatal Exposure PubMed ParsER) with applications to food additives.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.Database : the journal of biological databases and curation · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Today's biomedical research has become heavily dependent on access to the biological knowledge encoded in expert curated biological databases. As the volume of biological literature grows rapidly, it becomes increasingly difficult for biocurators to keep up with the literature because manual curation is an expensive and time-consuming endeavour. Past research has suggested that computer-assisted curation can improve efficiency, but few text-mining systems have been formally evaluated in this regard. Through participation in the interactive text-mining track of the BioCreative 2012 workshop, we developed PubTator, a PubMed-like system that assists with two specific human curation tasks: document triage and bioconcept annotation. On the basis of evaluation results from two external user groups, we find that the accuracy of PubTator-assisted curation is comparable with that of manual curation and that PubTator can significantly increase human curatorial speed. These encouraging findings warrant further investigation with a larger number of publications to be annotated. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/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.