ArticleDatabase : the journal of biological databases and curation2014
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
20 citing papers in PubMed.
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- MilkOligoCorpus: A semantically annotated resource for knowledge extraction on mammalian milk oligosaccharides.PloS one · 2025Article
- BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024Article
- MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.BMC bioinformatics · 2024Article
- Towards a unified search: Improving PubMed retrieval with full text.Journal of biomedical informatics · 2022Article
- MedTAG: a portable and customizable annotation tool for biomedical documents.BMC medical informatics and decision making · 2021Article
- An extensive review of tools for manual annotation of documents.Briefings in bioinformatics · 2021Review
- UPCLASS: a deep learning-based classifier for UniProtKB entry publications.Database : the journal of biological databases and curation · 2020Article
- PMC text mining subset in BioC: about three million full-text articles and growing.Bioinformatics (Oxford, England) · 2019Article
- Using distant supervision to augment manually annotated data for relation extraction.PloS one · 2019Article
- Automated Extraction of Diagnostic Criteria From Electronic Health Records for Autism Spectrum Disorders: Development, Evaluation, and Application.Journal of medical Internet research · 2018Article
- ezTag: tagging biomedical concepts via interactive learning.Nucleic acids research · 2018Article
- Biocuration: Distilling data into knowledge.PLoS biology · 2018Article
- LocText: relation extraction of protein localizations to assist database curation.BMC bioinformatics · 2018Article
- nala: text mining natural language mutation mentions.Bioinformatics (Oxford, England) · 2017Article
- EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.Database : the journal of biological databases and curation · 2016Article
- Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.Database : the journal of biological databases and curation · 2016Article
- Mining clinical attributes of genomic variants through assisted literature curation in Egas.Database : the journal of biological databases and curation · 2016Article
- Community challenges in biomedical text mining over 10 years: success, failure and the future.Briefings in bioinformatics · 2016Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
The breadth and depth of biomedical literature are increasing year upon year. To keep abreast of these increases, FlyBase, a database for Drosophila genomic and genetic information, is constantly exploring new ways to mine the published literature to increase the efficiency and accuracy of manual curation and to automate some aspects, such as triaging and entity extraction. Toward this end, we present the 'tagtog' system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text articles. tagtog leverages manual user annotation in combination with automatic machine-learned annotation to provide accurate identification of gene symbols and gene names. As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from the PLOS stable of journals. We show here the results of three experiments with different sized corpora and assess gene recognition performance and curation speed. We conclude that tagtog-named entity recognition improves with a larger corpus and that tagtog-assisted curation is quicker than manual curation. DATABASE URL: www.tagtog.net, www.flybase.org.
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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.