ArticleDatabase : the journal of biological databases and curation2016
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- SAND: a comprehensive annotation of class D β-lactamases using structural alignment-based numbering.Antimicrobial agents and chemotherapy · 2025Article
- Leveraging generative AI to assist biocuration of medical actions for rare disease.Bioinformatics advances · 2025Article
- ProMENDA: an updated resource for proteomic and metabolomic characterization in depression.Translational psychiatry · 2024Article
- Large language model based framework for automated extraction of genetic interactions from unstructured data.PloS one · 2024Article
- Toward reporting standards for the pathogenicity of variant combinations involved in multilocus/oligogenic diseases.HGG advances · 2023Review
- Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology.BMC medical informatics and decision making · 2022Article
- A Computational Text Mining-Guided Meta-Analysis Approach to Identify Potential Xerostomia Drug Targets.Journal of clinical medicine · 2022Article
- Text Mining for Building Biomedical Networks Using Cancer as a Case Study.Biomolecules · 2021Review
- NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.Journal of biomedical informatics · 2021Article
- ADE Eval: An Evaluation of Text Processing Systems for Adverse Event Extraction from Drug Labels for Pharmacovigilance.Drug safety · 2021Article
- ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.Frontiers in research metrics and analytics · 2021Article
- SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.Nucleic acids research · 2020Article
- BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.PLoS computational biology · 2020Article
- Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase.Database : the journal of biological databases and curation · 2020Article
- UPCLASS: a deep learning-based classifier for UniProtKB entry publications.Database : the journal of biological databases and curation · 2020Article
- PubTator central: automated concept annotation for biomedical full text articles.Nucleic acids research · 2019Article
- Ten quick tips for biocuration.PLoS computational biology · 2019Article
- Navigating the disease landscape: knowledge representations for contextualizing molecular signatures.Briefings in bioinformatics · 2019Review
- Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool.PloS one · 2019Article
- Making the right calls in precision oncology.Nature biotechnology · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application. In this article, we argue that text-mining technologies have become essential tools in real-world biomedical research. We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. We draw on these applications as case studies to characterize common requirements for successfully applying text-mining techniques to practical biocuration needs. We note that system 'accuracy' remains a challenge and identify several additional common difficulties and potential research directions including (i) the 'scalability' issue due to the increasing need of mining information from millions of full-text articles, (ii) the 'interoperability' issue of integrating various text-mining systems into existing curation workflows and (iii) the 'reusability' issue on the difficulty of applying trained systems to text genres that are not seen previously during development. We then describe related efforts within the text-mining community, with a special focus on the BioCreative series of challenge workshops. We believe that focusing on the near-term challenges identified in this work will amplify the opportunities afforded by the continued adoption of text-mining tools. Finally, in order to sustain the curation ecosystem and have text-mining systems adopted for practical benefits, we call for increased collaboration between text-mining researchers and various stakeholders, including researchers, publishers and biocurators.
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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.