ArticleDatabase : the journal of biological databases and curation2012
Text mining for the biocuration workflow.
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 94 papers.
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Who cites it
94 citing papers in PubMed.
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- The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII.Database : the journal of biological databases and curation · 2024Article
- MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.Bioinformatics (Oxford, England) · 2023Article
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- Automatic identification of scientific publications describing digital reconstructions of neural morphology.bioRxiv : the preprint server for biology · 2023Article
- Text mining for identification of biological entities related to antibiotic resistant organisms.PeerJ · 2022Article
- Classifying domain-specific text documents containing ambiguous keywords.Database : the journal of biological databases and curation · 2021Article
- NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.Scientific data · 2021Article
- Evaluation of literature searching tools for curation of mismatch repair gene variants in hereditary colon cancer.Advanced genetics (Hoboken, N.J.) · 2021Article
- ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.Frontiers in research metrics and analytics · 2021Article
- Data libraries - the missing element for modeling biological systems.The FEBS journal · 2020Review
- A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts.Immunology · 2020Article
- Predictive article recommendation using natural language processing and machine learning to support evidence updates in domain-specific knowledge graphs.JAMIA open · 2020Article
- SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.Nucleic acids research · 2020Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.
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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.