ReviewBriefings in functional genomics2015
Event-based text mining for biology and functional genomics.
Review in Briefings in functional genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed.
- Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature.Frontiers in artificial intelligence · 2026Article
- Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach.Database : the journal of biological databases and curation · 2024Article
- Text mining for contexts and relationships in cancer genomics literature.Bioinformatics (Oxford, England) · 2024Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- A survey on clinical natural language processing in the United Kingdom from 2007 to 2022.NPJ digital medicine · 2022Review
- A biomedical event extraction method based on fine-grained and attention mechanism.BMC bioinformatics · 2022Article
- Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference.Briefings in bioinformatics · 2022Review
- Comparing neural models for nested and overlapping biomedical event detection.BMC bioinformatics · 2022Article
- A Text Mining Protocol for Mining Biological Pathways and Regulatory Networks from Biomedical Literature.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.Database : the journal of biological databases and curation · 2020Article
- Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation.Database : the journal of biological databases and curation · 2019Article
- Annotation and detection of drug effects in text for pharmacovigilance.Journal of cheminformatics · 2018Article
- FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.BMC bioinformatics · 2018Article
- A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.PLoS computational biology · 2018Article
- Using uncertainty to link and rank evidence from biomedical literature for model curation.Bioinformatics (Oxford, England) · 2017Article
- Multiple kernels learning-based biological entity relationship extraction method.Journal of biomedical semantics · 2017Article
- A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries.International journal of genomics · 2017Review
- The landscape of microbial phenotypic traits and associated genes.Nucleic acids research · 2016Article
- SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.Wellcome open research · 2016Article
- Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature.Research integrity and peer review · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.
Indexed as
Identifiers
What OpenQuestion holds
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.